Starting phenix.real_space_refine on Sat Aug 8 12:36:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ry1_19584/08_2026/8ry1_19584.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ry1_19584/08_2026/8ry1_19584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ry1_19584/08_2026/8ry1_19584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ry1_19584/08_2026/8ry1_19584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ry1_19584/08_2026/8ry1_19584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ry1_19584/08_2026/8ry1_19584.map" } resolution = 3.85 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= 0.003 sd= 0.023 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 112 5.16 5 C 17136 2.51 5 N 4976 2.21 5 O 5376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27616 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3404 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'5GP%rna3p': 2} Classifications: {'RNA_mixed': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 1} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 3.56, per 1000 atoms: 0.13 Number of scatterers: 27616 At special positions: 0 Unit cell: (133.504, 133.504, 120.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 16 15.00 O 5376 8.00 N 4976 7.00 C 17136 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: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6688 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 40 sheets defined 44.1% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 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 69 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 108 through 117 removed outlier: 4.037A pdb=" N HIS A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.682A pdb=" N ASP A 152 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 197 through 206 removed outlier: 4.135A pdb=" N GLY A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 252 through 266 removed outlier: 3.683A pdb=" N ASP A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.564A pdb=" N VAL A 345 " --> pdb=" O HIS A 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 402 through 411 removed outlier: 3.970A pdb=" N PHE A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 448 removed outlier: 3.721A pdb=" N LEU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 459 Processing helix chain 'A' and resid 466 through 471 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 69 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 108 through 117 removed outlier: 4.037A pdb=" N HIS B 117 " --> pdb=" O ASN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.682A pdb=" N ASP B 152 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 197 through 206 removed outlier: 4.136A pdb=" N GLY B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 252 through 266 removed outlier: 3.683A pdb=" N ASP B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 288 Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 341 through 352 removed outlier: 3.565A pdb=" N VAL B 345 " --> pdb=" O HIS B 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 402 through 411 removed outlier: 3.970A pdb=" N PHE B 411 " --> pdb=" O ARG B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 448 removed outlier: 3.721A pdb=" N LEU B 432 " --> pdb=" O GLY B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 459 Processing helix chain 'B' and resid 466 through 471 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 69 Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 108 through 117 removed outlier: 4.037A pdb=" N HIS C 117 " --> pdb=" O ASN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.682A pdb=" N ASP C 152 " --> pdb=" O ARG C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 197 through 206 removed outlier: 4.135A pdb=" N GLY C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 252 through 266 removed outlier: 3.682A pdb=" N ASP C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 288 Processing helix chain 'C' and resid 304 through 310 Processing helix chain 'C' and resid 314 through 330 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.564A pdb=" N VAL C 345 " --> pdb=" O HIS C 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 402 through 411 removed outlier: 3.970A pdb=" N PHE C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 448 removed outlier: 3.720A pdb=" N LEU C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 459 Processing helix chain 'C' and resid 466 through 471 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 69 Processing helix chain 'D' and resid 79 through 92 Processing helix chain 'D' and resid 108 through 117 removed outlier: 4.037A pdb=" N HIS D 117 " --> pdb=" O ASN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.682A pdb=" N ASP D 152 " --> pdb=" O ARG D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 197 through 206 removed outlier: 4.136A pdb=" N GLY D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 252 through 266 removed outlier: 3.682A pdb=" N ASP D 266 " --> pdb=" O VAL D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 288 Processing helix chain 'D' and resid 304 through 310 Processing helix chain 'D' and resid 314 through 330 Processing helix chain 'D' and resid 341 through 352 removed outlier: 3.565A pdb=" N VAL D 345 " --> pdb=" O HIS D 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 352 " --> pdb=" O ALA D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 402 through 411 removed outlier: 3.970A pdb=" N PHE D 411 " --> pdb=" O ARG D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 448 removed outlier: 3.721A pdb=" N LEU D 432 " --> pdb=" O GLY D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 459 Processing helix chain 'D' and resid 466 through 471 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 69 Processing helix chain 'E' and resid 79 through 92 Processing helix chain 'E' and resid 108 through 117 removed outlier: 4.036A pdb=" N HIS E 117 " --> pdb=" O ASN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.682A pdb=" N ASP E 152 " --> pdb=" O ARG E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 174 Processing helix chain 'E' and resid 197 through 206 removed outlier: 4.135A pdb=" N GLY E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 252 through 266 removed outlier: 3.682A pdb=" N ASP E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 288 Processing helix chain 'E' and resid 304 through 310 Processing helix chain 'E' and resid 314 through 330 Processing helix chain 'E' and resid 341 through 352 removed outlier: 3.564A pdb=" N VAL E 345 " --> pdb=" O HIS E 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 402 through 411 removed outlier: 3.969A pdb=" N PHE E 411 " --> pdb=" O ARG E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 448 removed outlier: 3.721A pdb=" N LEU E 432 " --> pdb=" O GLY E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 459 Processing helix chain 'E' and resid 466 through 471 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 69 Processing helix chain 'F' and resid 79 through 92 Processing helix chain 'F' and resid 108 through 117 removed outlier: 4.037A pdb=" N HIS F 117 " --> pdb=" O ASN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 Processing helix chain 'F' and resid 149 through 153 removed outlier: 3.682A pdb=" N ASP F 152 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 174 Processing helix chain 'F' and resid 197 through 206 removed outlier: 4.135A pdb=" N GLY F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE F 205 " --> pdb=" O ILE F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 252 through 266 removed outlier: 3.682A pdb=" N ASP F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 288 Processing helix chain 'F' and resid 304 through 310 Processing helix chain 'F' and resid 314 through 330 Processing helix chain 'F' and resid 341 through 352 removed outlier: 3.564A pdb=" N VAL F 345 " --> pdb=" O HIS F 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 387 through 392 Processing helix chain 'F' and resid 402 through 411 removed outlier: 3.969A pdb=" N PHE F 411 " --> pdb=" O ARG F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 448 removed outlier: 3.722A pdb=" N LEU F 432 " --> pdb=" O GLY F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 459 Processing helix chain 'F' and resid 466 through 471 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 69 Processing helix chain 'G' and resid 79 through 92 Processing helix chain 'G' and resid 108 through 117 removed outlier: 4.037A pdb=" N HIS G 117 " --> pdb=" O ASN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 142 Processing helix chain 'G' and resid 149 through 153 removed outlier: 3.681A pdb=" N ASP G 152 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 174 Processing helix chain 'G' and resid 197 through 206 removed outlier: 4.135A pdb=" N GLY G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE G 205 " --> pdb=" O ILE G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 238 Processing helix chain 'G' and resid 252 through 266 removed outlier: 3.682A pdb=" N ASP G 266 " --> pdb=" O VAL G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 288 Processing helix chain 'G' and resid 304 through 310 Processing helix chain 'G' and resid 314 through 330 Processing helix chain 'G' and resid 341 through 352 removed outlier: 3.564A pdb=" N VAL G 345 " --> pdb=" O HIS G 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY G 352 " --> pdb=" O ALA G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 364 Processing helix chain 'G' and resid 387 through 392 Processing helix chain 'G' and resid 402 through 411 removed outlier: 3.969A pdb=" N PHE G 411 " --> pdb=" O ARG G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 428 through 448 removed outlier: 3.722A pdb=" N LEU G 432 " --> pdb=" O GLY G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 459 Processing helix chain 'G' and resid 466 through 471 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 69 Processing helix chain 'H' and resid 79 through 92 Processing helix chain 'H' and resid 108 through 117 removed outlier: 4.037A pdb=" N HIS H 117 " --> pdb=" O ASN H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 142 Processing helix chain 'H' and resid 149 through 153 removed outlier: 3.683A pdb=" N ASP H 152 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 174 Processing helix chain 'H' and resid 197 through 206 removed outlier: 4.135A pdb=" N GLY H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE H 205 " --> pdb=" O ILE H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 238 Processing helix chain 'H' and resid 252 through 266 removed outlier: 3.682A pdb=" N ASP H 266 " --> pdb=" O VAL H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 288 Processing helix chain 'H' and resid 304 through 310 Processing helix chain 'H' and resid 314 through 330 Processing helix chain 'H' and resid 341 through 352 removed outlier: 3.565A pdb=" N VAL H 345 " --> pdb=" O HIS H 341 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY H 352 " --> pdb=" O ALA H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 364 Processing helix chain 'H' and resid 387 through 392 Processing helix chain 'H' and resid 402 through 411 removed outlier: 3.970A pdb=" N PHE H 411 " --> pdb=" O ARG H 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 428 through 448 removed outlier: 3.721A pdb=" N LEU H 432 " --> pdb=" O GLY H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 459 Processing helix chain 'H' and resid 466 through 471 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 6.459A pdb=" N ARG A 3 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL A 463 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 460 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.461A pdb=" N VAL A 50 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 272 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU A 271 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS A 294 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA A 273 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 293 " --> pdb=" O TRP A 334 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP A 336 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL A 295 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 333 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N MET A 357 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 335 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 103 removed outlier: 6.709A pdb=" N ALA A 124 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU A 135 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 126 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 160 through 162 removed outlier: 6.021A pdb=" N ALA A 161 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 removed outlier: 3.753A pdb=" N LEU A 373 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 381 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 4 removed outlier: 6.460A pdb=" N ARG B 3 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL B 463 " --> pdb=" O ARG B 3 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 460 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 50 removed outlier: 6.461A pdb=" N VAL B 50 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 272 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 271 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS B 294 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA B 273 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 293 " --> pdb=" O TRP B 334 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP B 336 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL B 295 " --> pdb=" O ASP B 336 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 333 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N MET B 357 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 335 " --> pdb=" O MET B 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 103 removed outlier: 6.709A pdb=" N ALA B 124 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 135 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 126 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 162 removed outlier: 6.022A pdb=" N ALA B 161 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 373 through 374 removed outlier: 3.754A pdb=" N LEU B 373 " --> pdb=" O TYR B 381 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 381 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 4 removed outlier: 6.460A pdb=" N ARG C 3 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL C 463 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL C 460 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 49 through 50 removed outlier: 6.461A pdb=" N VAL C 50 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 272 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU C 271 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS C 294 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA C 273 " --> pdb=" O LYS C 294 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 293 " --> pdb=" O TRP C 334 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP C 336 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL C 295 " --> pdb=" O ASP C 336 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 333 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N MET C 357 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA C 335 " --> pdb=" O MET C 357 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.709A pdb=" N ALA C 124 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU C 135 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL C 126 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 160 through 162 removed outlier: 6.021A pdb=" N ALA C 161 " --> pdb=" O THR C 185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 373 through 374 removed outlier: 3.752A pdb=" N LEU C 373 " --> pdb=" O TYR C 381 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 381 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 4 removed outlier: 6.459A pdb=" N ARG D 3 " --> pdb=" O LEU D 461 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL D 463 " --> pdb=" O ARG D 3 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL D 460 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 49 through 50 removed outlier: 6.461A pdb=" N VAL D 50 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 272 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU D 271 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS D 294 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA D 273 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 293 " --> pdb=" O TRP D 334 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP D 336 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL D 295 " --> pdb=" O ASP D 336 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL D 333 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N MET D 357 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA D 335 " --> pdb=" O MET D 357 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 102 through 103 removed outlier: 6.710A pdb=" N ALA D 124 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU D 135 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL D 126 " --> pdb=" O ILE D 133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 160 through 162 removed outlier: 6.021A pdb=" N ALA D 161 " --> pdb=" O THR D 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 373 through 374 removed outlier: 3.753A pdb=" N LEU D 373 " --> pdb=" O TYR D 381 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR D 381 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 4 removed outlier: 6.460A pdb=" N ARG E 3 " --> pdb=" O LEU E 461 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL E 463 " --> pdb=" O ARG E 3 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL E 460 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 49 through 50 removed outlier: 6.461A pdb=" N VAL E 50 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 272 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU E 271 " --> pdb=" O ILE E 292 