Starting phenix.real_space_refine on Fri Feb 6 21:00:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ry7_19589/02_2026/8ry7_19589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ry7_19589/02_2026/8ry7_19589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ry7_19589/02_2026/8ry7_19589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ry7_19589/02_2026/8ry7_19589.map" model { file = "/net/cci-nas-00/data/ceres_data/8ry7_19589/02_2026/8ry7_19589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ry7_19589/02_2026/8ry7_19589.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 112 5.16 5 C 17008 2.51 5 N 4920 2.21 5 O 5272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27312 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3414 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 446} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 3.24, per 1000 atoms: 0.12 Number of scatterers: 27312 At special positions: 0 Unit cell: (134.924, 134.924, 132.304, 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 112 16.00 O 5272 8.00 N 4920 7.00 C 17008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6720 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 40 sheets defined 43.3% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 58 through 68 removed outlier: 3.703A pdb=" N ALA A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.709A pdb=" N GLY A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 252 through 266 removed outlier: 3.625A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.648A pdb=" N VAL A 345 " --> pdb=" O HIS A 341 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.829A pdb=" N GLY A 364 " --> pdb=" O TRP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 397 Processing helix chain 'A' and resid 401 through 412 removed outlier: 4.409A pdb=" N PHE A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 448 removed outlier: 4.163A pdb=" N HIS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.894A pdb=" N GLY A 468 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 470 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 58 through 68 removed outlier: 3.703A pdb=" N ALA B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.708A pdb=" N GLY B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 252 through 266 removed outlier: 3.624A pdb=" N LEU B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 289 Processing helix chain 'B' and resid 303 through 309 Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 341 through 352 removed outlier: 3.648A pdb=" N VAL B 345 " --> pdb=" O HIS B 341 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.829A pdb=" N GLY B 364 " --> pdb=" O TRP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 397 Processing helix chain 'B' and resid 401 through 412 removed outlier: 4.409A pdb=" N PHE B 411 " --> pdb=" O ARG B 407 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU B 412 " --> pdb=" O LYS B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 448 removed outlier: 4.164A pdb=" N HIS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 458 Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.893A pdb=" N GLY B 468 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 470 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 58 through 68 removed outlier: 3.703A pdb=" N ALA C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.709A pdb=" N GLY C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 252 through 266 removed outlier: 3.625A pdb=" N LEU C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 289 Processing helix chain 'C' and resid 303 through 309 Processing helix chain 'C' and resid 314 through 330 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.648A pdb=" N VAL C 345 " --> pdb=" O HIS C 341 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.829A pdb=" N GLY C 364 " --> pdb=" O TRP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 397 Processing helix chain 'C' and resid 401 through 412 removed outlier: 4.409A pdb=" N PHE C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU C 412 " --> pdb=" O LYS C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 448 removed outlier: 4.163A pdb=" N HIS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.893A pdb=" N GLY C 468 " --> pdb=" O SER C 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 470 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 58 through 68 removed outlier: 3.703A pdb=" N ALA D 62 " --> pdb=" O GLY D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 92 Processing helix chain 'D' and resid 108 through 117 Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.708A pdb=" N GLY D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 252 through 266 removed outlier: 3.625A pdb=" N LEU D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP D 266 " --> pdb=" O VAL D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 289 Processing helix chain 'D' and resid 303 through 309 Processing helix chain 'D' and resid 314 through 330 Processing helix chain 'D' and resid 341 through 352 removed outlier: 3.648A pdb=" N VAL D 345 " --> pdb=" O HIS D 341 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY D 352 " --> pdb=" O ALA D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.829A pdb=" N GLY D 364 " --> pdb=" O TRP D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 397 Processing helix chain 'D' and resid 401 through 412 removed outlier: 4.408A pdb=" N PHE D 411 " --> pdb=" O ARG D 407 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU D 412 " --> pdb=" O LYS D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 448 removed outlier: 4.163A pdb=" N HIS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 458 Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.894A pdb=" N GLY D 468 " --> pdb=" O SER D 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 470 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 58 through 68 removed outlier: 3.703A pdb=" N ALA E 62 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 92 Processing helix chain 'E' and resid 108 through 117 Processing helix chain 'E' and resid 149 through 154 Processing helix chain 'E' and resid 166 through 174 Processing helix chain 'E' and resid 196 through 204 removed outlier: 3.709A pdb=" N GLY E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 252 through 266 removed outlier: 3.624A pdb=" N LEU E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 289 Processing helix chain 'E' and resid 303 through 309 Processing helix chain 'E' and resid 314 through 330 Processing helix chain 'E' and resid 341 through 352 removed outlier: 3.648A pdb=" N VAL E 345 " --> pdb=" O HIS E 341 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 removed outlier: 3.830A pdb=" N GLY E 364 " --> pdb=" O TRP E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 397 Processing helix chain 'E' and resid 401 through 412 removed outlier: 4.409A pdb=" N PHE E 411 " --> pdb=" O ARG E 407 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU E 412 " --> pdb=" O LYS E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 448 removed outlier: 4.163A pdb=" N HIS E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 458 Processing helix chain 'E' and resid 465 through 470 removed outlier: 3.894A pdb=" N GLY E 468 " --> pdb=" O SER E 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 470 " --> pdb=" O ALA E 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 30 through 34 Processing helix chain 'F' and resid 58 through 68 removed outlier: 3.704A pdb=" N ALA F 62 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 92 Processing helix chain 'F' and resid 108 through 117 Processing helix chain 'F' and resid 149 through 154 Processing helix chain 'F' and resid 166 through 174 Processing helix chain 'F' and resid 196 through 204 removed outlier: 3.709A pdb=" N GLY F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 252 through 266 removed outlier: 3.624A pdb=" N LEU F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 289 Processing helix chain 'F' and resid 303 through 309 Processing helix chain 'F' and resid 314 through 330 Processing helix chain 'F' and resid 341 through 352 removed outlier: 3.647A pdb=" N VAL F 345 " --> pdb=" O HIS F 341 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 removed outlier: 3.830A pdb=" N GLY F 364 " --> pdb=" O TRP F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 397 Processing helix chain 'F' and resid 401 through 412 removed outlier: 4.408A pdb=" N PHE F 411 " --> pdb=" O ARG F 407 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU F 412 " --> pdb=" O LYS F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 448 removed outlier: 4.163A pdb=" N HIS F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 458 Processing helix chain 'F' and resid 465 through 470 removed outlier: 3.894A pdb=" N GLY F 468 " --> pdb=" O SER F 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 470 " --> pdb=" O ALA F 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 30 through 34 Processing helix chain 'G' and resid 58 through 68 removed outlier: 3.703A pdb=" N ALA G 62 " --> pdb=" O GLY G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 92 Processing helix chain 'G' and resid 108 through 117 Processing helix chain 'G' and resid 149 through 154 Processing helix chain 'G' and resid 166 through 174 Processing helix chain 'G' and resid 196 through 204 removed outlier: 3.708A pdb=" N GLY G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 238 Processing helix chain 'G' and resid 252 through 266 removed outlier: 3.624A pdb=" N LEU G 265 " --> pdb=" O ALA G 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP G 266 " --> pdb=" O VAL G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 289 Processing helix chain 'G' and resid 303 through 309 Processing helix chain 'G' and resid 314 through 330 Processing helix chain 'G' and resid 341 through 352 removed outlier: 3.648A pdb=" N VAL G 345 " --> pdb=" O HIS G 341 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY G 352 " --> pdb=" O ALA G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 364 removed outlier: 3.830A pdb=" N GLY G 364 " --> pdb=" O TRP G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 397 Processing helix chain 'G' and resid 401 through 412 removed outlier: 4.409A pdb=" N PHE G 411 " --> pdb=" O ARG G 407 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU G 412 " --> pdb=" O LYS G 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 448 removed outlier: 4.164A pdb=" N HIS G 435 " --> pdb=" O ASP G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 458 Processing helix chain 'G' and resid 465 through 470 removed outlier: 3.894A pdb=" N GLY G 468 " --> pdb=" O SER G 465 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA G 470 " --> pdb=" O ALA G 467 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 30 through 34 Processing helix chain 'H' and resid 58 through 68 removed outlier: 3.703A pdb=" N ALA H 62 " --> pdb=" O GLY H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 92 Processing helix chain 'H' and resid 108 through 117 Processing helix chain 'H' and resid 149 through 154 Processing helix chain 'H' and resid 166 through 174 Processing helix chain 'H' and resid 196 through 204 removed outlier: 3.709A pdb=" N GLY H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 238 Processing helix chain 'H' and resid 252 through 266 removed outlier: 3.625A pdb=" N LEU H 265 " --> pdb=" O ALA H 261 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP H 266 " --> pdb=" O VAL H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 289 Processing helix chain 'H' and resid 303 through 309 Processing helix chain 'H' and resid 314 through 330 Processing helix chain 'H' and resid 341 through 352 removed outlier: 3.648A pdb=" N VAL H 345 " --> pdb=" O HIS H 341 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY H 352 " --> pdb=" O ALA H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 364 removed outlier: 3.829A pdb=" N GLY H 364 " --> pdb=" O TRP H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 397 Processing helix chain 'H' and resid 401 through 412 removed outlier: 4.409A pdb=" N PHE H 411 " --> pdb=" O ARG H 407 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU H 412 " --> pdb=" O LYS H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 448 removed outlier: 4.162A pdb=" N HIS H 435 " --> pdb=" O ASP H 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 458 Processing helix chain 'H' and resid 465 through 470 removed outlier: 3.894A pdb=" N GLY H 468 " --> pdb=" O SER H 465 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA H 470 " --> pdb=" O ALA H 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 6.719A pdb=" N ARG A 3 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N VAL A 463 " --> pdb=" O ARG A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.664A pdb=" N VAL A 73 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 271 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYS A 294 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA A 273 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 293 " --> pdb=" O TRP A 334 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 333 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N MET A 357 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA A 335 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 49 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 103 removed outlier: 4.234A pdb=" N GLY A 134 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE A 128 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.265A pdb=" N ALA A 161 " --> pdb=" O THR A 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 4 removed outlier: 6.719A pdb=" N ARG B 3 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N VAL B 463 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 50 removed outlier: 3.665A pdb=" N VAL B 73 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU B 271 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYS B 294 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA B 273 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 293 " --> pdb=" O TRP B 334 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 333 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N MET B 357 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA B 335 " --> pdb=" O MET B 357 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL B 49 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 103 removed outlier: 4.235A pdb=" N GLY B 134 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE B 128 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 161 through 162 removed outlier: 6.265A pdb=" N ALA B 161 " --> pdb=" O THR B 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 373 through 374 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 4 removed outlier: 6.719A pdb=" N ARG C 3 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N VAL C 463 " --> pdb=" O ARG C 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.664A pdb=" N VAL C 73 