Starting phenix.real_space_refine on Fri Feb 6 20:49:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ry1_19584/02_2026/8ry1_19584.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ry1_19584/02_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_19584/02_2026/8ry1_19584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ry1_19584/02_2026/8ry1_19584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ry1_19584/02_2026/8ry1_19584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ry1_19584/02_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.06, per 1000 atoms: 0.15 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: 2.88 Conformation dependent library (CDL) restraints added in 1.4 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: 1.22 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: 5.63 Time building geometry restraints manager: 3.66 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=" O5' 5GP C 501 " pdb=" P 5GP C 501 " ideal model delta sigma weight residual 1.678 1.590 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" O5' 5GP E 501 " pdb=" P 5GP E 501 " ideal model delta sigma weight residual 1.678 1.590 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" O5' 5GP A 501 " pdb=" P 5GP A 501 " ideal model delta sigma weight residual 1.678 1.590 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" O5' 5GP D 501 " pdb=" P 5GP D 501 " ideal model delta sigma weight residual 1.678 1.590 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" O5' 5GP G 501 " pdb=" P 5GP G 501 " ideal model delta sigma weight residual 1.678 1.590 0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 28091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 37322 1.93 - 3.85: 822 3.85 - 5.78: 96 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: 3004 0.037 - 0.075: 955 0.075 - 0.112: 477 0.112 - 0.149: 76 0.149 - 0.187: 24 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: 1.530 Set stop_for_unknowns flag: 0.010 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: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.210 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 28096 Z= 0.176 Angle : 0.687 9.635 38312 Z= 0.326 Chirality : 0.046 0.187 4536 Planarity : 0.005 0.051 5000 Dihedral : 15.067 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 covalent geometry : bond 0.00371 (28096) covalent geometry : angle 0.68733 (38312) hydrogen bonds : bond 0.19803 ( 1160) hydrogen bonds : angle 7.39862 ( 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 : 1.258 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: 0.2062 time to fit residues: 405.7298 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 : 0.799 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.128976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.108635 restraints weight = 65091.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.112917 restraints weight = 39651.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.115941 restraints weight = 26750.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118403 restraints weight = 19352.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.120163 restraints weight = 14442.492| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28096 Z= 0.221 Angle : 0.708 7.862 38312 Z= 0.369 Chirality : 0.048 0.278 4536 Planarity : 0.006 0.076 5000 Dihedral : 6.967 58.316 4466 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.56 % Allowed : 21.79 % Favored : 73.65 % 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: 0.35 (0.14), residues: 3704 helix: 0.36 (0.14), residues: 1480 sheet: -0.01 (0.21), residues: 568 loop : 0.43 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 407 TYR 0.018 0.002 TYR C 12 PHE 0.025 0.002 PHE G 469 TRP 0.019 0.002 TRP G 334 HIS 0.007 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00486 (28096) covalent geometry : angle 0.70838 (38312) hydrogen bonds : bond 0.04309 ( 1160) hydrogen bonds : angle 5.78801 ( 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 1109 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 981 time to evaluate : 1.232 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: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.7792 (p0) cc_final: 0.7281 (p0) REVERT: A 77 ASP cc_start: 0.8353 (m-30) cc_final: 0.8076 (m-30) REVERT: A 107 ASP cc_start: 0.8467 (m-30) cc_final: 0.7905 (p0) REVERT: A 111 ASP cc_start: 0.8898 (t0) cc_final: 0.8659 (t0) REVERT: A 113 ASN cc_start: 0.8920 (t0) cc_final: 0.8668 (t0) REVERT: A 138 GLU cc_start: 0.8791 (mp0) cc_final: 0.8163 (tm-30) REVERT: A 155 LEU cc_start: 0.9108 (mm) cc_final: 0.8579 (pp) REVERT: A 184 MET cc_start: 0.8605 (mmm) cc_final: 0.8127 (mmm) REVERT: A 217 ARG cc_start: 0.7551 (mtt-85) cc_final: 0.6650 (mmm-85) REVERT: A 225 ASN cc_start: 0.8751 (p0) cc_final: 0.8060 (m-40) REVERT: A 313 ARG cc_start: 0.7756 (ttt90) cc_final: 0.7242 (tpt-90) REVERT: A 343 ARG cc_start: 0.8602 (ptm160) cc_final: 0.7818 (ttp-170) REVERT: A 408 LYS cc_start: 0.9243 (tptp) cc_final: 0.8796 (ptmt) REVERT: A 434 ASP cc_start: 0.8946 (m-30) cc_final: 0.8723 (m-30) REVERT: A 446 TYR cc_start: 0.8827 (m-80) cc_final: 0.8139 (m-80) REVERT: A 458 LYS cc_start: 0.9412 (mmmt) cc_final: 0.9061 (mmtm) REVERT: A 471 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7450 (tt0) REVERT: B 18 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6490 (t70) REVERT: B 68 ARG cc_start: 0.8176 (mmp80) cc_final: 0.7437 (mmm160) REVERT: B 117 HIS cc_start: 0.9160 (m-70) cc_final: 0.8738 (m-70) REVERT: B 153 ILE cc_start: 0.9249 (tp) cc_final: 0.8951 (tp) REVERT: B 155 LEU cc_start: 0.8536 (mm) cc_final: 0.8286 (mm) REVERT: B 158 PHE cc_start: 0.8062 (p90) cc_final: 0.7667 (p90) REVERT: B 213 LYS cc_start: 0.9247 (ttmm) cc_final: 0.9029 (ttpt) REVERT: B 231 LYS cc_start: 0.8849 (mtmt) cc_final: 0.8635 (ptpp) REVERT: B 302 MET cc_start: 0.7401 (mmp) cc_final: 0.6041 (mmt) REVERT: B 306 ARG cc_start: 0.8545 (mtp-110) cc_final: 0.7096 (mmt90) REVERT: B 376 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6216 (mpt180) REVERT: B 379 ARG cc_start: 0.8739 (mtm180) cc_final: 0.8500 (mtm180) REVERT: B 443 THR cc_start: 0.8937 (m) cc_final: 0.8700 (p) REVERT: B 451 ASN cc_start: 0.8712 (p0) cc_final: 0.8331 (p0) REVERT: B 452 LEU cc_start: 0.8007 (mt) cc_final: 0.7707 (mp) REVERT: B 458 LYS cc_start: 0.8859 (mttt) cc_final: 0.8498 (ptpt) REVERT: B 473 HIS cc_start: 0.8864 (t70) cc_final: 0.8559 (t70) REVERT: C 52 ASN cc_start: 0.7781 (p0) cc_final: 0.7280 (p0) REVERT: C 77 ASP cc_start: 0.8355 (m-30) cc_final: 0.8085 (m-30) REVERT: C 107 ASP cc_start: 0.8443 (m-30) cc_final: 0.7885 (p0) REVERT: C 111 ASP cc_start: 0.8873 (t0) cc_final: 0.8637 (t0) REVERT: C 138 GLU cc_start: 0.8792 (mp0) cc_final: 0.8154 (tm-30) REVERT: C 155 LEU cc_start: 0.9113 (mm) cc_final: 0.8584 (pp) REVERT: C 184 MET cc_start: 0.8604 (mmm) cc_final: 0.8123 (mmm) REVERT: C 217 ARG cc_start: 0.7555 (mtt-85) cc_final: 0.6656 (mmm-85) REVERT: C 254 LYS cc_start: 0.8369 (tttp) cc_final: 0.8054 (tttm) REVERT: C 313 ARG cc_start: 0.7752 (ttt90) cc_final: 0.7334 (tpt-90) REVERT: C 343 ARG cc_start: 0.8600 (ptm160) cc_final: 0.7824 (ttp-170) REVERT: C 434 ASP cc_start: 0.8951 (m-30) cc_final: 0.8735 (m-30) REVERT: C 446 TYR cc_start: 0.8824 (m-80) cc_final: 0.8135 (m-80) REVERT: C 458 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9048 (mmtm) REVERT: C 471 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7328 (tt0) REVERT: D 18 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6479 (t70) REVERT: D 68 ARG cc_start: 0.8170 (mmp80) cc_final: 0.7437 (mmm160) REVERT: D 117 HIS cc_start: 0.9155 (m-70) cc_final: 0.8741 (m-70) REVERT: D 153 ILE cc_start: 0.9249 (tp) cc_final: 0.8952 (tp) REVERT: D 155 LEU cc_start: 0.8547 (mm) cc_final: 0.8289 (mm) REVERT: D 158 PHE cc_start: 0.8047 (p90) cc_final: 0.7660 (p90) REVERT: D 213 LYS cc_start: 0.9221 (ttmm) cc_final: 0.9017 (ttpt) REVERT: D 231 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8633 (ptpp) REVERT: D 302 MET cc_start: 0.7394 (mmp) cc_final: 0.6038 (mmt) REVERT: D 306 ARG cc_start: 0.8534 (mtp-110) cc_final: 0.7055 (mmm160) REVERT: D 379 ARG cc_start: 0.8745 (mtm180) cc_final: 0.8488 (mtm180) REVERT: D 443 THR cc_start: 0.8930 (m) cc_final: 0.8698 (p) REVERT: D 451 ASN cc_start: 0.8712 (p0) cc_final: 0.8327 (p0) REVERT: D 452 LEU cc_start: 0.8018 (mt) cc_final: 0.7712 (mp) REVERT: D 458 LYS cc_start: 0.8860 (mttt) cc_final: 0.8498 (ptpt) REVERT: D 473 HIS cc_start: 0.8863 (t70) cc_final: 0.8552 (t70) REVERT: E 18 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7240 (t0) REVERT: E 86 THR cc_start: 0.9389 (m) cc_final: 0.9171 (p) REVERT: E 135 LEU cc_start: 0.8914 (tp) cc_final: 0.8399 (mt) REVERT: E 155 LEU cc_start: 0.8445 (mm) cc_final: 0.7782 (pt) REVERT: E 174 LEU cc_start: 0.8670 (mm) cc_final: 0.8321 (mm) REVERT: E 184 MET cc_start: 0.8002 (mmm) cc_final: 0.7372 (mmm) REVERT: E 197 ARG cc_start: 0.8690 (ttt90) cc_final: 0.8478 (mtp180) REVERT: E 246 ASP cc_start: 0.8026 (t0) cc_final: 0.7475 (t0) REVERT: E 259 ILE cc_start: 0.9080 (mm) cc_final: 0.8801 (mm) REVERT: E 277 VAL cc_start: 0.9012 (m) cc_final: 0.8795 (t) REVERT: E 306 ARG cc_start: 0.8553 (mtp-110) cc_final: 0.7557 (mtt-85) REVERT: E 341 HIS cc_start: 0.8338 (m170) cc_final: 0.7975 (m-70) REVERT: E 355 ASN cc_start: 0.8912 (t0) cc_final: 0.8665 (t0) REVERT: E 383 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: E 390 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8915 (mtpp) REVERT: E 438 SER cc_start: 0.8863 (t) cc_final: 0.8285 (p) REVERT: E 452 LEU cc_start: 0.7776 (mt) cc_final: 0.7538 (mt) REVERT: F 63 GLU cc_start: 0.8837 (pt0) cc_final: 0.8345 (pp20) REVERT: F 74 LEU cc_start: 0.8489 (mm) cc_final: 0.8151 (mm) REVERT: F 85 GLU cc_start: 0.8682 (tt0) cc_final: 0.8307 (tm-30) REVERT: F 115 LEU cc_start: 0.9394 (mt) cc_final: 0.8948 (mt) REVERT: F 118 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8093 (tttp) REVERT: F 135 LEU cc_start: 0.8490 (mt) cc_final: 0.8279 (mt) REVERT: F 184 MET cc_start: 0.8828 (mmm) cc_final: 0.8482 (tpt) REVERT: F 225 ASN cc_start: 0.8601 (p0) cc_final: 0.8319 (m-40) REVERT: F 254 LYS cc_start: 0.8077 (tttt) cc_final: 0.7754 (tttt) REVERT: F 276 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8435 (p) REVERT: F 302 MET cc_start: 0.6838 (mmp) cc_final: 0.6150 (mmp) REVERT: F 308 MET cc_start: 0.8002 (mmt) cc_final: 0.7685 (mmp) REVERT: F 376 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6355 (mmt-90) REVERT: F 430 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8349 (mm-30) REVERT: G 18 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7223 (t0) REVERT: G 61 MET cc_start: 0.8195 (mtt) cc_final: 0.7948 (ttm) REVERT: G 86 THR cc_start: 0.9385 (m) cc_final: 0.9165 (p) REVERT: G 155 LEU cc_start: 0.8448 (mm) cc_final: 0.7784 (pt) REVERT: G 174 LEU cc_start: 0.8696 (mm) cc_final: 0.8361 (mm) REVERT: G 184 MET cc_start: 0.8005 (mmm) cc_final: 0.7365 (mmm) REVERT: G 246 ASP cc_start: 0.8068 (t0) cc_final: 0.7557 (t0) REVERT: G 277 VAL cc_start: 0.9001 (m) cc_final: 0.8785 (t) REVERT: G 306 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.7554 (mtt-85) REVERT: G 341 HIS cc_start: 0.8318 (m170) cc_final: 0.7940 (m-70) REVERT: G 376 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.6122 (mpt-90) REVERT: G 383 GLU cc_start: 0.8712 (pm20) cc_final: 0.8429 (mp0) REVERT: G 390 LYS cc_start: 0.9186 (mmtm) cc_final: 0.8899 (mtpp) REVERT: G 438 SER cc_start: 0.8879 (t) cc_final: 0.8318 (p) REVERT: G 452 LEU cc_start: 0.7755 (mt) cc_final: 0.7531 (mt) REVERT: H 6 ASP cc_start: 0.8284 (m-30) cc_final: 0.8049 (p0) REVERT: H 63 GLU cc_start: 0.8840 (pt0) cc_final: 0.8324 (pp20) REVERT: H 71 ILE cc_start: 0.8533 (mm) cc_final: 0.8328 (mt) REVERT: H 74 LEU cc_start: 0.8494 (mm) cc_final: 0.8158 (mm) REVERT: H 85 GLU cc_start: 0.8680 (tt0) cc_final: 0.8309 (tm-30) REVERT: H 115 LEU cc_start: 0.9390 (mt) cc_final: 0.9017 (mt) REVERT: H 118 LYS cc_start: 0.8572 (mmtt) cc_final: 0.8047 (tttp) REVERT: H 184 MET cc_start: 0.8891 (mmm) cc_final: 0.8545 (tpt) REVERT: H 233 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8244 (pp30) REVERT: H 276 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8424 (p) REVERT: H 302 MET cc_start: 0.6773 (mmp) cc_final: 0.5865 (mmp) REVERT: H 308 MET cc_start: 0.8025 (mmt) cc_final: 0.7677 (mmp) REVERT: H 357 MET cc_start: 0.8244 (tpp) cc_final: 0.7835 (tpp) REVERT: H 374 PHE cc_start: 0.7756 (m-80) cc_final: 0.7491 (m-80) REVERT: H 376 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6350 (mmt-90) REVERT: H 430 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8341 (mm-30) REVERT: H 458 LYS cc_start: 0.9056 (mtmm) cc_final: 0.8704 (mtmt) outliers start: 128 outliers final: 62 residues processed: 1053 average time/residue: 0.2042 time to fit residues: 328.2571 Evaluate side-chains 903 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 830 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 B residue 17 ASN Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 376 ARG 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 297 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 185 THR 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 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 383 GLU 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 210 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 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 198 THR Chi-restraints excluded: chain G residue 242 LEU 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 210 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: 6.9990 chunk 331 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 302 optimal weight: 0.7980 chunk 178 optimal weight: 0.4980 chunk 247 optimal weight: 8.9990 chunk 266 optimal weight: 0.7980 chunk 334 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 318 optimal weight: 3.9990 chunk 242 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 328 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.132280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.111733 restraints weight = 63749.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.116136 restraints weight = 38730.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.119383 restraints weight = 26047.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.121727 restraints weight = 18648.