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS E 294 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA E 273 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL E 293 " --> pdb=" O TRP E 334 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP E 336 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL E 295 " --> pdb=" O ASP E 336 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL E 333 " --> pdb=" O ASN E 355 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N MET E 357 " --> pdb=" O VAL E 333 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA E 335 " --> pdb=" O MET E 357 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 102 through 103 removed outlier: 6.709A pdb=" N ALA E 124 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU E 135 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL E 126 " --> pdb=" O ILE E 133 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 160 through 162 removed outlier: 6.021A pdb=" N ALA E 161 " --> pdb=" O THR E 185 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 373 through 374 removed outlier: 3.753A pdb=" N LEU E 373 " --> pdb=" O TYR E 381 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR E 381 " --> pdb=" O LEU E 373 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 3 through 4 removed outlier: 6.460A pdb=" N ARG F 3 " --> pdb=" O LEU F 461 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL F 463 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL F 460 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 49 through 50 removed outlier: 6.462A pdb=" N VAL F 50 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 272 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU F 271 " --> pdb=" O ILE F 292 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS F 294 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA F 273 " --> pdb=" O LYS F 294 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL F 293 " --> pdb=" O TRP F 334 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP F 336 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL F 295 " --> pdb=" O ASP F 336 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL F 333 " --> pdb=" O ASN F 355 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N MET F 357 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA F 335 " --> pdb=" O MET F 357 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 102 through 103 removed outlier: 6.709A pdb=" N ALA F 124 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU F 135 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL F 126 " --> pdb=" O ILE F 133 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 160 through 162 removed outlier: 6.022A pdb=" N ALA F 161 " --> pdb=" O THR F 185 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 373 through 374 removed outlier: 3.753A pdb=" N LEU F 373 " --> pdb=" O TYR F 381 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR F 381 " --> pdb=" O LEU F 373 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 4 removed outlier: 6.460A pdb=" N ARG G 3 " --> pdb=" O LEU G 461 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL G 463 " --> pdb=" O ARG G 3 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL G 460 " --> pdb=" O VAL G 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 49 through 50 removed outlier: 6.461A pdb=" N VAL G 50 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL G 272 " --> pdb=" O LEU G 243 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU G 271 " --> pdb=" O ILE G 292 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS G 294 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA G 273 " --> pdb=" O LYS G 294 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL G 293 " --> pdb=" O TRP G 334 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP G 336 " --> pdb=" O VAL G 293 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL G 295 " --> pdb=" O ASP G 336 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL G 333 " --> pdb=" O ASN G 355 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N MET G 357 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA G 335 " --> pdb=" O MET G 357 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 102 through 103 removed outlier: 6.709A pdb=" N ALA G 124 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU G 135 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL G 126 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 160 through 162 removed outlier: 6.021A pdb=" N ALA G 161 " --> pdb=" O THR G 185 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 373 through 374 removed outlier: 3.753A pdb=" N LEU G 373 " --> pdb=" O TYR G 381 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR G 381 " --> pdb=" O LEU G 373 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 4 removed outlier: 6.460A pdb=" N ARG H 3 " --> pdb=" O LEU H 461 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL H 463 " --> pdb=" O ARG H 3 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL H 460 " --> pdb=" O VAL H 22 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 49 through 50 removed outlier: 6.462A pdb=" N VAL H 50 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 272 " --> pdb=" O LEU H 243 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU H 271 " --> pdb=" O ILE H 292 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS H 294 " --> pdb=" O LEU H 271 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA H 273 " --> pdb=" O LYS H 294 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL H 293 " --> pdb=" O TRP H 334 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP H 336 " --> pdb=" O VAL H 293 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL H 295 " --> pdb=" O ASP H 336 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL H 333 " --> pdb=" O ASN H 355 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N MET H 357 " --> pdb=" O VAL H 333 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA H 335 " --> pdb=" O MET H 357 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 102 through 103 removed outlier: 6.709A pdb=" N ALA H 124 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU H 135 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL H 126 " --> pdb=" O ILE H 133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 160 through 162 removed outlier: 6.021A pdb=" N ALA H 161 " --> pdb=" O THR H 185 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 373 through 374 removed outlier: 3.752A pdb=" N LEU H 373 " --> pdb=" O TYR H 381 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR H 381 " --> pdb=" O LEU H 373 " (cutoff:3.500A) 1160 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: 5.72 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9584 1.34 - 1.46: 5895 1.46 - 1.58: 12409 1.58 - 1.70: 16 1.70 - 1.82: 192 Bond restraints: 28096 Sorted by residual: bond pdb=" C8 5GP F 502 " pdb=" N7 5GP F 502 " ideal model delta sigma weight residual 1.306 1.347 -0.041 2.00e-02 2.50e+03 4.29e+00 bond pdb=" C8 5GP H 501 " pdb=" N7 5GP H 501 " ideal model delta sigma weight residual 1.306 1.347 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" C8 5GP G 502 " pdb=" N7 5GP G 502 " ideal model delta sigma weight residual 1.306 1.347 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C8 5GP A 502 " pdb=" N7 5GP A 502 " ideal model delta sigma weight residual 1.306 1.347 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C8 5GP C 502 " pdb=" N7 5GP C 502 " ideal model delta sigma weight residual 1.306 1.347 -0.041 2.00e-02 2.50e+03 4.19e+00 ... (remaining 28091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 37420 1.93 - 3.85: 740 3.85 - 5.78: 80 5.78 - 7.71: 48 7.71 - 9.63: 24 Bond angle restraints: 38312 Sorted by residual: angle pdb=" CA GLN B 233 " pdb=" CB GLN B 233 " pdb=" CG GLN B 233 " ideal model delta sigma weight residual 114.10 120.78 -6.68 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA GLN A 233 " pdb=" CB GLN A 233 " pdb=" CG GLN A 233 " ideal model delta sigma weight residual 114.10 120.73 -6.63 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA GLN D 233 " pdb=" CB GLN D 233 " pdb=" CG GLN D 233 " ideal model delta sigma weight residual 114.10 120.73 -6.63 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA GLN H 233 " pdb=" CB GLN H 233 " pdb=" CG GLN H 233 " ideal model delta sigma weight residual 114.10 120.72 -6.62 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CA GLN G 233 " pdb=" CB GLN G 233 " pdb=" CG GLN G 233 " ideal model delta sigma weight residual 114.10 120.72 -6.62 2.00e+00 2.50e-01 1.09e+01 ... (remaining 38307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 15009 17.06 - 34.11: 1447 34.11 - 51.17: 352 51.17 - 68.23: 120 68.23 - 85.29: 24 Dihedral angle restraints: 16952 sinusoidal: 6488 harmonic: 10464 Sorted by residual: dihedral pdb=" CG ARG E 60 " pdb=" CD ARG E 60 " pdb=" NE ARG E 60 " pdb=" CZ ARG E 60 " ideal model delta sinusoidal sigma weight residual 90.00 132.50 -42.50 2 1.50e+01 4.44e-03 9.74e+00 dihedral pdb=" CG ARG C 60 " pdb=" CD ARG C 60 " pdb=" NE ARG C 60 " pdb=" CZ ARG C 60 " ideal model delta sinusoidal sigma weight residual 90.00 132.47 -42.47 2 1.50e+01 4.44e-03 9.73e+00 dihedral pdb=" CG ARG G 60 " pdb=" CD ARG G 60 " pdb=" NE ARG G 60 " pdb=" CZ ARG G 60 " ideal model delta sinusoidal sigma weight residual 90.00 132.46 -42.46 2 1.50e+01 4.44e-03 9.72e+00 ... (remaining 16949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3052 0.037 - 0.075: 939 0.075 - 0.112: 461 0.112 - 0.149: 76 0.149 - 0.187: 8 Chirality restraints: 4536 Sorted by residual: chirality pdb=" CG LEU D 349 " pdb=" CB LEU D 349 " pdb=" CD1 LEU D 349 " pdb=" CD2 LEU D 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CG LEU G 349 " pdb=" CB LEU G 349 " pdb=" CD1 LEU G 349 " pdb=" CD2 LEU G 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" CG LEU H 349 " pdb=" CB LEU H 349 " pdb=" CD1 LEU H 349 " pdb=" CD2 LEU H 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.62e-01 ... (remaining 4533 not shown) Planarity restraints: 5000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 5GP D 501 " -0.007 2.00e-02 2.50e+03 1.32e-02 5.26e+00 pdb=" C2 5GP D 501 " 0.000 2.00e-02 2.50e+03 pdb=" C4 5GP D 501 " 0.024 2.00e-02 2.50e+03 pdb=" C5 5GP D 501 " 0.018 2.00e-02 2.50e+03 pdb=" C6 5GP D 501 " 0.004 2.00e-02 2.50e+03 pdb=" C8 5GP D 501 " -0.019 2.00e-02 2.50e+03 pdb=" N1 5GP D 501 " -0.005 2.00e-02 2.50e+03 pdb=" N2 5GP D 501 " -0.020 2.00e-02 2.50e+03 pdb=" N3 5GP D 501 " 0.016 2.00e-02 2.50e+03 pdb=" N7 5GP D 501 " -0.008 2.00e-02 2.50e+03 pdb=" N9 5GP D 501 " 0.000 2.00e-02 2.50e+03 pdb=" O6 5GP D 501 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 5GP C 501 " -0.007 2.00e-02 2.50e+03 1.32e-02 5.19e+00 pdb=" C2 5GP C 501 " 0.001 2.00e-02 2.50e+03 pdb=" C4 5GP C 501 " 0.024 2.00e-02 2.50e+03 pdb=" C5 5GP C 501 " 0.018 2.00e-02 2.50e+03 pdb=" C6 5GP C 501 " 0.004 2.00e-02 2.50e+03 pdb=" C8 5GP C 501 " -0.019 2.00e-02 2.50e+03 pdb=" N1 5GP C 501 " -0.006 2.00e-02 2.50e+03 pdb=" N2 5GP C 501 " -0.020 2.00e-02 2.50e+03 pdb=" N3 5GP C 501 " 0.016 2.00e-02 2.50e+03 pdb=" N7 5GP C 501 " -0.008 2.00e-02 2.50e+03 pdb=" N9 5GP C 501 " -0.000 2.00e-02 2.50e+03 pdb=" O6 5GP C 501 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 5GP F 501 " -0.007 2.00e-02 2.50e+03 1.31e-02 5.18e+00 pdb=" C2 5GP F 501 " 0.000 2.00e-02 2.50e+03 pdb=" C4 5GP F 501 " 0.024 2.00e-02 2.50e+03 pdb=" C5 5GP F 501 " 0.018 2.00e-02 2.50e+03 pdb=" C6 5GP F 501 " 0.004 2.00e-02 2.50e+03 pdb=" C8 5GP F 501 " -0.019 2.00e-02 2.50e+03 pdb=" N1 5GP F 501 " -0.005 2.00e-02 2.50e+03 pdb=" N2 5GP F 501 " -0.019 2.00e-02 2.50e+03 pdb=" N3 5GP F 501 " 0.015 2.00e-02 2.50e+03 pdb=" N7 5GP F 501 " -0.007 2.00e-02 2.50e+03 pdb=" N9 5GP F 501 " 0.000 2.00e-02 2.50e+03 pdb=" O6 5GP F 501 " -0.004 2.00e-02 2.50e+03 ... (remaining 4997 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2065 2.73 - 3.27: 29605 3.27 - 3.82: 50169 3.82 - 4.36: 57595 4.36 - 4.90: 97608 Nonbonded interactions: 237042 Sorted by model distance: nonbonded pdb=" OG1 THR G 137 " pdb=" OE1 GLU G 138 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR B 137 " pdb=" OE1 GLU B 138 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR C 137 " pdb=" OE1 GLU C 138 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR F 137 " pdb=" OE1 GLU F 138 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR A 137 " pdb=" OE1 GLU A 138 " model vdw 2.191 3.040 ... (remaining 237037 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: 0.10 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.570 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 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 : 0.003 0.041 28096 Z= 0.137 Angle : 0.669 9.635 38312 Z= 0.322 Chirality : 0.045 0.187 4536 Planarity : 0.005 0.051 5000 Dihedral : 15.058 85.286 10264 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.39 % Allowed : 21.76 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 3704 helix: 0.79 (0.14), residues: 1464 sheet: 0.17 (0.22), residues: 424 loop : 0.33 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 131 TYR 0.014 0.002 TYR F 12 PHE 0.020 0.002 PHE B 469 TRP 0.014 0.002 TRP F 334 HIS 0.002 0.000 HIS C 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (28096) covalent geometry : angle 0.66879 / 0.32 (38312) hydrogen bonds : bond 0.19803 / 13.53 ( 1160) hydrogen bonds : angle 7.39862 / 5.33 ( 3120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 1299 time to evaluate : 0.915 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: 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 52 ASN cc_start: 0.7171 (p0) cc_final: 0.6653 (p0) REVERT: A 77 ASP cc_start: 0.8226 (m-30) cc_final: 0.7943 (m-30) REVERT: A 86 THR cc_start: 0.9446 (m) cc_final: 0.9228 (p) REVERT: A 107 ASP cc_start: 0.8092 (m-30) cc_final: 0.7695 (p0) REVERT: A 109 VAL cc_start: 0.8555 (t) cc_final: 0.8143 (t) REVERT: A 111 ASP cc_start: 0.8990 (t0) cc_final: 0.8581 (t0) REVERT: A 155 LEU cc_start: 0.9048 (mm) cc_final: 0.8530 (pp) REVERT: A 184 MET cc_start: 0.8223 (mmm) cc_final: 0.7527 (mmm) REVERT: A 197 ARG cc_start: 0.8609 (ttt90) cc_final: 0.8384 (tpt-90) REVERT: A 225 ASN cc_start: 0.8938 (p0) cc_final: 0.7935 (m-40) REVERT: A 285 LEU cc_start: 0.8422 (mt) cc_final: 0.8135 (mt) REVERT: A 305 THR cc_start: 0.9097 (p) cc_final: 0.8764 (t) REVERT: A 357 MET cc_start: 0.5715 (tpp) cc_final: 0.3852 (ttt) REVERT: A 384 SER cc_start: 0.9061 (t) cc_final: 0.8791 (p) REVERT: A 408 LYS cc_start: 0.9135 (tptp) cc_final: 0.8724 (ptmt) REVERT: A 421 SER cc_start: 0.8927 (m) cc_final: 0.8709 (p) REVERT: A 446 TYR cc_start: 0.8734 (m-80) cc_final: 0.7973 (m-80) REVERT: A 473 HIS cc_start: 0.8096 (t70) cc_final: 0.7667 (t70) REVERT: B 18 ASP cc_start: 0.7081 (m-30) cc_final: 0.6510 (t0) REVERT: B 117 HIS cc_start: 0.9071 (m-70) cc_final: 0.8710 (m-70) REVERT: B 118 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8464 (tptt) REVERT: B 121 HIS cc_start: 0.8044 (m-70) cc_final: 0.7645 (m-70) REVERT: B 133 ILE cc_start: 0.8618 (pt) cc_final: 0.8404 (mm) REVERT: B 153 ILE cc_start: 0.8899 (tp) cc_final: 0.8662 (tp) REVERT: B 231 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8702 (mtmm) REVERT: B 302 MET cc_start: 0.7320 (mmp) cc_final: 0.5942 (mmt) REVERT: B 303 CYS cc_start: 0.7843 (t) cc_final: 0.7471 (t) REVERT: B 306 ARG cc_start: 0.8061 (mtp-110) cc_final: 0.7681 (ttp80) REVERT: B 307 MET cc_start: 0.3197 (OUTLIER) cc_final: 0.2516 (ptt) REVERT: B 357 MET cc_start: 0.7768 (tpp) cc_final: 0.7194 (mmm) REVERT: B 384 SER cc_start: 0.8022 (t) cc_final: 0.7625 (p) REVERT: B 403 PHE cc_start: 0.8574 (t80) cc_final: 0.8337 (t80) REVERT: B 451 ASN cc_start: 0.8506 (p0) cc_final: 0.8161 (p0) REVERT: B 473 HIS cc_start: 0.8711 (t70) cc_final: 0.8444 (t70) REVERT: C 52 ASN cc_start: 0.7198 (p0) cc_final: 0.6675 (p0) REVERT: C 77 ASP cc_start: 0.8231 (m-30) cc_final: 0.7950 (m-30) REVERT: C 86 THR cc_start: 0.9443 (m) cc_final: 0.9236 (p) REVERT: C 107 ASP cc_start: 0.8095 (m-30) cc_final: 0.7695 (p0) REVERT: C 109 VAL cc_start: 0.8563 (t) cc_final: 0.8153 (t) REVERT: C 111 ASP cc_start: 0.8983 (t0) cc_final: 0.8577 (t0) REVERT: C 115 LEU cc_start: 0.8498 (mt) cc_final: 0.8224 (mp) REVERT: C 155 LEU cc_start: 0.9044 (mm) cc_final: 0.8505 (pp) REVERT: C 184 MET cc_start: 0.8218 (mmm) cc_final: 0.7516 (mmm) REVERT: C 197 ARG cc_start: 0.8601 (ttt90) cc_final: 0.8382 (tpt-90) REVERT: C 225 ASN cc_start: 0.8930 (p0) cc_final: 0.7939 (m-40) REVERT: C 285 LEU cc_start: 0.8437 (mt) cc_final: 0.8137 (mt) REVERT: C 305 THR cc_start: 0.9115 (p) cc_final: 0.8785 (t) REVERT: C 357 MET cc_start: 0.5696 (tpp) cc_final: 0.3877 (ttt) REVERT: C 384 SER cc_start: 0.9055 (t) cc_final: 0.8776 (p) REVERT: C 408 LYS cc_start: 0.9137 (tptp) cc_final: 0.8721 (ptmt) REVERT: C 421 SER cc_start: 0.8929 (m) cc_final: 0.8699 (p) REVERT: C 446 TYR cc_start: 0.8735 (m-80) cc_final: 0.8051 (m-80) REVERT: C 473 HIS cc_start: 0.8029 (t70) cc_final: 0.7600 (t70) REVERT: D 18 ASP cc_start: 0.7083 (m-30) cc_final: 0.6509 (t0) REVERT: D 117 HIS cc_start: 0.9077 (m-70) cc_final: 0.8716 (m-70) REVERT: D 118 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8459 (tptt) REVERT: D 121 HIS cc_start: 0.8040 (m-70) cc_final: 0.7643 (m-70) REVERT: D 133 ILE cc_start: 0.8618 (pt) cc_final: 0.8403 (mm) REVERT: D 153 ILE cc_start: 0.8891 (tp) cc_final: 0.8656 (tp) REVERT: D 231 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8706 (mtmm) REVERT: D 302 MET cc_start: 0.7338 (mmp) cc_final: 0.5972 (mmt) REVERT: D 303 CYS cc_start: 0.7839 (t) cc_final: 0.7474 (t) REVERT: D 306 ARG cc_start: 0.8059 (mtp-110) cc_final: 0.7677 (ttp80) REVERT: D 307 MET cc_start: 0.3202 (OUTLIER) cc_final: 0.2513 (ptt) REVERT: D 357 MET cc_start: 0.7766 (tpp) cc_final: 0.7194 (mmm) REVERT: D 384 SER cc_start: 0.8025 (t) cc_final: 0.7624 (p) REVERT: D 403 PHE cc_start: 0.8571 (t80) cc_final: 0.8354 (t80) REVERT: D 451 ASN cc_start: 0.8509 (p0) cc_final: 0.8162 (p0) REVERT: D 473 HIS cc_start: 0.8713 (t70) cc_final: 0.8442 (t70) REVERT: E 18 ASP cc_start: 0.7571 (m-30) cc_final: 0.6997 (t0) REVERT: E 59 ARG cc_start: 0.7837 (ptm160) cc_final: 0.7417 (ptt-90) REVERT: E 