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU C 271 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYS C 294 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA C 273 " --> pdb=" O LYS C 294 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 293 " --> pdb=" O TRP C 334 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C 333 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N MET C 357 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA C 335 " --> pdb=" O MET C 357 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 49 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 102 through 103 removed outlier: 4.234A pdb=" N GLY C 134 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE C 128 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 161 through 162 removed outlier: 6.265A pdb=" N ALA C 161 " --> pdb=" O THR C 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 373 through 374 Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 4 removed outlier: 6.718A pdb=" N ARG D 3 " --> pdb=" O LEU D 461 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N VAL D 463 " --> pdb=" O ARG D 3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.663A pdb=" N VAL D 73 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU D 271 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS D 294 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA D 273 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL D 293 " --> pdb=" O TRP D 334 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL D 333 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N MET D 357 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA D 335 " --> pdb=" O MET D 357 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 49 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 103 removed outlier: 4.234A pdb=" N GLY D 134 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE D 128 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 161 through 162 removed outlier: 6.265A pdb=" N ALA D 161 " --> pdb=" O THR D 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 373 through 374 Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 4 removed outlier: 6.718A pdb=" N ARG E 3 " --> pdb=" O LEU E 461 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N VAL E 463 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 49 through 50 removed outlier: 3.664A pdb=" N VAL E 73 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU E 271 " --> pdb=" O ILE E 292 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYS E 294 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA E 273 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL E 293 " --> pdb=" O TRP E 334 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL E 333 " --> pdb=" O ASN E 355 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N MET E 357 " --> pdb=" O VAL E 333 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA E 335 " --> pdb=" O MET E 357 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL E 49 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.234A pdb=" N GLY E 134 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE E 128 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 161 through 162 removed outlier: 6.265A pdb=" N ALA E 161 " --> pdb=" O THR E 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 373 through 374 Processing sheet with id=AC8, first strand: chain 'F' and resid 3 through 4 removed outlier: 6.719A pdb=" N ARG F 3 " --> pdb=" O LEU F 461 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N VAL F 463 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 49 through 50 removed outlier: 3.665A pdb=" N VAL F 73 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU F 271 " --> pdb=" O ILE F 292 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYS F 294 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA F 273 " --> pdb=" O LYS F 294 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL F 293 " --> pdb=" O TRP F 334 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL F 333 " --> pdb=" O ASN F 355 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N MET F 357 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA F 335 " --> pdb=" O MET F 357 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL F 49 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 102 through 103 removed outlier: 4.234A pdb=" N GLY F 134 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE F 128 " --> pdb=" O PRO F 132 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 161 through 162 removed outlier: 6.265A pdb=" N ALA F 161 " --> pdb=" O THR F 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 373 through 374 Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 4 removed outlier: 6.719A pdb=" N ARG G 3 " --> pdb=" O LEU G 461 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N VAL G 463 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 49 through 50 removed outlier: 3.664A pdb=" N VAL G 73 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU G 271 " --> pdb=" O ILE G 292 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS G 294 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA G 273 " --> pdb=" O LYS G 294 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL G 293 " --> pdb=" O TRP G 334 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL G 333 " --> pdb=" O ASN G 355 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N MET G 357 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA G 335 " --> pdb=" O MET G 357 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL G 49 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 102 through 103 removed outlier: 4.234A pdb=" N GLY G 134 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE G 128 " --> pdb=" O PRO G 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 161 through 162 removed outlier: 6.266A pdb=" N ALA G 161 " --> pdb=" O THR G 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 373 through 374 Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 4 removed outlier: 6.718A pdb=" N ARG H 3 " --> pdb=" O LEU H 461 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N VAL H 463 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 49 through 50 removed outlier: 3.664A pdb=" N VAL H 73 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU H 271 " --> pdb=" O ILE H 292 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYS H 294 " --> pdb=" O LEU H 271 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA H 273 " --> pdb=" O LYS H 294 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL H 293 " --> pdb=" O TRP H 334 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL H 333 " --> pdb=" O ASN H 355 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N MET H 357 " --> pdb=" O VAL H 333 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA H 335 " --> pdb=" O MET H 357 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL H 49 " --> pdb=" O ILE H 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 102 through 103 removed outlier: 4.234A pdb=" N GLY H 134 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE H 128 " --> pdb=" O PRO H 132 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 161 through 162 removed outlier: 6.266A pdb=" N ALA H 161 " --> pdb=" O THR H 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 373 through 374 1104 hydrogen bonds defined for protein. 3120 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: 4.49 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9568 1.34 - 1.46: 5726 1.46 - 1.58: 12266 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 27752 Sorted by residual: bond pdb=" C THR H 207 " pdb=" O THR H 207 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.63e-01 bond pdb=" C THR E 207 " pdb=" O THR E 207 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.55e-01 bond pdb=" C GLY B 312 " pdb=" N ARG B 313 " ideal model delta sigma weight residual 1.336 1.324 0.012 1.48e-02 4.57e+03 7.11e-01 bond pdb=" C THR D 207 " pdb=" O THR D 207 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.00e-01 bond pdb=" C THR C 207 " pdb=" O THR C 207 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 6.98e-01 ... (remaining 27747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 37219 2.26 - 4.52: 480 4.52 - 6.79: 53 6.79 - 9.05: 16 9.05 - 11.31: 8 Bond angle restraints: 37776 Sorted by residual: angle pdb=" CB MET D 420 " pdb=" CG MET D 420 " pdb=" SD MET D 420 " ideal model delta sigma weight residual 112.70 124.01 -11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CB MET H 420 " pdb=" CG MET H 420 " pdb=" SD MET H 420 " ideal model delta sigma weight residual 112.70 124.00 -11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CB MET C 420 " pdb=" CG MET C 420 " pdb=" SD MET C 420 " ideal model delta sigma weight residual 112.70 123.97 -11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CB MET A 420 " pdb=" CG MET A 420 " pdb=" SD MET A 420 " ideal model delta sigma weight residual 112.70 123.97 -11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CB MET F 420 " pdb=" CG MET F 420 " pdb=" SD MET F 420 " ideal model delta sigma weight residual 112.70 123.96 -11.26 3.00e+00 1.11e-01 1.41e+01 ... (remaining 37771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.18: 14702 13.18 - 26.36: 1156 26.36 - 39.54: 589 39.54 - 52.73: 121 52.73 - 65.91: 24 Dihedral angle restraints: 16592 sinusoidal: 6072 harmonic: 10520 Sorted by residual: dihedral pdb=" CA ASP F 107 " pdb=" CB ASP F 107 " pdb=" CG ASP F 107 " pdb=" OD1 ASP F 107 " ideal model delta sinusoidal sigma weight residual -30.00 -83.23 53.23 1 2.00e+01 2.50e-03 9.63e+00 dihedral pdb=" CA ASP H 107 " pdb=" CB ASP H 107 " pdb=" CG ASP H 107 " pdb=" OD1 ASP H 107 " ideal model delta sinusoidal sigma weight residual -30.00 -83.21 53.21 1 2.00e+01 2.50e-03 9.63e+00 dihedral pdb=" CA ASP A 107 " pdb=" CB ASP A 107 " pdb=" CG ASP A 107 " pdb=" OD1 ASP A 107 " ideal model delta sinusoidal sigma weight residual -30.00 -83.19 53.19 1 2.00e+01 2.50e-03 9.62e+00 ... (remaining 16589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2805 0.032 - 0.063: 1013 0.063 - 0.095: 409 0.095 - 0.126: 248 0.126 - 0.158: 21 Chirality restraints: 4496 Sorted by residual: chirality pdb=" CA VAL B 272 " pdb=" N VAL B 272 " pdb=" C VAL B 272 " pdb=" CB VAL B 272 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA VAL D 272 " pdb=" N VAL D 272 " pdb=" C VAL D 272 " pdb=" CB VAL D 272 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA VAL H 272 " pdb=" N VAL H 272 " pdb=" C VAL H 272 " pdb=" CB VAL H 272 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 4493 not shown) Planarity restraints: 5000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA H 466 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.86e+00 pdb=" C ALA H 466 " -0.024 2.00e-02 2.50e+03 pdb=" O ALA H 466 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA H 467 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 466 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.86e+00 pdb=" C ALA E 466 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA E 466 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA E 467 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 466 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C ALA G 466 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA G 466 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA G 467 " 0.008 2.00e-02 2.50e+03 ... (remaining 4997 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 11031 2.88 - 3.38: 27860 3.38 - 3.89: 45180 3.89 - 4.39: 52784 4.39 - 4.90: 85451 Nonbonded interactions: 222306 Sorted by model distance: nonbonded pdb=" OG SER E 368 " pdb=" NZ LYS E 382 " model vdw 2.372 3.120 nonbonded pdb=" OG SER G 368 " pdb=" NZ LYS G 382 " model vdw 2.372 3.120 nonbonded pdb=" OG SER F 368 " pdb=" NZ LYS F 382 " model vdw 2.372 3.120 nonbonded pdb=" OG SER H 368 " pdb=" NZ LYS H 382 " model vdw 2.372 3.120 nonbonded pdb=" OG SER B 368 " pdb=" NZ LYS B 382 " model vdw 2.372 3.120 ... (remaining 222301 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.900 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 0.025 27752 Z= 0.184 Angle : 0.648 11.309 37776 Z= 0.318 Chirality : 0.044 0.158 4496 Planarity : 0.004 0.023 5000 Dihedral : 12.713 65.907 9872 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.82 % Allowed : 15.71 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.14), residues: 3736 helix: 1.43 (0.14), residues: 1480 sheet: -0.41 (0.21), residues: 624 loop : 0.91 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 396 TYR 0.008 0.001 TYR D 366 PHE 0.008 0.001 PHE D 147 TRP 0.003 0.001 TRP G 334 HIS 0.004 0.001 HIS H 435 Details of bonding type rmsd covalent geometry : bond 0.00386 (27752) covalent geometry : angle 0.64778 (37776) hydrogen bonds : bond 0.13843 ( 1104) hydrogen bonds : angle 5.41640 ( 3120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1007 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 VAL cc_start: 0.9238 (t) cc_final: 0.9024 (p) REVERT: A 118 LYS cc_start: 0.8477 (ptpp) cc_final: 0.7885 (ptpt) REVERT: A 158 PHE cc_start: 0.8283 (p90) cc_final: 0.7661 (p90) REVERT: A 176 HIS cc_start: 0.7881 (p90) cc_final: 0.7664 (p90) REVERT: A 184 MET cc_start: 0.7597 (tpp) cc_final: 0.7331 (tpp) REVERT: A 225 ASN cc_start: 0.9113 (m110) cc_final: 0.8660 (p0) REVERT: A 231 LYS cc_start: 0.9151 (mtmt) cc_final: 0.8676 (mttp) REVERT: A 233 GLN cc_start: 0.9216 (tt0) cc_final: 0.8849 (tp-100) REVERT: A 357 MET cc_start: 0.8633 (tpp) cc_final: 0.8423 (tpp) REVERT: A 358 ILE cc_start: 0.8977 (mt) cc_final: 0.8442 (mt) REVERT: A 367 GLU cc_start: 0.8563 (mp0) cc_final: 0.7781 (mp0) REVERT: A 430 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8096 (mp0) REVERT: A 431 ASP cc_start: 0.8671 (m-30) cc_final: 0.8468 (m-30) REVERT: A 451 ASN cc_start: 0.8093 (p0) cc_final: 0.7816 (p0) REVERT: B 35 ASP cc_start: 0.7818 (t70) cc_final: 0.7605 (t0) REVERT: B 52 ASN cc_start: 0.8820 (p0) cc_final: 0.8270 (p0) REVERT: B 53 MET cc_start: 0.8247 (mtp) cc_final: 0.8015 (mmm) REVERT: B 128 PHE cc_start: 0.8893 (t80) cc_final: 0.7340 (t80) REVERT: B 175 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8183 (pm20) REVERT: B 292 ILE cc_start: 0.9208 (mt) cc_final: 0.8944 (mm) REVERT: B 293 VAL cc_start: 0.9215 (t) cc_final: 0.8965 (p) REVERT: B 321 GLU cc_start: 0.8192 (tt0) cc_final: 0.7944 (tt0) REVERT: B 373 LEU cc_start: 0.8219 (mp) cc_final: 0.7697 (tp) REVERT: B 374 PHE cc_start: 0.8636 (m-80) cc_final: 0.7964 (m-80) REVERT: B 381 TYR cc_start: 0.8336 (p90) cc_final: 0.7622 (p90) REVERT: B 384 SER cc_start: 0.8439 (t) cc_final: 0.7751 (p) REVERT: B 405 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8323 (mtm180) REVERT: B 431 ASP cc_start: 0.8328 (m-30) cc_final: 0.8086 (t0) REVERT: B 451 ASN cc_start: 0.8391 (p0) cc_final: 0.7342 (p0) REVERT: C 56 VAL cc_start: 0.9233 (t) cc_final: 0.9024 (p) REVERT: C 118 LYS cc_start: 0.8475 (ptpp) cc_final: 0.7867 (ptpt) REVERT: C 158 PHE cc_start: 0.8297 (p90) cc_final: 0.7670 (p90) REVERT: C 176 HIS cc_start: 0.7876 (p90) cc_final: 0.7652 (p90) REVERT: C 184 MET cc_start: 0.7604 (tpp) cc_final: 0.7331 (tpp) REVERT: C 225 ASN cc_start: 0.9110 (m110) cc_final: 0.8642 (p0) REVERT: C 231 LYS cc_start: 0.9152 (mtmt) cc_final: 0.8677 (mttp) REVERT: C 233 GLN cc_start: 0.9215 (tt0) cc_final: 0.8849 (tp-100) REVERT: C 357 MET cc_start: 0.8618 (tpp) cc_final: 0.8399 (tpp) REVERT: C 367 GLU cc_start: 0.8566 (mp0) cc_final: 0.7671 (mp0) REVERT: C 451 ASN cc_start: 0.8094 (p0) cc_final: 0.7817 (p0) REVERT: D 35 ASP cc_start: 0.7826 (t70) cc_final: 0.7608 (t0) REVERT: D 52 ASN cc_start: 0.8821 (p0) cc_final: 0.8260 (p0) REVERT: D 53 MET cc_start: 0.8237 (mtp) cc_final: 0.8010 (mmm) REVERT: D 128 PHE cc_start: 0.8886 (t80) cc_final: 0.7345 (t80) REVERT: D 131 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.8042 (mmt90) REVERT: D 175 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8180 (pm20) REVERT: D 292 ILE cc_start: 0.9211 (mt) cc_final: 0.8945 (mm) REVERT: D 293 VAL cc_start: 0.9213 (t) cc_final: 0.8966 (p) REVERT: D 321 GLU cc_start: 0.8200 (tt0) cc_final: 0.7951 (tt0) REVERT: D 373 LEU cc_start: 0.8241 (mp) cc_final: 0.7736 (tp) REVERT: D 374 PHE cc_start: 0.8636 (m-80) cc_final: 0.7952 (m-80) REVERT: D 381 TYR cc_start: 0.8338 (p90) cc_final: 0.7569 (p90) REVERT: D 384 SER cc_start: 0.8578 (t) cc_final: 0.7975 (p) REVERT: D 405 ARG cc_start: 0.8536 (ttp-110) cc_final: 0.8322 (mtm180) REVERT: D 431 ASP cc_start: 0.8330 (m-30) cc_final: 0.8084 (t0) REVERT: D 451 ASN cc_start: 0.8387 (p0) cc_final: 0.7344 (p0) REVERT: E 13 ASP cc_start: 0.8040 (m-30) cc_final: 0.7356 (m-30) REVERT: E 174 LEU cc_start: 0.9109 (mt) cc_final: 0.8685 (tp) REVERT: E 249 HIS cc_start: 0.6936 (t70) cc_final: 0.6124 (t70) REVERT: E 307 MET cc_start: 0.8370 (mmm) cc_final: 0.7559 (ptp) REVERT: E 367 GLU cc_start: 0.7846 (mp0) cc_final: 0.7643 (mp0) REVERT: E 381 TYR cc_start: 0.7618 (p90) cc_final: 0.6677 (p90) REVERT: E 418 SER cc_start: 0.7798 (t) cc_final: 0.7572 (p) REVERT: F 18 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: F 53 MET cc_start: 0.8398 (mtp) cc_final: 0.8030 (mmm) REVERT: F 59 ARG cc_start: 0.7397 (ptm160) cc_final: 0.6961 (ttm-80) REVERT: F 76 GLN cc_start: 0.8164 (pt0) cc_final: 0.7950 (tt0) REVERT: F 176 HIS cc_start: 0.8143 (p90) cc_final: 0.7818 (p-80) REVERT: F 184 MET cc_start: 0.7094 (tpp) cc_final: 0.6877 (tpp) REVERT: F 275 ASN cc_start: 0.7458 (m-40) cc_final: 0.7228 (m110) REVERT: F 278 SER cc_start: 0.8772 (t) cc_final: 0.8384 (t) REVERT: F 339 VAL cc_start: 0.9259 (t) cc_final: 0.8931 (p) REVERT: F 358 ILE cc_start: 0.8344 (mt) cc_final: 0.8105 (mm) REVERT: F 371 ASP cc_start: 0.7211 (p0) cc_final: 0.6860 (p0) REVERT: F 431 ASP cc_start: 0.8399 (m-30) cc_final: 0.7792 (t0) REVERT: G 13 ASP cc_start: 0.8017 (m-30) cc_final: 0.7337 (m-30) REVERT: G 174 LEU cc_start: 0.9110 (mt) cc_final: 0.8696 (tp) REVERT: G 249 HIS cc_start: 0.6869 (t70) cc_final: 0.6127 (t70) REVERT: G 367 GLU cc_start: 0.7898 (mp0) cc_final: 0.7695 (mp0) REVERT: G 381 TYR cc_start: 0.7612 (p90) cc_final: 0.6663 (p90) REVERT: G 418 SER cc_start: 0.7813 (t) cc_final: 0.7593 (p) REVERT: H 18 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8193 (m-30) REVERT: H 53 MET cc_start: 0.8372 (mtp) cc_final: 0.8042 (mmm) REVERT: H 59 ARG cc_start: 0.7434 (ptm160) cc_final: 0.6949 (ttm-80) REVERT: H 176 HIS cc_start: 0.8142 (p90) cc_final: 0.7820 (p-80) REVERT: H 184 MET cc_start: 0.6979 (tpp) cc_final: 0.6744 (tpp) REVERT: H 275 ASN cc_start: 0.7416 (m-40) cc_final: 0.7119 (m110) REVERT: H 278 SER cc_start: 0.8750 (t) cc_final: 0.8380 (t) REVERT: H 339 VAL cc_start: 0.9253 (t) cc_final: 0.8903 (p) REVERT: H 355 ASN cc_start: 0.8865 (t0) cc_final: 0.8647 (t0) REVERT: H 371 ASP cc_start: 0.7217 (p0) cc_final: 0.6854 (p0) REVERT: H 372 LEU cc_start: 0.8826 (tt) cc_final: 0.8466 (mm) REVERT: H 431 ASP cc_start: 0.8378 (m-30) cc_final: 0.7808 (t0) outliers start: 23 outliers final: 2 residues processed: 1016 average time/residue: 0.1823 time to fit residues: 276.8980 Evaluate side-chains 695 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 691 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain F residue 18 ASP Chi-restraints excluded: chain H residue 18 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS B 435 HIS B 456 HIS C 8 HIS ** D 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 HIS E 17 ASN E 117 HIS E 332 HIS F 8 HIS ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN G 117 HIS G 332 HIS H 8 HIS ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.160838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107695 restraints weight = 54400.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112380 restraints weight = 29128.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115418 restraints weight = 19723.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117309 restraints weight = 15460.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118494 restraints weight = 13337.067| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27752 Z= 0.137 Angle : 0.629 11.627 37776 Z= 0.317 Chirality : 0.044 0.184 4496 Planarity : 0.005 0.046 5000 Dihedral : 3.983 43.286 4072 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.31 % Allowed : 21.15 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3736 helix: 0.86 (0.13), residues: 1504 sheet: 0.22 (0.21), residues: 656 loop : 0.25 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 343 TYR 0.008 0.001 TYR C 385 PHE 0.023 0.001 PHE F 89 TRP 0.011 0.001 TRP H 361 HIS 0.010 0.001 HIS G 117 Details of bonding type rmsd covalent geometry : bond 0.00314 (27752) covalent geometry : angle 0.62906 (37776) hydrogen bonds : bond 0.03773 ( 1104) hydrogen bonds : angle 4.89958 ( 3120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 741 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8518 (ptpp) cc_final: 0.8212 (ptpt) REVERT: A 158 PHE cc_start: 0.8382 (p90) cc_final: 0.7802 (p90) REVERT: A 184 MET cc_start: 0.7833 (tpp) cc_final: 0.7612 (tpp) REVERT: A 225 ASN cc_start: 0.9151 (m110) cc_final: 0.8610 (p0) REVERT: A 231 LYS cc_start: 0.9143 (mtmt) cc_final: 0.8786 (mtmm) REVERT: A 233 GLN cc_start: 0.9204 (tt0) cc_final: 0.8880 (tp-100) REVERT: A 355 ASN cc_start: 0.9143 (t0) cc_final: 0.8705 (m-40) REVERT: A 371 ASP cc_start: 0.7860 (p0) cc_final: 0.7598 (p0) REVERT: A 377 ASP cc_start: 0.9028 (t0) cc_final: 0.8806 (t0) REVERT: A 426 ARG cc_start: 0.8609 (mtm110) cc_final: 0.8351 (ptp-170) REVERT: B 27 ASP cc_start: 0.8179 (t0) cc_final: 0.7852 (t0) REVERT: B 52 ASN cc_start: 0.8665 (p0) cc_final: 0.8072 (p0) REVERT: B 53 MET cc_start: 0.8488 (mtp) cc_final: 0.8168 (mmm) REVERT: B 115 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8568 (tp) REVERT: B 118 LYS cc_start: 0.8933 (pptt) cc_final: 0.8429 (tmmt) REVERT: B 174 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8935 (tp) REVERT: B 224 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9015 (pt) REVERT: B 254 LYS cc_start: 0.8072 (tppt) cc_final: 0.7756 (tppt) REVERT: B 321 GLU cc_start: 0.7871 (tt0) cc_final: 0.7648 (tt0) REVERT: B 357 MET cc_start: 0.9115 (tpp) cc_final: 0.8579 (ttm) REVERT: B 367 GLU cc_start: 0.8513 (mp0) cc_final: 0.8202 (mp0) REVERT: B 373 LEU cc_start: 0.8380 (mp) cc_final: 0.7868 (tp) REVERT: B 374 PHE cc_start: 0.8664 (m-80) cc_final: 0.8005 (m-80) REVERT: B 381 TYR cc_start: 0.8570 (p90) cc_final: 0.7860 (p90) REVERT: B 382 LYS cc_start: 0.7690 (mttt) cc_final: 0.7264 (mttt) REVERT: B 438 SER cc_start: 0.9063 (OUTLIER) cc_final: 0.8751 (p) REVERT: B 451 ASN cc_start: 0.8607 (p0) cc_final: 0.8329 (p0) REVERT: C 118 LYS cc_start: 0.8520 (ptpp) cc_final: 0.8214 (ptpt) REVERT: C 158 PHE cc_start: 0.8382 (p90) cc_final: 0.7794 (p90) REVERT: C 184 MET cc_start: 0.7783 (tpp) cc_final: 0.7566 (tpp) REVERT: C 225 ASN cc_start: 0.9138 (m110) cc_final: 0.8597 (p0) REVERT: C 231 LYS cc_start: 0.9153 (mtmt) cc_final: 0.8796 (mtmm) REVERT: C 233 GLN cc_start: 0.9193 (tt0) cc_final: 0.8877 (tp-100) REVERT: C 355 ASN cc_start: 0.9145 (t0) cc_final: 0.8708 (m-40) REVERT: C 358 ILE cc_start: 0.9182 (mt) cc_final: 0.8688 (mt) REVERT: C 371 ASP cc_start: 0.7868 (p0) cc_final: 0.7620 (p0) REVERT: C 377 ASP cc_start: 0.8989 (t0) cc_final: 0.8780 (t0) REVERT: C 426 ARG cc_start: 0.8592 (mtm110) cc_final: 0.8337 (ptp-170) REVERT: D 27 ASP cc_start: 0.8125 (t0) cc_final: 0.7804 (t0) REVERT: D 52 ASN cc_start: 0.8705 (p0) cc_final: 0.8030 (p0) REVERT: D 53 MET cc_start: 0.8522 (mtp) cc_final: 0.8211 (mmm) REVERT: D 118 LYS cc_start: 0.8924 (pptt) cc_final: 0.8636 (tmmt) REVERT: D 128 PHE cc_start: 0.8510 (t80) cc_final: 0.8289 (t80) REVERT: D 131 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8106 (mmt90) REVERT: D 174 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8908 (tp) REVERT: D 254 LYS cc_start: 0.8163 (tppt) cc_final: 0.7950 (tppt) REVERT: D 321 GLU cc_start: 0.7876 (tt0) cc_final: 0.7649 (tt0) REVERT: D 357 MET cc_start: 0.9117 (tpp) cc_final: 0.8578 (ttm) REVERT: D 367 GLU cc_start: 0.8510 (mp0) cc_final: 0.8208 (mp0) REVERT: D 373 LEU cc_start: 0.8381 (mp) cc_final: 0.7867 (tp) REVERT: D 374 PHE cc_start: 0.8648 (m-80) cc_final: 0.7994 (m-80) REVERT: D 381 TYR cc_start: 0.8568 (p90) cc_final: 0.7844 (p90) REVERT: D 382 LYS cc_start: 0.7705 (mttt) cc_final: 0.7273 (mttt) REVERT: D 438 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8741 (p) REVERT: D 451 ASN cc_start: 0.8613 (p0) cc_final: 0.8337 (p0) REVERT: E 13 ASP cc_start: 0.8472 (m-30) cc_final: 0.7615 (m-30) REVERT: E 115 LEU cc_start: 0.9563 (mm) cc_final: 0.9098 (tp) REVERT: E 174 LEU cc_start: 0.9285 (mt) cc_final: 0.8829 (tp) REVERT: E 184 MET cc_start: -0.2449 (mmm) cc_final: -0.2798 (mmm) REVERT: E 191 LEU cc_start: 0.7708 (mt) cc_final: 0.7488 (mp) REVERT: E 249 HIS cc_start: 0.7077 (t70) cc_final: 0.6739 (t70) REVERT: E 381 TYR cc_start: 0.7298 (p90) cc_final: 0.5516 (p90) REVERT: E 438 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7692 (p) REVERT: E 441 ARG cc_start: 0.8781 (mtt-85) cc_final: 0.8306 (mtt-85) REVERT: E 458 LYS cc_start: 0.8447 (pttt) cc_final: 0.8083 (pttt) REVERT: E 464 GLN cc_start: 0.7065 (pm20) cc_final: 0.6667 (pm20) REVERT: F 53 MET cc_start: 0.8572 (mtp) cc_final: 0.8133 (mmm) REVERT: F 76 GLN cc_start: 0.8569 (pt0) cc_final: 0.8164 (tt0) REVERT: F 176 HIS cc_start: 0.8481 (p90) cc_final: 0.8250 (p-80) REVERT: F 206 TYR cc_start: 0.8759 (m-80) cc_final: 0.8382 (m-80) REVERT: F 278 SER cc_start: 0.8958 (t) cc_final: 0.8626 (t) REVERT: F 339 VAL cc_start: 0.9514 (t) cc_final: 0.9292 (p) REVERT: F 340 ARG cc_start: 0.8184 (mmm160) cc_final: 0.7841 (mmm160) REVERT: F 349 LEU cc_start: 0.9082 (mm) cc_final: 0.8880 (mm) REVERT: F 357 MET cc_start: 0.8246 (tpp) cc_final: 0.7998 (tpp) REVERT: F 372 LEU cc_start: 0.8907 (tt) cc_final: 0.8376 (mm) REVERT: F 431 ASP cc_start: 0.8658 (m-30) cc_final: 0.8116 (t0) REVERT: G 13 ASP cc_start: 0.8471 (m-30) cc_final: 0.7588 (m-30) REVERT: G 174 LEU cc_start: 0.9281 (mt) cc_final: 0.8823 (tp) REVERT: G 184 MET cc_start: -0.2444 (mmm) cc_final: -0.2808 (mmm) REVERT: G 191 LEU cc_start: 0.7711 (mt) cc_final: 0.7498 (mp) REVERT: G 249 HIS cc_start: 0.7023 (t70) cc_final: 0.6702 (t70) REVERT: G 381 TYR cc_start: 0.7292 (p90) cc_final: 0.5494 (p90) REVERT: G 438 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7699 (p) REVERT: G 441 ARG cc_start: 0.8789 (mtt-85) cc_final: 0.8313 (mtt-85) REVERT: G 458 LYS cc_start: 0.8449 (pttt) cc_final: 0.8079 (pttt) REVERT: G 464 GLN cc_start: 0.7071 (pm20) cc_final: 0.6638 (pm20) REVERT: H 53 MET cc_start: 0.8541 (mtp) cc_final: 0.8153 (mmm) REVERT: H 91 LYS cc_start: 0.8473 (mmmt) cc_final: 0.6360 (mmmt) REVERT: H 176 HIS cc_start: 0.8491 (p90) cc_final: 0.8241 (p-80) REVERT: H 206 TYR cc_start: 0.8778 (m-80) cc_final: 0.8398 (m-80) REVERT: H 252 GLN cc_start: 0.7735 (pt0) cc_final: 0.7019 (pt0) REVERT: H 255 MET cc_start: 0.7796 (mmm) cc_final: 0.7363 (tpp) REVERT: H 278 SER cc_start: 0.8966 (t) cc_final: 0.8635 (t) REVERT: H 334 TRP cc_start: 0.8802 (m-10) cc_final: 0.8401 (m-10) REVERT: H 339 VAL cc_start: 0.9452 (t) cc_final: 0.9213 (t) REVERT: H 340 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7734 (mmm160) REVERT: H 357 MET cc_start: 0.8340 (tpp) cc_final: 0.7938 (tpp) REVERT: H 372 LEU cc_start: 0.8975 (tt) cc_final: 0.8473 (mm) REVERT: H 431 ASP cc_start: 0.8659 (m-30) cc_final: 0.8116 (t0) outliers start: 93 outliers final: 44 residues processed: 801 average time/residue: 0.1794 time to fit residues: 220.9023 Evaluate side-chains 708 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 656 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 438 SER Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 305 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 252 optimal weight: 10.0000 chunk 320 optimal weight: 5.9990 chunk 7 optimal weight: 0.0770 chunk 240 optimal weight: 9.9990 chunk 343 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 358 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 HIS B 252 GLN B 456 HIS C 332 HIS D 252 GLN D 456 HIS E 117 HIS E 140 ASN E 341 HIS F 121 HIS F 140 ASN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS G 17 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN G 341 HIS H 140 ASN ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.154635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.100807 restraints weight = 54663.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105220 restraints weight = 29566.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108048 restraints weight = 20240.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.109846 restraints weight = 16029.