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.123409 restraints weight = 13988.922| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28096 Z= 0.131 Angle : 0.663 7.989 38312 Z= 0.334 Chirality : 0.047 0.275 4536 Planarity : 0.005 0.063 5000 Dihedral : 6.439 55.020 4448 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.20 % Allowed : 24.68 % Favored : 71.12 % 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: 0.51 (0.14), residues: 3704 helix: 0.66 (0.14), residues: 1424 sheet: 0.15 (0.21), residues: 600 loop : 0.31 (0.15), residues: 1680 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 0.025 0.002 PHE D 316 TRP 0.014 0.001 TRP G 334 HIS 0.006 0.001 HIS G 8 Details of bonding type rmsd covalent geometry : bond 0.00310 (28096) covalent geometry : angle 0.66281 (38312) hydrogen bonds : bond 0.03666 ( 1160) hydrogen bonds : angle 5.50326 ( 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 1068 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 950 time to evaluate : 0.748 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: A 52 ASN cc_start: 0.7427 (p0) cc_final: 0.6907 (p0) REVERT: A 53 MET cc_start: 0.7649 (mmt) cc_final: 0.7322 (mmt) REVERT: A 59 ARG cc_start: 0.8308 (ptm160) cc_final: 0.7980 (ptt-90) REVERT: A 77 ASP cc_start: 0.8233 (m-30) cc_final: 0.7944 (m-30) REVERT: A 99 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8289 (p) REVERT: A 107 ASP cc_start: 0.8451 (m-30) cc_final: 0.7956 (p0) REVERT: A 111 ASP cc_start: 0.8871 (t0) cc_final: 0.8629 (t0) REVERT: A 155 LEU cc_start: 0.9092 (mm) cc_final: 0.8583 (pp) REVERT: A 174 LEU cc_start: 0.8981 (mm) cc_final: 0.8654 (mm) REVERT: A 184 MET cc_start: 0.8509 (mmm) cc_final: 0.8140 (mmm) REVERT: A 197 ARG cc_start: 0.8955 (ttt90) cc_final: 0.8558 (mtp180) REVERT: A 225 ASN cc_start: 0.8540 (p0) cc_final: 0.8031 (m-40) REVERT: A 313 ARG cc_start: 0.7693 (ttt90) cc_final: 0.7353 (ttt90) REVERT: A 343 ARG cc_start: 0.8567 (ptm160) cc_final: 0.7492 (ttp-170) REVERT: A 387 MET cc_start: 0.8652 (pmm) cc_final: 0.8441 (pmm) REVERT: A 434 ASP cc_start: 0.8939 (m-30) cc_final: 0.8726 (m-30) REVERT: A 446 TYR cc_start: 0.8712 (m-80) cc_final: 0.7966 (m-80) REVERT: A 458 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9007 (mmtm) REVERT: B 18 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6164 (t70) REVERT: B 68 ARG cc_start: 0.8088 (mmp80) cc_final: 0.7524 (mmm160) REVERT: B 74 LEU cc_start: 0.8809 (mm) cc_final: 0.8591 (mm) REVERT: B 91 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8437 (mmmt) REVERT: B 117 HIS cc_start: 0.9138 (m-70) cc_final: 0.8851 (p90) REVERT: B 118 LYS cc_start: 0.8908 (tptt) cc_final: 0.8591 (tptt) REVERT: B 128 PHE cc_start: 0.9303 (t80) cc_final: 0.8991 (t80) REVERT: B 153 ILE cc_start: 0.9204 (tp) cc_final: 0.8909 (tp) REVERT: B 155 LEU cc_start: 0.8569 (mm) cc_final: 0.8299 (mm) REVERT: B 158 PHE cc_start: 0.8054 (p90) cc_final: 0.7737 (p90) REVERT: B 179 ILE cc_start: 0.7947 (mm) cc_final: 0.7485 (mm) REVERT: B 184 MET cc_start: 0.8613 (tpp) cc_final: 0.8385 (tpt) REVERT: B 197 ARG cc_start: 0.9036 (mtp180) cc_final: 0.8633 (ptp-110) REVERT: B 302 MET cc_start: 0.7116 (mmp) cc_final: 0.6079 (mmp) REVERT: B 306 ARG cc_start: 0.8437 (mtp-110) cc_final: 0.6433 (mtp-110) REVERT: B 332 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6527 (p-80) REVERT: B 357 MET cc_start: 0.8067 (mmm) cc_final: 0.7834 (mmm) REVERT: B 366 TYR cc_start: 0.8894 (m-80) cc_final: 0.8670 (m-80) REVERT: B 379 ARG cc_start: 0.8746 (mtm180) cc_final: 0.8504 (mtm180) REVERT: B 403 PHE cc_start: 0.9047 (t80) cc_final: 0.8451 (t80) REVERT: B 451 ASN cc_start: 0.8669 (p0) cc_final: 0.8281 (p0) REVERT: B 458 LYS cc_start: 0.8877 (mttt) cc_final: 0.8469 (ptpt) REVERT: B 473 HIS cc_start: 0.8866 (t70) cc_final: 0.8575 (t70) REVERT: C 52 ASN cc_start: 0.7411 (p0) cc_final: 0.6895 (p0) REVERT: C 53 MET cc_start: 0.7667 (mmt) cc_final: 0.7338 (mmt) REVERT: C 77 ASP cc_start: 0.8209 (m-30) cc_final: 0.7991 (m-30) REVERT: C 107 ASP cc_start: 0.8424 (m-30) cc_final: 0.7947 (p0) REVERT: C 111 ASP cc_start: 0.8850 (t0) cc_final: 0.8617 (t0) REVERT: C 116 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8895 (tp) REVERT: C 138 GLU cc_start: 0.8752 (mp0) cc_final: 0.8242 (tm-30) REVERT: C 155 LEU cc_start: 0.9100 (mm) cc_final: 0.8605 (pp) REVERT: C 174 LEU cc_start: 0.8984 (mm) cc_final: 0.8484 (mm) REVERT: C 184 MET cc_start: 0.8495 (mmm) cc_final: 0.8128 (mmm) REVERT: C 197 ARG cc_start: 0.8939 (ttt90) cc_final: 0.8511 (mtp180) REVERT: C 225 ASN cc_start: 0.8624 (p0) cc_final: 0.8026 (m-40) REVERT: C 313 ARG cc_start: 0.7724 (ttt90) cc_final: 0.7444 (ttt90) REVERT: C 343 ARG cc_start: 0.8577 (ptm160) cc_final: 0.7533 (ttp-170) REVERT: C 387 MET cc_start: 0.8674 (pmm) cc_final: 0.8442 (pmm) REVERT: C 434 ASP cc_start: 0.8936 (m-30) cc_final: 0.8702 (m-30) REVERT: C 446 TYR cc_start: 0.8702 (m-80) cc_final: 0.7965 (m-80) REVERT: C 458 LYS cc_start: 0.9396 (mmmt) cc_final: 0.9076 (mmtm) REVERT: D 18 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6247 (t70) REVERT: D 68 ARG cc_start: 0.8082 (mmp80) cc_final: 0.7530 (mmm160) REVERT: D 74 LEU cc_start: 0.8800 (mm) cc_final: 0.8584 (mm) REVERT: D 91 LYS cc_start: 0.8691 (mmmt) cc_final: 0.8443 (mmmt) REVERT: D 117 HIS cc_start: 0.9138 (m-70) cc_final: 0.8856 (p90) REVERT: D 118 LYS cc_start: 0.8911 (tptt) cc_final: 0.8590 (tptt) REVERT: D 128 PHE cc_start: 0.9299 (t80) cc_final: 0.8987 (t80) REVERT: D 153 ILE cc_start: 0.9189 (tp) cc_final: 0.8900 (tp) REVERT: D 155 LEU cc_start: 0.8575 (mm) cc_final: 0.8305 (mm) REVERT: D 158 PHE cc_start: 0.8051 (p90) cc_final: 0.7731 (p90) REVERT: D 179 ILE cc_start: 0.7962 (mm) cc_final: 0.7499 (mm) REVERT: D 184 MET cc_start: 0.8623 (tpp) cc_final: 0.8395 (tpt) REVERT: D 197 ARG cc_start: 0.9037 (mtp180) cc_final: 0.8572 (ptp-110) REVERT: D 225 ASN cc_start: 0.7456 (OUTLIER) cc_final: 0.7254 (m-40) REVERT: D 302 MET cc_start: 0.7140 (mmp) cc_final: 0.6102 (mmp) REVERT: D 303 CYS cc_start: 0.8134 (t) cc_final: 0.7933 (m) REVERT: D 306 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.6506 (mtp-110) REVERT: D 332 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6557 (p-80) REVERT: D 357 MET cc_start: 0.8062 (mmm) cc_final: 0.7834 (mmm) REVERT: D 366 TYR cc_start: 0.8889 (m-80) cc_final: 0.8668 (m-80) REVERT: D 379 ARG cc_start: 0.8763 (mtm180) cc_final: 0.8437 (mtm180) REVERT: D 411 PHE cc_start: 0.8668 (m-10) cc_final: 0.8229 (m-10) REVERT: D 451 ASN cc_start: 0.8667 (p0) cc_final: 0.8277 (p0) REVERT: D 458 LYS cc_start: 0.8880 (mttt) cc_final: 0.8471 (ptpt) REVERT: D 473 HIS cc_start: 0.8870 (t70) cc_final: 0.8576 (t70) REVERT: E 18 ASP cc_start: 0.7981 (m-30) cc_final: 0.7069 (t70) REVERT: E 59 ARG cc_start: 0.8043 (ptm160) cc_final: 0.7776 (ptt180) REVERT: E 86 THR cc_start: 0.9386 (m) cc_final: 0.9133 (p) REVERT: E 103 LEU cc_start: 0.9341 (mm) cc_final: 0.9103 (mm) REVERT: E 155 LEU cc_start: 0.8442 (mm) cc_final: 0.7786 (pt) REVERT: E 174 LEU cc_start: 0.8578 (mm) cc_final: 0.8225 (mm) REVERT: E 242 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.5821 (mm) REVERT: E 246 ASP cc_start: 0.7880 (t0) cc_final: 0.7531 (t0) REVERT: E 306 ARG cc_start: 0.8522 (mtp-110) cc_final: 0.7561 (mtt-85) REVERT: E 341 HIS cc_start: 0.8339 (m170) cc_final: 0.7963 (m-70) REVERT: E 355 ASN cc_start: 0.8575 (t0) cc_final: 0.8117 (t0) REVERT: E 368 SER cc_start: 0.8725 (t) cc_final: 0.8043 (p) REVERT: E 383 GLU cc_start: 0.8559 (pm20) cc_final: 0.8233 (mp0) REVERT: E 387 MET cc_start: 0.8516 (pmm) cc_final: 0.8311 (pmm) REVERT: E 390 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8663 (mtpp) REVERT: E 412 GLU cc_start: 0.8746 (tp30) cc_final: 0.8495 (tp30) REVERT: E 438 SER cc_start: 0.8861 (t) cc_final: 0.8449 (p) REVERT: E 452 LEU cc_start: 0.7774 (mt) cc_final: 0.7552 (mt) REVERT: E 464 GLN cc_start: 0.8424 (tp-100) cc_final: 0.8096 (tp-100) REVERT: F 17 ASN cc_start: 0.6538 (OUTLIER) cc_final: 0.6315 (m110) REVERT: F 63 GLU cc_start: 0.8710 (pt0) cc_final: 0.8235 (tp30) REVERT: F 68 ARG cc_start: 0.8550 (mmm160) cc_final: 0.7858 (mmm160) REVERT: F 74 LEU cc_start: 0.8478 (mm) cc_final: 0.8053 (mm) REVERT: F 85 GLU cc_start: 0.8729 (tt0) cc_final: 0.8261 (tm-30) REVERT: F 115 LEU cc_start: 0.9315 (mt) cc_final: 0.8872 (mt) REVERT: F 118 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8227 (mtpt) REVERT: F 233 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8199 (pp30) REVERT: F 302 MET cc_start: 0.6735 (mmp) cc_final: 0.5984 (mmp) REVERT: F 308 MET cc_start: 0.7969 (mmt) cc_final: 0.7760 (mmt) REVERT: F 328 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8144 (pp30) REVERT: F 387 MET cc_start: 0.7153 (pmm) cc_final: 0.6911 (pmm) REVERT: F 390 LYS cc_start: 0.9127 (mmtm) cc_final: 0.8674 (tttm) REVERT: F 430 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8426 (mm-30) REVERT: F 458 LYS cc_start: 0.9075 (ptpt) cc_final: 0.8790 (pttt) REVERT: G 18 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7075 (t70) REVERT: G 59 ARG cc_start: 0.8052 (ptm160) cc_final: 0.7782 (ptt180) REVERT: G 86 THR cc_start: 0.9376 (m) cc_final: 0.9120 (p) REVERT: G 103 LEU cc_start: 0.9343 (mm) cc_final: 0.9115 (mm) REVERT: G 155 LEU cc_start: 0.8433 (mm) cc_final: 0.7766 (pt) REVERT: G 175 GLU cc_start: 0.7405 (tp30) cc_final: 0.7126 (mm-30) REVERT: G 184 MET cc_start: 0.7750 (mmm) cc_final: 0.7377 (mmm) REVERT: G 306 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.6972 (mtm180) REVERT: G 316 PHE cc_start: 0.8600 (t80) cc_final: 0.8184 (t80) REVERT: G 336 ASP cc_start: 0.6956 (t70) cc_final: 0.6582 (t0) REVERT: G 341 HIS cc_start: 0.8357 (m170) cc_final: 0.7968 (m-70) REVERT: G 355 ASN cc_start: 0.8326 (t0) cc_final: 0.8038 (t0) REVERT: G 368 SER cc_start: 0.8742 (t) cc_final: 0.8126 (p) REVERT: G 383 GLU cc_start: 0.8587 (pm20) cc_final: 0.8272 (mp0) REVERT: G 387 MET cc_start: 0.8545 (pmm) cc_final: 0.7724 (pmm) REVERT: G 390 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8823 (ttpt) REVERT: G 412 GLU cc_start: 0.8752 (tp30) cc_final: 0.8508 (tp30) REVERT: G 438 SER cc_start: 0.8850 (t) cc_final: 0.8437 (p) REVERT: G 452 LEU cc_start: 0.7782 (mt) cc_final: 0.7552 (mt) REVERT: H 17 ASN cc_start: 0.6545 (OUTLIER) cc_final: 0.6334 (m110) REVERT: H 59 ARG cc_start: 0.7444 (ptt-90) cc_final: 0.7149 (ptt90) REVERT: H 68 ARG cc_start: 0.8516 (mmm160) cc_final: 0.7813 (mmm160) REVERT: H 74 LEU cc_start: 0.8435 (mm) cc_final: 0.8017 (mm) REVERT: H 85 GLU cc_start: 0.8710 (tt0) cc_final: 0.8243 (tm-30) REVERT: H 95 LEU cc_start: 0.8927 (mm) cc_final: 0.8668 (mm) REVERT: H 115 LEU cc_start: 0.9302 (mt) cc_final: 0.8860 (mt) REVERT: H 118 