86 THR cc_start: 0.9307 (m) cc_final: 0.9086 (p) REVERT: E 109 VAL cc_start: 0.8478 (t) cc_final: 0.7990 (t) REVERT: E 155 LEU cc_start: 0.8241 (mm) cc_final: 0.8027 (pt) REVERT: E 169 GLU cc_start: 0.9003 (mp0) cc_final: 0.8561 (mp0) REVERT: E 184 MET cc_start: 0.7691 (mmm) cc_final: 0.6873 (mmm) REVERT: E 197 ARG cc_start: 0.8714 (ttt90) cc_final: 0.8311 (tpt-90) REVERT: E 237 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8621 (mm-30) REVERT: E 246 ASP cc_start: 0.7526 (t0) cc_final: 0.7117 (t0) REVERT: E 256 LEU cc_start: 0.8920 (mt) cc_final: 0.8544 (mt) REVERT: E 259 ILE cc_start: 0.8935 (mm) cc_final: 0.8305 (mm) REVERT: E 306 ARG cc_start: 0.8362 (mtp-110) cc_final: 0.7345 (mtt-85) REVERT: E 315 GLN cc_start: 0.6932 (tp-100) cc_final: 0.6695 (tp-100) REVERT: E 328 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8273 (tm-30) REVERT: E 341 HIS cc_start: 0.8314 (m170) cc_final: 0.7985 (m-70) REVERT: E 385 TYR cc_start: 0.7568 (m-10) cc_final: 0.7268 (m-10) REVERT: E 387 MET cc_start: 0.8647 (pmm) cc_final: 0.8318 (pmm) REVERT: E 419 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7415 (ptt-90) REVERT: E 438 SER cc_start: 0.8554 (t) cc_final: 0.8183 (p) REVERT: F 50 VAL cc_start: 0.8868 (t) cc_final: 0.8570 (p) REVERT: F 52 ASN cc_start: 0.6646 (p0) cc_final: 0.6314 (p0) REVERT: F 74 LEU cc_start: 0.8039 (mm) cc_final: 0.7659 (mm) REVERT: F 98 ASP cc_start: 0.8611 (m-30) cc_final: 0.8172 (t0) REVERT: F 115 LEU cc_start: 0.9366 (mt) cc_final: 0.8884 (mt) REVERT: F 118 LYS cc_start: 0.8379 (mmtt) cc_final: 0.7937 (tttp) REVERT: F 155 LEU cc_start: 0.8414 (mm) cc_final: 0.7992 (mm) REVERT: F 169 GLU cc_start: 0.8962 (mp0) cc_final: 0.8564 (mp0) REVERT: F 176 HIS cc_start: 0.8949 (m-70) cc_final: 0.8616 (m-70) REVERT: F 225 ASN cc_start: 0.8320 (p0) cc_final: 0.7745 (m-40) REVERT: F 249 HIS cc_start: 0.7287 (t-170) cc_final: 0.6943 (t-170) REVERT: F 302 MET cc_start: 0.7099 (mmp) cc_final: 0.6059 (mmp) REVERT: F 367 GLU cc_start: 0.7996 (mp0) cc_final: 0.7347 (mp0) REVERT: F 382 LYS cc_start: 0.8972 (mttt) cc_final: 0.8710 (mttp) REVERT: F 384 SER cc_start: 0.8468 (t) cc_final: 0.7557 (t) REVERT: F 387 MET cc_start: 0.7463 (pmm) cc_final: 0.6989 (pmm) REVERT: F 434 ASP cc_start: 0.8572 (m-30) cc_final: 0.8292 (m-30) REVERT: G 18 ASP cc_start: 0.7671 (m-30) cc_final: 0.7049 (t0) REVERT: G 59 ARG cc_start: 0.7841 (ptm160) cc_final: 0.7408 (ptt-90) REVERT: G 86 THR cc_start: 0.9300 (m) cc_final: 0.9079 (p) REVERT: G 109 VAL cc_start: 0.8506 (t) cc_final: 0.8013 (t) REVERT: G 155 LEU cc_start: 0.8215 (mm) cc_final: 0.8003 (pt) REVERT: G 169 GLU cc_start: 0.8999 (mp0) cc_final: 0.8559 (mp0) REVERT: G 184 MET cc_start: 0.7703 (mmm) cc_final: 0.6887 (mmm) REVERT: G 197 ARG cc_start: 0.8687 (ttt90) cc_final: 0.8294 (tpt-90) REVERT: G 237 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8612 (mm-30) REVERT: G 246 ASP cc_start: 0.7502 (t0) cc_final: 0.7114 (t0) REVERT: G 256 LEU cc_start: 0.8936 (mt) cc_final: 0.8515 (mp) REVERT: G 259 ILE cc_start: 0.8929 (mm) cc_final: 0.8146 (mm) REVERT: G 306 ARG cc_start: 0.8368 (mtp-110) cc_final: 0.7340 (mtt-85) REVERT: G 315 GLN cc_start: 0.6937 (tp-100) cc_final: 0.6707 (tp-100) REVERT: G 328 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8272 (tm-30) REVERT: G 341 HIS cc_start: 0.8321 (m170) cc_final: 0.7992 (m-70) REVERT: G 385 TYR cc_start: 0.7549 (m-10) cc_final: 0.7265 (m-10) REVERT: G 387 MET cc_start: 0.8622 (pmm) cc_final: 0.8310 (pmm) REVERT: G 419 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7411 (ptt-90) REVERT: G 438 SER cc_start: 0.8585 (t) cc_final: 0.8205 (p) REVERT: H 50 VAL cc_start: 0.8867 (t) cc_final: 0.8545 (p) REVERT: H 52 ASN cc_start: 0.6608 (p0) cc_final: 0.6327 (p0) REVERT: H 74 LEU cc_start: 0.8099 (mm) cc_final: 0.7725 (mm) REVERT: H 98 ASP cc_start: 0.8611 (m-30) cc_final: 0.8172 (t0) REVERT: H 115 LEU cc_start: 0.9355 (mt) cc_final: 0.8872 (mt) REVERT: H 118 LYS cc_start: 0.8372 (mmtt) cc_final: 0.7927 (tttp) REVERT: H 155 LEU cc_start: 0.8416 (mm) cc_final: 0.8000 (mm) REVERT: H 158 PHE cc_start: 0.7967 (p90) cc_final: 0.7508 (p90) REVERT: H 169 GLU cc_start: 0.8952 (mp0) cc_final: 0.8555 (mp0) REVERT: H 176 HIS cc_start: 0.8935 (m-70) cc_final: 0.8598 (m-70) REVERT: H 225 ASN cc_start: 0.8289 (p0) cc_final: 0.7706 (m-40) REVERT: H 249 HIS cc_start: 0.7242 (t-170) cc_final: 0.6751 (t70) REVERT: H 302 MET cc_start: 0.7084 (mmp) cc_final: 0.6067 (mmp) REVERT: H 367 GLU cc_start: 0.7988 (mp0) cc_final: 0.7356 (mp0) REVERT: H 374 PHE cc_start: 0.7811 (m-80) cc_final: 0.7522 (m-10) REVERT: H 382 LYS cc_start: 0.8972 (mttt) cc_final: 0.8716 (mttp) REVERT: H 383 GLU cc_start: 0.8206 (mp0) cc_final: 0.7990 (pm20) REVERT: H 384 SER cc_start: 0.8498 (t) cc_final: 0.7576 (t) REVERT: H 387 MET cc_start: 0.7405 (pmm) cc_final: 0.6994 (pmm) REVERT: H 434 ASP cc_start: 0.8557 (m-30) cc_final: 0.8281 (m-30) outliers start: 11 outliers final: 4 residues processed: 1301 average time/residue: 0.1909 time to fit residues: 379.8599 Evaluate side-chains 941 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 935 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 307 MET Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain G residue 307 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 117 HIS ** A 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN B 456 HIS C 17 ASN C 117 HIS ** C 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 ASN D 456 HIS G 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.128827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.108512 restraints weight = 65177.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.112784 restraints weight = 39662.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.115917 restraints weight = 26747.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.118237 restraints weight = 19171.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.119932 restraints weight = 14403.611| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28096 Z= 0.218 Angle : 0.701 8.062 38312 Z= 0.367 Chirality : 0.048 0.285 4536 Planarity : 0.006 0.074 5000 Dihedral : 7.204 58.426 4466 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.13 % Allowed : 22.72 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.38 (0.14), residues: 3704 helix: 0.38 (0.14), residues: 1480 sheet: 0.00 (0.21), residues: 568 loop : 0.45 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 407 TYR 0.017 0.002 TYR C 366 PHE 0.022 0.002 PHE G 469 TRP 0.019 0.002 TRP G 334 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (28096) covalent geometry : angle 0.70088 / 0.37 (38312) hydrogen bonds : bond 0.04284 / 2.97 ( 1160) hydrogen bonds : angle 5.77498 / 4.14 ( 3120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 980 time to evaluate : 0.952 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 52 ASN cc_start: 0.7786 (p0) cc_final: 0.7281 (p0) REVERT: A 77 ASP cc_start: 0.8348 (m-30) cc_final: 0.8075 (m-30) REVERT: A 107 ASP cc_start: 0.8468 (m-30) cc_final: 0.7884 (p0) REVERT: A 111 ASP cc_start: 0.8904 (t0) cc_final: 0.8653 (t0) REVERT: A 113 ASN cc_start: 0.8921 (t0) cc_final: 0.8661 (t0) REVERT: A 118 LYS cc_start: 0.7305 (mmtt) cc_final: 0.7087 (mmmm) REVERT: A 138 GLU cc_start: 0.8791 (mp0) cc_final: 0.8162 (tm-30) REVERT: A 155 LEU cc_start: 0.9118 (mm) cc_final: 0.8589 (pp) REVERT: A 184 MET cc_start: 0.8608 (mmm) cc_final: 0.8127 (mmm) REVERT: A 217 ARG cc_start: 0.7556 (mtt-85) cc_final: 0.6551 (mmm-85) REVERT: A 254 LYS cc_start: 0.8362 (tttp) cc_final: 0.8090 (tttm) REVERT: A 313 ARG cc_start: 0.7763 (ttt90) cc_final: 0.7355 (tpt-90) REVERT: A 343 ARG cc_start: 0.8600 (ptm160) cc_final: 0.7812 (ttp-170) REVERT: A 408 LYS cc_start: 0.9226 (tptp) cc_final: 0.8675 (ttmt) REVERT: A 434 ASP cc_start: 0.8947 (m-30) cc_final: 0.8732 (m-30) REVERT: A 446 TYR cc_start: 0.8828 (m-80) cc_final: 0.8133 (m-80) REVERT: A 458 LYS cc_start: 0.9414 (mmmt) cc_final: 0.9062 (mmtm) REVERT: A 471 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7375 (tt0) REVERT: B 18 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6505 (t70) REVERT: B 68 ARG cc_start: 0.8169 (mmp80) cc_final: 0.7443 (mmm160) REVERT: B 117 HIS cc_start: 0.9159 (m-70) cc_final: 0.8744 (m-70) REVERT: B 118 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8445 (tptt) REVERT: B 121 HIS cc_start: 0.8413 (m-70) cc_final: 0.7986 (m-70) REVERT: B 153 ILE cc_start: 0.9257 (tp) cc_final: 0.8963 (tp) REVERT: B 155 LEU cc_start: 0.8535 (mm) cc_final: 0.8285 (mm) REVERT: B 158 PHE cc_start: 0.8072 (p90) cc_final: 0.7701 (p90) REVERT: B 159 VAL cc_start: 0.7755 (t) cc_final: 0.7261 (m) REVERT: B 213 LYS cc_start: 0.9250 (ttmm) cc_final: 0.9015 (ttmt) REVERT: B 302 MET cc_start: 0.7418 (mmp) cc_final: 0.6065 (mmt) REVERT: B 306 ARG cc_start: 0.8541 (mtp-110) cc_final: 0.7138 (mmt180) REVERT: B 379 ARG cc_start: 0.8731 (mtm180) cc_final: 0.8479 (mtm180) REVERT: B 443 THR cc_start: 0.8935 (m) cc_final: 0.8699 (p) REVERT: B 451 ASN cc_start: 0.8703 (p0) cc_final: 0.8328 (p0) REVERT: B 452 LEU cc_start: 0.8007 (mt) cc_final: 0.7709 (mp) REVERT: B 458 LYS cc_start: 0.8869 (mttt) cc_final: 0.8513 (ptpt) REVERT: B 473 HIS cc_start: 0.8869 (t70) cc_final: 0.8560 (t70) REVERT: C 52 ASN cc_start: 0.7768 (p0) cc_final: 0.7276 (p0) REVERT: C 59 ARG cc_start: 0.8313 (ptm160) cc_final: 0.7983 (ptt180) REVERT: C 77 ASP cc_start: 0.8346 (m-30) cc_final: 0.8072 (m-30) REVERT: C 107 ASP cc_start: 0.8446 (m-30) cc_final: 0.7888 (p0) REVERT: C 111 ASP cc_start: 0.8882 (t0) cc_final: 0.8649 (t0) REVERT: C 138 GLU cc_start: 0.8790 (mp0) cc_final: 0.8154 (tm-30) REVERT: C 155 LEU cc_start: 0.9122 (mm) cc_final: 0.8592 (pp) REVERT: C 184 MET cc_start: 0.8610 (mmm) cc_final: 0.8121 (mmm) REVERT: C 217 ARG cc_start: 0.7561 (mtt-85) cc_final: 0.6557 (mmm-85) REVERT: C 254 LYS cc_start: 0.8363 (tttp) cc_final: 0.8098 (tttm) REVERT: C 313 ARG cc_start: 0.7759 (ttt90) cc_final: 0.7327 (tpt-90) REVERT: C 343 ARG cc_start: 0.8591 (ptm160) cc_final: 0.7804 (ttp-170) REVERT: C 434 ASP cc_start: 0.8945 (m-30) cc_final: 0.8725 (m-30) REVERT: C 446 TYR cc_start: 0.8824 (m-80) cc_final: 0.8132 (m-80) REVERT: C 458 LYS cc_start: 0.9411 (mmmt) cc_final: 0.9051 (mmtm) REVERT: C 471 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7309 (tt0) REVERT: D 18 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6492 (t70) REVERT: D 68 ARG cc_start: 0.8164 (mmp80) cc_final: 0.7441 (mmm160) REVERT: D 117 HIS cc_start: 0.9157 (m-70) cc_final: 0.8749 (m-70) REVERT: D 118 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8446 (tptt) REVERT: D 121 HIS cc_start: 0.8417 (m-70) cc_final: 0.7992 (m-70) REVERT: D 153 ILE cc_start: 0.9254 (tp) cc_final: 0.8961 (tp) REVERT: D 155 LEU cc_start: 0.8546 (mm) cc_final: 0.8284 (mm) REVERT: D 158 PHE cc_start: 0.8055 (p90) cc_final: 0.7675 (p90) REVERT: D 213 LYS cc_start: 0.9223 (ttmm) cc_final: 0.9019 (ttmt) REVERT: D 231 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8641 (ptpp) REVERT: D 302 MET cc_start: 0.7413 (mmp) cc_final: 0.6060 (mmt) REVERT: D 306 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.7030 (mmm160) REVERT: D 332 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6475 (p-80) REVERT: D 379 ARG cc_start: 0.8735 (mtm180) cc_final: 0.8485 (mtm180) REVERT: D 443 THR cc_start: 0.8928 (m) cc_final: 0.8694 (p) REVERT: D 451 ASN cc_start: 0.8702 (p0) cc_final: 0.8323 (p0) REVERT: D 452 LEU cc_start: 0.8014 (mt) cc_final: 0.7711 (mp) REVERT: D 458 LYS cc_start: 0.8871 (mttt) cc_final: 0.8512 (ptpt) REVERT: D 473 HIS cc_start: 0.8866 (t70) cc_final: 0.8555 (t70) REVERT: E 8 HIS cc_start: 0.5584 (m-70) cc_final: 0.5278 (m90) REVERT: E 18 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7247 (t0) REVERT: E 86 THR cc_start: 0.9392 (m) cc_final: 0.9149 (p) REVERT: E 135 LEU cc_start: 0.8909 (tp) cc_final: 0.8398 (mt) REVERT: E 155 LEU cc_start: 0.8447 (mm) cc_final: 0.7784 (pt) REVERT: E 174 LEU cc_start: 0.8688 (mm) cc_final: 0.8335 (mm) REVERT: E 184 MET cc_start: 0.7997 (mmm) cc_final: 0.7374 (mmm) REVERT: E 197 ARG cc_start: 0.8685 (ttt90) cc_final: 0.8483 (mtp180) REVERT: E 246 ASP cc_start: 0.8036 (t0) cc_final: 0.7485 (t0) REVERT: E 259 ILE cc_start: 0.9076 (mm) cc_final: 0.8794 (mm) REVERT: E 277 VAL cc_start: 0.9028 (m) cc_final: 0.8803 (t) REVERT: E 306 ARG cc_start: 0.8555 (mtp-110) cc_final: 0.7565 (mtt-85) REVERT: E 341 HIS cc_start: 0.8334 (m170) cc_final: 0.7968 (m-70) REVERT: E 355 ASN cc_start: 0.8903 (t0) cc_final: 0.8666 (t0) REVERT: E 383 GLU cc_start: 0.8699 (pm20) cc_final: 0.8417 (mp0) REVERT: E 390 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8906 (mtpp) REVERT: E 438 SER cc_start: 0.8866 (t) cc_final: 0.8309 (p) REVERT: E 452 LEU cc_start: 0.7777 (mt) cc_final: 0.7545 (mt) REVERT: F 63 GLU cc_start: 0.8836 (pt0) cc_final: 0.8349 (pp20) REVERT: F 74 LEU cc_start: 0.8486 (mm) cc_final: 0.8144 (mm) REVERT: F 85 GLU cc_start: 0.8698 (tt0) cc_final: 0.8318 (tm-30) REVERT: F 115 LEU cc_start: 0.9397 (mt) cc_final: 0.8959 (mt) REVERT: F 118 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8094 (tttp) REVERT: F 184 MET cc_start: 0.8832 (mmm) cc_final: 0.8605 (tpp) REVERT: F 225 ASN cc_start: 0.8617 (p0) cc_final: 0.8342 (m-40) REVERT: F 254 LYS cc_start: 0.8080 (tttt) cc_final: 0.7733 (tttt) REVERT: F 276 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8426 (p) REVERT: F 302 MET cc_start: 0.6843 (mmp) cc_final: 0.6152 (mmp) REVERT: F 308 MET cc_start: 0.7992 (mmt) cc_final: 0.7652 (mmp) REVERT: F 376 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6337 (mmt-90) REVERT: F 430 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8252 (mm-30) REVERT: G 18 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7289 (t0) REVERT: G 61 MET cc_start: 0.8200 (mtt) cc_final: 0.7955 (ttm) REVERT: G 86 THR cc_start: 0.9385 (m) cc_final: 0.9141 (p) REVERT: G 155 LEU cc_start: 0.8447 (mm) cc_final: 0.7783 (pt) REVERT: G 174 LEU cc_start: 0.8705 (mm) cc_final: 0.8378 (mm) REVERT: G 184 MET cc_start: 0.8006 (mmm) cc_final: 0.7367 (mmm) REVERT: G 246 ASP cc_start: 0.8082 (t0) cc_final: 0.7563 (t0) REVERT: G 277 VAL cc_start: 0.9010 (m) cc_final: 0.8788 (t) REVERT: G 306 ARG cc_start: 0.8544 (mtp-110) cc_final: 0.7561 (mtt-85) REVERT: G 341 HIS cc_start: 0.8315 (m170) cc_final: 0.7950 (m-70) REVERT: G 355 ASN cc_start: 0.8920 (t0) cc_final: 0.8691 (t0) REVERT: G 383 GLU cc_start: 0.8709 (pm20) cc_final: 0.8429 (mp0) REVERT: G 390 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8904 (mtpp) REVERT: G 438 SER cc_start: 0.8870 (t) cc_final: 0.8305 (p) REVERT: G 452 LEU cc_start: 0.7758 (mt) cc_final: 0.7533 (mt) REVERT: H 6 ASP cc_start: 0.8284 (m-30) cc_final: 0.8048 (p0) REVERT: H 63 GLU cc_start: 0.8840 (pt0) cc_final: 0.8353 (pp20) REVERT: H 74 LEU cc_start: 0.8494 (mm) cc_final: 0.8157 (mm) REVERT: H 85 GLU cc_start: 0.8679 (tt0) cc_final: 0.8312 (tm-30) REVERT: H 115 LEU cc_start: 0.9395 (mt) cc_final: 0.9019 (mt) REVERT: H 118 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8057 (tttp) REVERT: H 184 MET cc_start: 0.8897 (mmm) cc_final: 0.8540 (tpt) REVERT: H 233 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8244 (pp30) REVERT: H 276 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8411 (p) REVERT: H 302 MET cc_start: 0.6776 (mmp) cc_final: 0.5869 (mmp) REVERT: H 308 MET cc_start: 0.8012 (mmt) cc_final: 0.7659 (mmp) REVERT: H 357 MET cc_start: 0.8256 (tpp) cc_final: 0.7870 (tpp) REVERT: H 374 PHE cc_start: 0.7764 (m-80) cc_final: 0.7489 (m-80) REVERT: H 376 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6370 (mmt-90) REVERT: H 430 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8273 (mm-30) REVERT: H 458 LYS cc_start: 0.9058 (mtmm) cc_final: 0.8704 (mtmt) outliers start: 116 outliers final: 58 residues processed: 1044 average time/residue: 0.1825 time to fit residues: 293.4354 Evaluate side-chains 893 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 826 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 376 ARG Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 376 ARG Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 275 ASN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 332 HIS Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain H residue 376 ARG Chi-restraints excluded: chain H residue 393 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 78 optimal weight: 2.9990 chunk 331 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 302 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 266 optimal weight: 0.9980 chunk 334 optimal weight: 7.9990 chunk 314 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 242 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 HIS C 456 HIS ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN F 121 HIS F 328 GLN ** G 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN H 121 HIS H 328 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.131007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.110322 restraints weight = 64755.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.114601 restraints weight = 39585.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.117774 restraints weight = 26835.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.120094 restraints weight = 19383.