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110929 restraints weight = 13878.266| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27752 Z= 0.212 Angle : 0.635 9.349 37776 Z= 0.325 Chirality : 0.045 0.163 4496 Planarity : 0.005 0.049 5000 Dihedral : 4.225 44.904 4068 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.38 % Allowed : 21.40 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3736 helix: 0.50 (0.13), residues: 1560 sheet: -0.18 (0.20), residues: 664 loop : -0.02 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG H 343 TYR 0.013 0.001 TYR G 381 PHE 0.021 0.001 PHE B 128 TRP 0.009 0.001 TRP G 361 HIS 0.006 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00481 (27752) covalent geometry : angle 0.63490 (37776) hydrogen bonds : bond 0.03838 ( 1104) hydrogen bonds : angle 5.08046 ( 3120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 691 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8581 (ptpp) cc_final: 0.8296 (ptpt) REVERT: A 158 PHE cc_start: 0.8467 (p90) cc_final: 0.8099 (p90) REVERT: A 225 ASN cc_start: 0.9080 (m110) cc_final: 0.8412 (p0) REVERT: A 231 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8837 (mttp) REVERT: A 233 GLN cc_start: 0.9212 (tt0) cc_final: 0.8737 (tp-100) REVERT: A 302 MET cc_start: 0.8105 (mmm) cc_final: 0.7723 (tpp) REVERT: A 355 ASN cc_start: 0.9193 (t0) cc_final: 0.8807 (m-40) REVERT: A 379 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7627 (mtm180) REVERT: A 426 ARG cc_start: 0.8659 (mtm110) cc_final: 0.8246 (mtm-85) REVERT: B 53 MET cc_start: 0.8649 (mtp) cc_final: 0.8272 (mmm) REVERT: B 63 GLU cc_start: 0.8747 (tt0) cc_final: 0.8523 (tt0) REVERT: B 98 ASP cc_start: 0.7794 (t70) cc_final: 0.7177 (t70) REVERT: B 115 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8589 (tp) REVERT: B 118 LYS cc_start: 0.8970 (pptt) cc_final: 0.8361 (ttpp) REVERT: B 202 ARG cc_start: 0.9162 (mtm-85) cc_final: 0.8455 (mtm-85) REVERT: B 224 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.8765 (tt) REVERT: B 254 LYS cc_start: 0.8469 (tppt) cc_final: 0.7817 (tppt) REVERT: B 302 MET cc_start: 0.7783 (ttt) cc_final: 0.7419 (tmm) REVERT: B 308 MET cc_start: 0.8557 (tpp) cc_final: 0.8307 (mmm) REVERT: B 321 GLU cc_start: 0.7904 (tt0) cc_final: 0.7690 (tt0) REVERT: B 357 MET cc_start: 0.8952 (tpp) cc_final: 0.8694 (ttm) REVERT: B 367 GLU cc_start: 0.8524 (mp0) cc_final: 0.8203 (mp0) REVERT: B 373 LEU cc_start: 0.8624 (mp) cc_final: 0.8066 (tp) REVERT: B 374 PHE cc_start: 0.8761 (m-80) cc_final: 0.8081 (m-80) REVERT: B 381 TYR cc_start: 0.8727 (p90) cc_final: 0.8365 (p90) REVERT: B 382 LYS cc_start: 0.7615 (mttt) cc_final: 0.7202 (mtpt) REVERT: B 430 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7351 (mt-10) REVERT: B 431 ASP cc_start: 0.8743 (m-30) cc_final: 0.8226 (t0) REVERT: B 451 ASN cc_start: 0.8616 (p0) cc_final: 0.8394 (p0) REVERT: C 68 ARG cc_start: 0.8280 (mmt180) cc_final: 0.7664 (mmt180) REVERT: C 118 LYS cc_start: 0.8579 (ptpp) cc_final: 0.8306 (ptpt) REVERT: C 158 PHE cc_start: 0.8462 (p90) cc_final: 0.8091 (p90) REVERT: C 231 LYS cc_start: 0.9117 (mtmt) cc_final: 0.8847 (mttp) REVERT: C 233 GLN cc_start: 0.9202 (tt0) cc_final: 0.8733 (tp-100) REVERT: C 302 MET cc_start: 0.8100 (mmm) cc_final: 0.7711 (tpp) REVERT: C 321 GLU cc_start: 0.7740 (tt0) cc_final: 0.7531 (tt0) REVERT: C 355 ASN cc_start: 0.9201 (t0) cc_final: 0.8820 (m-40) REVERT: C 379 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7663 (mtm180) REVERT: C 426 ARG cc_start: 0.8746 (mtm110) cc_final: 0.8417 (ptp-170) REVERT: C 430 GLU cc_start: 0.8505 (mp0) cc_final: 0.8220 (mm-30) REVERT: D 53 MET cc_start: 0.8686 (mtp) cc_final: 0.8121 (mmm) REVERT: D 63 GLU cc_start: 0.8750 (tt0) cc_final: 0.8527 (tt0) REVERT: D 98 ASP cc_start: 0.7816 (t70) cc_final: 0.7202 (t70) REVERT: D 115 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8850 (mt) REVERT: D 118 LYS cc_start: 0.8975 (pptt) cc_final: 0.8721 (pptt) REVERT: D 174 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9128 (tp) REVERT: D 202 ARG cc_start: 0.9166 (mtm-85) cc_final: 0.8455 (mtm-85) REVERT: D 302 MET cc_start: 0.7786 (ttt) cc_final: 0.7421 (tmm) REVERT: D 308 MET cc_start: 0.8528 (tpp) cc_final: 0.8278 (mmm) REVERT: D 321 GLU cc_start: 0.7907 (tt0) cc_final: 0.7695 (tt0) REVERT: D 357 MET cc_start: 0.8964 (tpp) cc_final: 0.8711 (ttm) REVERT: D 367 GLU cc_start: 0.8536 (mp0) cc_final: 0.8194 (mp0) REVERT: D 373 LEU cc_start: 0.8620 (mp) cc_final: 0.8064 (tp) REVERT: D 374 PHE cc_start: 0.8761 (m-80) cc_final: 0.8083 (m-80) REVERT: D 381 TYR cc_start: 0.8727 (p90) cc_final: 0.8360 (p90) REVERT: D 382 LYS cc_start: 0.7609 (mttt) cc_final: 0.7199 (mtpt) REVERT: D 430 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7352 (mt-10) REVERT: D 431 ASP cc_start: 0.8756 (m-30) cc_final: 0.7947 (t0) REVERT: D 451 ASN cc_start: 0.8600 (p0) cc_final: 0.8393 (p0) REVERT: E 13 ASP cc_start: 0.8546 (m-30) cc_final: 0.7771 (m-30) REVERT: E 117 HIS cc_start: 0.6969 (m170) cc_final: 0.6700 (m-70) REVERT: E 135 LEU cc_start: 0.8371 (mm) cc_final: 0.8168 (mm) REVERT: E 174 LEU cc_start: 0.9263 (mt) cc_final: 0.8887 (tp) REVERT: E 184 MET cc_start: -0.2210 (mmm) cc_final: -0.2809 (mmm) REVERT: E 227 ASP cc_start: 0.8016 (p0) cc_final: 0.7717 (p0) REVERT: E 249 HIS cc_start: 0.7415 (t70) cc_final: 0.6750 (t70) REVERT: E 278 SER cc_start: 0.7954 (t) cc_final: 0.7665 (t) REVERT: E 308 MET cc_start: 0.8367 (mmm) cc_final: 0.8093 (tpt) REVERT: E 340 ARG cc_start: 0.8045 (tpp80) cc_final: 0.7672 (tpp80) REVERT: E 357 MET cc_start: 0.7269 (tpp) cc_final: 0.6780 (tpp) REVERT: E 381 TYR cc_start: 0.7323 (p90) cc_final: 0.6638 (p90) REVERT: E 420 MET cc_start: 0.7941 (tpt) cc_final: 0.7725 (tpp) REVERT: E 426 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.6973 (ttm170) REVERT: E 438 SER cc_start: 0.8125 (OUTLIER) cc_final: 0.7813 (p) REVERT: E 458 LYS cc_start: 0.8468 (pttt) cc_final: 0.8155 (pttt) REVERT: E 464 GLN cc_start: 0.8423 (pm20) cc_final: 0.8097 (pm20) REVERT: F 16 TYR cc_start: 0.9338 (m-10) cc_final: 0.8123 (m-10) REVERT: F 53 MET cc_start: 0.8356 (mtp) cc_final: 0.7767 (mmm) REVERT: F 184 MET cc_start: 0.7420 (tpp) cc_final: 0.7044 (tpp) REVERT: F 202 ARG cc_start: 0.9239 (mtm-85) cc_final: 0.8985 (mpp80) REVERT: F 218 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7887 (mp) REVERT: F 222 VAL cc_start: 0.8911 (m) cc_final: 0.8594 (p) REVERT: F 231 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8556 (ptpt) REVERT: F 255 MET cc_start: 0.8185 (tpp) cc_final: 0.7962 (tpt) REVERT: F 278 SER cc_start: 0.9056 (t) cc_final: 0.8729 (t) REVERT: F 339 VAL cc_start: 0.9559 (t) cc_final: 0.9243 (p) REVERT: F 340 ARG cc_start: 0.8283 (mmm160) cc_final: 0.7928 (mmm160) REVERT: F 349 LEU cc_start: 0.9124 (mm) cc_final: 0.8813 (mm) REVERT: F 357 MET cc_start: 0.8362 (tpp) cc_final: 0.8047 (tpp) REVERT: F 358 ILE cc_start: 0.8715 (mt) cc_final: 0.8274 (mt) REVERT: F 431 ASP cc_start: 0.8792 (m-30) cc_final: 0.8338 (t0) REVERT: G 13 ASP cc_start: 0.8535 (m-30) cc_final: 0.7809 (m-30) REVERT: G 135 LEU cc_start: 0.8448 (mm) cc_final: 0.8236 (mm) REVERT: G 174 LEU cc_start: 0.9283 (mt) cc_final: 0.8936 (tp) REVERT: G 213 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8962 (ptmt) REVERT: G 227 ASP cc_start: 0.7896 (p0) cc_final: 0.7601 (p0) REVERT: G 249 HIS cc_start: 0.7464 (t70) cc_final: 0.6780 (t70) REVERT: G 278 SER cc_start: 0.7975 (t) cc_final: 0.7676 (t) REVERT: G 336 ASP cc_start: 0.8256 (t0) cc_final: 0.8010 (m-30) REVERT: G 340 ARG cc_start: 0.8033 (tpp80) cc_final: 0.7672 (tpp80) REVERT: G 357 MET cc_start: 0.7300 (tpp) cc_final: 0.6994 (tpp) REVERT: G 381 TYR cc_start: 0.7281 (p90) cc_final: 0.7061 (p90) REVERT: G 419 ARG cc_start: 0.6594 (mmm-85) cc_final: 0.6360 (mmm-85) REVERT: G 426 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.6919 (ttm170) REVERT: G 438 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7854 (p) REVERT: G 458 LYS cc_start: 0.8453 (pttt) cc_final: 0.8134 (pttt) REVERT: G 464 GLN cc_start: 0.8466 (pm20) cc_final: 0.8131 (pm20) REVERT: H 16 TYR cc_start: 0.9329 (m-10) cc_final: 0.8053 (m-10) REVERT: H 53 MET cc_start: 0.8356 (mtp) cc_final: 0.7776 (mmm) REVERT: H 59 ARG cc_start: 0.7623 (ptm160) cc_final: 0.7246 (ttm110) REVERT: H 76 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: H 119 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7845 (mmm160) REVERT: H 184 MET cc_start: 0.7317 (tpp) cc_final: 0.6917 (tpp) REVERT: H 202 ARG cc_start: 0.9243 (mtm-85) cc_final: 0.8989 (mpp80) REVERT: H 218 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7951 (mp) REVERT: H 231 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8613 (ptpt) REVERT: H 255 MET cc_start: 0.7816 (mmm) cc_final: 0.7579 (tpt) REVERT: H 278 SER cc_start: 0.9042 (t) cc_final: 0.8718 (t) REVERT: H 315 GLN cc_start: 0.8275 (tp40) cc_final: 0.7963 (tp-100) REVERT: H 334 TRP cc_start: 0.8940 (m-10) cc_final: 0.8442 (m-10) REVERT: H 340 ARG cc_start: 0.7917 (mmm160) cc_final: 0.7602 (tpp-160) REVERT: H 357 MET cc_start: 0.8359 (tpp) cc_final: 0.8006 (tpp) REVERT: H 362 PHE cc_start: 0.8919 (m-80) cc_final: 0.8500 (m-80) REVERT: H 373 LEU cc_start: 0.8348 (mp) cc_final: 0.8132 (tp) REVERT: H 412 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8568 (mm-30) REVERT: H 431 ASP cc_start: 0.8793 (m-30) cc_final: 0.8336 (t0) outliers start: 123 outliers final: 67 residues processed: 758 average time/residue: 0.1835 time to fit residues: 212.1969 Evaluate side-chains 728 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 652 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 259 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 396 ARG Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 396 ARG Chi-restraints excluded: chain G residue 438 SER Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 433 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 4 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 320 optimal weight: 4.9990 chunk 311 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 351 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 GLN F 435 HIS ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.157691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103878 restraints weight = 53880.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108125 restraints weight = 29561.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110878 restraints weight = 20486.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112610 restraints weight = 16293.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113711 restraints weight = 14178.335| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27752 Z= 0.180 Angle : 0.606 8.937 37776 Z= 0.309 Chirality : 0.044 0.158 4496 Planarity : 0.004 0.045 5000 Dihedral : 4.151 46.730 4068 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.42 % Allowed : 22.76 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3736 helix: 0.74 (0.13), residues: 1504 sheet: -0.33 (0.20), residues: 664 loop : -0.13 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 60 TYR 0.014 0.001 TYR F 12 PHE 0.023 0.001 PHE D 128 TRP 0.011 0.001 TRP G 361 HIS 0.005 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00412 (27752) covalent geometry : angle 0.60561 (37776) hydrogen bonds : bond 0.03582 ( 1104) hydrogen bonds : angle 4.93969 ( 3120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 693 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 PHE cc_start: 0.8524 (p90) cc_final: 0.8116 (p90) REVERT: A 184 MET cc_start: 0.7858 (tpp) cc_final: 0.7611 (tpp) REVERT: A 231 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8768 (mttp) REVERT: A 233 GLN cc_start: 0.9197 (tt0) cc_final: 0.8801 (tp-100) REVERT: A 355 ASN cc_start: 0.9148 (t0) cc_final: 0.8829 (m-40) REVERT: A 377 ASP cc_start: 0.8924 (t0) cc_final: 0.8520 (t0) REVERT: A 379 ARG cc_start: 0.7920 (mtm180) cc_final: 0.7578 (mtm180) REVERT: A 426 ARG cc_start: 0.8766 (mtm110) cc_final: 0.8382 (ptp-170) REVERT: B 53 MET cc_start: 0.8599 (mtp) cc_final: 0.8293 (mmm) REVERT: B 115 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8735 (tp) REVERT: B 118 LYS cc_start: 0.8957 (pptt) cc_final: 0.8609 (pptt) REVERT: B 184 MET cc_start: 0.8367 (mmm) cc_final: 0.8119 (mmm) REVERT: B 202 ARG cc_start: 0.9165 (mtm-85) cc_final: 0.8161 (mtm-85) REVERT: B 224 ILE cc_start: 0.9436 (pt) cc_final: 0.9170 (pt) REVERT: B 254 LYS cc_start: 0.8469 (tppt) cc_final: 0.7913 (tppt) REVERT: B 302 MET cc_start: 0.7694 (ttt) cc_final: 0.7247 (tmm) REVERT: B 308 MET cc_start: 0.8511 (tpp) cc_final: 0.8294 (mmm) REVERT: B 321 GLU cc_start: 0.7853 (tt0) cc_final: 0.7640 (tt0) REVERT: B 373 LEU cc_start: 0.8682 (mp) cc_final: 0.8167 (tp) REVERT: B 374 PHE cc_start: 0.8776 (m-80) cc_final: 0.8162 (m-10) REVERT: B 381 TYR cc_start: 0.8809 (p90) cc_final: 0.8249 (p90) REVERT: B 430 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7204 (mt-10) REVERT: B 431 ASP cc_start: 0.8707 (m-30) cc_final: 0.7890 (t0) REVERT: B 438 SER cc_start: 0.9271 (OUTLIER) cc_final: 0.8861 (p) REVERT: C 68 ARG cc_start: 0.8299 (mmt180) cc_final: 0.7699 (mmt90) REVERT: C 118 LYS cc_start: 0.8594 (ptpp) cc_final: 0.8374 (ptpp) REVERT: C 158 PHE cc_start: 0.8497 (p90) cc_final: 0.8076 (p90) REVERT: C 184 MET cc_start: 0.7871 (tpp) cc_final: 0.7622 (tpp) REVERT: C 231 LYS cc_start: 0.9115 (mtmt) cc_final: 0.8764 (mttp) REVERT: C 233 GLN cc_start: 0.9200 (tt0) cc_final: 0.8819 (tp-100) REVERT: C 355 ASN cc_start: 0.9157 (t0) cc_final: 0.8850 (m-40) REVERT: C 377 ASP cc_start: 0.8959 (t0) cc_final: 0.8546 (t0) REVERT: C 379 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7663 (mtm180) REVERT: C 426 ARG cc_start: 0.8908 (mtm110) cc_final: 0.8697 (mtm-85) REVERT: D 53 MET cc_start: 0.8663 (mtp) cc_final: 0.8322 (mmm) REVERT: D 98 ASP cc_start: 0.7799 (t70) cc_final: 0.7442 (t70) REVERT: D 115 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8814 (mt) REVERT: D 118 LYS cc_start: 0.8967 (pptt) cc_final: 0.8667 (pptt) REVERT: D 174 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9154 (tp) REVERT: D 202 ARG cc_start: 0.9171 (mtm-85) cc_final: 0.8178 (mtm-85) REVERT: D 260 LYS cc_start: 0.9091 (pptt) cc_final: 0.8833 (pttp) REVERT: D 302 MET cc_start: 0.7787 (ttt) cc_final: 0.7252 (tmm) REVERT: D 308 MET cc_start: 0.8488 (tpp) cc_final: 0.8286 (mmm) REVERT: D 321 GLU cc_start: 0.7855 (tt0) cc_final: 0.7638 (tt0) REVERT: D 344 ASP cc_start: 0.8489 (m-30) cc_final: 0.8198 (m-30) REVERT: D 373 LEU cc_start: 0.8674 (mp) cc_final: 0.8153 (tp) REVERT: D 374 PHE cc_start: 0.8782 (m-80) cc_final: 0.8168 (m-10) REVERT: D 381 TYR cc_start: 0.8821 (p90) cc_final: 0.8277 (p90) REVERT: D 430 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7212 (mt-10) REVERT: D 431 ASP cc_start: 0.8707 (m-30) cc_final: 0.7886 (t0) REVERT: D 438 SER cc_start: 0.9275 (OUTLIER) cc_final: 0.8858 (p) REVERT: E 13 ASP cc_start: 0.8538 (m-30) cc_final: 0.8058 (m-30) REVERT: E 103 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7961 (mm) REVERT: E 174 LEU cc_start: 0.9320 (mt) cc_final: 0.8948 (tp) REVERT: E 227 ASP cc_start: 0.7970 (p0) cc_final: 0.7591 (p0) REVERT: E 249 HIS cc_start: 0.7557 (t70) cc_final: 0.7305 (t70) REVERT: E 307 MET cc_start: 0.8039 (mtp) cc_final: 0.7220 (ptp) REVERT: E 308 MET cc_start: 0.8444 (mmm) cc_final: 0.8079 (tpt) REVERT: E 316 PHE cc_start: 0.9467 (t80) cc_final: 0.9232 (t80) REVERT: E 340 ARG cc_start: 0.7903 (tpp80) cc_final: 0.7439 (tpp80) REVERT: E 373 LEU cc_start: 0.8225 (tt) cc_final: 0.7742 (pt) REVERT: E 381 TYR cc_start: 0.7434 (p90) cc_final: 0.6865 (p90) REVERT: E 408 LYS cc_start: 0.8795 (mttt) cc_final: 0.8547 (mptt) REVERT: E 426 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7233 (ttm170) REVERT: E 438 SER cc_start: 0.8162 (OUTLIER) cc_final: 0.7901 (p) REVERT: E 458 LYS cc_start: 0.8527 (pttt) cc_final: 0.8246 (pttt) REVERT: F 16 TYR cc_start: 0.9367 (m-10) cc_final: 0.8225 (m-10) REVERT: F 76 GLN cc_start: 0.8077 (pt0) cc_final: 0.7660 (tt0) REVERT: F 184 MET cc_start: 0.7767 (tpp) cc_final: 0.7445 (tpp) REVERT: F 206 TYR cc_start: 0.8811 (m-80) cc_final: 0.8496 (m-10) REVERT: F 218 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7891 (mp) REVERT: F 222 VAL cc_start: 0.8906 (m) cc_final: 0.8251 (p) REVERT: F 231 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8528 (mtmt) REVERT: F 260 LYS cc_start: 0.9006 (mtmt) cc_final: 0.8793 (ptpp) REVERT: F 275 ASN cc_start: 0.7467 (m110) cc_final: 0.6848 (m110) REVERT: F 278 SER cc_start: 0.9057 (t) cc_final: 0.8198 (p) REVERT: F 339 VAL cc_start: 0.9560 (t) cc_final: 0.9103 (t) REVERT: F 340 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7870 (mmm160) REVERT: F 