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8200 (mtpt) REVERT: H 233 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8258 (pp30) REVERT: H 260 LYS cc_start: 0.8542 (pttp) cc_final: 0.8026 (pttp) REVERT: H 267 LEU cc_start: 0.8670 (mt) cc_final: 0.8419 (mt) REVERT: H 302 MET cc_start: 0.6692 (mmp) cc_final: 0.5967 (mmp) REVERT: H 328 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8181 (pp30) REVERT: H 344 ASP cc_start: 0.8407 (m-30) cc_final: 0.7510 (m-30) REVERT: H 390 LYS cc_start: 0.9034 (mmtm) cc_final: 0.8586 (tttm) REVERT: H 430 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8395 (mm-30) REVERT: H 458 LYS cc_start: 0.9069 (mtmm) cc_final: 0.8705 (mtmt) REVERT: H 469 PHE cc_start: 0.5870 (m-10) cc_final: 0.5670 (m-10) outliers start: 118 outliers final: 58 residues processed: 1018 average time/residue: 0.1914 time to fit residues: 300.8220 Evaluate side-chains 913 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 842 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 421 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 127 VAL 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 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 378 ASP Chi-restraints excluded: chain C residue 421 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 225 ASN 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 417 THR Chi-restraints excluded: chain E residue 14 LEU 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 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 307 MET Chi-restraints excluded: chain G residue 309 THR 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 225 optimal weight: 0.0270 chunk 138 optimal weight: 8.9990 chunk 268 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 239 optimal weight: 0.0770 chunk 279 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 186 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 328 GLN C 456 HIS ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.133669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.112205 restraints weight = 64051.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.116628 restraints weight = 38761.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119973 restraints weight = 26165.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122443 restraints weight = 18833.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.124359 restraints weight = 14176.564| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4288 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= 0.127 Angle : 0.666 8.293 38312 Z= 0.334 Chirality : 0.047 0.258 4536 Planarity : 0.005 0.051 5000 Dihedral : 6.235 57.096 4448 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.70 % Allowed : 26.57 % Favored : 69.73 % 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: 0.42 (0.14), residues: 3704 helix: 0.50 (0.14), residues: 1424 sheet: 0.43 (0.22), residues: 520 loop : 0.21 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 391 TYR 0.021 0.002 TYR F 366 PHE 0.025 0.002 PHE D 403 TRP 0.016 0.002 TRP E 334 HIS 0.008 0.001 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00296 (28096) covalent geometry : angle 0.66641 (38312) hydrogen bonds : bond 0.03506 ( 1160) hydrogen bonds : angle 5.39507 ( 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 996 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 892 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7514 (p0) cc_final: 0.7115 (p0) REVERT: A 77 ASP cc_start: 0.8242 (m-30) cc_final: 0.8031 (m-30) REVERT: A 99 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.7967 (p) REVERT: A 107 ASP cc_start: 0.8442 (m-30) cc_final: 0.7915 (p0) REVERT: A 111 ASP cc_start: 0.8938 (t0) cc_final: 0.8672 (t0) REVERT: A 138 GLU cc_start: 0.8731 (mp0) cc_final: 0.8467 (mm-30) REVERT: A 155 LEU cc_start: 0.9127 (mm) cc_final: 0.8551 (pp) REVERT: A 174 LEU cc_start: 0.8963 (mm) cc_final: 0.8426 (mm) REVERT: A 184 MET cc_start: 0.8656 (mmm) cc_final: 0.8241 (mmm) REVERT: A 197 ARG cc_start: 0.9026 (ttt90) cc_final: 0.8489 (mmm160) REVERT: A 241 ASP cc_start: 0.7314 (t0) cc_final: 0.6816 (m-30) REVERT: A 243 LEU cc_start: 0.9175 (pp) cc_final: 0.8857 (mm) REVERT: A 283 ARG cc_start: 0.9141 (mtm110) cc_final: 0.8916 (mtp180) REVERT: A 343 ARG cc_start: 0.8534 (ptm160) cc_final: 0.7791 (ttp-170) REVERT: A 446 TYR cc_start: 0.8716 (m-80) cc_final: 0.7923 (m-80) REVERT: A 458 LYS cc_start: 0.9391 (mmmt) cc_final: 0.9004 (mmtm) REVERT: A 461 LEU cc_start: 0.8912 (mt) cc_final: 0.8702 (mt) REVERT: B 68 ARG cc_start: 0.8086 (mmp80) cc_final: 0.7592 (mmm160) REVERT: B 74 LEU cc_start: 0.8771 (mm) cc_final: 0.8449 (mm) REVERT: B 117 HIS cc_start: 0.9159 (m-70) cc_final: 0.8859 (p90) REVERT: B 118 LYS cc_start: 0.8911 (tptt) cc_final: 0.8587 (tptt) REVERT: B 128 PHE cc_start: 0.9271 (t80) cc_final: 0.8964 (t80) REVERT: B 135 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7176 (mm) REVERT: B 153 ILE cc_start: 0.9250 (tp) cc_final: 0.8935 (tp) REVERT: B 155 LEU cc_start: 