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.121813 restraints weight = 14683.722| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28096 Z= 0.138 Angle : 0.659 8.006 38312 Z= 0.336 Chirality : 0.047 0.284 4536 Planarity : 0.005 0.062 5000 Dihedral : 6.972 58.910 4448 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.49 % Allowed : 25.14 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.45 (0.14), residues: 3704 helix: 0.59 (0.14), residues: 1416 sheet: 0.16 (0.21), residues: 600 loop : 0.29 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 340 TYR 0.029 0.002 TYR F 366 PHE 0.024 0.002 PHE D 316 TRP 0.014 0.001 TRP G 334 HIS 0.007 0.001 HIS A 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (28096) covalent geometry : angle 0.65935 / 0.34 (38312) hydrogen bonds : bond 0.03718 / 2.58 ( 1160) hydrogen bonds : angle 5.54089 / 3.97 ( 3120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 917 time to evaluate : 0.820 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: A 52 ASN cc_start: 0.7550 (p0) cc_final: 0.6985 (p0) REVERT: A 53 MET cc_start: 0.7808 (mmt) cc_final: 0.7406 (mmt) REVERT: A 77 ASP cc_start: 0.8257 (m-30) cc_final: 0.8037 (m-30) REVERT: A 99 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8257 (p) REVERT: A 107 ASP cc_start: 0.8440 (m-30) cc_final: 0.7947 (p0) REVERT: A 111 ASP cc_start: 0.8889 (t0) cc_final: 0.8653 (t0) REVERT: A 138 GLU cc_start: 0.8762 (mp0) cc_final: 0.8249 (tm-30) REVERT: A 155 LEU cc_start: 0.9099 (mm) cc_final: 0.8604 (pp) REVERT: A 184 MET cc_start: 0.8528 (mmm) cc_final: 0.8146 (mmm) REVERT: A 225 ASN cc_start: 0.8654 (p0) cc_final: 0.8044 (m-40) REVERT: A 313 ARG cc_start: 0.7678 (ttt90) cc_final: 0.7295 (ttt90) REVERT: A 343 ARG cc_start: 0.8548 (ptm160) cc_final: 0.7474 (ttp-170) REVERT: A 387 MET cc_start: 0.8644 (pmm) cc_final: 0.8345 (pmm) REVERT: A 434 ASP cc_start: 0.8932 (m-30) cc_final: 0.8727 (m-30) REVERT: A 446 TYR cc_start: 0.8683 (m-80) cc_final: 0.7978 (m-80) REVERT: A 458 LYS cc_start: 0.9391 (mmmt) cc_final: 0.9085 (mmtm) REVERT: B 18 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6332 (t70) REVERT: B 68 ARG cc_start: 0.8070 (mmp80) cc_final: 0.7491 (mmm160) REVERT: B 91 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8443 (mmmt) REVERT: B 117 HIS cc_start: 0.9139 (m-70) cc_final: 0.8750 (m-70) REVERT: B 121 HIS cc_start: 0.8232 (m-70) cc_final: 0.6846 (m-70) REVERT: B 128 PHE cc_start: 0.9315 (t80) cc_final: 0.8991 (t80) REVERT: B 153 ILE cc_start: 0.9233 (tp) cc_final: 0.8946 (tp) REVERT: B 155 LEU cc_start: 0.8579 (mm) cc_final: 0.8328 (mm) REVERT: B 158 PHE cc_start: 0.8046 (p90) cc_final: 0.7731 (p90) REVERT: B 159 VAL cc_start: 0.7849 (t) cc_final: 0.7374 (m) REVERT: B 184 MET cc_start: 0.8616 (tpp) cc_final: 0.8385 (tpt) REVERT: B 302 MET cc_start: 0.7194 (mmp) cc_final: 0.6147 (mmp) REVERT: B 303 CYS cc_start: 0.8185 (t) cc_final: 0.7974 (m) REVERT: B 306 ARG cc_start: 0.8411 (mtp-110) cc_final: 0.6391 (mtp-110) REVERT: B 332 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6576 (p-80) REVERT: B 344 ASP cc_start: 0.8235 (m-30) cc_final: 0.7883 (m-30) REVERT: B 379 ARG cc_start: 0.8766 (mtm180) cc_final: 0.8437 (mtm180) REVERT: B 403 PHE cc_start: 0.9060 (t80) cc_final: 0.8448 (t80) REVERT: B 451 ASN cc_start: 0.8656 (p0) cc_final: 0.8293 (p0) REVERT: B 452 LEU cc_start: 0.7927 (mt) cc_final: 0.7701 (mp) REVERT: B 458 LYS cc_start: 0.8883 (mttt) cc_final: 0.8480 (ptpt) REVERT: B 473 HIS cc_start: 0.8879 (t70) cc_final: 0.8595 (t70) REVERT: C 52 ASN cc_start: 0.7535 (p0) cc_final: 0.6975 (p0) REVERT: C 53 MET cc_start: 0.7821 (mmt) cc_final: 0.7420 (mmt) REVERT: C 59 ARG cc_start: 0.8333 (ptm160) cc_final: 0.7990 (ptt180) REVERT: C 107 ASP cc_start: 0.8423 (m-30) cc_final: 0.7946 (p0) REVERT: C 111 ASP cc_start: 0.8854 (t0) cc_final: 0.8631 (t0) REVERT: C 116 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8911 (tp) REVERT: C 138 GLU cc_start: 0.8747 (mp0) cc_final: 0.8244 (tm-30) REVERT: C 155 LEU cc_start: 0.9104 (mm) cc_final: 0.8610 (pp) REVERT: C 184 MET cc_start: 0.8517 (mmm) cc_final: 0.8139 (mmm) REVERT: C 197 ARG cc_start: 0.8939 (ttt90) cc_final: 0.8509 (mtp180) REVERT: C 306 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8242 (mtt90) REVERT: C 343 ARG cc_start: 0.8562 (ptm160) cc_final: 0.7778 (ttp-170) REVERT: C 387 MET cc_start: 0.8646 (pmm) cc_final: 0.8354 (pmm) REVERT: C 422 LEU cc_start: 0.8425 (mm) cc_final: 0.8095 (mm) REVERT: C 434 ASP cc_start: 0.8930 (m-30) cc_final: 0.8719 (m-30) REVERT: C 446 TYR cc_start: 0.8680 (m-80) cc_final: 0.7969 (m-80) REVERT: C 458 LYS cc_start: 0.9383 (mmmt) cc_final: 0.9074 (mmtm) REVERT: D 18 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6320 (t70) REVERT: D 68 ARG cc_start: 0.8056 (mmp80) cc_final: 0.7489 (mmm160) REVERT: D 91 LYS cc_start: 0.8702 (mmmt) cc_final: 0.8451 (mmmt) REVERT: D 117 HIS cc_start: 0.9124 (m-70) cc_final: 0.8738 (m-70) REVERT: D 121 HIS cc_start: 0.8222 (m-70) cc_final: 0.6855 (m-70) REVERT: D 128 PHE cc_start: 0.9311 (t80) cc_final: 0.8987 (t80) REVERT: D 153 ILE cc_start: 0.9229 (tp) cc_final: 0.8940 (tp) REVERT: D 155 LEU cc_start: 0.8594 (mm) cc_final: 0.8343 (mm) REVERT: D 158 PHE cc_start: 0.8061 (p90) cc_final: 0.7804 (p90) REVERT: D 159 VAL cc_start: 0.7988 (t) cc_final: 0.7373 (m) REVERT: D 184 MET cc_start: 0.8629 (tpp) cc_final: 0.8390 (tpt) REVERT: D 231 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8603 (ptpp) REVERT: D 302 MET cc_start: 0.7242 (mmp) cc_final: 0.6196 (mmp) REVERT: D 332 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6489 (p-80) REVERT: D 379 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8420 (mtm180) REVERT: D 403 PHE cc_start: 0.9078 (t80) cc_final: 0.8457 (t80) REVERT: D 451 ASN cc_start: 0.8661 (p0) cc_final: 0.8293 (p0) REVERT: D 452 LEU cc_start: 0.7930 (mt) cc_final: 0.7703 (mp) REVERT: D 458 LYS cc_start: 0.8890 (mttt) cc_final: 0.8487 (ptpt) REVERT: D 473 HIS cc_start: 0.8878 (t70) cc_final: 0.8592 (t70) REVERT: E 18 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7140 (t70) REVERT: E 86 THR cc_start: 0.9367 (m) cc_final: 0.9154 (p) REVERT: E 135 LEU cc_start: 0.8869 (tp) cc_final: 0.8399 (mt) REVERT: E 155 LEU cc_start: 0.8451 (mm) cc_final: 0.7785 (pt) REVERT: E 174 LEU cc_start: 0.8599 (mm) cc_final: 0.8257 (mm) REVERT: E 246 ASP cc_start: 0.7891 (t0) cc_final: 0.7612 (t0) REVERT: E 277 VAL cc_start: 0.8967 (m) cc_final: 0.8745 (t) REVERT: E 306 ARG cc_start: 0.8530 (mtp-110) cc_final: 0.7593 (mtt-85) REVERT: E 341 HIS cc_start: 0.8337 (m170) cc_final: 0.7946 (m-70) REVERT: E 355 ASN cc_start: 0.8652 (t0) cc_final: 0.8243 (t0) REVERT: E 368 SER cc_start: 0.8765 (t) cc_final: 0.8452 (m) REVERT: E 383 GLU cc_start: 0.8610 (pm20) cc_final: 0.8287 (mp0) REVERT: E 387 MET cc_start: 0.8586 (pmm) cc_final: 0.7665 (pmm) REVERT: E 390 LYS cc_start: 0.9133 (mmtm) cc_final: 0.8718 (mtpp) REVERT: E 438 SER cc_start: 0.8868 (t) cc_final: 0.8447 (p) REVERT: E 452 LEU cc_start: 0.7805 (mt) cc_final: 0.7583 (mt) REVERT: E 464 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8211 (tp-100) REVERT: F 17 ASN cc_start: 0.6656 (OUTLIER) cc_final: 0.6298 (m110) REVERT: F 68 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8056 (mmm160) REVERT: F 74 LEU cc_start: 0.8470 (mm) cc_final: 0.8112 (mm) REVERT: F 85 GLU cc_start: 0.8735 (tt0) cc_final: 0.8266 (tm-30) REVERT: F 115 LEU cc_start: 0.9339 (mt) cc_final: 0.8929 (mt) REVERT: F 118 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8000 (tttp) REVERT: F 233 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8188 (pp30) REVERT: F 302 MET cc_start: 0.6690 (mmp) cc_final: 0.5931 (mmp) REVERT: F 328 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8153 (pp30) REVERT: F 430 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8406 (mm-30) REVERT: F 469 PHE cc_start: 0.5984 (m-10) cc_final: 0.5507 (m-10) REVERT: G 18 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7129 (t70) REVERT: G 86 THR cc_start: 0.9358 (m) cc_final: 0.9141 (p) REVERT: G 135 LEU cc_start: 0.8861 (tp) cc_final: 0.8389 (mt) REVERT: G 155 LEU cc_start: 0.8441 (mm) cc_final: 0.7762 (pt) REVERT: G 175 GLU cc_start: 0.7390 (tp30) cc_final: 0.7117 (mm-30) REVERT: G 184 MET cc_start: 0.7830 (mmm) cc_final: 0.7403 (mmm) REVERT: G 306 ARG cc_start: 0.8522 (mtp-110) cc_final: 0.6960 (mtm180) REVERT: G 316 PHE cc_start: 0.8556 (t80) cc_final: 0.7863 (t80) REVERT: G 336 ASP cc_start: 0.6933 (t70) cc_final: 0.6567 (t0) REVERT: G 341 HIS cc_start: 0.8312 (m170) cc_final: 0.7921 (m-70) REVERT: G 355 ASN cc_start: 0.8623 (t0) cc_final: 0.8190 (t0) REVERT: G 368 SER cc_start: 0.8770 (t) cc_final: 0.8463 (m) REVERT: G 383 GLU cc_start: 0.8599 (pm20) cc_final: 0.8284 (mp0) REVERT: G 387 MET cc_start: 0.8576 (pmm) cc_final: 0.7605 (pmm) REVERT: G 390 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8697 (mtpp) REVERT: G 431 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7601 (p0) REVERT: G 438 SER cc_start: 0.8861 (t) cc_final: 0.8440 (p) REVERT: G 452 LEU cc_start: 0.7790 (mt) cc_final: 0.7576 (mt) REVERT: H 6 ASP cc_start: 0.8254 (m-30) cc_final: 0.8040 (p0) REVERT: H 17 ASN cc_start: 0.6632 (OUTLIER) cc_final: 0.6402 (m110) REVERT: H 63 GLU cc_start: 0.8762 (pt0) cc_final: 0.8367 (tp30) REVERT: H 68 ARG cc_start: 0.8664 (mmm160) cc_final: 0.8062 (mmm160) REVERT: H 74 LEU cc_start: 0.8463 (mm) cc_final: 0.8031 (mm) REVERT: H 85 GLU cc_start: 0.8713 (tt0) cc_final: 0.8250 (tm-30) REVERT: H 95 LEU cc_start: 0.8931 (mm) cc_final: 0.8688 (mm) REVERT: H 115 LEU cc_start: 0.9335 (mt) cc_final: 0.8898 (mt) REVERT: H 118 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8202 (mtpt) REVERT: H 260 LYS cc_start: 0.8583 (pttp) cc_final: 0.8077 (pttp) REVERT: H 267 LEU cc_start: 0.8657 (mt) cc_final: 0.8400 (mt) REVERT: H 302 MET cc_start: 0.6686 (mmp) cc_final: 0.5952 (mmp) REVERT: H 308 MET cc_start: 0.8003 (mmt) cc_final: 0.7791 (mmt) REVERT: H 328 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8195 (pp30) REVERT: H 390 LYS cc_start: 0.9151 (mmtm) cc_final: 0.8655 (tttm) REVERT: H 430 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8403 (mm-30) REVERT: H 469 PHE cc_start: 0.6007 (m-10) cc_final: 0.5801 (m-10) outliers start: 126 outliers final: 72 residues processed: 990 average time/residue: 0.1760 time to fit residues: 272.5124 Evaluate side-chains 894 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 809 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 328 GLN Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 431 ASP Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 17 ASN Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 275 ASN Chi-restraints excluded: chain H residue 328 GLN Chi-restraints excluded: chain H residue 332 HIS Chi-restraints excluded: chain H residue 376 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 138 optimal weight: 0.5980 chunk 268 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 239 optimal weight: 0.7980 chunk 279 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 186 optimal weight: 0.0000 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 HIS ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 ASN ** E 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** 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 = 0.3939 r_free = 0.3939 target = 0.131857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111035 restraints weight = 63864.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.115329 restraints weight = 39384.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.118524 restraints weight = 26757.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.120832 restraints weight = 19376.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.122756 restraints weight = 14681.024| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28096 Z= 0.133 Angle : 0.656 11.064 38312 Z= 0.332 Chirality : 0.046 0.256 4536 Planarity : 0.005 0.054 5000 Dihedral : 6.729 59.882 4448 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.99 % Allowed : 26.96 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.29 (0.14), residues: 3704 helix: 0.44 (0.14), residues: 1424 sheet: 0.02 (0.21), residues: 600 loop : 0.25 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 391 TYR 0.021 0.002 TYR F 366 PHE 0.015 0.002 PHE H 362 TRP 0.017 0.002 TRP G 334 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (28096) covalent geometry : angle 0.65621 / 0.33 (38312) hydrogen bonds : bond 0.03499 / 2.43 ( 1160) hydrogen bonds : angle 5.39111 / 3.86 ( 3120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 881 time to evaluate : 0.995 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 52 ASN cc_start: 0.7603 (p0) cc_final: 0.6951 (p0) REVERT: A 59 ARG cc_start: 0.8313 (ptm160) cc_final: 0.8013 (ptt180) REVERT: A 76 GLN cc_start: 0.8060 (pm20) cc_final: 0.7576 (pm20) REVERT: A 99 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8277 (p) REVERT: A 107 ASP cc_start: 0.8451 (m-30) cc_final: 0.7979 (p0) REVERT: A 111 ASP cc_start: 0.8861 (t0) cc_final: 0.8598 (t0) REVERT: A 138 GLU cc_start: 0.8839 (mp0) cc_final: 0.8298 (tm-30) REVERT: A 155 LEU cc_start: 0.9101 (mm) cc_final: 0.8593 (pp) REVERT: A 184 MET cc_start: 0.8550 (mmm) cc_final: 0.8236 (mmm) REVERT: A 197 ARG cc_start: 0.8907 (mtp180) cc_final: 0.8498 (mtp180) REVERT: A 217 ARG cc_start: 0.7208 (mtt-85) cc_final: 0.6714 (mmm-85) REVERT: A 283 ARG cc_start: 0.9124 (mtm110) cc_final: 0.8917 (mtp180) REVERT: A 313 ARG cc_start: 0.7738 (ttt90) cc_final: 0.7487 (ttt90) REVERT: A 343 ARG cc_start: 0.8531 (ptm160) cc_final: 0.7768 (ttp-170) REVERT: A 421 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8652 (t) REVERT: A 434 ASP cc_start: 0.8943 (m-30) cc_final: 0.8736 (m-30) REVERT: A 446 TYR cc_start: 0.8726 (m-80) cc_final: 0.7905 (m-80) REVERT: A 458 LYS cc_start: 0.9393 (mmmt) cc_final: 0.9026 (mmtm) REVERT: B 18 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.5820 (t70) REVERT: B 68 ARG cc_start: 0.8044 (mmp80) cc_final: 0.7530 (mmm160) REVERT: B 74 LEU cc_start: 0.8855 (mm) cc_final: 0.8563 (mm) REVERT: B 103 LEU cc_start: 0.9401 (mm) cc_final: 0.9111 (mm) REVERT: B 117 HIS cc_start: 0.9105 (m-70) cc_final: 0.8740 (m-70) REVERT: B 118 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8520 (tptt) REVERT: B 128 PHE cc_start: 0.9284 (t80) cc_final: 0.8963 (t80) REVERT: B 135 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7218 (mm) REVERT: B 153 ILE cc_start: 0.9208 (tp) cc_final: 0.8923 (tp) REVERT: B 155 LEU cc_start: 0.8587 (mm) cc_final: 0.8366 (mm) REVERT: B 158 PHE cc_start: 0.8053 (p90) cc_final: 0.7841 (p90) REVERT: B 213 LYS cc_start: 0.9172 (ttmm) cc_final: 0.8924 (ttpt) REVERT: B 241 ASP cc_start: 0.8034 (t0) cc_final: 0.7805 (t0) REVERT: B 302 MET cc_start: 0.7135 (mmp) cc_final: 0.6035 (mmp) REVERT: B 332 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6511 (p-80) REVERT: B 344 ASP cc_start: 0.8228 (m-30) cc_final: 0.7867 (m-30) REVERT: B 379 ARG cc_start: 0.8795 (mtm180) cc_final: 0.8427 (mtm180) REVERT: B 408 LYS cc_start: 0.8568 (pttt) cc_final: 0.8318 (pttm) REVERT: B 451 ASN cc_start: 0.8668 (p0) cc_final: 0.8293 (p0) REVERT: B 452 LEU cc_start: 0.8009 (mt) cc_final: 0.7642 (mp) REVERT: B 458 LYS cc_start: 0.8873 (mttt) cc_final: 0.8481 (ptpt) REVERT: B 473 HIS cc_start: 0.8906 (t70) cc_final: 0.8616 (t70) REVERT: C 52 ASN cc_start: 0.7605 (p0) cc_final: 0.7281 (p0) REVERT: C 53 MET cc_start: 0.7798 (mmt) cc_final: 0.7426 (mmt) REVERT: C 59 ARG cc_start: 0.8311 (ptm160) cc_final: 0.8014 (ptt180) REVERT: C 76 GLN cc_start: 0.7921 (pm20) cc_final: 0.7332 (pm20) REVERT: C 99 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8359 (p) REVERT: C 107 ASP cc_start: 0.8438 (m-30) cc_final: 0.7967 (p0) REVERT: C 111 ASP cc_start: 0.8840 (t0) cc_final: 0.8619 (t0) REVERT: C 116 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8885 (tp) REVERT: C 138 GLU cc_start: 0.8749 (mp0) cc_final: 0.8298 (tm-30) REVERT: C 155 LEU cc_start: 0.9104 (mm) cc_final: 0.8611 (pp) REVERT: C 184 MET cc_start: 0.8566 (mmm) cc_final: 0.8217 (mmm) REVERT: C 217 ARG cc_start: 0.7203 (mtt-85) cc_final: 0.6707 (mmm-85) REVERT: C 283 ARG cc_start: 0.9120 (mtm110) cc_final: 0.8914 (mmm160) REVERT: C 327 ARG cc_start: 0.9049 (mtp180) cc_final: 0.8780 (mtt180) REVERT: C 343 ARG cc_start: 0.8546 (ptm160) cc_final: 0.7782 (ttp-170) REVERT: C 387 MET cc_start: 0.8528 (pmm) cc_final: 0.7866 (pmm) REVERT: C 390 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8913 (pttt) REVERT: C 421 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8653 (t) REVERT: C 434 ASP cc_start: 0.8953 (m-30) cc_final: 0.8750 (m-30) REVERT: C 446 TYR cc_start: 0.8732 (m-80) cc_final: 0.7924 (m-80) REVERT: C 456 HIS cc_start: 0.7758 (t70) cc_final: 0.7233 (t70) REVERT: C 458 LYS cc_start: 0.9398 (mmmt) cc_final: 0.9022 (mmtm) REVERT: D 18 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.5826 (t70) REVERT: D 68 ARG cc_start: 0.8026 (mmp80) cc_final: 0.7495 (mmm160) REVERT: D 74 LEU cc_start: 0.8843 (mm) cc_final: 0.8561 (mm) REVERT: D 117 HIS cc_start: 0.9092 (m-70) cc_final: 0.8734 (m-70) REVERT: D 118 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8492 (tptt) REVERT: D 128 PHE cc_start: 0.9284 (t80) cc_final: 0.8961 (t80) REVERT: D 153 ILE cc_start: 0.9201 (tp) cc_final: 0.8911 (tp) REVERT: D 155 LEU cc_start: 0.8614 (mm) cc_final: 0.8358 (mm) REVERT: D 158 PHE cc_start: 0.8121 (p90) cc_final: 0.7792 (p90) REVERT: D 159 VAL cc_start: 0.8027 (t) cc_final: 0.7375 (m) REVERT: D 213 LYS cc_start: 0.9163 (ttmm) cc_final: 0.8921 (ttpt) REVERT: D 241 ASP cc_start: 0.8041 (t0) cc_final: 0.7815 (t0) REVERT: D 302 MET cc_start: 0.7307 (mmp) cc_final: 0.6234 (mmp) REVERT: D 303 CYS cc_start: 0.7431 (m) cc_final: 0.6821 (m) REVERT: D 332 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.6481 (p-80) REVERT: D 344 ASP cc_start: 0.8132 (m-30) cc_final: 0.7725 (m-30) REVERT: D 379 ARG cc_start: 0.8790 (mtm180) cc_final: 0.8391 (mtm180) REVERT: D 408 LYS cc_start: 0.8585 (pttt) cc_final: 0.8298 (pttm) REVERT: D 451 ASN cc_start: 0.8674 (p0) cc_final: 0.8294 (p0) REVERT: D 452 LEU cc_start: 0.8014 (mt) cc_final: 0.7645 (mp) REVERT: D 458 LYS cc_start: 0.8878 (mttt) cc_final: 0.8488 (ptpt) REVERT: D 473 HIS cc_start: 0.8910 (t70) cc_final: 0.8621 (t70) REVERT: E 6 ASP cc_start: 0.9070 (t0) cc_final: 0.8829 (t0) REVERT: E 18 ASP cc_start: 0.7964 (m-30) cc_final: 0.7067 (t70) REVERT: E 61 MET cc_start: 0.8219 (mtt) cc_final: 0.7663 (tpp) REVERT: E 86 THR cc_start: 0.9367 (m) cc_final: 0.9160 (p) REVERT: E 135 LEU cc_start: 0.8849 (tp) cc_final: 0.8406 (mt) REVERT: E 155 LEU cc_start: 0.8450 (mm) cc_final: 0.7930 (pp) REVERT: E 175 GLU cc_start: 0.7486 (tp30) cc_final: 0.7168 (mm-30) REVERT: E 202 ARG cc_start: 0.7687 (ptp-110) cc_final: 0.7290 (ptm160) REVERT: E 246 ASP cc_start: 0.8219 (t0) cc_final: 0.7645 (t0) REVERT: E 277 VAL cc_start: 0.8937 (m) cc_final: 0.8696 (t) REVERT: E 292 ILE cc_start: 0.8819 (mm) cc_final: 0.8470 (mm) REVERT: E 306 ARG cc_start: 0.8503 (mtp-110) cc_final: 0.7618 (mtt-85) REVERT: E 341 HIS cc_start: 0.8342 (m170) cc_final: 0.7970 (m-70) REVERT: E 355 ASN