349 LEU cc_start: 0.9136 (mm) cc_final: 0.8851 (mm) REVERT: F 358 ILE cc_start: 0.8929 (mt) cc_final: 0.8381 (mm) REVERT: F 374 PHE cc_start: 0.8815 (m-80) cc_final: 0.8445 (m-10) REVERT: F 458 LYS cc_start: 0.8582 (ptmm) cc_final: 0.8315 (pttp) REVERT: G 13 ASP cc_start: 0.8520 (m-30) cc_final: 0.8053 (m-30) REVERT: G 103 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7979 (mm) REVERT: G 174 LEU cc_start: 0.9315 (mt) cc_final: 0.8923 (tp) REVERT: G 227 ASP cc_start: 0.7860 (p0) cc_final: 0.7475 (p0) REVERT: G 249 HIS cc_start: 0.7601 (t70) cc_final: 0.6869 (t70) REVERT: G 294 LYS cc_start: 0.5794 (mmmt) cc_final: 0.5590 (mmmt) REVERT: G 308 MET cc_start: 0.8764 (tpp) cc_final: 0.8536 (tpp) REVERT: G 340 ARG cc_start: 0.7912 (tpp80) cc_final: 0.7400 (tpp80) REVERT: G 373 LEU cc_start: 0.8201 (tt) cc_final: 0.7670 (pt) REVERT: G 381 TYR cc_start: 0.7555 (p90) cc_final: 0.6617 (p90) REVERT: G 426 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7132 (ttm170) REVERT: G 438 SER cc_start: 0.8184 (OUTLIER) cc_final: 0.7930 (p) REVERT: G 458 LYS cc_start: 0.8493 (pttt) cc_final: 0.8213 (pttt) REVERT: H 16 TYR cc_start: 0.9306 (m-10) cc_final: 0.8194 (m-10) REVERT: H 91 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8405 (mmmt) REVERT: H 119 ARG cc_start: 0.8511 (mmm160) cc_final: 0.7978 (mmm160) REVERT: H 184 MET cc_start: 0.7777 (tpp) cc_final: 0.7455 (tpp) REVERT: H 206 TYR cc_start: 0.8816 (m-80) cc_final: 0.8348 (m-10) REVERT: H 218 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7904 (mp) REVERT: H 224 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5320 (mt) REVERT: H 231 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8536 (ptpt) REVERT: H 255 MET cc_start: 0.7854 (mmm) cc_final: 0.7620 (tpt) REVERT: H 278 SER cc_start: 0.9052 (t) cc_final: 0.8181 (p) REVERT: H 315 GLN cc_start: 0.8241 (tp40) cc_final: 0.7890 (tp-100) REVERT: H 334 TRP cc_start: 0.8966 (m-10) cc_final: 0.8384 (m-10) REVERT: H 336 ASP cc_start: 0.8598 (t0) cc_final: 0.8080 (m-30) REVERT: H 340 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7491 (tpp-160) REVERT: H 343 ARG cc_start: 0.8240 (ptp90) cc_final: 0.7616 (ptp90) REVERT: H 357 MET cc_start: 0.8423 (tpp) cc_final: 0.7999 (tpp) REVERT: H 372 LEU cc_start: 0.9179 (tt) cc_final: 0.8605 (mm) REVERT: H 373 LEU cc_start: 0.8517 (mp) cc_final: 0.8225 (mt) REVERT: H 374 PHE cc_start: 0.8581 (m-80) cc_final: 0.8201 (m-10) REVERT: H 412 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8616 (mm-30) REVERT: H 431 ASP cc_start: 0.8707 (m-30) cc_final: 0.7905 (t0) outliers start: 124 outliers final: 71 residues processed: 767 average time/residue: 0.1985 time to fit residues: 231.3168 Evaluate side-chains 732 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 649 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 396 ARG Chi-restraints excluded: chain G residue 438 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain H residue 224 ILE Chi-restraints excluded: chain H residue 259 ILE Chi-restraints excluded: chain H residue 275 ASN Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 432 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 184 optimal weight: 5.9990 chunk 164 optimal weight: 0.0040 chunk 201 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 326 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN B 252 GLN F 251 HIS ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 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 = 0.4092 r_free = 0.4092 target = 0.157494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103096 restraints weight = 54670.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107798 restraints weight = 31440.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110025 restraints weight = 19956.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111616 restraints weight = 16563.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111879 restraints weight = 16114.992| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 27752 Z= 0.189 Angle : 0.628 9.227 37776 Z= 0.318 Chirality : 0.044 0.194 4496 Planarity : 0.004 0.045 5000 Dihedral : 4.160 47.910 4068 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.88 % Allowed : 23.93 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3736 helix: 0.78 (0.13), residues: 1496 sheet: -0.61 (0.22), residues: 584 loop : -0.09 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 327 TYR 0.016 0.001 TYR H 12 PHE 0.019 0.001 PHE B 128 TRP 0.007 0.001 TRP E 361 HIS 0.005 0.001 HIS E 435 Details of bonding type rmsd covalent geometry : bond 0.00432 (27752) covalent geometry : angle 0.62777 (37776) hydrogen bonds : bond 0.03610 ( 1104) hydrogen bonds : angle 4.95472 ( 3120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 668 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8565 (ptpt) cc_final: 0.8314 (ptpp) REVERT: A 158 PHE cc_start: 0.8509 (p90) cc_final: 0.8058 (p90) REVERT: A 184 MET cc_start: 0.7880 (tpp) cc_final: 0.7446 (tpp) REVERT: A 231 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8724 (mttp) REVERT: A 233 GLN cc_start: 0.9232 (tt0) cc_final: 0.8793 (tp-100) REVERT: A 355 ASN cc_start: 0.9140 (t0) cc_final: 0.8827 (m-40) REVERT: A 377 ASP cc_start: 0.8994 (t0) cc_final: 0.8625 (t0) REVERT: A 379 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7517 (mtm180) REVERT: A 426 ARG cc_start: 0.8821 (mtm110) cc_final: 0.8486 (ptp-170) REVERT: B 46 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8435 (pt) REVERT: B 53 MET cc_start: 0.8741 (mtp) cc_final: 0.8277 (mmm) REVERT: B 115 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8734 (tp) REVERT: B 118 LYS cc_start: 0.8955 (pptt) cc_final: 0.8624 (pttp) REVERT: B 202 ARG cc_start: 0.9254 (mtm-85) cc_final: 0.8160 (mtm-85) REVERT: B 224 ILE cc_start: 0.9466 (pt) cc_final: 0.8875 (mt) REVERT: B 254 LYS cc_start: 0.8505 (tppt) cc_final: 0.7984 (tppt) REVERT: B 264 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8822 (p) REVERT: B 302 MET cc_start: 0.7714 (ttt) cc_final: 0.7250 (tmm) REVERT: B 344 ASP cc_start: 0.8548 (m-30) cc_final: 0.8309 (m-30) REVERT: B 357 MET cc_start: 0.8910 (ttm) cc_final: 0.8555 (mtp) REVERT: B 367 GLU cc_start: 0.8475 (mp0) cc_final: 0.7738 (mp0) REVERT: B 373 LEU cc_start: 0.8642 (mp) cc_final: 0.8253 (mt) REVERT: B 374 PHE cc_start: 0.8873 (m-80) cc_final: 0.8203 (m-10) REVERT: B 430 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7379 (mt-10) REVERT: B 431 ASP cc_start: 0.8741 (m-30) cc_final: 0.7898 (t0) REVERT: B 438 SER cc_start: 0.9259 (OUTLIER) cc_final: 0.8838 (p) REVERT: C 56 VAL cc_start: 0.9471 (t) cc_final: 0.9238 (p) REVERT: C 68 ARG cc_start: 0.8337 (mmt180) cc_final: 0.7730 (mmt90) REVERT: C 118 LYS cc_start: 0.8508 (ptpp) cc_final: 0.8212 (ptpp) REVERT: C 158 PHE cc_start: 0.8489 (p90) cc_final: 0.8047 (p90) REVERT: C 184 MET cc_start: 0.7889 (tpp) cc_final: 0.7454 (tpp) REVERT: C 231 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8720 (mttp) REVERT: C 233 GLN cc_start: 0.9235 (tt0) cc_final: 0.8789 (tp-100) REVERT: C 355 ASN cc_start: 0.9142 (t0) cc_final: 0.8831 (m-40) REVERT: C 377 ASP cc_start: 0.9004 (t0) cc_final: 0.8628 (t0) REVERT: C 379 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7525 (mtm180) REVERT: C 426 ARG cc_start: 0.8979 (mtm110) cc_final: 0.8752 (mtm-85) REVERT: D 53 MET cc_start: 0.8758 (mtp) cc_final: 0.8272 (mmm) REVERT: D 115 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8770 (tp) REVERT: D 118 LYS cc_start: 0.8972 (pptt) cc_final: 0.8665 (pptt) REVERT: D 174 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9136 (tp) REVERT: D 184 MET cc_start: 0.8289 (mmm) cc_final: 0.8027 (mmm) REVERT: D 202 ARG cc_start: 0.9274 (mtm-85) cc_final: 0.8152 (mtm-85) REVERT: D 241 ASP cc_start: 0.7933 (t0) cc_final: 0.7728 (t0) REVERT: D 255 MET cc_start: 0.8667 (tpp) cc_final: 0.8351 (tpp) REVERT: D 302 MET cc_start: 0.7713 (ttt) cc_final: 0.7271 (tmm) REVERT: D 344 ASP cc_start: 0.8569 (m-30) cc_final: 0.8345 (m-30) REVERT: D 357 MET cc_start: 0.8925 (ttm) cc_final: 0.8570 (mtp) REVERT: D 367 GLU cc_start: 0.8489 (mp0) cc_final: 0.7761 (mp0) REVERT: D 373 LEU cc_start: 0.8664 (mp) cc_final: 0.8274 (mt) REVERT: D 374 PHE cc_start: 0.8861 (m-80) cc_final: 0.8201 (m-10) REVERT: D 430 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7375 (mt-10) REVERT: D 431 ASP cc_start: 0.8737 (m-30) cc_final: 0.7899 (t0) REVERT: E 13 ASP cc_start: 0.8492 (m-30) cc_final: 0.8062 (m-30) REVERT: E 103 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8088 (mm) REVERT: E 174 LEU cc_start: 0.9346 (mt) cc_final: 0.8719 (tt) REVERT: E 184 MET cc_start: -0.2288 (mmm) cc_final: -0.2551 (mmm) REVERT: E 213 LYS cc_start: 0.9187 (mtpp) cc_final: 0.8883 (mtmm) REVERT: E 227 ASP cc_start: 0.8082 (p0) cc_final: 0.7689 (p0) REVERT: E 249 HIS cc_start: 0.7756 (t70) cc_final: 0.7315 (t70) REVERT: E 307 MET cc_start: 0.8028 (mtp) cc_final: 0.7564 (ptp) REVERT: E 308 MET cc_start: 0.8425 (mmm) cc_final: 0.8007 (tpt) REVERT: E 340 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7481 (tpp80) REVERT: E 357 MET cc_start: 0.7287 (tpp) cc_final: 0.7002 (tpp) REVERT: E 373 LEU cc_start: 0.8049 (tt) cc_final: 0.7556 (pt) REVERT: E 381 TYR cc_start: 0.7688 (p90) cc_final: 0.5660 (p90) REVERT: E 383 GLU cc_start: 0.8713 (mt-10) cc_final: 0.7787 (mp0) REVERT: E 438 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7918 (p) REVERT: E 458 LYS cc_start: 0.8569 (pttt) cc_final: 0.8264 (pttt) REVERT: F 16 TYR cc_start: 0.9349 (m-10) cc_final: 0.8330 (m-10) REVERT: F 184 MET cc_start: 0.8030 (tpp) cc_final: 0.7659 (tpp) REVERT: F 202 ARG cc_start: 0.9074 (mtm-85) cc_final: 0.8805 (mtm-85) REVERT: F 218 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7951 (mp) REVERT: F 222 VAL cc_start: 0.9037 (m) cc_final: 0.8771 (p) REVERT: F 224 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.5811 (mt) REVERT: F 231 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8489 (mtmt) REVERT: F 278 SER cc_start: 0.8841 (t) cc_final: 0.8273 (p) REVERT: F 339 VAL cc_start: 0.9533 (t) cc_final: 0.9097 (p) REVERT: F 340 ARG cc_start: 0.8293 (mmm160) cc_final: 0.7939 (mmm160) REVERT: F 349 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8842 (mm) REVERT: F 374 PHE cc_start: 0.8739 (m-80) cc_final: 0.8429 (m-10) REVERT: G 13 ASP cc_start: 0.8500 (m-30) cc_final: 0.8055 (m-30) REVERT: G 103 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8178 (mm) REVERT: G 174 LEU cc_start: 0.9328 (mt) cc_final: 0.8686 (tt) REVERT: G 184 MET cc_start: -0.2475 (mmm) cc_final: -0.2724 (mmm) REVERT: G 202 ARG cc_start: 0.8389 (mtt90) cc_final: 0.7960 (mtm-85) REVERT: G 213 LYS cc_start: 0.9248 (mtpp) cc_final: 0.8967 (ptmt) REVERT: G 227 ASP cc_start: 0.8030 (p0) cc_final: 0.7634 (p0) REVERT: G 249 HIS cc_start: 0.7642 (t70) cc_final: 0.6795 (t70) REVERT: G 255 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6555 (mpp) REVERT: G 307 MET cc_start: 0.7994 (mpp) cc_final: 0.7658 (mpp) REVERT: G 308 MET cc_start: 0.8582 (tpp) cc_final: 0.8173 (tpp) REVERT: G 340 ARG cc_start: 0.7854 (tpp80) cc_final: 0.7490 (tpp80) REVERT: G 357 MET cc_start: 0.7262 (tpp) cc_final: 0.6986 (tpp) REVERT: G 373 LEU cc_start: 0.8108 (tt) cc_final: 0.7664 (pt) REVERT: G 379 ARG cc_start: 0.7681 (tpt-90) cc_final: 0.7358 (tpt-90) REVERT: G 381 TYR cc_start: 0.7323 (p90) cc_final: 0.6687 (p90) REVERT: G 426 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7057 (ttm170) REVERT: G 438 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7884 (p) REVERT: G 458 LYS cc_start: 0.8569 (pttt) cc_final: 0.8260 (pttt) REVERT: H 16 TYR cc_start: 0.9316 (m-10) cc_final: 0.8275 (m-10) REVERT: H 61 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6176 (pmm) REVERT: H 91 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8619 (mmmt) REVERT: H 119 ARG cc_start: 0.8467 (mmm160) cc_final: 0.8196 (mmp80) REVERT: H 184 MET cc_start: 0.8043 (tpp) cc_final: 0.7720 (tpp) REVERT: H 202 ARG cc_start: 0.9178 (mtm-85) cc_final: 0.8754 (mtm-85) REVERT: H 224 ILE cc_start: 0.5902 (OUTLIER) cc_final: 0.5333 (mt) REVERT: H 231 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8489 (ptpt) REVERT: H 255 MET cc_start: 0.7925 (mmm) cc_final: 0.7649 (tpt) REVERT: H 278 SER cc_start: 0.8836 (t) cc_final: 0.8269 (p) REVERT: H 315 GLN cc_start: 0.8307 (tp40) cc_final: 0.7941 (tp-100) REVERT: H 334 TRP cc_start: 0.8985 (m-10) cc_final: 0.8429 (m-10) REVERT: H 340 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7551 (tpp-160) REVERT: H 357 MET cc_start: 0.8395 (tpp) cc_final: 0.8009 (tpp) REVERT: H 373 LEU cc_start: 0.8439 (mp) cc_final: 0.8108 (mt) REVERT: H 374 PHE cc_start: 0.8629 (m-80) cc_final: 0.8320 (m-10) REVERT: H 458 LYS cc_start: 0.8751 (ptmm) cc_final: 0.8535 (pttp) outliers start: 137 outliers final: 91 residues processed: 751 average time/residue: 0.1981 time to fit residues: 226.7408 Evaluate side-chains 747 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 640 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain C residue 53 MET Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 396 ARG Chi-restraints excluded: chain G residue 438 SER Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 176 HIS Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 224 ILE Chi-restraints excluded: chain H residue 259 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 263 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 353 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 304 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 GLN F 328 GLN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 328 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.157382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103325 restraints weight = 54170.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107536 restraints weight = 29920.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.110226 restraints weight = 20781.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111892 restraints weight = 16605.