0.8553 (mm) cc_final: 0.8294 (mm) REVERT: B 158 PHE cc_start: 0.8076 (p90) cc_final: 0.7809 (p90) REVERT: B 179 ILE cc_start: 0.7767 (mm) cc_final: 0.7060 (mm) REVERT: B 197 ARG cc_start: 0.9135 (mtp180) cc_final: 0.8651 (ptp-110) REVERT: B 213 LYS cc_start: 0.9212 (ttmm) cc_final: 0.8963 (ttpt) REVERT: B 231 LYS cc_start: 0.8717 (mttm) cc_final: 0.8383 (mtmm) REVERT: B 302 MET cc_start: 0.7142 (mmp) cc_final: 0.6074 (mmp) REVERT: B 303 CYS cc_start: 0.7290 (m) cc_final: 0.6764 (m) REVERT: B 332 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.6571 (p-80) REVERT: B 357 MET cc_start: 0.7816 (mmm) cc_final: 0.7581 (mmm) REVERT: B 379 ARG cc_start: 0.8791 (mtm180) cc_final: 0.8429 (mtm180) REVERT: B 451 ASN cc_start: 0.8698 (p0) cc_final: 0.8278 (p0) REVERT: B 458 LYS cc_start: 0.8847 (mttt) cc_final: 0.8428 (ptpt) REVERT: B 473 HIS cc_start: 0.8829 (t70) cc_final: 0.8574 (t70) REVERT: C 52 ASN cc_start: 0.7491 (p0) cc_final: 0.7095 (p0) REVERT: C 59 ARG cc_start: 0.8278 (ptm160) cc_final: 0.7920 (ptt180) REVERT: C 77 ASP cc_start: 0.8175 (m-30) cc_final: 0.7938 (m-30) REVERT: C 99 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8363 (p) REVERT: C 107 ASP cc_start: 0.8402 (m-30) cc_final: 0.7910 (p0) REVERT: C 111 ASP cc_start: 0.8898 (t0) cc_final: 0.8658 (t0) REVERT: C 116 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8684 (tp) REVERT: C 141 CYS cc_start: 0.8951 (p) cc_final: 0.8554 (p) REVERT: C 155 LEU cc_start: 0.9136 (mm) cc_final: 0.8596 (pp) REVERT: C 174 LEU cc_start: 0.8961 (mm) cc_final: 0.8433 (mm) REVERT: C 184 MET cc_start: 0.8633 (mmm) cc_final: 0.8219 (mmm) REVERT: C 197 ARG cc_start: 0.9019 (ttt90) cc_final: 0.8490 (mmm160) REVERT: C 217 ARG cc_start: 0.7097 (mtt-85) cc_final: 0.6622 (mmm-85) REVERT: C 243 LEU cc_start: 0.9167 (pp) cc_final: 0.8859 (mm) REVERT: C 313 ARG cc_start: 0.7784 (ttt90) cc_final: 0.7438 (ttt90) REVERT: C 328 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8443 (tm-30) REVERT: C 343 ARG cc_start: 0.8540 (ptm160) cc_final: 0.7758 (ttp-170) REVERT: C 446 TYR cc_start: 0.8715 (m-80) cc_final: 0.7929 (m-80) REVERT: C 458 LYS cc_start: 0.9384 (mmmt) cc_final: 0.8981 (mmtm) REVERT: D 68 ARG cc_start: 0.8080 (mmp80) cc_final: 0.7582 (mmm160) REVERT: D 74 LEU cc_start: 0.8769 (mm) cc_final: 0.8449 (mm) REVERT: D 117 HIS cc_start: 0.9151 (m-70) cc_final: 0.8861 (p90) REVERT: D 118 LYS cc_start: 0.8916 (tptt) cc_final: 0.8588 (tptt) REVERT: D 128 PHE cc_start: 0.9263 (t80) cc_final: 0.8958 (t80) REVERT: D 135 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7180 (mm) REVERT: D 153 ILE cc_start: 0.9219 (tp) cc_final: 0.8900 (tp) REVERT: D 155 LEU cc_start: 0.8553 (mm) cc_final: 0.8294 (mm) REVERT: D 158 PHE cc_start: 0.8083 (p90) cc_final: 0.7812 (p90) REVERT: D 179 ILE cc_start: 0.7786 (mm) cc_final: 0.7307 (mm) REVERT: D 197 ARG cc_start: 0.9057 (mtp180) cc_final: 0.8585 (ptp-110) REVERT: D 213 LYS cc_start: 0.9201 (ttmm) cc_final: 0.8986 (ttmt) REVERT: D 231 LYS cc_start: 0.8700 (mttm) cc_final: 0.8370 (mtmm) REVERT: D 302 MET cc_start: 0.7047 (mmp) cc_final: 0.6052 (mmp) REVERT: D 303 CYS cc_start: 0.8009 (t) cc_final: 0.7634 (m) REVERT: D 332 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.6552 (p-80) REVERT: D 357 MET cc_start: 0.7814 (mmm) cc_final: 0.7571 (mmm) REVERT: D 408 LYS cc_start: 0.8565 (pttt) cc_final: 0.8260 (pttm) REVERT: D 451 ASN cc_start: 0.8704 (p0) cc_final: 0.8276 (p0) REVERT: D 458 LYS cc_start: 0.8849 (mttt) cc_final: 0.8434 (ptpt) REVERT: D 473 HIS cc_start: 0.8860 (t70) cc_final: 0.8570 (t70) REVERT: E 6 ASP cc_start: 0.8955 (t0) cc_final: 0.8682 (t0) REVERT: E 18 ASP cc_start: 0.8020 (m-30) cc_final: 0.7012 (t70) REVERT: E 61 MET cc_start: 0.8240 (mtt) cc_final: 0.7706 (tpp) REVERT: E 86 THR cc_start: 0.9416 (m) cc_final: 0.9202 (p) REVERT: E 103 LEU cc_start: 0.9310 (mm) cc_final: 0.9051 (mm) REVERT: E 155 LEU cc_start: 0.8428 (mm) cc_final: 0.7914 (pp) REVERT: E 175 GLU cc_start: 0.7452 (tp30) cc_final: 0.7102 (mm-30) REVERT: E 195 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8457 (tt) REVERT: E 233 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7703 (tm-30) REVERT: E 242 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5777 (mm) REVERT: E 246 ASP cc_start: 0.8129 (t0) cc_final: 0.7547 (t0) REVERT: E 292 ILE cc_start: 0.8764 (mm) cc_final: 0.8448 (mm) REVERT: E 306 ARG cc_start: 0.8543 (mtp-110) cc_final: 0.7559 (mtt90) REVERT: E 341 HIS cc_start: 0.8371 (m170) cc_final: 0.8024 (m-70) REVERT: E 355 ASN cc_start: 0.8517 (t0) cc_final: 0.8010 (t0) REVERT: E 383 GLU cc_start: 0.8545 (pm20) cc_final: 0.8142 (mp0) REVERT: E 390 LYS cc_start: 0.9174 (mmtm) cc_final: 0.8771 (ttpt) REVERT: E 438 SER cc_start: 0.8819 (t) cc_final: 0.8361 (p) REVERT: E 452 LEU cc_start: 0.7705 (mt) cc_final: 0.7500 (mt) REVERT: E 464 GLN cc_start: 0.8415 (tp-100) cc_final: 0.8187 (tp-100) REVERT: E 471 GLU cc_start: 0.7887 (pt0) cc_final: 0.7608 (tt0) REVERT: F 74 LEU cc_start: 0.8429 (mm) cc_final: 0.8114 (mm) REVERT: F 85 