cc_start: 0.8577 (t0) cc_final: 0.8135 (t0) REVERT: E 383 GLU cc_start: 0.8570 (pm20) cc_final: 0.8174 (mp0) REVERT: E 390 LYS cc_start: 0.9108 (mmtm) cc_final: 0.8671 (mtpp) REVERT: E 438 SER cc_start: 0.8842 (t) cc_final: 0.8340 (p) REVERT: E 452 LEU cc_start: 0.7829 (mt) cc_final: 0.7608 (mt) REVERT: F 15 THR cc_start: 0.6996 (t) cc_final: 0.6246 (m) REVERT: F 63 GLU cc_start: 0.8705 (pt0) cc_final: 0.8354 (tp30) REVERT: F 68 ARG cc_start: 0.8642 (mmm160) cc_final: 0.8038 (mmm160) REVERT: F 74 LEU cc_start: 0.8456 (mm) cc_final: 0.8020 (mm) REVERT: F 85 GLU cc_start: 0.8782 (tt0) cc_final: 0.8300 (tm-30) REVERT: F 95 LEU cc_start: 0.8953 (mm) cc_final: 0.8701 (mm) REVERT: F 115 LEU cc_start: 0.9309 (mt) cc_final: 0.8938 (mt) REVERT: F 302 MET cc_start: 0.6702 (mmp) cc_final: 0.5887 (mmp) REVERT: F 308 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7710 (mmt) REVERT: G 6 ASP cc_start: 0.9075 (t0) cc_final: 0.8839 (t0) REVERT: G 18 ASP cc_start: 0.7973 (m-30) cc_final: 0.7444 (t70) REVERT: G 61 MET cc_start: 0.8231 (mtt) cc_final: 0.7683 (tpp) REVERT: G 86 THR cc_start: 0.9365 (m) cc_final: 0.9158 (p) REVERT: G 135 LEU cc_start: 0.8843 (tp) cc_final: 0.8384 (mt) REVERT: G 155 LEU cc_start: 0.8468 (mm) cc_final: 0.7942 (pp) REVERT: G 175 GLU cc_start: 0.7467 (tp30) cc_final: 0.7165 (mm-30) REVERT: G 195 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8391 (tt) REVERT: G 233 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7918 (tm-30) REVERT: G 246 ASP cc_start: 0.7975 (t0) cc_final: 0.7537 (t0) REVERT: G 316 PHE cc_start: 0.8492 (t80) cc_final: 0.8064 (t80) REVERT: G 341 HIS cc_start: 0.8332 (m170) cc_final: 0.7955 (m-70) REVERT: G 355 ASN cc_start: 0.8641 (t0) cc_final: 0.8156 (t0) REVERT: G 383 GLU cc_start: 0.8571 (pm20) cc_final: 0.8174 (mp0) REVERT: G 390 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8662 (mtpp) REVERT: G 438 SER cc_start: 0.8877 (t) cc_final: 0.8365 (p) REVERT: G 452 LEU cc_start: 0.7827 (mt) cc_final: 0.7615 (mt) REVERT: G 464 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7752 (tp-100) REVERT: G 471 GLU cc_start: 0.7917 (pt0) cc_final: 0.7576 (tt0) REVERT: H 63 GLU cc_start: 0.8695 (pt0) cc_final: 0.8366 (tp30) REVERT: H 68 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8212 (mmm160) REVERT: H 74 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8115 (mm) REVERT: H 85 GLU cc_start: 0.8776 (tt0) cc_final: 0.8274 (tm-30) REVERT: H 95 LEU cc_start: 0.8949 (mm) cc_final: 0.8708 (mm) REVERT: H 115 LEU cc_start: 0.9306 (mt) cc_final: 0.8880 (mt) REVERT: H 118 LYS cc_start: 0.8534 (mmtt) cc_final: 0.7982 (tttp) REVERT: H 233 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8181 (pp30) REVERT: H 260 LYS cc_start: 0.8598 (pttp) cc_final: 0.8077 (pttp) REVERT: H 302 MET cc_start: 0.6739 (mmp) cc_final: 0.5910 (mmp) REVERT: H 458 LYS cc_start: 0.9088 (mtmm) cc_final: 0.8794 (mttt) outliers start: 112 outliers final: 78 residues processed: 947 average time/residue: 0.1830 time to fit residues: 270.5447 Evaluate side-chains 895 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 804 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 307 MET Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 308 MET Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 376 ARG Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 275 ASN Chi-restraints excluded: chain H residue 332 HIS Chi-restraints excluded: chain H residue 376 ARG Chi-restraints excluded: chain H residue 433 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 355 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 332 optimal weight: 20.0000 chunk 348 optimal weight: 8.9990 chunk 258 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 277 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN ** E 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 ASN ** H 315 GLN ** 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 = 0.3863 r_free = 0.3863 target = 0.126092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.105259 restraints weight = 66296.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.109355 restraints weight = 41326.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.112398 restraints weight = 28516.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.114640 restraints weight = 20897.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.116309 restraints weight = 16046.352| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 28096 Z= 0.205 Angle : 0.686 8.944 38312 Z= 0.354 Chirality : 0.046 0.238 4536 Planarity : 0.005 0.052 5000 Dihedral : 6.641 57.699 4448 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.06 % Allowed : 27.10 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.08 (0.14), residues: 3704 helix: 0.22 (0.14), residues: 1432 sheet: -0.18 (0.21), residues: 600 loop : 0.22 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 426 TYR 0.021 0.002 TYR A 366 PHE 0.028 0.002 PHE B 316 TRP 0.020 0.001 TRP G 334 HIS 0.006 0.001 HIS G 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (28096) covalent geometry : angle 0.68567 / 0.35 (38312) hydrogen bonds : bond 0.03642 / 2.51 ( 1160) hydrogen bonds : angle 5.45485 / 3.91 ( 3120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 802 time to evaluate : 0.717 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: A 53 MET cc_start: 0.8132 (mmt) cc_final: 0.7328 (mmt) REVERT: A 76 GLN cc_start: 0.8137 (pm20) cc_final: 0.7893 (pm20) REVERT: A 99 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8272 (p) REVERT: A 107 ASP cc_start: 0.8514 (m-30) cc_final: 0.8075 (p0) REVERT: A 111 ASP cc_start: 0.8905 (t0) cc_final: 0.8687 (t0) REVERT: A 138 GLU cc_start: 0.8888 (mp0) cc_final: 0.8422 (tm-30) REVERT: A 155 LEU cc_start: 0.9147 (mm) cc_final: 0.8623 (pp) REVERT: A 174 LEU cc_start: 0.8941 (mm) cc_final: 0.8628 (mm) REVERT: A 184 MET cc_start: 0.8640 (mmm) cc_final: 0.8365 (mmm) REVERT: A 197 ARG cc_start: 0.8923 (mtp180) cc_final: 0.8452 (mtp180) REVERT: A 217 ARG cc_start: 0.7369 (mtt-85) cc_final: 0.6864 (mmm-85) REVERT: A 254 LYS cc_start: 0.8583 (tttp) cc_final: 0.8257 (tttt) REVERT: A 283 ARG cc_start: 0.9120 (mtm110) cc_final: 0.8828 (mmm-85) REVERT: A 313 ARG cc_start: 0.7744 (ttt90) cc_final: 0.7311 (ttt90) REVERT: A 343 ARG cc_start: 0.8557 (ptm160) cc_final: 0.7748 (ttp-170) REVERT: A 372 LEU cc_start: 0.8507 (tt) cc_final: 0.8223 (tt) REVERT: A 387 MET cc_start: 0.8539 (pmm) cc_final: 0.7854 (pmm) REVERT: A 421 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8667 (t) REVERT: A 434 ASP cc_start: 0.8994 (m-30) cc_final: 0.8740 (m-30) REVERT: A 446 TYR cc_start: 0.8792 (m-80) cc_final: 0.8146 (m-80) REVERT: A 458 LYS cc_start: 0.9432 (mmmt) cc_final: 0.9105 (mmtm) REVERT: B 68 ARG cc_start: 0.8082 (mmp80) cc_final: 0.7639 (mmm160) REVERT: B 74 LEU cc_start: 0.8973 (mm) cc_final: 0.8668 (mm) REVERT: B 117 HIS cc_start: 0.9094 (m-70) cc_final: 0.8734 (m-70) REVERT: B 153 ILE cc_start: 0.9281 (tp) cc_final: 0.9013 (tp) REVERT: B 158 PHE cc_start: 0.8181 (p90) cc_final: 0.7750 (p90) REVERT: B 159 VAL cc_start: 0.7910 (t) cc_final: 0.7650 (m) REVERT: B 184 MET cc_start: 0.8585 (tpp) cc_final: 0.8294 (tpt) REVERT: B 241 ASP cc_start: 0.8160 (t0) cc_final: 0.7894 (t0) REVERT: B 302 MET cc_start: 0.7518 (mmp) cc_final: 0.6508 (mmp) REVERT: B 303 CYS cc_start: 0.7733 (m) cc_final: 0.6920 (m) REVERT: B 332 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6484 (p-80) REVERT: B 379 ARG cc_start: 0.8721 (mtm180) cc_final: 0.8387 (mtm180) REVERT: B 403 PHE cc_start: 0.9078 (t80) cc_final: 0.8868 (t80) REVERT: B 408 LYS cc_start: 0.8548 (pttt) cc_final: 0.8300 (pttm) REVERT: B 451 ASN cc_start: 0.8660 (p0) cc_final: 0.8335 (p0) REVERT: B 458 LYS cc_start: 0.8881 (mttt) cc_final: 0.8503 (ptpt) REVERT: B 473 HIS cc_start: 0.8954 (t70) cc_final: 0.8670 (t70) REVERT: C 18 ASP cc_start: 0.8444 (m-30) cc_final: 0.6796 (t0) REVERT: C 59 ARG cc_start: 0.8357 (ptm160) cc_final: 0.8067 (ptt180) REVERT: C 76 GLN cc_start: 0.8119 (pm20) cc_final: 0.7651 (pm20) REVERT: C 99 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8375 (p) REVERT: C 107 ASP cc_start: 0.8481 (m-30) cc_final: 0.8074 (p0) REVERT: C 111 ASP cc_start: 0.8888 (t0) cc_final: 0.8683 (t0) REVERT: C 116 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9047 (tp) REVERT: C 138 GLU cc_start: 0.8810 (mp0) cc_final: 0.8418 (tm-30) REVERT: C 155 LEU cc_start: 0.9152 (mm) cc_final: 0.8661 (pp) REVERT: C 184 MET cc_start: 0.8636 (mmm) cc_final: 0.8329 (mmm) REVERT: C 197 ARG cc_start: 0.8956 (ttt90) cc_final: 0.8611 (mtp180) REVERT: C 217 ARG cc_start: 0.7364 (mtt-85) cc_final: 0.6860 (mmm-85) REVERT: C 283 ARG cc_start: 0.9118 (mtm110) cc_final: 0.8843 (mmm-85) REVERT: C 306 ARG cc_start: 0.8540 (ttm170) cc_final: 0.8324 (ttm170) REVERT: C 343 ARG cc_start: 0.8577 (ptm160) cc_final: 0.7744 (ttp-170) REVERT: C 387 MET cc_start: 0.8532 (pmm) cc_final: 0.7130 (pmm) REVERT: C 421 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8646 (t) REVERT: C 434 ASP cc_start: 0.8994 (m-30) cc_final: 0.8724 (m-30) REVERT: C 446 TYR cc_start: 0.8771 (m-80) cc_final: 0.8136 (m-80) REVERT: C 458 LYS cc_start: 0.9435 (mmmt) cc_final: 0.9090 (mmtm) REVERT: D 68 ARG cc_start: 0.8079 (mmp80) cc_final: 0.7610 (mmm160) REVERT: D 74 LEU cc_start: 0.8981 (mm) cc_final: 0.8729 (mm) REVERT: D 117 HIS cc_start: 0.9078 (m-70) cc_final: 0.8726 (m-70) REVERT: D 128 PHE cc_start: 0.9310 (t80) cc_final: 0.8983 (t80) REVERT: D 153 ILE cc_start: 0.9287 (tp) cc_final: 0.9006 (tp) REVERT: D 158 PHE cc_start: 0.8294 (p90) cc_final: 0.7933 (p90) REVERT: D 174 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8511 (tp) REVERT: D 184 MET cc_start: 0.8611 (tpp) cc_final: 0.8331 (tpt) REVERT: D 231 LYS cc_start: 0.8889 (mttm) cc_final: 0.8673 (mtmm) REVERT: D 241 ASP cc_start: 0.8200 (t0) cc_final: 0.7942 (t0) REVERT: D 252 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8017 (tp40) REVERT: D 302 MET cc_start: 0.7539 (mmp) cc_final: 0.6464 (mmp) REVERT: D 332 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6394 (p-80) REVERT: D 357 MET cc_start: 0.8258 (mmm) cc_final: 0.7997 (mmm) REVERT: D 379 ARG cc_start: 0.8709 (mtm180) cc_final: 0.8400 (mtm180) REVERT: D 451 ASN cc_start: 0.8653 (p0) cc_final: 0.8331 (p0) REVERT: D 458 LYS cc_start: 0.8891 (mttt) cc_final: 0.8505 (ptpt) REVERT: D 473 HIS cc_start: 0.8972 (t70) cc_final: 0.8680 (t70) REVERT: E 6 ASP cc_start: 0.9144 (t0) cc_final: 0.8919 (t0) REVERT: E 18 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7427 (t0) REVERT: E 59 ARG cc_start: 0.8110 (ptt90) cc_final: 0.7733 (ptt-90) REVERT: E 61 MET cc_start: 0.8337 (mtt) cc_final: 0.7729 (tpp) REVERT: E 86 THR cc_start: 0.9384 (m) cc_final: 0.9170 (p) REVERT: E 135 LEU cc_start: 0.8871 (tp) cc_final: 0.8321 (mt) REVERT: E 155 LEU cc_start: 0.8510 (mm) cc_final: 0.7998 (pp) REVERT: E 175 GLU cc_start: 0.7548 (tp30) cc_final: 0.7199 (mm-30) REVERT: E 195 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8485 (tt) REVERT: E 242 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5246 (tt) REVERT: E 246 ASP cc_start: 0.8646 (t0) cc_final: 0.8357 (t0) REVERT: E 292 ILE cc_start: 0.8965 (mm) cc_final: 0.8532 (mm) REVERT: E 306 ARG cc_start: 0.8542 (mtp-110) cc_final: 0.7719 (mtt90) REVERT: E 327 ARG cc_start: 0.8387 (ppt170) cc_final: 0.8179 (ppt170) REVERT: E 341 HIS cc_start: 0.8308 (m170) cc_final: 0.7937 (m-70) REVERT: E 355 ASN cc_start: 0.8743 (t0) cc_final: 0.8314 (t0) REVERT: E 383 GLU cc_start: 0.8503 (pm20) cc_final: 0.8158 (mp0) REVERT: E 390 LYS cc_start: 0.9188 (mmtm) cc_final: 0.8768 (mtpp) REVERT: E 422 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8098 (mt) REVERT: E 438 SER cc_start: 0.8855 (t) cc_final: 0.8340 (p) REVERT: E 458 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8196 (mmtm) REVERT: E 471 GLU cc_start: 0.7935 (pt0) cc_final: 0.7665 (tt0) REVERT: F 85 GLU cc_start: 0.8831 (tt0) cc_final: 0.8338 (tm-30) REVERT: F 98 ASP cc_start: 0.8462 (t0) cc_final: 0.7794 (t0) REVERT: F 118 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8092 (mmtp) REVERT: F 169 GLU cc_start: 0.9146 (mp0) cc_final: 0.8614 (mp0) REVERT: F 233 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8370 (pp30) REVERT: F 260 LYS cc_start: 0.8699 (pttp) cc_final: 0.8225 (pttp) REVERT: F 302 MET cc_start: 0.7019 (mmp) cc_final: 0.6186 (mmt) REVERT: F 344 ASP cc_start: 0.8544 (m-30) cc_final: 0.7872 (m-30) REVERT: F 430 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8135 (mm-30) REVERT: G 6 ASP cc_start: 0.9127 (t0) cc_final: 0.8908 (t0) REVERT: G 18 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7673 (t70) REVERT: G 59 ARG cc_start: 0.8093 (ptt90) cc_final: 0.7688 (ptt-90) REVERT: G 61 MET cc_start: 0.8326 (mtt) cc_final: 0.7713 (tpp) REVERT: G 86 THR cc_start: 0.9388 (m) cc_final: 0.9169 (p) REVERT: G 135 LEU cc_start: 0.8901 (tp) cc_final: 0.8366 (mt) REVERT: G 155 LEU cc_start: 0.8496 (mm) cc_final: 0.7988 (pp) REVERT: G 175 GLU cc_start: 0.7524 (tp30) cc_final: 0.7233 (mm-30) REVERT: G 195 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8474 (tt) REVERT: G 202 ARG cc_start: 0.7793 (ptp90) cc_final: 0.7416 (ptm160) REVERT: G 246 ASP cc_start: 0.8426 (t0) cc_final: 0.7814 (t0) REVERT: G 306 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.8001 (mmm160) REVERT: G 316 PHE cc_start: 0.8594 (t80) cc_final: 0.7791 (t80) REVERT: G 341 HIS cc_start: 0.8292 (m170) cc_final: 0.7922 (m-70) REVERT: G 355 ASN cc_start: 0.8775 (t0) cc_final: 0.8384 (t0) REVERT: G 383 GLU cc_start: 0.8514 (pm20) cc_final: 0.8155 (mp0) REVERT: G 390 LYS cc_start: 0.9172 (mmtm) cc_final: 0.8731 (mtpp) REVERT: G 438 SER cc_start: 0.8885 (t) cc_final: 0.8380 (p) REVERT: G 452 LEU cc_start: 0.7864 (mt) cc_final: 0.7635 (mt) REVERT: G 458 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8234 (mmtm) REVERT: G 464 GLN cc_start: 0.8546 (tp-100) cc_final: 0.7946 (tp-100) REVERT: H 85 GLU cc_start: 0.8826 (tt0) cc_final: 0.8329 (tm-30) REVERT: H 98 ASP cc_start: 0.8476 (t0) cc_final: 0.7802 (t0) REVERT: H 135 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8072 (mm) REVERT: H 233 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8267 (pp30) REVERT: H 302 MET cc_start: 0.6954 (mmp) cc_final: 0.6133 (mmt) REVERT: H 304 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8188 (m) REVERT: H 308 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7662 (mmt) REVERT: H 355 ASN cc_start: 0.9010 (t0) cc_final: 0.8654 (m-40) REVERT: H 430 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8113 (mm-30) outliers start: 142 outliers final: 94 residues processed: 876 average time/residue: 0.1835 time to fit residues: 252.4924 Evaluate side-chains 859 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 747 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 384 SER Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 275 ASN Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain H residue 433 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 251 optimal weight: 5.9990 chunk 72 optimal weight: 0.0570 chunk 169 optimal weight: 9.9990 chunk 321 optimal weight: 20.0000 chunk 274 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 203 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN C 17 ASN C 76 GLN D 252 GLN E 233 GLN ** E 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 ASN ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.130640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.109515 restraints weight = 64354.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.113833 restraints weight = 40008.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.116998 restraints weight = 27347.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.119310 restraints weight = 19900.