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.112962 restraints weight = 14509.909| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27752 Z= 0.184 Angle : 0.638 8.314 37776 Z= 0.322 Chirality : 0.044 0.188 4496 Planarity : 0.004 0.055 5000 Dihedral : 4.170 49.121 4068 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.27 % Allowed : 25.43 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3736 helix: 0.71 (0.13), residues: 1520 sheet: -0.91 (0.21), residues: 600 loop : -0.13 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 327 TYR 0.015 0.001 TYR B 381 PHE 0.021 0.001 PHE G 128 TRP 0.007 0.001 TRP G 334 HIS 0.005 0.001 HIS F 251 Details of bonding type rmsd covalent geometry : bond 0.00426 (27752) covalent geometry : angle 0.63789 (37776) hydrogen bonds : bond 0.03620 ( 1104) hydrogen bonds : angle 4.94050 ( 3120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 648 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 56 VAL cc_start: 0.9472 (t) cc_final: 0.9259 (p) REVERT: A 118 LYS cc_start: 0.8633 (ptpt) cc_final: 0.8361 (ptpp) REVERT: A 158 PHE cc_start: 0.8509 (p90) cc_final: 0.8121 (p90) REVERT: A 184 MET cc_start: 0.7924 (tpp) cc_final: 0.7507 (tpp) REVERT: A 231 LYS cc_start: 0.9109 (mtmt) cc_final: 0.8791 (mttp) REVERT: A 233 GLN cc_start: 0.9208 (tt0) cc_final: 0.8787 (tp-100) REVERT: A 340 ARG cc_start: 0.8464 (tpp80) cc_final: 0.8197 (tpp80) REVERT: A 355 ASN cc_start: 0.9119 (t0) cc_final: 0.8823 (m-40) REVERT: A 377 ASP cc_start: 0.8981 (t0) cc_final: 0.8584 (t0) REVERT: A 379 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7563 (mtm180) REVERT: A 426 ARG cc_start: 0.8849 (mtm110) cc_final: 0.8381 (ptp-170) REVERT: B 53 MET cc_start: 0.8683 (mtp) cc_final: 0.8305 (mmm) REVERT: B 98 ASP cc_start: 0.8188 (t0) cc_final: 0.7907 (t70) REVERT: B 115 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8719 (tp) REVERT: B 118 LYS cc_start: 0.9043 (pptt) cc_final: 0.8793 (pptt) REVERT: B 202 ARG cc_start: 0.9246 (mtm-85) cc_final: 0.8194 (mtm-85) REVERT: B 224 ILE cc_start: 0.9409 (pt) cc_final: 0.9024 (tt) REVERT: B 254 LYS cc_start: 0.8510 (tppt) cc_final: 0.7817 (tppt) REVERT: B 302 MET cc_start: 0.7656 (ttt) cc_final: 0.7277 (tmm) REVERT: B 344 ASP cc_start: 0.8547 (m-30) cc_final: 0.8335 (m-30) REVERT: B 357 MET cc_start: 0.8995 (ttm) cc_final: 0.8609 (mtp) REVERT: B 374 PHE cc_start: 0.8820 (m-80) cc_final: 0.8228 (m-10) REVERT: B 430 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7249 (mt-10) REVERT: B 431 ASP cc_start: 0.8743 (m-30) cc_final: 0.7907 (t0) REVERT: C 68 ARG cc_start: 0.8290 (mmt180) cc_final: 0.7697 (mmt90) REVERT: C 118 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8326 (ptpp) REVERT: C 158 PHE cc_start: 0.8496 (p90) cc_final: 0.8115 (p90) REVERT: C 184 MET cc_start: 0.7938 (tpp) cc_final: 0.7522 (tpp) REVERT: C 231 LYS cc_start: 0.9115 (mtmt) cc_final: 0.8788 (mttp) REVERT: C 233 GLN cc_start: 0.9211 (tt0) cc_final: 0.8787 (tp-100) REVERT: C 340 ARG cc_start: 0.8458 (tpp80) cc_final: 0.8198 (tpp80) REVERT: C 355 ASN cc_start: 0.9129 (t0) cc_final: 0.8832 (m-40) REVERT: C 377 ASP cc_start: 0.8980 (t0) cc_final: 0.8585 (t0) REVERT: C 379 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7570 (mtm180) REVERT: C 426 ARG cc_start: 0.8990 (mtm110) cc_final: 0.8762 (mtm-85) REVERT: D 53 MET cc_start: 0.8706 (mtp) cc_final: 0.8327 (mmm) REVERT: D 115 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8767 (tp) REVERT: D 118 LYS cc_start: 0.9012 (pptt) cc_final: 0.8727 (pptt) REVERT: D 174 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9142 (tp) REVERT: D 202 ARG cc_start: 0.9255 (mtm-85) cc_final: 0.8177 (mtm180) REVERT: D 302 MET cc_start: 0.7644 (ttt) cc_final: 0.7275 (tmm) REVERT: D 344 ASP cc_start: 0.8571 (m-30) cc_final: 0.8347 (m-30) REVERT: D 357 MET cc_start: 0.9013 (ttm) cc_final: 0.8641 (mtp) REVERT: D 374 PHE cc_start: 0.8821 (m-80) cc_final: 0.8233 (m-10) REVERT: D 430 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7332 (mt-10) REVERT: D 431 ASP cc_start: 0.8729 (m-30) cc_final: 0.7913 (t0) REVERT: D 438 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.8833 (p) REVERT: E 13 ASP cc_start: 0.8489 (m-30) cc_final: 0.8118 (m-30) REVERT: E 103 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8176 (mm) REVERT: E 174 LEU cc_start: 0.9303 (mt) cc_final: 0.8728 (tt) REVERT: E 202 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7770 (mtm-85) REVERT: E 227 ASP cc_start: 0.8151 (p0) cc_final: 0.7723 (p0) REVERT: E 249 HIS cc_start: 0.7813 (t70) cc_final: 0.6969 (t70) REVERT: E 307 MET cc_start: 0.8106 (mtp) cc_final: 0.7245 (ptp) REVERT: E 308 MET cc_start: 0.8394 (mmm) cc_final: 0.8088 (mmm) REVERT: E 327 ARG cc_start: 0.7708 (mmm160) cc_final: 0.6910 (mmp-170) REVERT: E 340 ARG cc_start: 0.7798 (tpp80) cc_final: 0.7519 (tpp80) REVERT: E 381 TYR cc_start: 0.7758 (p90) cc_final: 0.7132 (p90) REVERT: E 408 LYS cc_start: 0.8782 (mptt) cc_final: 0.8402 (mppt) REVERT: E 419 ARG cc_start: 0.6688 (tpp80) cc_final: 0.6288 (tpp80) REVERT: E 420 MET cc_start: 0.8023 (tpt) cc_final: 0.7705 (mmm) REVERT: E 433 LEU cc_start: 0.9034 (mm) cc_final: 0.8822 (mm) REVERT: E 438 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7977 (p) REVERT: F 16 TYR cc_start: 0.9347 (m-10) cc_final: 0.8282 (m-10) REVERT: F 184 MET cc_start: 0.8400 (tpp) cc_final: 0.8078 (tpp) REVERT: F 218 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7871 (mp) REVERT: F 224 ILE cc_start: 0.5062 (OUTLIER) cc_final: 0.4645 (mt) REVERT: F 231 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8484 (mtmt) REVERT: F 278 SER cc_start: 0.8898 (t) cc_final: 0.8371 (p) REVERT: F 315 GLN cc_start: 0.8287 (tp40) cc_final: 0.7765 (tp-100) REVERT: F 339 VAL cc_start: 0.9526 (t) cc_final: 0.9066 (p) REVERT: F 340 ARG cc_start: 0.8298 (mmm160) cc_final: 0.7877 (mmm160) REVERT: F 349 LEU cc_start: 0.9127 (mm) cc_final: 0.8823 (mm) REVERT: F 357 MET cc_start: 0.8295 (tpp) cc_final: 0.7858 (tpp) REVERT: F 373 LEU cc_start: 0.8895 (tt) cc_final: 0.8553 (pt) REVERT: G 13 ASP cc_start: 0.8516 (m-30) cc_final: 0.8054 (m-30) REVERT: G 103 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8325 (mm) REVERT: G 174 LEU cc_start: 0.9302 (mt) cc_final: 0.8686 (tt) REVERT: G 202 ARG cc_start: 0.8323 (mtt90) cc_final: 0.7873 (mtm-85) REVERT: G 227 ASP cc_start: 0.8095 (p0) cc_final: 0.7680 (p0) REVERT: G 249 HIS cc_start: 0.7579 (t70) cc_final: 0.7275 (t70) REVERT: G 307 MET cc_start: 0.7947 (mpp) cc_final: 0.7626 (mpp) REVERT: G 308 MET cc_start: 0.8598 (tpp) cc_final: 0.8198 (tpp) REVERT: G 340 ARG cc_start: 0.7924 (tpp80) cc_final: 0.7441 (tpp80) REVERT: G 379 ARG cc_start: 0.7818 (tpt-90) cc_final: 0.7571 (tpt-90) REVERT: G 381 TYR cc_start: 0.7824 (p90) cc_final: 0.6934 (p90) REVERT: G 438 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.8012 (p) REVERT: H 16 TYR cc_start: 0.9316 (m-10) cc_final: 0.8343 (m-10) REVERT: H 59 ARG cc_start: 0.7660 (ptm160) cc_final: 0.7334 (ptm160) REVERT: H 61 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6096 (pmm) REVERT: H 119 ARG cc_start: 0.8517 (mmm160) cc_final: 0.8076 (mmm160) REVERT: H 184 MET cc_start: 0.8439 (tpp) cc_final: 0.8114 (tpp) REVERT: H 202 ARG cc_start: 0.9221 (mtm-85) cc_final: 0.8803 (mtm-85) REVERT: H 218 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7954 (mp) REVERT: H 224 ILE cc_start: 0.5622 (OUTLIER) cc_final: 0.5302 (mt) REVERT: H 231 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8523 (mtmt) REVERT: H 255 MET cc_start: 0.7985 (mmm) cc_final: 0.7644 (tpt) REVERT: H 278 SER cc_start: 0.8886 (t) cc_final: 0.8343 (p) REVERT: H 315 GLN cc_start: 0.8354 (tp40) cc_final: 0.7991 (tp-100) REVERT: H 334 TRP cc_start: 0.9010 (m-10) cc_final: 0.8309 (m-10) REVERT: H 336 ASP cc_start: 0.8713 (t0) cc_final: 0.8016 (m-30) REVERT: H 340 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7581 (tpp-160) REVERT: H 343 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7574 (ptp90) REVERT: H 357 MET cc_start: 0.8429 (tpp) cc_final: 0.8043 (tpp) REVERT: H 458 LYS cc_start: 0.8780 (ptmm) cc_final: 0.8525 (pttp) outliers start: 120 outliers final: 85 residues processed: 716 average time/residue: 0.2006 time to fit residues: 218.3092 Evaluate side-chains 711 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 612 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 176 HIS Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 218 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 438 SER Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 176 HIS Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain H residue 224 ILE Chi-restraints excluded: chain H residue 259 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 328 GLN Chi-restraints excluded: chain H residue 343 ARG Chi-restraints excluded: chain H residue 382 LYS Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 7 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 258 optimal weight: 0.7980 chunk 362 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 345 optimal weight: 9.9990 chunk 255 optimal weight: 1.9990 chunk 349 optimal weight: 1.9990 chunk 326 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 456 HIS ** E 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 328 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.157876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.104132 restraints weight = 53631.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108336 restraints weight = 29544.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111053 restraints weight = 20453.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.112761 restraints weight = 16316.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113639 restraints weight = 14202.853| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27752 Z= 0.160 Angle : 0.648 9.711 37776 Z= 0.324 Chirality : 0.044 0.220 4496 Planarity : 0.004 0.043 5000 Dihedral : 4.110 49.781 4068 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.99 % Allowed : 26.10 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3736 helix: 0.75 (0.13), residues: 1520 sheet: -0.94 (0.21), residues: 600 loop : -0.16 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 396 TYR 0.014 0.001 TYR F 12 PHE 0.020 0.001 PHE B 128 TRP 0.006 0.001 TRP G 334 HIS 0.004 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00374 (27752) covalent geometry : angle 0.64790 (37776) hydrogen bonds : bond 0.03491 ( 1104) hydrogen bonds : angle 4.90318 ( 3120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 628 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 VAL cc_start: 0.9464 (t) cc_final: 0.9189 (p) REVERT: A 61 MET cc_start: 0.8473 (mmt) cc_final: 0.8167 (mmt) REVERT: A 118 LYS cc_start: 0.8592 (ptpt) cc_final: 0.8278 (ptpp) REVERT: A 158 PHE cc_start: 0.8486 (p90) cc_final: 0.8111 (p90) REVERT: A 184 MET cc_start: 0.7911 (tpp) cc_final: 0.7486 (tpp) REVERT: A 231 LYS cc_start: 0.9106 (mtmt) cc_final: 0.8788 (mttp) REVERT: A 233 GLN cc_start: 0.9215 (tt0) cc_final: 0.8806 (tp-100) REVERT: A 355 ASN cc_start: 0.9096 (t0) cc_final: 0.8798 (m-40) REVERT: A 377 ASP cc_start: 0.8987 (t0) cc_final: 0.8575 (t0) REVERT: A 379 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7561 (mtm180) REVERT: A 426 ARG cc_start: 0.8860 (mtm110) cc_final: 0.8406 (ptp-170) REVERT: B 53 MET cc_start: 0.8680 (mtp) cc_final: 0.8315 (mmm) REVERT: B 98 ASP cc_start: 0.8208 (t0) cc_final: 0.7906 (t70) REVERT: B 115 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8698 (tp) REVERT: B 118 LYS cc_start: 0.9043 (pptt) cc_final: 0.8778 (pptt) REVERT: B 202 ARG cc_start: 0.9248 (mtm-85) cc_final: 0.8167 (mtm-85) REVERT: B 224 ILE cc_start: 0.9468 (pt) cc_final: 0.9123 (tt) REVERT: B 302 MET cc_start: 0.7642 (ttt) cc_final: 0.7273 (tmm) REVERT: B 344 ASP cc_start: 0.8528 (m-30) cc_final: 0.8315 (m-30) REVERT: B 357 MET cc_start: 0.9003 (ttm) cc_final: 0.8601 (mtp) REVERT: B 367 GLU cc_start: 0.8482 (mp0) cc_final: 0.7640 (mp0) REVERT: B 374 PHE cc_start: 0.8804 (m-80) cc_final: 0.8254 (m-10) REVERT: B 408 LYS cc_start: 0.8243 (mmtm) cc_final: 0.8016 (mmtm) REVERT: B 430 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7413 (mt-10) REVERT: C 56 VAL cc_start: 0.9465 (t) cc_final: 0.9241 (p) REVERT: C 68 ARG cc_start: 0.8247 (mmt180) cc_final: 0.7528 (mmt90) REVERT: C 118 LYS cc_start: 0.8549 (ptpp) cc_final: 0.8280 (ptpp) REVERT: C 158 PHE cc_start: 0.8485 (p90) cc_final: 0.8111 (p90) REVERT: C 184 MET cc_start: 0.7918 (tpp) cc_final: 0.7496 (tpp) REVERT: C 231 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8833 (mttp) REVERT: C 233 GLN cc_start: 0.9219 (tt0) cc_final: 0.8779 (tp-100) REVERT: C 355 ASN cc_start: 0.9114 (t0) cc_final: 0.8825 (m-40) REVERT: C 377 ASP cc_start: 0.8986 (t0) cc_final: 0.8578 (t0) REVERT: C 379 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7564 (mtm180) REVERT: C 426 ARG cc_start: 0.9003 (mtm110) cc_final: 0.8386 (mtp180) REVERT: D 53 MET cc_start: 0.8718 (mtp) cc_final: 0.8323 (mmm) REVERT: D 115 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8755 (tp) REVERT: D 118 LYS cc_start: 0.9055 (pptt) cc_final: 0.8785 (pptt) REVERT: D 157 ASP cc_start: 0.8170 (t0) cc_final: 0.7840 (p0) REVERT: D 202 ARG cc_start: 0.9265 (mtm-85) cc_final: 0.8174 (mtm-85) REVERT: D 302 MET cc_start: 0.7644 (ttt) cc_final: 0.7276 (tmm) REVERT: D 327 ARG cc_start: 0.8467 (ttm170) cc_final: 0.8256 (tpp80) REVERT: D 344 ASP cc_start: 0.8553 (m-30) cc_final: 0.8344 (m-30) REVERT: D 357 MET cc_start: 0.9013 (ttm) cc_final: 0.8647 (mtp) REVERT: D 367 GLU cc_start: 0.8487 (mp0) cc_final: 0.7646 (mp0) REVERT: D 374 PHE cc_start: 0.8790 (m-80) cc_final: 0.8252 (m-10) REVERT: D 408 LYS cc_start: 0.8246 (mmtm) cc_final: 0.8022 (mmtm) REVERT: D 430 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7423 (mt-10) REVERT: D 454 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: E 13 ASP cc_start: 0.8500 (m-30) cc_final: 0.8102 (m-30) REVERT: E 103 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8107 (mm) REVERT: E 111 ASP cc_start: 0.8453 (t0) cc_final: 0.8244 (p0) REVERT: E 174 LEU cc_start: 0.9300 (mt) cc_final: 0.8695 (tt) REVERT: E 184 MET cc_start: -0.2870 (mmm) cc_final: -0.3272 (mmm) REVERT: E 202 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7807 (mtm-85) REVERT: E 227 ASP cc_start: 0.8163 (p0) cc_final: 0.7745 (p0) REVERT: E 249 HIS cc_start: 0.7840 (t70) cc_final: 0.7168 (t70) REVERT: E 307 MET cc_start: 0.7996 (mtp) cc_final: 0.7225 (ptp) REVERT: E 308 MET cc_start: 0.8404 (mmm) cc_final: 0.8085 (mmm) REVERT: E 327 ARG cc_start: 0.7665 (mmm160) cc_final: 0.7396 (mmp-170) REVERT: E 340 ARG cc_start: 0.7772 (tpp80) cc_final: 0.7508 (tpp80) REVERT: E 381 TYR cc_start: 0.7990 (p90) cc_final: 0.7734 (p90) REVERT: E 408 LYS cc_start: 0.8744 (mptt) cc_final: 0.8470 (mmtm) REVERT: E 419 ARG cc_start: 0.6661 (tpp80) cc_final: 0.6306 (tpp80) REVERT: E 420 MET cc_start: 0.8106 (tpt) cc_final: 0.7779 (mmm) REVERT: E 438 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7950 (p) REVERT: F 16 TYR cc_start: 0.9342 (m-10) cc_final: 0.8334 (m-10) REVERT: F 184 MET cc_start: 0.8394 (tpp) cc_final: 0.8030 (tpp) REVERT: F 224 ILE cc_start: 0.4609 (OUTLIER) cc_final: 0.4182 (mt) REVERT: F 231 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8474 (mtmt) REVERT: F 275 ASN cc_start: 0.7757 (m110) cc_final: 0.7121 (m110) REVERT: F 278 SER cc_start: 0.8911 (t) cc_final: 0.8288 (p) REVERT: F 340 ARG cc_start: 0.8265 (mmm160) cc_final: 0.7865 (mmm160) REVERT: F 349 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8823 (mm) REVERT: F 357 MET cc_start: 0.8248 (tpp) cc_final: 0.7892 (tpp) REVERT: G 13 ASP cc_start: 0.8509 (m-30) cc_final: 0.8057 (m-30) REVERT: G 103 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8358 (mm) REVERT: G 174 LEU cc_start: 0.9286 (mt) cc_final: 0.8638 (tt) REVERT: G 184 MET cc_start: -0.2608 (mmm) cc_final: -0.3239 (mmm) REVERT: G 202 ARG cc_start: 0.8306 (mtt90) cc_final: 0.7872 (mtm-85) REVERT: G 227 ASP cc_start: 0.8141 (p0) cc_final: 0.7742 (p0) REVERT: G 249 HIS cc_start: 0.7618 (t70) cc_final: 0.6751 (t70) REVERT: G 255 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6378 (mpp) REVERT: G 266 ASP cc_start: 0.7561 (t0) cc_final: 0.7287 (m-30) REVERT: G 307 MET cc_start: 0.7997 (mpp) cc_final: 