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.121134 restraints weight = 15189.939| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 : 0.003 0.036 28096 Z= 0.130 Angle : 0.685 9.618 38312 Z= 0.344 Chirality : 0.047 0.221 4536 Planarity : 0.005 0.065 5000 Dihedral : 6.578 54.981 4448 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.81 % Allowed : 29.20 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.07 (0.14), residues: 3704 helix: 0.27 (0.14), residues: 1424 sheet: -0.28 (0.21), residues: 600 loop : 0.19 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 426 TYR 0.022 0.002 TYR C 366 PHE 0.028 0.002 PHE D 403 TRP 0.018 0.001 TRP G 334 HIS 0.005 0.001 HIS E 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (28096) covalent geometry : angle 0.68549 / 0.34 (38312) hydrogen bonds : bond 0.03417 / 2.36 ( 1160) hydrogen bonds : angle 5.40755 / 3.88 ( 3120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 816 time to evaluate : 1.091 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: A 52 ASN cc_start: 0.7277 (p0) cc_final: 0.6784 (p0) REVERT: A 76 GLN cc_start: 0.8008 (pm20) cc_final: 0.7748 (pm20) REVERT: A 107 ASP cc_start: 0.8503 (m-30) cc_final: 0.8075 (p0) REVERT: A 111 ASP cc_start: 0.8893 (t0) cc_final: 0.8655 (t0) REVERT: A 138 GLU cc_start: 0.8876 (mp0) cc_final: 0.8552 (tm-30) REVERT: A 141 CYS cc_start: 0.8863 (p) cc_final: 0.8290 (p) REVERT: A 153 ILE cc_start: 0.9269 (tp) cc_final: 0.9036 (mm) REVERT: A 155 LEU cc_start: 0.9092 (mm) cc_final: 0.8472 (pp) REVERT: A 184 MET cc_start: 0.8683 (mmm) cc_final: 0.8434 (mmm) REVERT: A 197 ARG cc_start: 0.8933 (mtp180) cc_final: 0.8436 (mtp180) REVERT: A 217 ARG cc_start: 0.7332 (mtt-85) cc_final: 0.6936 (mmm-85) REVERT: A 254 LYS cc_start: 0.8540 (tttp) cc_final: 0.8213 (tttt) REVERT: A 283 ARG cc_start: 0.9100 (mtm110) cc_final: 0.8855 (mmm160) REVERT: A 343 ARG cc_start: 0.8334 (ptm160) cc_final: 0.7660 (ttm170) REVERT: A 374 PHE cc_start: 0.8288 (m-10) cc_final: 0.8014 (m-10) REVERT: A 420 MET cc_start: 0.8388 (mmm) cc_final: 0.8098 (mmp) REVERT: A 421 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8615 (t) REVERT: A 434 ASP cc_start: 0.8947 (m-30) cc_final: 0.8673 (m-30) REVERT: A 446 TYR cc_start: 0.8704 (m-80) cc_final: 0.8058 (m-80) REVERT: A 458 LYS cc_start: 0.9427 (mmmt) cc_final: 0.9099 (mmtm) REVERT: B 52 ASN cc_start: 0.7851 (p0) cc_final: 0.7471 (p0) REVERT: B 68 ARG cc_start: 0.8339 (mmp80) cc_final: 0.7613 (mmm160) REVERT: B 103 LEU cc_start: 0.9483 (mm) cc_final: 0.9169 (mm) REVERT: B 117 HIS cc_start: 0.9048 (m-70) cc_final: 0.8748 (m-70) REVERT: B 128 PHE cc_start: 0.9269 (t80) cc_final: 0.8977 (t80) REVERT: B 135 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7285 (mp) REVERT: B 153 ILE cc_start: 0.9238 (tp) cc_final: 0.8934 (tp) REVERT: B 158 PHE cc_start: 0.8157 (p90) cc_final: 0.7915 (p90) REVERT: B 159 VAL cc_start: 0.7938 (t) cc_final: 0.7735 (m) REVERT: B 184 MET cc_start: 0.8656 (tpp) cc_final: 0.8435 (tpt) REVERT: B 241 ASP cc_start: 0.8131 (t0) cc_final: 0.7880 (t0) REVERT: B 267 LEU cc_start: 0.9211 (mt) cc_final: 0.8967 (tp) REVERT: B 302 MET cc_start: 0.7472 (mmp) cc_final: 0.6395 (mmp) REVERT: B 332 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6476 (p-80) REVERT: B 379 ARG cc_start: 0.8767 (mtm180) cc_final: 0.8382 (mtm180) REVERT: B 403 PHE cc_start: 0.9047 (t80) cc_final: 0.8836 (t80) REVERT: B 408 LYS cc_start: 0.8545 (pttt) cc_final: 0.8260 (pttm) REVERT: B 451 ASN cc_start: 0.8624 (p0) cc_final: 0.8306 (p0) REVERT: B 452 LEU cc_start: 0.8018 (mt) cc_final: 0.7706 (mp) REVERT: B 458 LYS cc_start: 0.8885 (mttt) cc_final: 0.8531 (ptpt) REVERT: B 473 HIS cc_start: 0.8933 (t70) cc_final: 0.8658 (t70) REVERT: C 59 ARG cc_start: 0.8299 (ptm160) cc_final: 0.8022 (ptt180) REVERT: C 99 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8456 (p) REVERT: C 107 ASP cc_start: 0.8515 (m-30) cc_final: 0.8073 (p0) REVERT: C 111 ASP cc_start: 0.8878 (t0) cc_final: 0.8649 (t0) REVERT: C 116 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8850 (tp) REVERT: C 138 GLU cc_start: 0.8817 (mp0) cc_final: 0.8568 (tm-30) REVERT: C 141 CYS cc_start: 0.8809 (p) cc_final: 0.8349 (p) REVERT: C 155 LEU cc_start: 0.9117 (mm) cc_final: 0.8648 (pp) REVERT: C 184 MET cc_start: 0.8670 (mmm) cc_final: 0.8379 (mmm) REVERT: C 197 ARG cc_start: 0.8975 (ttt90) cc_final: 0.8656 (mtp180) REVERT: C 217 ARG cc_start: 0.7319 (mtt-85) cc_final: 0.6920 (mmm-85) REVERT: C 254 LYS cc_start: 0.8556 (tttp) cc_final: 0.8241 (tttt) REVERT: C 283 ARG cc_start: 0.9105 (mtm110) cc_final: 0.8791 (mmm-85) REVERT: C 302 MET cc_start: 0.8139 (mmp) cc_final: 0.6935 (mmm) REVERT: C 306 ARG cc_start: 0.8522 (ttm170) cc_final: 0.8175 (mtt90) REVERT: C 313 ARG cc_start: 0.7356 (tpt-90) cc_final: 0.7079 (ttt90) REVERT: C 343 ARG cc_start: 0.8350 (ptm160) cc_final: 0.7671 (ttm170) REVERT: C 420 MET cc_start: 0.8371 (mmm) cc_final: 0.8090 (mmp) REVERT: C 421 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8602 (t) REVERT: C 422 LEU cc_start: 0.8476 (mm) cc_final: 0.8009 (mm) REVERT: C 434 ASP cc_start: 0.8957 (m-30) cc_final: 0.8688 (m-30) REVERT: C 446 TYR cc_start: 0.8718 (m-80) cc_final: 0.8070 (m-80) REVERT: C 458 LYS cc_start: 0.9417 (mmmt) cc_final: 0.9081 (mmtm) REVERT: D 31 ARG cc_start: 0.7230 (mtm180) cc_final: 0.6945 (mtm180) REVERT: D 52 ASN cc_start: 0.7764 (p0) cc_final: 0.7545 (p0) REVERT: D 68 ARG cc_start: 0.8379 (mmp80) cc_final: 0.7656 (mmm160) REVERT: D 74 LEU cc_start: 0.8977 (mm) cc_final: 0.8688 (mm) REVERT: D 91 LYS cc_start: 0.8519 (mmmt) cc_final: 0.8259 (mmmt) REVERT: D 117 HIS cc_start: 0.9037 (m-70) cc_final: 0.8738 (m-70) REVERT: D 128 PHE cc_start: 0.9290 (t80) cc_final: 0.8993 (t80) REVERT: D 153 ILE cc_start: 0.9232 (tp) cc_final: 0.8934 (tp) REVERT: D 158 PHE cc_start: 0.8122 (p90) cc_final: 0.7882 (p90) REVERT: D 184 MET cc_start: 0.8677 (tpp) cc_final: 0.8417 (tpt) REVERT: D 241 ASP cc_start: 0.8172 (t0) cc_final: 0.7915 (t0) REVERT: D 302 MET cc_start: 0.7510 (mmp) cc_final: 0.6389 (mmp) REVERT: D 332 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6422 (p-80) REVERT: D 379 ARG cc_start: 0.8774 (mtm180) cc_final: 0.8375 (mtm180) REVERT: D 408 LYS cc_start: 0.8542 (pttt) cc_final: 0.8242 (pttm) REVERT: D 451 ASN cc_start: 0.8623 (p0) cc_final: 0.8302 (p0) REVERT: D 452 LEU cc_start: 0.8004 (mt) cc_final: 0.7695 (mp) REVERT: D 458 LYS cc_start: 0.8894 (mttt) cc_final: 0.8537 (ptpt) REVERT: D 473 HIS cc_start: 0.8943 (t70) cc_final: 0.8659 (t70) REVERT: E 6 ASP cc_start: 0.9116 (t0) cc_final: 0.8865 (t0) REVERT: E 18 ASP cc_start: 0.8116 (m-30) cc_final: 0.7007 (t70) REVERT: E 59 ARG cc_start: 0.8043 (ptt90) cc_final: 0.7615 (ptt-90) REVERT: E 61 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7667 (tpp) REVERT: E 86 THR cc_start: 0.9380 (m) cc_final: 0.9162 (p) REVERT: E 135 LEU cc_start: 0.8938 (tp) cc_final: 0.8477 (mt) REVERT: E 155 LEU cc_start: 0.8498 (mm) cc_final: 0.7976 (pp) REVERT: E 175 GLU cc_start: 0.7438 (tp30) cc_final: 0.7058 (mm-30) REVERT: E 195 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8532 (tt) REVERT: E 246 ASP cc_start: 0.8656 (t0) cc_final: 0.8334 (t0) REVERT: E 292 ILE cc_start: 0.8929 (mm) cc_final: 0.8511 (mm) REVERT: E 306 ARG cc_start: 0.8539 (mtp-110) cc_final: 0.7633 (mtt90) REVERT: E 341 HIS cc_start: 0.8295 (m170) cc_final: 0.7952 (m-70) REVERT: E 355 ASN cc_start: 0.8773 (t0) cc_final: 0.8398 (t0) REVERT: E 383 GLU cc_start: 0.8498 (pm20) cc_final: 0.8112 (mp0) REVERT: E 390 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8721 (mtpp) REVERT: E 438 SER cc_start: 0.8833 (t) cc_final: 0.8325 (p) REVERT: F 61 MET cc_start: 0.8387 (ttm) cc_final: 0.8141 (ttm) REVERT: F 74 LEU cc_start: 0.8530 (mm) cc_final: 0.8220 (mm) REVERT: F 85 GLU cc_start: 0.8838 (tt0) cc_final: 0.8329 (tm-30) REVERT: F 95 LEU cc_start: 0.8938 (mm) cc_final: 0.8736 (mm) REVERT: F 98 ASP cc_start: 0.8368 (t0) cc_final: 0.7683 (t70) REVERT: F 115 LEU cc_start: 0.9339 (mt) cc_final: 0.8744 (mt) REVERT: F 118 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8157 (mmmm) REVERT: F 155 LEU cc_start: 0.8580 (mm) cc_final: 0.8165 (mt) REVERT: F 169 GLU cc_start: 0.9113 (mp0) cc_final: 0.8581 (mp0) REVERT: F 254 LYS cc_start: 0.9052 (tttt) cc_final: 0.8829 (tttt) REVERT: F 260 LYS cc_start: 0.8661 (pttp) cc_final: 0.8159 (pttp) REVERT: F 269 LEU cc_start: 0.7901 (mp) cc_final: 0.7651 (mp) REVERT: F 276 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.7981 (p) REVERT: F 302 MET cc_start: 0.6963 (mmp) cc_final: 0.6091 (mmt) REVERT: F 308 MET cc_start: 0.7876 (mmp) cc_final: 0.7621 (mmp) REVERT: F 328 GLN cc_start: 0.8148 (pp30) cc_final: 0.7659 (pp30) REVERT: F 344 ASP cc_start: 0.8451 (m-30) cc_final: 0.8133 (m-30) REVERT: F 357 MET cc_start: 0.7782 (tpp) cc_final: 0.7511 (tpp) REVERT: F 458 LYS cc_start: 0.9138 (pttt) cc_final: 0.8901 (pttm) REVERT: G 6 ASP cc_start: 0.9096 (t0) cc_final: 0.8841 (t0) REVERT: G 59 ARG cc_start: 0.8026 (ptt90) cc_final: 0.7588 (ptt-90) REVERT: G 68 ARG cc_start: 0.7900 (mmp-170) cc_final: 0.7480 (mmm160) REVERT: G 86 THR cc_start: 0.9380 (m) cc_final: 0.9163 (p) REVERT: G 135 LEU cc_start: 0.8879 (tp) cc_final: 0.8404 (mt) REVERT: G 155 LEU cc_start: 0.8468 (mm) cc_final: 0.7947 (pp) REVERT: G 175 GLU cc_start: 0.7466 (tp30) cc_final: 0.7119 (mm-30) REVERT: G 246 ASP cc_start: 0.8300 (t0) cc_final: 0.7599 (t0) REVERT: G 306 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.7672 (mtm180) REVERT: G 316 PHE cc_start: 0.8569 (t80) cc_final: 0.7784 (t80) REVERT: G 327 ARG cc_start: 0.8315 (ppt170) cc_final: 0.8106 (ppt170) REVERT: G 341 HIS cc_start: 0.8318 (m170) cc_final: 0.7967 (m-70) REVERT: G 355 ASN cc_start: 0.8789 (t0) cc_final: 0.8419 (t0) REVERT: G 383 GLU cc_start: 0.8487 (pm20) cc_final: 0.8103 (mp0) REVERT: G 390 LYS cc_start: 0.9128 (mmtm) cc_final: 0.8710 (mtpp) REVERT: G 438 SER cc_start: 0.8870 (t) cc_final: 0.8254 (p) REVERT: G 452 LEU cc_start: 0.7810 (mt) cc_final: 0.7568 (mt) REVERT: G 458 LYS cc_start: 0.8473 (mmtm) cc_final: 0.8171 (mmtm) REVERT: G 471 GLU cc_start: 0.7933 (pt0) cc_final: 0.7549 (tt0) REVERT: H 85 GLU cc_start: 0.8820 (tt0) cc_final: 0.8317 (tm-30) REVERT: H 98 ASP cc_start: 0.8379 (t0) cc_final: 0.7661 (t70) REVERT: H 169 GLU cc_start: 0.9105 (mp0) cc_final: 0.8571 (mp0) REVERT: H 233 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8246 (pp30) REVERT: H 276 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8449 (p) REVERT: H 302 MET cc_start: 0.6914 (mmp) cc_final: 0.6135 (mmt) REVERT: H 304 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8236 (m) REVERT: H 308 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7638 (mmt) REVERT: H 328 GLN cc_start: 0.8179 (pp30) cc_final: 0.7750 (pp30) REVERT: H 329 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8712 (mt) outliers start: 107 outliers final: 73 residues processed: 872 average time/residue: 0.1802 time to fit residues: 248.2449 Evaluate side-chains 831 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 744 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 307 MET Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 13 ASP Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 275 ASN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 433 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 175 optimal weight: 0.6980 chunk 312 optimal weight: 0.7980 chunk 358 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 289 optimal weight: 8.9990 chunk 308 optimal weight: 10.0000 chunk 350 optimal weight: 6.9990 chunk 335 optimal weight: 4.9990 chunk 160 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN C 17 ASN D 252 GLN E 17 ASN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.3888 r_free = 0.3888 target = 0.128106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.106860 restraints weight = 65316.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.111053 restraints weight = 40751.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.114156 restraints weight = 28128.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.116398 restraints weight = 20678.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.118216 restraints weight = 15966.032| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28096 Z= 0.159 Angle : 0.685 11.277 38312 Z= 0.346 Chirality : 0.047 0.245 4536 Planarity : 0.005 0.051 5000 Dihedral : 6.521 52.765 4448 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.45 % Allowed : 29.84 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.11 (0.14), residues: 3704 helix: 0.18 (0.14), residues: 1424 sheet: -0.47 (0.20), residues: 608 loop : 0.08 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 313 TYR 0.025 0.002 TYR C 12 PHE 0.027 0.002 PHE D 403 TRP 0.019 0.001 TRP G 334 HIS 0.013 0.001 HIS D 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (28096) covalent geometry : angle 0.68493 / 0.35 (38312) hydrogen bonds : bond 0.03396 / 2.36 ( 1160) hydrogen bonds : angle 5.44516 / 3.90 ( 3120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 797 time to evaluate : 0.806 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: A 52 ASN cc_start: 0.7386 (p0) cc_final: 0.7042 (p0) REVERT: A 53 MET cc_start: 0.8156 (mmt) cc_final: 0.7568 (mmt) REVERT: A 59 ARG cc_start: 0.8323 (ptm160) cc_final: 0.8030 (ptt180) REVERT: A 76 GLN cc_start: 0.8074 (pm20) cc_final: 0.7754 (pm20) REVERT: A 107 ASP cc_start: 0.8548 (m-30) cc_final: 0.8111 (p0) REVERT: A 111 ASP cc_start: 0.8917 (t0) cc_final: 0.8675 (t0) REVERT: A 138 GLU cc_start: 0.8875 (mp0) cc_final: 0.8570 (tm-30) REVERT: A 141 CYS cc_start: 0.8842 (p) cc_final: 0.8300 (p) REVERT: A 155 LEU cc_start: 0.9115 (mm) cc_final: 0.8575 (pp) REVERT: A 174 LEU cc_start: 0.8987 (mm) cc_final: 0.8621 (mm) REVERT: A 184 MET cc_start: 0.8733 (mmm) cc_final: 0.8414 (mmm) REVERT: A 197 ARG cc_start: 0.8932 (mtp180) cc_final: 0.8439 (mtp180) REVERT: A 241 ASP cc_start: 0.7494 (t0) cc_final: 0.6956 (m-30) REVERT: A 254 LYS cc_start: 0.8561 (tttp) cc_final: 0.8235 (tttt) REVERT: A 283 ARG cc_start: 0.9099 (mtm110) cc_final: 0.8858 (mmm160) REVERT: A 313 ARG cc_start: 0.7735 (tpt-90) cc_final: 0.7334 (tpt-90) REVERT: A 343 ARG cc_start: 0.8375 (ptm160) cc_final: 0.7676 (ttp-170) REVERT: A 421 SER cc_start: 0.8830 (m) cc_final: 0.8601 (t) REVERT: A 434 ASP cc_start: 0.8955 (m-30) cc_final: 0.8699 (m-30) REVERT: A 446 TYR cc_start: 0.8777 (m-80) cc_final: 0.8136 (m-80) REVERT: A 458 LYS cc_start: 0.9432 (mmmt) cc_final: 0.9096 (mmtm) REVERT: B 31 ARG cc_start: 0.7042 (mtm180) cc_final: 0.6789 (mtm180) REVERT: B 68 ARG cc_start: 0.8358 (mmp80) cc_final: 0.7641 (mmm160) REVERT: B 128 PHE cc_start: 0.9260 (t80) cc_final: 0.8974 (t80) REVERT: B 153 ILE cc_start: 0.9172 (tp) cc_final: 0.8895 (tp) REVERT: B 184 MET cc_start: 0.8663 (tpp) cc_final: 0.8459 (tpt) REVERT: B 241 ASP cc_start: 0.8222 (t0) cc_final: 0.7973 (t0) REVERT: B 302 MET cc_start: 0.7571 (mmp) cc_final: 0.6518 (mmp) REVERT: B 332 HIS cc_start: 0.7436 (OUTLIER) cc_final: 0.6402 (p-80) REVERT: B 379 ARG cc_start: 0.8752 (mtm180) cc_final: 0.8347 (mtm180) REVERT: B 415 ILE cc_start: 0.8280 (mm) cc_final: 0.8033 (mm) REVERT: B 451 ASN cc_start: 0.8626 (p0) cc_final: 0.8322 (p0) REVERT: B 458 LYS cc_start: 0.8894 (mttt) cc_final: 0.8536 (ptpt) REVERT: B 473 HIS cc_start: 0.8947 (t70) cc_final: 0.8711 (t70) REVERT: C 59 ARG cc_start: 0.8316 (ptm160) cc_final: 0.8080 (ptt180) REVERT: C 107 ASP cc_start: 0.8530 (m-30) cc_final: 0.8116 (p0) REVERT: C 111 ASP cc_start: 0.8879 (t0) cc_final: 0.8646 (t0) REVERT: C 116 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8663 (tp) REVERT: C 141 CYS cc_start: 0.8799 (p) cc_final: 0.8299 (p) REVERT: C 155 LEU cc_start: 0.9114 (mm) cc_final: 0.8542 (pp) REVERT: C 184 MET cc_start: 0.8732 (mmm) cc_final: 0.8409 (mmm) REVERT: C 197 ARG cc_start: 0.8975 (ttt90) cc_final: 0.8667 (mtp180) REVERT: C 241 ASP cc_start: 0.7513 (t0) cc_final: 0.6972 (m-30) REVERT: C 254 LYS cc_start: 0.8596 (tttp) cc_final: 0.8255 (tttt) REVERT: C 283 ARG cc_start: 0.9106 (mtm110) cc_final: 0.8838 (mmm160) REVERT: C 313 ARG cc_start: 0.7378 (tpt-90) cc_final: 0.6935 (ttt90) REVERT: C 343 ARG cc_start: 0.8387 (ptm160) cc_final: 0.7679 (ttp-170) REVERT: C 434 ASP cc_start: 0.8956 (m-30) cc_final: 0.8700 (m-30) REVERT: C 446 TYR cc_start: 0.8752 (m-80) cc_final: 0.8109 (m-80) REVERT: C 458 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9090 (mmtm) REVERT: D 52 ASN cc_start: 0.7943 (p0) cc_final: 0.7712 (p0) REVERT: D 68 ARG cc_start: 0.8369 (mmp80) cc_final: 0.7618 (mmm160) REVERT: D 74 LEU cc_start: 0.9098 (mm) cc_final: 0.8798 (mm) REVERT: D 91 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8254 (mmmt) REVERT: D 153 ILE cc_start: 0.9157 (tp) cc_final: 0.8887 (tp) REVERT: D 158 PHE cc_start: 0.8095 (p90) cc_final: 0.7848 (p90) REVERT: D 174 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8372 (tp) REVERT: D 184 MET cc_start: 0.8717 (tpp) cc_final: 0.8477 (tpt) REVERT: D 194 VAL cc_start: 0.9200 (t) cc_final: 0.8866 (t) REVERT: D 231 LYS cc_start: 0.8865 (mttm) cc_final: 0.8429 (ptpt) REVERT: D 241 ASP cc_start: 0.8270 (t0) cc_final: 0.8011 (t0) REVERT: D 302 MET cc_start: 0.7625 (mmp) cc_final: 0.6590 (mmp) REVERT: D 332 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.6384 (p-80) REVERT: D 379 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8393 (mtm180) REVERT: D 408 LYS cc_start: 0.8481 (pttt) cc_final: 0.8166 (pttm) REVERT: D 415 ILE cc_start: 0.8310 (mm) cc_final: 0.8006 (mm) REVERT: D 451 ASN cc_start: 0.8631 (p0) cc_final: 0.8321 (p0) REVERT: D 458 LYS cc_start: 0.8905 (mttt) cc_final: 0.8548 (ptpt) REVERT: D 473 HIS cc_start: 0.8982 (t70) cc_final: 0.8730 (t70) REVERT: E 6 ASP cc_start: 0.9141 (t0) cc_final: 0.8931 (t0) REVERT: E 59 ARG cc_start: 0.8055 (ptt90) cc_final: 0.7608 (ptt-90) REVERT: E 77 ASP cc_start: 0.8126 (m-30) cc_final: 0.7750 (m-30) REVERT: E 86 THR cc_start: 0.9382 (m) cc_final: 0.9159 (p) REVERT: E 135 LEU cc_start: 0.8927 (tp) cc_final: 0.8385 (mt) REVERT: E 155 LEU cc_start: 0.8520 (mm) cc_final: 0.8001 (pp) REVERT: E 175 GLU cc_start: 0.7475 (tp30) cc_final: 0.7101 (mm-30) REVERT: E 195 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8594 (tt) REVERT: E 202 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.7617 (ptp-170) REVERT: E 246 ASP cc_start: 0.8769 (t0) cc_final: 0.8407 (t0) REVERT: E 292 ILE cc_start: 0.8940 (mm) cc_final: 0.8571 (mm) REVERT: E 306 ARG cc_start: 0.8605 (mtp-110) cc_final: 0.7739 (mtt90) REVERT: E 341 HIS cc_start: 0.8245 (m170) cc_final: 0.7905 (m-70) REVERT: E 355 ASN cc_start: 0.8747 (t0) cc_final: 0.8421 (t0) REVERT: E 383 GLU cc_start: 0.8480 (pm20) cc_final: 0.8103 (mp0) REVERT: E 390 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8820 (mtpp) REVERT: E 438 SER cc_start: 0.8827 (t) cc_final: 0.8284 (p) REVERT: E 458 LYS cc_start: 0.8553 (mmtm) cc_final: 0.8226 (mmtm) REVERT: E 471 GLU cc_start: 0.7806 (pt0) cc_final: 0.7479 (tt0) REVERT: F 85 GLU cc_start: 0.8878 (tt0) cc_final: 0.8364 (tm-30) REVERT: F 98 ASP cc_start: 0.8491 (t0) cc_final: 0.7753 (t70) REVERT: F 118 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8128 (mmmm) REVERT: F 169 GLU cc_start: 0.9123 (mp0) cc_final: 0.8679 (mp0) REVERT: F 195 LEU cc_start: 0.8578 (mt) cc_final: 0.8184 (mp) REVERT: F 233 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8431 (pp30) REVERT: F 260 LYS cc_start: 0.8679 (pttp) cc_final: 0.8402 (pttp) REVERT: F 302 MET cc_start: 0.7111 (mmp) cc_final: 0.6341 (mmt) REVERT: F 328 GLN cc_start: 0.8157 (pp30) cc_final: 0.7676 (pp30) REVERT: F 344 ASP cc_start: 0.8437 (m-30) cc_final: 0.8195 (m-30) REVERT: F 458 LYS cc_start: 0.9122 (pttt) cc_final: 0.8906 (pttm) REVERT: G 6 ASP cc_start: 0.9128 (t0) cc_final: 0.8915 (t0) REVERT: G 59 ARG cc_start: 0.8073 (ptt90) cc_final: 0.7639 (ptt-90) REVERT: G 61 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7696 (tpp) REVERT: G 86 THR cc_start: 0.9383 (m) cc_final: 0.9164 (p) REVERT: G 135 LEU cc_start: 0.8893 (tp) cc_final: 0.8358 (mt) REVERT: G 155 LEU cc_start: 0.8468 (mm) cc_final: 0.7952 (pp) REVERT: G 175 GLU cc_start: 0.7421 (tp30) cc_final: 0.7068 (mm-30) REVERT: G 195 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8591 (tt) REVERT: G 246 ASP cc_start: 0.8506 (t0) cc_final: 0.8260 (t0) REVERT: G 306 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.7707 (mtm180) REVERT: G 316 PHE cc_start: 0.8643 (t80) cc_final: 0.7916 (t80) REVERT: G 341 HIS cc_start: 0.8295 (m170) cc_final: 0.7955 (m-70) REVERT: G 355 ASN cc_start: 0.8770 (t0) cc_final: 0.8384 (t0) REVERT: G 383 GLU cc_start: 0.8471 (pm20) cc_final: 0.8076 (mp0) REVERT: G 390 LYS cc_start: 0.9174 (mmtm) cc_final: 0.8794 (mtpp) REVERT: G 438 SER cc_start: 0.8810 (t) cc_final: 0.8252 (p) REVERT: G 452 LEU cc_start: 0.7838 (mt) cc_final: 0.7578 (mt) REVERT: G 471 GLU cc_start: 0.7959 (pt0) cc_final: 0.7585 (tt0) REVERT: H 85 GLU cc_start: 0.8853 (tt0) cc_final: 0.8356 (tm-30) REVERT: H 98 ASP cc_start: 0.8408 (t0) cc_final: 0.7722 (t70) REVERT: H 118 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8206 (mmmt) REVERT: H 169 GLU cc_start: 0.9117 (mp0) cc_final: 0.8581 (mp0) REVERT: H 276 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8305 (p) REVERT: H 302 MET cc_start: 0.7076 (mmp) cc_final: 0.6249 (mmt) REVERT: H 304 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8331 (m) REVERT: H 308 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7508 (mmp) REVERT: H 328 GLN cc_start: 0.8175 (pp30) cc_final: 0.7693 (pp30) REVERT: H 408 LYS cc_start: 0.8533 (tppt) cc_final: 0.8195 (tppt) REVERT: H 458 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8817 (mtmt) REVERT: H 473 HIS cc_start: 0.8855 (t70) cc_final: 0.8520 (t70) outliers start: 125 outliers final: 91 residues processed: 857 average time/residue: 0.1873 time to fit residues: 250.9297 Evaluate side-chains 868 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 767 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 275 ASN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 456 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 229 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 109 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 344 optimal weight: 0.9990 chunk 220 optimal weight: 0.5980 chunk 150 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN D 252 GLN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 ASN ** H 315 GLN ** 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 = 0.3932 r_free = 0.3932 target = 0.131399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.110214 restraints weight = 64046.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.114523 restraints weight = 39687.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.117726 restraints weight = 27145.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.120047 restraints weight = 19704.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.121902 restraints weight = 15046.936| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28096 Z= 0.130 Angle : 0.718 11.850 38312 Z= 0.356 Chirality : 0.047 0.265 4536 Planarity : 0.005 0.101 5000 Dihedral : 6.503 52.174 4448 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.63 % Allowed : 31.05 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.20 (0.14), residues: 3704 helix: 0.15 (0.14), residues: 1424 sheet: -0.60 (0.20), residues: 616 loop : 0.00 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 202 TYR 0.028 0.002 TYR A 12 PHE 0.032 0.002 PHE B 316 TRP 0.019 0.001 TRP G 334 HIS 0.025 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (28096) covalent geometry : angle 0.71797 / 0.36 (38312) hydrogen bonds : bond 0.03365 / 2.32 ( 1160) hydrogen bonds : angle 5.45810 / 3.91 ( 3120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 805 time to evaluate : 1.051 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: A 52 ASN cc_start: 0.7254 (p0) cc_final: 0.6865 (p0) REVERT: A 53 MET cc_start: 0.8081 (mmt) cc_final: 0.7520 (mmt) REVERT: A 59 ARG cc_start: 0.8285 (ptm160) cc_final: 0.8035 (mtt180) REVERT: A 76 GLN cc_start: 0.8020 (pm20) cc_final: 0.7720 (pm20) REVERT: A 107 ASP cc_start: 0.8569 (m-30) cc_final: 0.8135 (p0) REVERT: A 111 ASP cc_start: 0.8892 (t0) cc_final: 0.8617 (t0) REVERT: A 138 GLU cc_start: 0.8857 (mp0) cc_final: 0.8527 (tm-30) REVERT: A 141 CYS cc_start: 0.8805 (p) cc_final: 0.8268 (p) REVERT: A 146 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8522 (ptp90) REVERT: A 155 LEU cc_start: 0.9115 (mm) cc_final: 0.8502 (pp) REVERT: A 174 LEU cc_start: 0.8988 (mm) cc_final: 0.8618 (mm) REVERT: A 184 MET cc_start: 0.8686 (mmm) cc_final: 0.8486 (mmm) REVERT: A 197 ARG cc_start: 0.8922 (mtp180) cc_final: 0.8416 (mtp180) REVERT: A 254 LYS cc_start: 0.8542 (tttp) cc_final: 0.8235 (tttt) REVERT: A 283 ARG cc_start: 0.9081 (mtm110) cc_final: 0.8863 (mmm160) REVERT: A 313 ARG cc_start: 0.7664 (tpt-90) cc_final: 0.7253 (tpt-90) REVERT: A 343 ARG cc_start: 0.8378 (ptm160) cc_final: 0.7700 (ttp-170) REVERT: A 357 MET cc_start: 0.6142 (tpp) cc_final: 0.5799 (tpp) REVERT: A 434 ASP cc_start: 0.8919 (m-30) cc_final: 0.8639 (m-30) REVERT: A 446 TYR cc_start: 0.8722 (m-80) cc_final: 0.8142 (m-80) REVERT: A 458 LYS cc_start: 0.9441 (mmmt) cc_final: 0.9117 (mmtm) REVERT: B 52 ASN cc_start: 0.8012 (p0) cc_final: 0.7754 (p0) REVERT: B 68 ARG cc_start: 0.8303 (mmp80) cc_final: 0.7579 (mmm160) REVERT: B 103 LEU cc_start: 0.9465 (mm) cc_final: 0.9060 (mm) REVERT: B 128 PHE cc_start: 0.9228 (t80) cc_final: 0.8973 (t80) REVERT: B 153 ILE cc_start: 0.9069 (tp) cc_final: 0.8771 (tp) REVERT: B 241 ASP cc_start: 0.8160 (t0) cc_final: 0.7908 (t0) REVERT: B 267 LEU cc_start: 0.9248 (mt) cc_final: 0.9012 (tp) REVERT: B 302 MET cc_start: 0.7468 (mmp) cc_final: 0.6411 (mmp) REVERT: B 306 ARG cc_start: 0.7528 (ptm-80) cc_final: 0.6484 (ptm-80) REVERT: B 332 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6333 (p-80) REVERT: B 379 ARG cc_start: 0.8755 (mtm180) cc_final: 0.8348 (mtm180) REVERT: B 390 LYS cc_start: 0.9331 (mmtm) cc_final: 0.9068 (mppt) REVERT: B 408 LYS cc_start: 0.8563 (pttt) cc_final: 0.8244 (pttm) REVERT: B 415 ILE cc_start: 0.8316 (mm) cc_final: 0.8019 (mm) REVERT: B 451 ASN cc_start: 0.8648 (p0) cc_final: 0.8291 (p0) REVERT: B 458 LYS cc_start: 0.8884 (mttt) cc_final: 0.8565 (ptpt) REVERT: C 59 ARG cc_start: 0.8287 (ptm160) cc_final: 0.8045 (ptt180) REVERT: C 107 ASP cc_start: 0.8511 (m-30) cc_final: 0.8177 (p0) REVERT: C 111 ASP cc_start: 0.8843 (t0) cc_final: 0.8609 (t0) REVERT: C 141 CYS cc_start: 0.8744 (p) cc_final: 0.8181 (p) REVERT: C 155 LEU cc_start: 0.9064 (mm) cc_final: 0.8771 (mm) REVERT: C 184 MET cc_start: 0.8668 (mmm) cc_final: 0.8438 (mmm) REVERT: C 197 ARG cc_start: 0.8927 (ttt90) cc_final: 0.8585 (mtp180) REVERT: C 254 LYS cc_start: 0.8552 (tttp) cc_final: 0.8228 (tttt) REVERT: C 283 ARG cc_start: 0.9078 (mtm110) cc_final: 0.8789 (mmm160) REVERT: C 313 ARG cc_start: 0.7301 (tpt-90) cc_final: 0.7032 (ttt90) REVERT: C 340 ARG cc_start: 0.7544 (tpt90) cc_final: 0.6968 (tpm170) REVERT: C 343 ARG cc_start: 0.8343 (ptm160) cc_final: 0.7585 (ttp-170) REVERT: C 434 ASP cc_start: 0.8919 (m-30) cc_final: 0.8651 (m-30) REVERT: C 446 TYR cc_start: 0.8713 (m-80) cc_final: 0.8165 (m-80) REVERT: C 458 LYS cc_start: 0.9427 (mmmt) cc_final: 0.9077 (mmtm) REVERT: D 31 ARG cc_start: 0.7126 (mtm180) cc_final: 0.6731 (mtm180) REVERT: D 68 ARG cc_start: 0.8388 (mmp80) cc_final: 0.7617 (mmm160) REVERT: D 74 LEU cc_start: 0.9010 (mm) cc_final: 0.8738 (mm) REVERT: D 91 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8266 (mmmt) REVERT: D 153 ILE cc_start: 0.9077 (tp) cc_final: 0.8783 (tp) REVERT: D 184 MET cc_start: 0.8681 (tpp) cc_final: 0.8440 (tpt) REVERT: D 231 LYS cc_start: 0.8873 (mttm) cc_final: 0.8411 (ptpt) REVERT: D 241 ASP cc_start: 0.8217 (t0) cc_final: 0.7964 (t0) REVERT: D 302 MET cc_start: 0.7519 (mmp) cc_final: 0.6541 (mmp) REVERT: D 332 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6334 (p-80) REVERT: D 379 ARG cc_start: 0.8743 (mtm180) cc_final: 0.8342 (mtm180) REVERT: D 390 LYS cc_start: 0.9307 (mmtm) cc_final: 0.9074 (mppt) REVERT: D 408 LYS cc_start: 0.8510 (pttt) cc_final: 0.8188 (pttm) REVERT: D 415 ILE cc_start: 0.8326 (mm) cc_final: 0.8014 (mm) REVERT: D 451 ASN cc_start: 0.8644 (p0) cc_final: 0.8306 (p0) REVERT: D 458 LYS cc_start: 0.8890 (mttt) cc_final: 0.8560 (ptpt) REVERT: E 6 ASP cc_start: 0.9112 (t0) cc_final: 0.8898 (t0) REVERT: E 59 ARG cc_start: 0.8058 (ptt90) cc_final: 0.7615 (ptt-90) REVERT: E 61 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7629 (tpp) REVERT: E 77 ASP cc_start: 0.7992 (m-30) cc_final: 0.7656 (m-30) REVERT: E 86 THR cc_start: 0.9381 (m) cc_final: 0.9166 (p) REVERT: E 135 LEU cc_start: 0.8954 (tp) cc_final: 0.8472 (mt) REVERT: E 155 LEU cc_start: 0.8492 (mm) cc_final: 0.7974 (pp) REVERT: E 175 GLU cc_start: 0.7394 (tp30) cc_final: 0.7063 (mm-30) REVERT: E 195 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8649 (tt) REVERT: E 246 ASP cc_start: 0.8777 (t0) cc_final: 0.8380 (t0) REVERT: E 292 ILE cc_start: 0.8906 (mm) cc_final: 0.8535 (mm) REVERT: E 306 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.7808 (mtt90) REVERT: E 341 HIS cc_start: 0.8317 (m170) cc_final: 0.7973 (m-70) REVERT: E 355 ASN cc_start: 0.8825 (t0) cc_final: 0.8358 (t0) REVERT: E 383 GLU cc_start: 0.8450 (pm20) cc_final: 0.8098 (mp0) REVERT: E 390 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8726 (mtpp) REVERT: E 438 SER cc_start: 0.8774 (t) cc_final: 0.8240 (p) REVERT: F 85 GLU cc_start: 0.8851 (tt0) cc_final: 0.8336 (tm-30) REVERT: F 98 ASP cc_start: 0.8425 (t0) cc_final: 0.7739 (t70) REVERT: F 118 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8023 (tptt) REVERT: F 169 GLU cc_start: 0.9082 (mp0) cc_final: 0.8588 (mp0) REVERT: F 233 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8456 (pp30) REVERT: F 302 MET cc_start: 0.7157 (mmp) cc_final: 0.6469 (mmt) REVERT: F 308 MET cc_start: 0.7820 (mmp) cc_final: 0.7597 (mmp) REVERT: F 344 ASP cc_start: 0.8434 (m-30) cc_final: 0.8212 (m-30) REVERT: F 458 LYS cc_start: 0.9130 (pttt) cc_final: 0.8867 (pttm) REVERT: G 6 ASP cc_start: 0.9103 (t0) cc_final: 0.8892 (t0) REVERT: G 31 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7516 (ptt180) REVERT: G 59 ARG cc_start: 0.8055 (ptt90) cc_final: 0.7614 (ptt-90) REVERT: G 61 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7642 (tpp) REVERT: G 77 ASP cc_start: 0.8037 (m-30) cc_final: 0.7665 (m-30) REVERT: G 86 THR cc_start: 0.9385 (m) cc_final: 0.9175 (p) REVERT: G 135 LEU cc_start: 0.8897 (tp) cc_final: 0.8416 (mt) REVERT: G 155 LEU cc_start: 0.8450 (mm) cc_final: 0.7927 (pp) REVERT: G 175 GLU cc_start: 0.7363 (tp30) cc_final: 0.6977 (mm-30) REVERT: G 195 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8670 (tt) REVERT: G 246 ASP cc_start: 0.8489 (t0) cc_final: 0.8189 (t0) REVERT: G 306 ARG cc_start: 0.8353 (mtp-110) cc_final: 0.8016 (mmm160) REVERT: G 316 PHE cc_start: 0.8673 (t80) cc_final: 0.7914 (t80) REVERT: G 341 HIS cc_start: 0.8339 (m170) cc_final: 0.7984 (m-70) REVERT: G 355 ASN cc_start: 0.8695 (t0) cc_final: 0.8284 (t0) REVERT: G 383 GLU cc_start: 0.8451 (pm20) cc_final: 0.8067 (mp0) REVERT: G 387 MET cc_start: 0.8729 (pmm) cc_final: 0.8416 (ppp) REVERT: G 438 SER cc_start: 0.8766 (t) cc_final: 0.8048 (p) REVERT: G 452 LEU cc_start: 0.7718 (mt) cc_final: 0.7447 (mt) REVERT: G 471 GLU cc_start: 0.7959 (pt0) cc_final: 0.7556 (tt0) REVERT: H 85 GLU cc_start: 0.8835 (tt0) cc_final: 0.8338 (tm-30) REVERT: H 98 ASP cc_start: 0.8351 (t0) cc_final: 0.7669 (t70) REVERT: H 118 LYS cc_start: 0.8597 (mmtt) cc_final: 0.8203 (mmmt) REVERT: H 169 GLU cc_start: 0.9094 (mp0) cc_final: 0.8650 (mp0) REVERT: H 233 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8412 (pp30) REVERT: H 255 MET cc_start: 0.8909 (tpt) cc_final: 0.8569 (tpp) REVERT: H 260 LYS cc_start: 0.8631 (pttp) cc_final: 0.8161 (pttp) REVERT: H 276 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8070 (p) REVERT: H 302 MET cc_start: 0.7139 (mmp) cc_final: 0.6288 (mmt) REVERT: H 304 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8368 (m) REVERT: H 329 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8546 (tt) REVERT: H 458 LYS cc_start: 0.9121 (mtmm) cc_final: 0.8821 (mtmt) REVERT: H 473 HIS cc_start: 0.8836 (t70) cc_final: 0.8524 (t70) outliers start: 102 outliers final: 77 residues processed: 851 average time/residue: 0.1914 time to fit residues: 253.3942 Evaluate side-chains 843 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 756 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 275 ASN Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 332 HIS Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 456 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 89 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 289 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 ASN ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.125989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.104853 restraints weight = 66162.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.108894 restraints weight = 41470.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.111924 restraints weight = 28774.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114143 restraints weight = 21222.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.115933 restraints weight = 16424.541| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28096 Z= 0.222 Angle : 0.771 12.267 38312 Z= 0.391 Chirality : 0.048 0.291 4536 Planarity : 0.005 0.081 5000 Dihedral : 6.586 51.498 4448 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.38 % Allowed : 31.20 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.36 (0.14), residues: 3704 helix: -0.06 (0.14), residues: 1424 sheet: -0.66 (0.20), residues: 608 loop : -0.03 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 426 TYR 0.031 0.003 TYR C 12 PHE 0.030 0.002 PHE D 316 TRP 0.022 0.002 TRP G 334 HIS 0.013 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (28096) covalent geometry : angle 0.77051 / 0.39 (38312) hydrogen bonds : bond 0.03650 / 2.53 ( 1160) hydrogen bonds : angle 5.63641 / 4.04 ( 3120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 792 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 52 ASN cc_start: 0.7370 (p0) cc_final: 0.6862 (p0) REVERT: A 59 ARG cc_start: 0.8356 (ptm160) cc_final: 0.8085 (ptt180) REVERT: A 76 GLN cc_start: 0.8122 (pm20) cc_final: 0.7515 (pm20) REVERT: A 107 ASP cc_start: 0.8653 (m-30) cc_final: 0.8232 (p0) REVERT: A 111 ASP cc_start: 0.8875 (t0) cc_final: 0.8632 (t0) REVERT: A 138 GLU cc_start: 0.8881 (mp0) cc_final: 0.8566 (tm-30) REVERT: A 141 CYS cc_start: 0.8772 (p) cc_final: 0.8248 (p) REVERT: A 146 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8592 (ptp90) REVERT: A 155 LEU cc_start: 0.9161 (mm) cc_final: 0.8870 (mm) REVERT: A 174 LEU cc_start: 0.9078 (mm) cc_final: 0.8740 (mm) REVERT: A 195 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9081 (tt) REVERT: A 197 ARG cc_start: 0.8907 (mtp180) cc_final: 0.8390 (mtp180) REVERT: A 254 LYS cc_start: 0.8605 (tttp) cc_final: 0.8308 (tttt) REVERT: A 283 ARG cc_start: 0.9083 (mtm110) cc_final: 0.8853 (mmm160) REVERT: A 313 ARG cc_start: 0.7744 (tpt-90) cc_final: 0.7235 (tpt-90) REVERT: A 343 ARG cc_start: 0.8438 (ptm160) cc_final: 0.7750 (ttp-170) REVERT: A 357 MET cc_start: 0.6462 (tpp) cc_final: 0.6116 (tpp) REVERT: A 434 ASP cc_start: 0.8916 (m-30) cc_final: 0.8554 (m-30) REVERT: A 446 TYR cc_start: 0.8851 (m-80) cc_final: 0.8251 (m-80) REVERT: A 458 LYS cc_start: 0.9446 (mmmt) cc_final: 0.9134 (mmtm) REVERT: B 4 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8650 (t80) REVERT: B 31 ARG cc_start: 0.7086 (mtm180) cc_final: 0.6883 (mtm180) REVERT: B 37 SER cc_start: 0.8854 (m) cc_final: 0.8575 (p) REVERT: B 68 ARG cc_start: 0.8340 (mmp80) cc_final: 0.7539 (mmm160) REVERT: B 74 LEU cc_start: 0.9066 (mm) cc_final: 0.8805 (mm) REVERT: B 91 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8324 (mmmt) REVERT: B 128 PHE cc_start: 0.9262 (t80) cc_final: 0.9045 (t80) REVERT: B 153 ILE cc_start: 0.9156 (tp) cc_final: 0.8954 (tp) REVERT: B 174 LEU cc_start: 0.9238 (mm) cc_final: 0.8452 (tp) REVERT: B 241 ASP cc_start: 0.8234 (t0) cc_final: 0.7953 (t0) REVERT: B 302 MET cc_start: 0.7581 (mmp) cc_final: 0.6615 (mmp) REVERT: B 306 ARG cc_start: 0.7507 (ptm-80) cc_final: 0.6423 (ptm-80) REVERT: B 379 ARG cc_start: 0.8686 (mtm180) cc_final: 0.8294 (mtm110) REVERT: B 387 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8472 (mmp) REVERT: B 408 LYS cc_start: 0.8549 (pttt) cc_final: 0.8195 (pttm) REVERT: B 451 ASN cc_start: 0.8635 (p0) cc_final: 0.8354 (p0) REVERT: B 458 LYS cc_start: 0.8914 (mttt) cc_final: 0.8562 (ptpt) REVERT: C 59 ARG cc_start: 0.8347 (ptm160) cc_final: 0.8120 (ptt180) REVERT: C 107 ASP cc_start: 0.8575 (m-30) cc_final: 0.8250 (p0) REVERT: C 111 ASP cc_start: 0.8834 (t0) cc_final: 0.8621 (t0) REVERT: C 141 CYS cc_start: 0.8752 (p) cc_final: 0.8199 (p) REVERT: C 155 LEU cc_start: 0.9210 (mm) cc_final: 0.8889 (mm) REVERT: C 306 ARG cc_start: 0.8700 (mtt90) cc_final: 0.8379 (mtt180) REVERT: C 313 ARG cc_start: 0.7682 (tpt-90) cc_final: 0.7237 (tpt-90) REVERT: C 327 ARG cc_start: 0.8970 (mtp180) cc_final: 0.8767 (mtt180) REVERT: C 343 ARG cc_start: 0.8418 (ptm160) cc_final: 0.7659 (ttp-170) REVERT: C 357 MET cc_start: 0.6368 (tpp) cc_final: 0.5738 (tpp) REVERT: C 434 ASP cc_start: 0.8911 (m-30) cc_final: 0.8548 (m-30) REVERT: C 446 TYR cc_start: 0.8880 (m-80) cc_final: 0.8279 (m-80) REVERT: C 458 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9116 (mmtm) REVERT: D 31 ARG cc_start: 0.7115 (mtm180) cc_final: 0.6827 (mtm180) REVERT: D 68 ARG cc_start: 0.8401 (mmp80) cc_final: 0.7547 (mmm160) REVERT: D 174 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8339 (tp) REVERT: D 231 LYS cc_start: 0.8983 (mttm) cc_final: 0.8595 (mtmm) REVERT: D 241 ASP cc_start: 0.8268 (t0) cc_final: 0.8014 (t0) REVERT: D 255 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8233 (tpt) REVERT: D 302 MET cc_start: 0.7643 (mmp) cc_final: 0.6791 (mmp) REVERT: D 306 ARG cc_start: 0.7519 (ptm-80) cc_final: 0.6326 (ptm-80) REVERT: D 332 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6374 (p-80) REVERT: D 379 ARG cc_start: 0.8670 (mtm180) cc_final: 0.8296 (mtm110) REVERT: D 387 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8461 (mmp) REVERT: D 408 LYS cc_start: 0.8545 (pttt) cc_final: 0.8231 (pttm) REVERT: D 451 ASN cc_start: 0.8665 (p0) cc_final: 0.8391 (p0) REVERT: D 458 LYS cc_start: 0.8914 (mttt) cc_final: 0.8539 (ptpt) REVERT: E 6 ASP cc_start: 0.9200 (t0) cc_final: 0.8900 (m-30) REVERT: E 14 LEU cc_start: 0.8532 (mm) cc_final: 0.8284 (mm) REVERT: E 59 ARG cc_start: 0.8116 (ptt90) cc_final: 0.7674 (ptt-90) REVERT: E 61 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7701 (tpp) REVERT: E 86 THR cc_start: 