0.7629 (mpp) REVERT: G 308 MET cc_start: 0.8584 (tpp) cc_final: 0.8162 (tpp) REVERT: G 327 ARG cc_start: 0.7038 (mmp-170) cc_final: 0.6162 (mmp-170) REVERT: G 340 ARG cc_start: 0.7816 (tpp80) cc_final: 0.7459 (tpp80) REVERT: G 381 TYR cc_start: 0.7981 (p90) cc_final: 0.7255 (p90) REVERT: G 426 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7312 (ttm170) REVERT: G 438 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7975 (p) REVERT: H 16 TYR cc_start: 0.9323 (m-10) cc_final: 0.8363 (m-10) REVERT: H 61 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.6526 (pmm) REVERT: H 119 ARG cc_start: 0.8582 (mmm160) cc_final: 0.8054 (mmp-170) REVERT: H 184 MET cc_start: 0.8419 (tpp) cc_final: 0.8061 (tpp) REVERT: H 202 ARG cc_start: 0.9245 (mtm-85) cc_final: 0.8729 (mtm-85) REVERT: H 218 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7936 (mp) REVERT: H 231 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8491 (mtmt) REVERT: H 255 MET cc_start: 0.7973 (mmm) cc_final: 0.7631 (tpt) REVERT: H 278 SER cc_start: 0.8911 (t) cc_final: 0.8367 (p) REVERT: H 315 GLN cc_start: 0.8316 (tp40) cc_final: 0.7977 (tp-100) REVERT: H 334 TRP cc_start: 0.8988 (m-10) cc_final: 0.8445 (m-10) REVERT: H 340 ARG cc_start: 0.8189 (mmm160) cc_final: 0.7656 (tpp-160) REVERT: H 343 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7485 (ptp90) REVERT: H 355 ASN cc_start: 0.9039 (t0) cc_final: 0.8776 (t0) REVERT: H 357 MET cc_start: 0.8363 (tpp) cc_final: 0.7954 (tpp) outliers start: 112 outliers final: 77 residues processed: 694 average time/residue: 0.1982 time to fit residues: 210.2465 Evaluate side-chains 699 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 609 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 396 ARG Chi-restraints excluded: chain G residue 438 SER Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 176 HIS Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain H residue 259 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 343 ARG Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 247 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 134 optimal weight: 0.0270 chunk 68 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 306 optimal weight: 0.0970 chunk 153 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 GLN F 249 HIS F 275 ASN F 315 GLN F 328 GLN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 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 = 0.4124 r_free = 0.4124 target = 0.160090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106542 restraints weight = 53524.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110818 restraints weight = 29306.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113602 restraints weight = 20246.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115348 restraints weight = 16057.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116452 restraints weight = 13949.548| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27752 Z= 0.118 Angle : 0.661 11.354 37776 Z= 0.324 Chirality : 0.045 0.258 4496 Planarity : 0.004 0.042 5000 Dihedral : 3.942 50.759 4068 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.13 % Allowed : 27.10 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3736 helix: 0.86 (0.13), residues: 1512 sheet: -0.92 (0.21), residues: 608 loop : -0.00 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 119 TYR 0.022 0.001 TYR F 381 PHE 0.022 0.001 PHE D 128 TRP 0.007 0.001 TRP G 361 HIS 0.005 0.001 HIS E 435 Details of bonding type rmsd covalent geometry : bond 0.00275 (27752) covalent geometry : angle 0.66058 (37776) hydrogen bonds : bond 0.03223 ( 1104) hydrogen bonds : angle 4.72202 ( 3120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 667 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 56 VAL cc_start: 0.9452 (t) cc_final: 0.9243 (p) REVERT: A 118 LYS cc_start: 0.8554 (ptpt) cc_final: 0.8241 (ptpt) REVERT: A 158 PHE cc_start: 0.8498 (p90) cc_final: 0.8190 (p90) REVERT: A 184 MET cc_start: 0.7960 (tpp) cc_final: 0.7526 (tpp) REVERT: A 233 GLN cc_start: 0.9199 (tt0) cc_final: 0.8792 (tp-100) REVERT: A 355 ASN cc_start: 0.9044 (t0) cc_final: 0.8730 (m-40) REVERT: A 377 ASP cc_start: 0.8981 (t0) cc_final: 0.8503 (t0) REVERT: A 379 ARG cc_start: 0.8035 (mtm180) cc_final: 0.7607 (mtm180) REVERT: A 426 ARG cc_start: 0.8868 (mtm110) cc_final: 0.8415 (ptp-170) REVERT: B 53 MET cc_start: 0.8579 (mtp) cc_final: 0.8296 (mmm) REVERT: B 63 GLU cc_start: 0.8523 (tt0) cc_final: 0.8243 (pp20) REVERT: B 98 ASP cc_start: 0.8228 (t0) cc_final: 0.7879 (t70) REVERT: B 115 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8611 (tp) REVERT: B 202 ARG cc_start: 0.9210 (mtm-85) cc_final: 0.8004 (mtm180) REVERT: B 260 LYS cc_start: 0.8950 (pttm) cc_final: 0.8620 (pttm) REVERT: B 302 MET cc_start: 0.7615 (ttt) cc_final: 0.7196 (tmm) REVERT: B 357 MET cc_start: 0.8926 (ttm) cc_final: 0.8525 (mtp) REVERT: B 374 PHE cc_start: 0.8786 (m-80) cc_final: 0.8247 (m-10) REVERT: B 382 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7410 (ttmt) REVERT: B 430 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7325 (mt-10) REVERT: B 454 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: C 158 PHE cc_start: 0.8504 (p90) cc_final: 0.8201 (p90) REVERT: C 184 MET cc_start: 0.7973 (tpp) cc_final: 0.7542 (tpp) REVERT: C 231 LYS cc_start: 0.9084 (mtmt) cc_final: 0.8841 (mttp) REVERT: C 233 GLN cc_start: 0.9202 (tt0) cc_final: 0.8794 (tp-100) REVERT: C 328 GLN cc_start: 0.9159 (tp40) cc_final: 0.8743 (tm-30) REVERT: C 355 ASN cc_start: 0.9044 (t0) cc_final: 0.8722 (m-40) REVERT: C 377 ASP cc_start: 0.8998 (t0) cc_final: 0.8518 (t0) REVERT: C 379 ARG cc_start: 0.8007 (mtm180) cc_final: 0.7574 (mtm180) REVERT: D 53 MET cc_start: 0.8610 (mtp) cc_final: 0.8292 (mmm) REVERT: D 63 GLU cc_start: 0.8521 (tt0) cc_final: 0.8107 (pp20) REVERT: D 98 ASP cc_start: 0.8010 (t0) cc_final: 0.7546 (t70) REVERT: D 115 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8821 (mm) REVERT: D 174 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9176 (tp) REVERT: D 202 ARG cc_start: 0.9224 (mtm-85) cc_final: 0.7869 (mtm180) REVERT: D 302 MET cc_start: 0.7605 (ttt) cc_final: 0.7195 (tmm) REVERT: D 357 MET cc_start: 0.8968 (ttm) cc_final: 0.8580 (mtp) REVERT: D 374 PHE cc_start: 0.8801 (m-80) cc_final: 0.8275 (m-10) REVERT: D 430 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7364 (mt-10) REVERT: D 454 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7678 (mt-10) REVERT: E 13 ASP cc_start: 0.8507 (m-30) cc_final: 0.8042 (m-30) REVERT: E 103 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8127 (mm) REVERT: E 174 LEU cc_start: 0.9263 (mt) cc_final: 0.8647 (tt) REVERT: E 184 MET cc_start: -0.3259 (mmm) cc_final: -0.3619 (mmm) REVERT: E 202 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7803 (mtm-85) REVERT: E 224 ILE cc_start: 0.3667 (OUTLIER) cc_final: 0.3007 (mt) REVERT: E 227 ASP cc_start: 0.8150 (p0) cc_final: 0.7753 (p0) REVERT: E 249 HIS cc_start: 0.7392 (t70) cc_final: 0.6272 (t70) REVERT: E 255 MET cc_start: 0.7101 (mpp) cc_final: 0.6277 (mmm) REVERT: E 266 ASP cc_start: 0.7539 (t0) cc_final: 0.7274 (m-30) REVERT: E 307 MET cc_start: 0.8008 (mtp) cc_final: 0.7171 (ptp) REVERT: E 308 MET cc_start: 0.8450 (mmm) cc_final: 0.7959 (mmm) REVERT: E 340 ARG cc_start: 0.7705 (tpp80) cc_final: 0.7487 (tpp80) REVERT: E 381 TYR cc_start: 0.8014 (p90) cc_final: 0.7698 (p90) REVERT: E 408 LYS cc_start: 0.8732 (mptt) cc_final: 0.8453 (mmtm) REVERT: E 419 ARG cc_start: 0.6736 (tpp80) cc_final: 0.6485 (tpp80) REVERT: E 420 MET cc_start: 0.8234 (tpt) cc_final: 0.7872 (mmm) REVERT: E 426 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7064 (ttm170) REVERT: F 16 TYR cc_start: 0.9332 (m-10) cc_final: 0.8405 (m-10) REVERT: F 61 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6643 (mtm) REVERT: F 184 MET cc_start: 0.8475 (tpp) cc_final: 0.8142 (tpp) REVERT: F 224 ILE cc_start: 0.4236 (OUTLIER) cc_final: 0.3767 (mt) REVERT: F 255 MET cc_start: 0.7979 (tpp) cc_final: 0.7772 (mmm) REVERT: F 278 SER cc_start: 0.8800 (t) cc_final: 0.8247 (p) REVERT: F 340 ARG cc_start: 0.8213 (mmm160) cc_final: 0.7878 (mmm160) REVERT: F 349 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8839 (mm) REVERT: F 357 MET cc_start: 0.8272 (tpp) cc_final: 0.7830 (tpp) REVERT: F 374 PHE cc_start: 0.8624 (m-10) cc_final: 0.8400 (m-10) REVERT: G 13 ASP cc_start: 0.8518 (m-30) cc_final: 0.8018 (m-30) REVERT: G 174 LEU cc_start: 0.9239 (mt) cc_final: 0.8598 (tt) REVERT: G 184 MET cc_start: -0.3392 (mmm) cc_final: -0.3968 (mmm) REVERT: G 202 ARG cc_start: 0.8276 (mtt90) cc_final: 0.7832 (mtm-85) REVERT: G 227 ASP cc_start: 0.8126 (p0) cc_final: 0.7745 (p0) REVERT: G 249 HIS cc_start: 0.7353 (t70) cc_final: 0.6771 (t-90) REVERT: G 255 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.6297 (mpp) REVERT: G 266 ASP cc_start: 0.7520 (t0) cc_final: 0.7255 (m-30) REVERT: G 307 MET cc_start: 0.7958 (mpp) cc_final: 0.7559 (mpp) REVERT: G 308 MET cc_start: 0.8609 (tpp) cc_final: 0.8147 (tpp) REVERT: G 340 ARG cc_start: 0.7802 (tpp80) cc_final: 0.7381 (tpp80) REVERT: G 381 TYR cc_start: 0.7902 (p90) cc_final: 0.7193 (p90) REVERT: G 420 MET cc_start: 0.8134 (tpp) cc_final: 0.7502 (tpt) REVERT: H 16 TYR cc_start: 0.9317 (m-10) cc_final: 0.8408 (m-10) REVERT: H 61 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.6343 (pmm) REVERT: H 119 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8329 (mmp80) REVERT: H 184 MET cc_start: 0.8384 (tpp) cc_final: 0.8071 (tpp) REVERT: H 218 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7846 (mp) REVERT: H 231 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8429 (ptpt) REVERT: H 255 MET cc_start: 0.7909 (mmm) cc_final: 0.7702 (tpt) REVERT: H 278 SER cc_start: 0.8844 (t) cc_final: 0.8284 (p) REVERT: H 315 GLN cc_start: 0.8272 (tp40) cc_final: 0.7898 (tp-100) REVERT: H 334 TRP cc_start: 0.9016 (m-10) cc_final: 0.8523 (m-10) REVERT: H 340 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7606 (tpp-160) REVERT: H 343 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7476 (ptp90) REVERT: H 355 ASN cc_start: 0.9052 (t0) cc_final: 0.8795 (t0) REVERT: H 357 MET cc_start: 0.8432 (tpp) cc_final: 0.8144 (tpp) REVERT: H 458 LYS cc_start: 0.8780 (ptmm) cc_final: 0.8563 (pttp) outliers start: 88 outliers final: 58 residues processed: 712 average time/residue: 0.1962 time to fit residues: 213.6927 Evaluate side-chains 709 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 637 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 396 ARG Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 343 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 62 optimal weight: 0.0570 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 9 optimal weight: 0.0050 chunk 287 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 367 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 overall best weight: 0.8114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 117 HIS F 275 ASN ** G 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 GLN ** G 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.160474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105989 restraints weight = 54189.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110291 restraints weight = 29691.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113104 restraints weight = 20586.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114817 restraints weight = 16402.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.115891 restraints weight = 14309.496| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27752 Z= 0.135 Angle : 0.701 12.147 37776 Z= 0.340 Chirality : 0.045 0.262 4496 Planarity : 0.004 0.057 5000 Dihedral : 3.917 49.438 4068 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.92 % Allowed : 27.99 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3736 helix: 0.79 (0.13), residues: 1520 sheet: -0.90 (0.21), residues: 608 loop : -0.04 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 327 TYR 0.018 0.001 TYR A 381 PHE 0.024 0.001 PHE A 128 TRP 0.005 0.001 TRP G 361 HIS 0.006 0.001 HIS E 117 Details of bonding type rmsd covalent geometry : bond 0.00317 (27752) covalent geometry : angle 0.70127 (37776) hydrogen bonds : bond 0.03362 ( 1104) hydrogen bonds : angle 4.77603 ( 3120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 646 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 118 LYS cc_start: 0.8540 (ptpt) cc_final: 0.8227 (ptpt) REVERT: A 158 PHE cc_start: 0.8510 (p90) cc_final: 0.8202 (p90) REVERT: A 184 MET cc_start: 0.7939 (tpp) cc_final: 0.7463 (tpp) REVERT: A 231 LYS cc_start: 0.8967 (mttp) cc_final: 0.8665 (mttp) REVERT: A 233 GLN cc_start: 0.9200 (tt0) cc_final: 0.8744 (tp-100) REVERT: A 254 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8230 (tttm) REVERT: A 328 GLN cc_start: 0.9125 (tp40) cc_final: 0.8807 (tm-30) REVERT: A 355 ASN cc_start: 0.9027 (t0) cc_final: 0.8710 (m-40) REVERT: A 377 ASP cc_start: 0.9027 (t0) cc_final: 0.8551 (t0) REVERT: A 379 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7566 (mtm180) REVERT: A 426 ARG cc_start: 0.8902 (mtm110) cc_final: 0.8366 (ptp-170) REVERT: B 53 MET cc_start: 0.8609 (mtp) cc_final: 0.8300 (mmm) REVERT: B 63 GLU cc_start: 0.8537 (tt0) cc_final: 0.8092 (pp20) REVERT: B 98 ASP cc_start: 0.8139 (t0) cc_final: 0.7648 (t70) REVERT: B 202 ARG cc_start: 0.9208 (mtm-85) cc_final: 0.7732 (mtm180) REVERT: B 260 LYS cc_start: 0.8954 (pttm) cc_final: 0.8607 (pttm) REVERT: B 302 MET cc_start: 0.7651 (ttt) cc_final: 0.7249 (tmm) REVERT: B 357 MET cc_start: 0.8905 (ttm) cc_final: 0.8516 (mtp) REVERT: B 374 PHE cc_start: 0.8826 (m-80) cc_final: 0.8305 (m-10) REVERT: B 382 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7378 (ttmt) REVERT: B 408 LYS cc_start: 0.8286 (mmtm) cc_final: 0.8071 (mmtm) REVERT: B 419 ARG cc_start: 0.8651 (ptm160) cc_final: 0.8171 (mtp-110) REVERT: B 430 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7242 (mt-10) REVERT: B 454 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: C 68 ARG cc_start: 0.7983 (mmt180) cc_final: 0.7527 (mmt180) REVERT: C 118 LYS cc_start: 0.8490 (ptpp) cc_final: 0.8086 (ptpt) REVERT: C 158 PHE cc_start: 0.8504 (p90) cc_final: 0.8183 (p90) REVERT: C 184 MET cc_start: 0.7954 (tpp) cc_final: 0.7499 (tpp) REVERT: C 231 LYS cc_start: 0.9083 (mtmt) cc_final: 0.8844 (mttp) REVERT: C 233 GLN cc_start: 0.9206 (tt0) cc_final: 0.8776 (tp-100) REVERT: C 328 GLN cc_start: 0.9168 (tp40) cc_final: 0.8796 (tm-30) REVERT: C 355 ASN cc_start: 0.9019 (t0) cc_final: 0.8709 (m-40) REVERT: C 377 ASP cc_start: 0.9014 (t0) cc_final: 0.8531 (t0) REVERT: C 379 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7598 (mtm180) REVERT: C 430 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7805 (mm-30) REVERT: D 53 MET cc_start: 0.8676 (mtp) cc_final: 0.8306 (mmm) REVERT: D 63 GLU cc_start: 0.8533 (tt0) cc_final: 0.8174 (pp20) REVERT: D 115 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8563 (tp) REVERT: D 118 LYS cc_start: 0.8816 (pptt) cc_final: 0.8476 (tmmt) REVERT: D 174 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9179 (tp) REVERT: D 202 ARG cc_start: 0.9225 (mtm-85) cc_final: 0.9022 (mtm180) REVERT: D 302 MET cc_start: 0.7642 (ttt) cc_final: 0.7249 (tmm) REVERT: D 357 MET cc_start: 0.8941 (ttm) cc_final: 0.8560 (mtp) REVERT: D 374 PHE cc_start: 0.8818 (m-80) cc_final: 0.8315 (m-10) REVERT: D 382 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7393 (ttmt) REVERT: D 408 LYS cc_start: 0.8296 (mmtm) cc_final: 0.8086 (mmtm) REVERT: D 419 ARG cc_start: 0.8623 (ptm160) cc_final: 0.8169 (mtp-110) REVERT: D 454 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: E 13 ASP cc_start: 0.8502 (m-30) cc_final: 0.8045 (m-30) REVERT: E 103 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8204 (mm) REVERT: E 174 LEU cc_start: 0.9261 (mt) cc_final: 0.8653 (tt) REVERT: E 184 MET cc_start: -0.3228 (mmm) cc_final: -0.3597 (mmm) REVERT: E 202 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.7952 (mtm-85) REVERT: E 227 ASP cc_start: 0.8147 (p0) cc_final: 0.7739 (p0) REVERT: E 249 HIS cc_start: 0.7386 (t70) cc_final: 0.6572 (t70) REVERT: E 266 ASP cc_start: 0.7568 (t0) cc_final: 0.7266 (m-30) REVERT: E 307 MET cc_start: 0.8011 (mtp) cc_final: 0.7145 (ptp) REVERT: E 308 MET cc_start: 0.8476 (mmm) cc_final: 0.7973 (mmm) REVERT: E 316 PHE cc_start: 0.9346 (t80) cc_final: 0.9124 (t80) REVERT: E 340 ARG cc_start: 0.7718 (tpp80) cc_final: 0.7502 (tpp80) REVERT: E 381 TYR cc_start: 0.7995 (p90) cc_final: 0.7710 (p90) REVERT: E 408 LYS cc_start: 0.8721 (mptt) cc_final: 0.8451 (mmtm) REVERT: E 420 MET cc_start: 0.8138 (tpt) cc_final: 0.7775 (mmm) REVERT: F 16 TYR cc_start: 0.9342 (m-10) cc_final: 0.8456 (m-10) REVERT: F 61 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6676 (mtm) REVERT: F 184 MET cc_start: 0.8488 (tpp) cc_final: 0.8210 (tpp) REVERT: F 255 MET cc_start: 0.7965 (tpp) cc_final: 0.7660 (tpp) REVERT: F 278 SER cc_start: 0.8698 (t) cc_final: 0.8169 (p) REVERT: F 340 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7891 (mmm160) REVERT: F 349 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8817 (mm) REVERT: F 357 MET cc_start: 0.8349 (tpp) cc_final: 0.7868 (tpp) REVERT: F 373 LEU cc_start: 0.8757 (tt) cc_final: 0.8483 (pt) REVERT: F 374 PHE cc_start: 0.8672 (m-10) cc_final: 0.8347 (m-10) REVERT: G 13 ASP cc_start: 0.8513 (m-30) cc_final: 0.8039 (m-30) REVERT: G 174 LEU cc_start: 0.9213 (mt) cc_final: 0.8602 (tt) REVERT: G 202 ARG cc_start: 0.8323 (mtt90) cc_final: 0.7805 (mtm-85) REVERT: G 227 ASP cc_start: 0.8122 (p0) cc_final: 0.7731 (p0) REVERT: G 249 HIS cc_start: 0.7328 (t70) cc_final: 0.7038 (t-90) REVERT: G 266 ASP cc_start: 0.7495 (t0) cc_final: 0.7167 (m-30) REVERT: G 307 MET cc_start: 0.7982 (mpp) cc_final: 0.7574 (mpp) REVERT: G 308 MET cc_start: 0.8575 (tpp) cc_final: 0.8175 (tpp) REVERT: G 340 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7441 (tpp80) REVERT: G 379 ARG cc_start: 0.7774 (tpt-90) cc_final: 0.7420 (tpt-90) REVERT: G 381 TYR cc_start: 0.7772 (p90) cc_final: 0.7497 (p90) REVERT: G 420 MET cc_start: 0.8198 (tpp) cc_final: 0.7564 (tpt) REVERT: H 16 TYR cc_start: 0.9322 (m-10) cc_final: 0.8404 (m-10) REVERT: H 50 VAL cc_start: 0.9076 (t) cc_final: 0.8830 (t) REVERT: H 59 ARG cc_start: 0.7657 (ptm160) cc_final: 0.7289 (mtp180) REVERT: H 61 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6317 (pmm) REVERT: H 119 ARG cc_start: 0.8649 (mmm160) cc_final: 0.8329 (mmm160) REVERT: H 184 MET cc_start: 0.8404 (tpp) cc_final: 0.8055 (tpp) REVERT: H 218 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7957 (mp) REVERT: H 255 MET cc_start: 0.7893 (mmm) cc_final: 0.7630 (tpp) REVERT: H 278 SER cc_start: 0.8851 (t) cc_final: 0.8333 (p) REVERT: H 315 GLN cc_start: 0.8239 (tp40) cc_final: 0.7944 (tp-100) REVERT: H 340 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7732 (tpp-160) REVERT: H 343 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7503 (ptp90) REVERT: H 355 ASN cc_start: 0.9118 (t0) cc_final: 0.8809 (t0) REVERT: H 357 MET cc_start: 0.8324 (tpp) cc_final: 0.8104 (tpp) REVERT: H 361 TRP cc_start: 0.8092 (t60) cc_final: 0.7850 (t60) REVERT: H 362 PHE cc_start: 0.8774 (m-80) cc_final: 0.8396 (m-80) REVERT: H 458 LYS cc_start: 0.8769 (ptmm) cc_final: 0.8568 (pttp) outliers start: 82 outliers final: 62 residues processed: 688 average time/residue: 0.1955 time to fit residues: 204.8856 Evaluate side-chains 707 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 635 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 396 ARG Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain H residue 259 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 343 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 249 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 chunk 293 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 366 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 435 HIS D 456 HIS F 275 ASN G 315 GLN ** H 252 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 = 0.4129 r_free = 0.4129 target = 0.160846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.106718 restraints weight = 53686.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.110990 restraints weight = 29579.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113784 restraints weight = 20508.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115512 restraints weight = 16282.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116651 restraints weight = 14151.283| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27752 Z= 0.132 Angle : 0.706 13.112 37776 Z= 0.342 Chirality : 0.045 0.266 4496 Planarity : 0.004 0.045 5000 Dihedral : 3.914 49.273 4068 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.67 % Allowed : 28.06 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3736 helix: 0.81 (0.13), residues: 1512 sheet: -0.73 (0.20), residues: 680 loop : -0.26 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 327 TYR 0.017 0.001 TYR A 381 PHE 0.022 0.001 PHE D 128 TRP 0.006 0.001 TRP G 361 HIS 0.006 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00312 (27752) covalent geometry : angle 0.70565 (37776) hydrogen bonds : bond 0.03343 ( 1104) hydrogen bonds : angle 4.77110 ( 3120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7472 Ramachandran restraints generated. 3736 Oldfield, 0 Emsley, 3736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 647 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 118 LYS cc_start: 0.8500 (ptpt) cc_final: 0.8172 (ptpt) REVERT: A 158 PHE cc_start: 0.8505 (p90) cc_final: 0.8223 (p90) REVERT: A 184 MET cc_start: 0.7991 (tpp) cc_final: 0.7555 (tpp) REVERT: A 231 LYS cc_start: 0.8996 (mttp) cc_final: 0.8725 (mttp) REVERT: A 233 GLN cc_start: 0.9201 (tt0) cc_final: 0.8746 (tp-100) REVERT: A 254 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8278 (tttm) REVERT: A 328 GLN cc_start: 0.9094 (tp40) cc_final: 0.8850 (tm-30) REVERT: A 355 ASN cc_start: 0.9048 (t0) cc_final: 0.8748 (m-40) REVERT: A 377 ASP cc_start: 0.9023 (t0) cc_final: 0.8501 (t0) REVERT: A 379 ARG cc_start: 0.7978 (mtm180) cc_final: 0.7521 (mtm180) REVERT: A 426 ARG cc_start: 0.9015 (mtm110) cc_final: 0.8486 (ptp-170) REVERT: B 53 MET cc_start: 0.8624 (mtp) cc_final: 0.8281 (mmm) REVERT: B 63 GLU cc_start: 0.8485 (tt0) cc_final: 0.8040 (pp20) REVERT: B 98 ASP cc_start: 0.8174 (t0) cc_final: 0.7698 (t70) REVERT: B 157 ASP cc_start: 0.8177 (t0) cc_final: 0.7873 (p0) REVERT: B 202 ARG cc_start: 0.9208 (mtm-85) cc_final: 0.8105 (mtm180) REVERT: B 302 MET cc_start: 0.7657 (ttt) cc_final: 0.7244 (tmm) REVERT: B 357 MET cc_start: 0.8920 (ttm) cc_final: 0.8517 (mtp) REVERT: B 374 PHE cc_start: 0.8811 (m-80) cc_final: 0.8325 (m-10) REVERT: B 382 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7358 (ttmt) REVERT: B 408 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8074 (mmtm) REVERT: B 419 ARG cc_start: 0.8599 (ptm160) cc_final: 0.8168 (mtp-110) REVERT: B 430 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7468 (mt-10) REVERT: B 451 ASN cc_start: 0.8045 (p0) cc_final: 0.6062 (p0) REVERT: B 454 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: C 68 ARG cc_start: 0.8021 (mmt180) cc_final: 0.7633 (mmt180) REVERT: C 118 LYS cc_start: 0.8435 (ptpp) cc_final: 0.8088 (ptpt) REVERT: C 158 PHE cc_start: 0.8527 (p90) cc_final: 0.8242 (p90) REVERT: C 184 MET cc_start: 0.7943 (tpp) cc_final: 0.7485 (tpp) REVERT: C 231 LYS cc_start: 0.9090 (mtmt) cc_final: 0.8832 (mttp) REVERT: C 233 GLN cc_start: 0.9207 (tt0) cc_final: 0.8774 (tp-100) REVERT: C 328 GLN cc_start: 0.9140 (tp40) cc_final: 0.8870 (tm-30) REVERT: C 355 ASN cc_start: 0.9039 (t0) cc_final: 0.8752 (m-40) REVERT: C 377 ASP cc_start: 0.9014 (t0) cc_final: 0.8474 (t0) REVERT: C 379 ARG cc_start: 0.8041 (mtm180) cc_final: 0.7587 (mtm180) REVERT: C 430 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7807 (mm-30) REVERT: D 53 MET cc_start: 0.8660 (mtp) cc_final: 0.8296 (mmm) REVERT: D 63 GLU cc_start: 0.8523 (tt0) cc_final: 0.8120 (pp20) REVERT: D 98 ASP cc_start: 0.7907 (t0) cc_final: 0.7612 (t70) REVERT: D 115 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8421 (tp) REVERT: D 118 LYS cc_start: 0.8816 (pptt) cc_final: 0.8470 (tmmt) REVERT: D 174 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9183 (tp) REVERT: D 302 MET cc_start: 0.7649 (ttt) cc_final: 0.7237 (tmm) REVERT: D 357 MET cc_start: 0.8957 (ttm) cc_final: 0.8564 (mtp) REVERT: D 374 PHE cc_start: 0.8808 (m-80) cc_final: 0.8298 (m-10) REVERT: D 382 LYS cc_start: 0.7881 (ttmt) cc_final: 0.7382 (ttmt) REVERT: D 408 LYS cc_start: 0.8316 (mmtm) cc_final: 0.8116 (mmtm) REVERT: D 419 ARG cc_start: 0.8635 (ptm160) cc_final: 0.8159 (mtp-110) REVERT: D 438 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8804 (p) REVERT: D 451 ASN cc_start: 0.7941 (p0) cc_final: 0.6962 (p0) REVERT: E 13 ASP cc_start: 0.8492 (m-30) cc_final: 0.8044 (m-30) REVERT: E 103 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8247 (mm) REVERT: E 174 LEU cc_start: 0.9261 (mt) cc_final: 0.8684 (tp) REVERT: E 202 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.8099 (mtm-85) REVERT: E 227 ASP cc_start: 0.8191 (p0) cc_final: 0.7766 (p0) REVERT: E 249 HIS cc_start: 0.7351 (t70) cc_final: 0.6954 (t70) REVERT: E 266 ASP cc_start: 0.7534 (t0) cc_final: 0.7204 (m-30) REVERT: E 308 MET cc_start: 0.8474 (mmm) cc_final: 0.8050 (mmm) REVERT: E 316 PHE cc_start: 0.9343 (t80) cc_final: 0.9119 (t80) REVERT: E 340 ARG cc_start: 0.7726 (tpp80) cc_final: 0.7518 (tpp80) REVERT: E 381 TYR cc_start: 0.7942 (p90) cc_final: 0.7224 (p90) REVERT: E 420 MET cc_start: 0.8104 (tpt) cc_final: 0.7708 (mmm) REVERT: E 458 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8615 (pttp) REVERT: F 16 TYR cc_start: 0.9301 (m-10) cc_final: 0.8196 (m-10) REVERT: F 61 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6592 (mtm) REVERT: F 184 MET cc_start: 0.8546 (tpp) cc_final: 0.8245 (tpp) REVERT: F 255 MET cc_start: 0.7965 (tpp) cc_final: 0.7664 (tpp) REVERT: F 278 SER cc_start: 0.8776 (t) cc_final: 0.8297 (p) REVERT: F 315 GLN cc_start: 0.8294 (tp40) cc_final: 0.7437 (tp-100) REVERT: F 340 ARG cc_start: 0.8298 (mmm160) cc_final: 0.7856 (mmm160) REVERT: F 349 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8810 (mm) REVERT: F 357 MET cc_start: 0.8364 (tpp) cc_final: 0.7925 (tpp) REVERT: F 373 LEU cc_start: 0.8775 (tt) cc_final: 0.8510 (pt) REVERT: F 374 PHE cc_start: 0.8654 (m-10) cc_final: 0.8346 (m-10) REVERT: G 13 ASP cc_start: 0.8514 (m-30) cc_final: 0.8045 (m-30) REVERT: G 174 LEU cc_start: 0.9219 (mt) cc_final: 0.8627 (tp) REVERT: G 202 ARG cc_start: 0.8357 (mtt90) cc_final: 0.7823 (mtm-85) REVERT: G 227 ASP cc_start: 0.8103 (p0) cc_final: 0.7708 (p0) REVERT: G 266 ASP cc_start: 0.7510 (t0) cc_final: 0.7181 (m-30) REVERT: G 307 MET cc_start: 0.7921 (mpp) cc_final: 0.7497 (mpp) REVERT: G 308 MET cc_start: 0.8543 (tpp) cc_final: 0.8111 (tpp) REVERT: G 340 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7419 (tpp80) REVERT: G 379 ARG cc_start: 0.7806 (tpt-90) cc_final: 0.7452 (tpt-90) REVERT: G 381 TYR cc_start: 0.7789 (p90) cc_final: 0.7532 (p90) REVERT: G 420 MET cc_start: 0.8238 (tpp) cc_final: 0.7491 (tpt) REVERT: H 16 TYR cc_start: 0.9317 (m-10) cc_final: 0.8470 (m-10) REVERT: H 59 ARG cc_start: 0.7654 (ptm160) cc_final: 0.7132 (mtp180) REVERT: H 119 ARG cc_start: 0.8606 (mmm160) cc_final: 0.7940 (mmm160) REVERT: H 184 MET cc_start: 0.8574 (tpp) cc_final: 0.8273 (tpp) REVERT: H 218 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7910 (mp) REVERT: H 278 SER cc_start: 0.8826 (t) cc_final: 0.8314 (p) REVERT: H 307 MET cc_start: 0.9039 (mmm) cc_final: 0.8579 (mmm) REVERT: H 334 TRP cc_start: 0.8933 (m-10) cc_final: 0.8479 (m-10) REVERT: H 343 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7499 (ptp90) REVERT: H 355 ASN cc_start: 0.9066 (t0) cc_final: 0.8806 (t0) REVERT: H 362 PHE cc_start: 0.8752 (m-80) cc_final: 0.8353 (m-80) REVERT: H 458 LYS cc_start: 0.8710 (ptmm) cc_final: 0.8478 (pttp) outliers start: 75 outliers final: 59 residues processed: 685 average time/residue: 0.1988 time to fit residues: 206.9870 Evaluate side-chains 705 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 637 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 396 ARG Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 396 ARG Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 53 MET Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 396 ARG Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain H residue 259 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 343 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 136 optimal weight: 0.6980 chunk 168 optimal weight: 0.5980 chunk 192 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 150 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 217 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 GLN ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.161239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107199 restraints weight = 53575.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111499 restraints weight = 29373.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114298 restraints weight = 20320.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116059 restraints weight = 16171.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117147 restraints weight = 14060.233| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27752 Z= 0.129 Angle : 0.721 13.104 37776 Z= 0.346 Chirality : 0.045 0.267 4496 Planarity : 0.004 0.043 5000 Dihedral : 3.890 49.191 4068 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.96 % Allowed : 28.06 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3736 helix: 0.90 (0.13), residues: 1496 sheet: -0.68 (0.19), residues: 680 loop : -0.12 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 68 TYR 0.017 0.001 TYR A 381 PHE 0.024 0.001 PHE C 128 TRP 0.006 0.001 TRP H 334 HIS 0.006 0.001 HIS B 435 Details of bonding type rmsd covalent geometry : bond 0.00305 (27752) covalent geometry : angle 0.72050 (37776) hydrogen bonds : bond 0.03295 ( 1104) hydrogen bonds : angle 4.75153 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6301.72 seconds wall clock time: 108 minutes 54.39 seconds (6534.39 seconds total)