0.9383 (m) cc_final: 0.9177 (p) REVERT: E 135 LEU cc_start: 0.8953 (tp) cc_final: 0.8373 (mt) REVERT: E 138 GLU cc_start: 0.8615 (mp0) cc_final: 0.8359 (mm-30) REVERT: E 155 LEU cc_start: 0.8572 (mm) cc_final: 0.7900 (pp) REVERT: E 158 PHE cc_start: 0.7841 (p90) cc_final: 0.7128 (p90) REVERT: E 175 GLU cc_start: 0.7420 (tp30) cc_final: 0.7031 (mm-30) REVERT: E 195 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8721 (tt) REVERT: E 242 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.5228 (tt) REVERT: E 246 ASP cc_start: 0.8935 (t0) cc_final: 0.8561 (t0) REVERT: E 292 ILE cc_start: 0.9008 (mm) cc_final: 0.8632 (mm) REVERT: E 306 ARG cc_start: 0.8579 (mtp-110) cc_final: 0.7778 (mmt90) REVERT: E 341 HIS cc_start: 0.8182 (m170) cc_final: 0.7831 (m-70) REVERT: E 355 ASN cc_start: 0.8729 (t0) cc_final: 0.8462 (t0) REVERT: E 357 MET cc_start: 0.7591 (tpp) cc_final: 0.7297 (mmm) REVERT: E 383 GLU cc_start: 0.8438 (pm20) cc_final: 0.8079 (mp0) REVERT: E 390 LYS cc_start: 0.9153 (mmtm) cc_final: 0.8730 (mtpp) REVERT: E 438 SER cc_start: 0.8818 (t) cc_final: 0.8236 (p) REVERT: F 85 GLU cc_start: 0.8852 (tt0) cc_final: 0.8382 (tm-30) REVERT: F 98 ASP cc_start: 0.8405 (t0) cc_final: 0.7608 (t70) REVERT: F 169 GLU cc_start: 0.9125 (mp0) cc_final: 0.8697 (mp0) REVERT: F 180 ASP cc_start: 0.8836 (t0) cc_final: 0.8618 (t0) REVERT: F 231 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7740 (pttm) REVERT: F 233 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8397 (pp30) REVERT: F 255 MET cc_start: 0.8703 (tpt) cc_final: 0.8397 (tpp) REVERT: F 260 LYS cc_start: 0.8752 (pttp) cc_final: 0.8351 (pttp) REVERT: F 302 MET cc_start: 0.7185 (mmp) cc_final: 0.6455 (mmt) REVERT: F 328 GLN cc_start: 0.8155 (pp30) cc_final: 0.7692 (pp30) REVERT: F 344 ASP cc_start: 0.8578 (m-30) cc_final: 0.8224 (m-30) REVERT: F 408 LYS cc_start: 0.8500 (tppt) cc_final: 0.8140 (tppt) REVERT: F 435 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7270 (m-70) REVERT: F 452 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6370 (mt) REVERT: F 458 LYS cc_start: 0.9152 (pttt) cc_final: 0.8905 (pttm) REVERT: G 6 ASP cc_start: 0.9181 (t0) cc_final: 0.8867 (m-30) REVERT: G 14 LEU cc_start: 0.8510 (mm) cc_final: 0.8304 (mm) REVERT: G 59 ARG cc_start: 0.8146 (ptt90) cc_final: 0.7707 (ptt-90) REVERT: G 61 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7732 (tpp) REVERT: G 68 ARG cc_start: 0.8042 (mmp-170) cc_final: 0.7687 (mmp80) REVERT: G 86 THR cc_start: 0.9384 (m) cc_final: 0.9178 (p) REVERT: G 135 LEU cc_start: 0.8914 (tp) cc_final: 0.8401 (mt) REVERT: G 138 GLU cc_start: 0.8600 (mp0) cc_final: 0.8347 (mm-30) REVERT: G 155 LEU cc_start: 0.8527 (mm) cc_final: 0.8015 (pp) REVERT: G 158 PHE cc_start: 0.7849 (p90) cc_final: 0.7086 (p90) REVERT: G 175 GLU cc_start: 0.7424 (tp30) cc_final: 0.7040 (mm-30) REVERT: G 195 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8755 (tt) REVERT: G 242 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.5187 (tt) REVERT: G 246 ASP cc_start: 0.8777 (t0) cc_final: 0.8528 (t0) REVERT: G 302 MET cc_start: 0.7620 (mmp) cc_final: 0.6322 (mmp) REVERT: G 306 ARG cc_start: 0.8394 (mtp-110) cc_final: 0.7777 (mtm180) REVERT: G 313 ARG cc_start: 0.7287 (tpt-90) cc_final: 0.6950 (tpt-90) REVERT: G 316 PHE cc_start: 0.8649 (t80) cc_final: 0.7994 (t80) REVERT: G 341 HIS cc_start: 0.8221 (m170) cc_final: 0.7884 (m-70) REVERT: G 383 GLU cc_start: 0.8436 (pm20) cc_final: 0.8038 (mp0) REVERT: G 438 SER cc_start: 0.8801 (t) cc_final: 0.8217 (p) REVERT: H 85 GLU cc_start: 0.8868 (tt0) cc_final: 0.8385 (tm-30) REVERT: H 118 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8104 (mmtp) REVERT: H 169 GLU cc_start: 0.9118 (mp0) cc_final: 0.8689 (mp0) REVERT: H 231 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7744 (pttm) REVERT: H 233 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8310 (pp30) REVERT: H 254 LYS cc_start: 0.8784 (pptt) cc_final: 0.8534 (pptt) REVERT: H 255 MET cc_start: 0.8658 (tpt) cc_final: 0.8383 (tpp) REVERT: H 276 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.7908 (p) REVERT: H 302 MET cc_start: 0.7206 (mmp) cc_final: 0.6441 (mmt) REVERT: H 304 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8334 (m) REVERT: H 328 GLN cc_start: 0.8145 (pp30) cc_final: 0.7688 (pp30) REVERT: H 408 LYS cc_start: 0.8618 (tppt) cc_final: 0.8304 (tppt) REVERT: H 435 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7540 (m-70) REVERT: H 458 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8881 (mttt) REVERT: H 473 HIS cc_start: 0.8832 (t70) cc_final: 0.8417 (t70) outliers start: 123 outliers final: 92 residues processed: 847 average time/residue: 0.1917 time to fit residues: 252.8524 Evaluate side-chains 863 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 752 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 456 HIS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 435 HIS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 357 MET Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 332 HIS Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 421 SER Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 435 HIS Chi-restraints excluded: chain H residue 456 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 354 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 276 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 281 optimal weight: 10.0000 chunk 63 optimal weight: 0.3980 chunk 221 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 315 GLN ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.129957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.108388 restraints weight = 64656.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.112615 restraints weight = 40545.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.115741 restraints weight = 28045.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.118119 restraints weight = 20650.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.119886 restraints weight = 15863.263| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28096 Z= 0.142 Angle : 0.791 13.100 38312 Z= 0.389 Chirality : 0.049 0.322 4536 Planarity : 0.005 0.080 5000 Dihedral : 6.539 53.584 4448 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.38 % Allowed : 32.51 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.40 (0.13), residues: 3704 helix: -0.03 (0.14), residues: 1424 sheet: -0.76 (0.20), residues: 608 loop : -0.07 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 327 TYR 0.025 0.002 TYR G 446 PHE 0.032 0.002 PHE B 316 TRP 0.021 0.002 TRP E 334 HIS 0.011 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (28096) covalent geometry : angle 0.79091 / 0.39 (38312) hydrogen bonds : bond 0.03523 / 2.45 ( 1160) hydrogen bonds : angle 5.58603 / 4.01 ( 3120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 771 time to evaluate : 0.933 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: A 52 ASN cc_start: 0.7308 (p0) cc_final: 0.6818 (p0) REVERT: A 53 MET cc_start: 0.8149 (mmt) cc_final: 0.7528 (mmt) REVERT: A 76 GLN cc_start: 0.8028 (pm20) cc_final: 0.7505 (pm20) REVERT: A 107 ASP cc_start: 0.8648 (m-30) cc_final: 0.8250 (p0) REVERT: A 111 ASP cc_start: 0.8864 (t0) cc_final: 0.8580 (t0) REVERT: A 138 GLU cc_start: 0.8885 (mp0) cc_final: 0.8549 (tm-30) REVERT: A 141 CYS cc_start: 0.8752 (p) cc_final: 0.8250 (p) REVERT: A 146 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8522 (ptp90) REVERT: A 174 LEU cc_start: 0.9033 (mm) cc_final: 0.8664 (mm) REVERT: A 195 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8997 (tt) REVERT: A 197 ARG cc_start: 0.8941 (mtp180) cc_final: 0.8419 (mtp180) REVERT: A 254 LYS cc_start: 0.8530 (tttp) cc_final: 0.8263 (tttt) REVERT: A 283 ARG cc_start: 0.9090 (mtm110) cc_final: 0.8821 (mmm160) REVERT: A 313 ARG cc_start: 0.7656 (tpt-90) cc_final: 0.7260 (tpt-90) REVERT: A 316 PHE cc_start: 0.8632 (t80) cc_final: 0.8428 (t80) REVERT: A 343 ARG cc_start: 0.8355 (ptm160) cc_final: 0.7731 (ttm170) REVERT: A 357 MET cc_start: 0.6292 (tpp) cc_final: 0.5950 (tpp) REVERT: A 434 ASP cc_start: 0.8860 (m-30) cc_final: 0.8576 (m-30) REVERT: A 446 TYR cc_start: 0.8674 (m-80) cc_final: 0.8006 (m-80) REVERT: A 458 LYS cc_start: 0.9450 (mmmt) cc_final: 0.9129 (mmtm) REVERT: B 37 SER cc_start: 0.8854 (m) cc_final: 0.8586 (p) REVERT: B 68 ARG cc_start: 0.8327 (mmp80) cc_final: 0.7563 (mmm160) REVERT: B 128 PHE cc_start: 0.9297 (t80) cc_final: 0.9091 (t80) REVERT: B 153 ILE cc_start: 0.9077 (tp) cc_final: 0.8801 (tp) REVERT: B 174 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8502 (tp) REVERT: B 231 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8909 (pttm) REVERT: B 302 MET cc_start: 0.7459 (mmp) cc_final: 0.6502 (mmp) REVERT: B 306 ARG cc_start: 0.7561 (ptm-80) cc_final: 0.6693 (ptm-80) REVERT: B 332 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6198 (p-80) REVERT: B 379 ARG cc_start: 0.8753 (mtm180) cc_final: 0.8337 (mtm180) REVERT: B 387 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8352 (mmp) REVERT: B 408 LYS cc_start: 0.8541 (pttt) cc_final: 0.8181 (pttm) REVERT: B 451 ASN cc_start: 0.8610 (p0) cc_final: 0.8346 (p0) REVERT: B 458 LYS cc_start: 0.8897 (mttt) cc_final: 0.8453 (ptpt) REVERT: C 53 MET cc_start: 0.8200 (mmt) cc_final: 0.7487 (mmt) REVERT: C 76 GLN cc_start: 0.7747 (mp10) cc_final: 0.7502 (mp10) REVERT: C 107 ASP cc_start: 0.8559 (m-30) cc_final: 0.8245 (p0) REVERT: C 111 ASP cc_start: 0.8849 (t0) cc_final: 0.8603 (t0) REVERT: C 141 CYS cc_start: 0.8697 (p) cc_final: 0.8125 (p) REVERT: C 155 LEU cc_start: 0.9252 (mm) cc_final: 0.8924 (mm) REVERT: C 197 ARG cc_start: 0.8933 (ttt90) cc_final: 0.8577 (mtp180) REVERT: C 254 LYS cc_start: 0.8553 (tttp) cc_final: 0.8240 (tttt) REVERT: C 283 ARG cc_start: 0.9086 (mtm110) cc_final: 0.8878 (mtm110) REVERT: C 313 ARG cc_start: 0.7606 (tpt-90) cc_final: 0.7287 (ttt90) REVERT: C 340 ARG cc_start: 0.7606 (tpt90) cc_final: 0.7022 (tpm170) REVERT: C 343 ARG cc_start: 0.8347 (ptm160) cc_final: 0.7741 (ttm170) REVERT: C 357 MET cc_start: 0.6067 (tpp) cc_final: 0.5723 (tpp) REVERT: C 426 ARG cc_start: 0.6275 (ptt90) cc_final: 0.5837 (ptt180) REVERT: C 434 ASP cc_start: 0.8852 (m-30) cc_final: 0.8574 (m-30) REVERT: C 446 TYR cc_start: 0.8773 (m-80) cc_final: 0.8195 (m-80) REVERT: C 458 LYS cc_start: 0.9420 (mmmt) cc_final: 0.9079 (mmtm) REVERT: D 68 ARG cc_start: 0.8387 (mmp80) cc_final: 0.7584 (mmm160) REVERT: D 174 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8488 (tp) REVERT: D 231 LYS cc_start: 0.8979 (mttm) cc_final: 0.8544 (ptpt) REVERT: D 241 ASP cc_start: 0.8240 (t0) cc_final: 0.7986 (t0) REVERT: D 255 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8158 (tpt) REVERT: D 302 MET cc_start: 0.7541 (mmp) cc_final: 0.6637 (mmp) REVERT: D 306 ARG cc_start: 0.7564 (ptm-80) cc_final: 0.6571 (ptm-80) REVERT: D 332 HIS cc_start: 0.7315 (OUTLIER) cc_final: 0.6122 (p-80) REVERT: D 379 ARG cc_start: 0.8730 (mtm180) cc_final: 0.8320 (mtm180) REVERT: D 387 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8361 (mmp) REVERT: D 408 LYS cc_start: 0.8571 (pttt) cc_final: 0.8236 (pttm) REVERT: D 451 ASN cc_start: 0.8637 (p0) cc_final: 0.8354 (p0) REVERT: D 458 LYS cc_start: 0.8906 (mttt) cc_final: 0.8577 (ptpt) REVERT: E 6 ASP cc_start: 0.9177 (t0) cc_final: 0.8923 (m-30) REVERT: E 14 LEU cc_start: 0.8386 (mm) cc_final: 0.8126 (mm) REVERT: E 31 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7519 (ptt180) REVERT: E 59 ARG cc_start: 0.8032 (ptt90) cc_final: 0.7572 (ptt-90) REVERT: E 61 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7636 (tpp) REVERT: E 77 ASP cc_start: 0.8148 (m-30) cc_final: 0.7746 (m-30) REVERT: E 86 THR cc_start: 0.9377 (m) cc_final: 0.9162 (p) REVERT: E 135 LEU cc_start: 0.8956 (tp) cc_final: 0.8479 (mt) REVERT: E 155 LEU cc_start: 0.8513 (mm) cc_final: 0.7983 (pp) REVERT: E 158 PHE cc_start: 0.7884 (p90) cc_final: 0.7237 (p90) REVERT: E 175 GLU cc_start: 0.7334 (tp30) cc_final: 0.6931 (mm-30) REVERT: E 195 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8696 (tt) REVERT: E 246 ASP cc_start: 0.8865 (t0) cc_final: 0.8463 (t0) REVERT: E 292 ILE cc_start: 0.8968 (mm) cc_final: 0.8591 (mm) REVERT: E 306 ARG cc_start: 0.8607 (mtp-110) cc_final: 0.7735 (mmt90) REVERT: E 313 ARG cc_start: 0.7473 (tpt-90) cc_final: 0.6847 (tmt-80) REVERT: E 341 HIS cc_start: 0.8214 (m170) cc_final: 0.7890 (m-70) REVERT: E 355 ASN cc_start: 0.8648 (t0) cc_final: 0.8185 (t0) REVERT: E 383 GLU cc_start: 0.8439 (pm20) cc_final: 0.8063 (mp0) REVERT: E 390 LYS cc_start: 0.9111 (mmtm) cc_final: 0.8678 (mtpp) REVERT: E 438 SER cc_start: 0.8766 (t) cc_final: 0.8050 (p) REVERT: F 85 GLU cc_start: 0.8847 (tt0) cc_final: 0.8332 (tm-30) REVERT: F 98 ASP cc_start: 0.8232 (t0) cc_final: 0.7691 (t0) REVERT: F 118 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8139 (mmmm) REVERT: F 169 GLU cc_start: 0.9092 (mp0) cc_final: 0.8664 (mp0) REVERT: F 180 ASP cc_start: 0.8857 (t0) cc_final: 0.8612 (t0) REVERT: F 231 LYS cc_start: 0.7939 (mtmm) cc_final: 0.7683 (pttm) REVERT: F 233 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8391 (pp30) REVERT: F 255 MET cc_start: 0.8628 (tpt) cc_final: 0.8266 (tpp) REVERT: F 260 LYS cc_start: 0.8693 (pttp) cc_final: 0.8283 (pttp) REVERT: F 302 MET cc_start: 0.7089 (mmp) cc_final: 0.6320 (mmt) REVERT: F 344 ASP cc_start: 0.8565 (m-30) cc_final: 0.8266 (m-30) REVERT: F 390 LYS cc_start: 0.8951 (mmtm) cc_final: 0.8353 (ptmm) REVERT: F 422 LEU cc_start: 0.8900 (mt) cc_final: 0.8629 (mt) REVERT: F 458 LYS cc_start: 0.9171 (pttt) cc_final: 0.8899 (pttm) REVERT: G 6 ASP cc_start: 0.9175 (t0) cc_final: 0.8909 (m-30) REVERT: G 14 LEU cc_start: 0.8398 (mm) cc_final: 0.8193 (mm) REVERT: G 59 ARG cc_start: 0.8058 (ptt90) cc_final: 0.7600 (ptt-90) REVERT: G 61 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7574 (tpp) REVERT: G 86 THR cc_start: 0.9377 (m) cc_final: 0.9166 (p) REVERT: G 135 LEU cc_start: 0.8932 (tp) cc_final: 0.8478 (mt) REVERT: G 155 LEU cc_start: 0.8446 (mm) cc_final: 0.7930 (pp) REVERT: G 158 PHE cc_start: 0.7872 (p90) cc_final: 0.7172 (p90) REVERT: G 175 GLU cc_start: 0.7328 (tp30) cc_final: 0.6949 (mm-30) REVERT: G 195 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8770 (tt) REVERT: G 246 ASP cc_start: 0.8680 (t0) cc_final: 0.8434 (t0) REVERT: G 306 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.7243 (mtm-85) REVERT: G 313 ARG cc_start: 0.7197 (tpt-90) cc_final: 0.6758 (tpt-90) REVERT: G 316 PHE cc_start: 0.8657 (t80) cc_final: 0.7972 (t80) REVERT: G 341 HIS cc_start: 0.8267 (m170) cc_final: 0.7942 (m-70) REVERT: G 355 ASN cc_start: 0.8713 (t0) cc_final: 0.8286 (t0) REVERT: G 387 MET cc_start: 0.8680 (pmm) cc_final: 0.8398 (ppp) REVERT: G 438 SER cc_start: 0.8751 (t) cc_final: 0.8201 (p) REVERT: G 471 GLU cc_start: 0.7830 (pt0) cc_final: 0.7455 (tt0) REVERT: H 85 GLU cc_start: 0.8855 (tt0) cc_final: 0.8352 (tm-30) REVERT: H 98 ASP cc_start: 0.8221 (t0) cc_final: 0.7661 (t0) REVERT: H 118 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8060 (mmtp) REVERT: H 169 GLU cc_start: 0.9096 (mp0) cc_final: 0.8593 (mp0) REVERT: H 231 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7693 (pttm) REVERT: H 233 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8304 (pp30) REVERT: H 254 LYS cc_start: 0.8779 (pptt) cc_final: 0.8515 (pptt) REVERT: H 260 LYS cc_start: 0.8744 (pttp) cc_final: 0.8268 (pttp) REVERT: H 276 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.7938 (p) REVERT: H 302 MET cc_start: 0.7099 (mmp) cc_final: 0.6334 (mmt) REVERT: H 308 MET cc_start: 0.7817 (mmt) cc_final: 0.7500 (mmp) REVERT: H 408 LYS cc_start: 0.8625 (tppt) cc_final: 0.8268 (tppt) REVERT: H 422 LEU cc_start: 0.8918 (mt) cc_final: 0.8646 (mt) REVERT: H 435 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7455 (m-70) REVERT: H 458 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8828 (mtmt) REVERT: H 473 HIS cc_start: 0.8811 (t70) cc_final: 0.8368 (t70) outliers start: 95 outliers final: 73 residues processed: 813 average time/residue: 0.1910 time to fit residues: 242.4164 Evaluate side-chains 829 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 740 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 146 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 275 ASN Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 393 VAL Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 433 LEU Chi-restraints excluded: chain H residue 435 HIS Chi-restraints excluded: chain H residue 456 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 173 optimal weight: 10.0000 chunk 363 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 187 optimal weight: 0.0060 chunk 135 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 HIS ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** 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 = 0.3934 r_free = 0.3934 target = 0.131513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.110023 restraints weight = 63707.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114257 restraints weight = 39861.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.117426 restraints weight = 27427.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.119733 restraints weight = 20088.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121563 restraints weight = 15454.933| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28096 Z= 0.139 Angle : 0.784 13.241 38312 Z= 0.384 Chirality : 0.049 0.323 4536 Planarity : 0.005 0.075 5000 Dihedral : 6.446 55.242 4448 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.24 % Allowed : 32.80 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: -0.38 (0.13), residues: 3704 helix: -0.03 (0.14), residues: 1416 sheet: -0.76 (0.20), residues: 600 loop : -0.04 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 419 TYR 0.025 0.002 TYR E 446 PHE 0.031 0.002 PHE D 316 TRP 0.021 0.002 TRP E 334 HIS 0.013 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (28096) covalent geometry : angle 0.78399 / 0.38 (38312) hydrogen bonds : bond 0.03430 / 2.38 ( 1160) hydrogen bonds : angle 5.56350 / 3.98 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5783.60 seconds wall clock time: 100 minutes 23.49 seconds (6023.49 seconds total)