GLU cc_start: 0.8801 (tt0) cc_final: 0.8283 (tm-30) REVERT: F 95 LEU cc_start: 0.8931 (mm) cc_final: 0.8680 (mm) REVERT: F 98 ASP cc_start: 0.8668 (m-30) cc_final: 0.8427 (t0) REVERT: F 115 LEU cc_start: 0.9322 (mt) cc_final: 0.8945 (mt) REVERT: F 118 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8255 (mmmt) REVERT: F 155 LEU cc_start: 0.8559 (mm) cc_final: 0.8118 (mm) REVERT: F 225 ASN cc_start: 0.8367 (p0) cc_final: 0.8121 (p0) REVERT: F 233 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8212 (pp30) REVERT: F 254 LYS cc_start: 0.8165 (tttt) cc_final: 0.7938 (ptmt) REVERT: F 260 LYS cc_start: 0.8531 (pttp) cc_final: 0.8009 (pttp) REVERT: F 302 MET cc_start: 0.6740 (mmp) cc_final: 0.5903 (mmp) REVERT: F 344 ASP cc_start: 0.8423 (m-30) cc_final: 0.7470 (m-30) REVERT: F 357 MET cc_start: 0.7787 (tpp) cc_final: 0.7586 (tpp) REVERT: F 383 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8026 (pm20) REVERT: F 455 LEU cc_start: 0.8525 (tt) cc_final: 0.8190 (tt) REVERT: G 6 ASP cc_start: 0.8942 (t0) cc_final: 0.8668 (t0) REVERT: G 18 ASP cc_start: 0.7920 (m-30) cc_final: 0.7028 (t0) REVERT: G 59 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7726 (ptt180) REVERT: G 68 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7471 (mmm160) REVERT: G 86 THR cc_start: 0.9411 (m) cc_final: 0.9155 (p) REVERT: G 135 LEU cc_start: 0.8854 (tp) cc_final: 0.8427 (mt) REVERT: G 155 LEU cc_start: 0.8429 (mm) cc_final: 0.7909 (pp) REVERT: G 195 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8446 (tt) REVERT: G 233 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7689 (tm-30) REVERT: G 246 ASP cc_start: 0.7917 (t0) cc_final: 0.7466 (t0) REVERT: G 341 HIS cc_start: 0.8401 (m170) cc_final: 0.8018 (m-70) REVERT: G 355 ASN cc_start: 0.8376 (t0) cc_final: 0.8006 (t0) REVERT: G 368 SER cc_start: 0.8725 (t) cc_final: 0.8006 (p) REVERT: G 383 GLU cc_start: 0.8567 (pm20) cc_final: 0.8165 (mp0) REVERT: G 390 LYS cc_start: 0.9119 (mmtm) cc_final: 0.8625 (mtpp) REVERT: G 438 SER cc_start: 0.8848 (t) cc_final: 0.8356 (p) REVERT: G 464 GLN cc_start: 0.8288 (tp-100) cc_final: 0.7731 (tp-100) REVERT: G 471 GLU cc_start: 0.7952 (pt0) cc_final: 0.7607 (tt0) REVERT: H 59 ARG cc_start: 0.7448 (ptt-90) cc_final: 0.6964 (ptt90) REVERT: H 74 LEU cc_start: 0.8405 (mm) cc_final: 0.8098 (mm) REVERT: H 85 GLU cc_start: 0.8801 (tt0) cc_final: 0.8272 (tm-30) REVERT: H 98 ASP cc_start: 0.8684 (m-30) cc_final: 0.8416 (t0) REVERT: H 115 LEU cc_start: 0.9318 (mt) cc_final: 0.8919 (mt) REVERT: H 118 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8256 (mmmt) REVERT: H 155 LEU cc_start: 0.8501 (mm) cc_final: 0.8061 (mm) REVERT: H 260 LYS cc_start: 0.8534 (pttp) cc_final: 0.8020 (pttp) REVERT: H 276 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8089 (p) REVERT: H 302 MET cc_start: 0.6623 (mmp) cc_final: 0.5820 (mmp) REVERT: H 308 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7610 (mmt) REVERT: H 344 ASP cc_start: 0.8469 (m-30) cc_final: 0.7572 (m-30) REVERT: H 458 LYS cc_start: 0.9116 (mtmm) cc_final: 0.8789 (ptpt) outliers start: 104 outliers final: 72 residues processed: 951 average time/residue: 0.1907 time to fit residues: 279.0564 Evaluate side-chains 893 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 807 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 252 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 422 LEU 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 135 LEU 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 349 LEU 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 242 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 378 ASP Chi-restraints excluded: chain C residue 422 LEU 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 135 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 349 LEU 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 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 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 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 224 ILE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 275 ASN Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 383 GLU Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 21 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 309 THR Chi-restraints excluded: chain G residue 376 ARG 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 125 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 224 ILE 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 308 MET Chi-restraints excluded: chain H residue 332 HIS 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: 3.9990 chunk 143 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 332 optimal weight: 8.9990 chunk 348 optimal weight: 20.0000 chunk 258 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN C 456 HIS ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 ASN ** E 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.124665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.103670 restraints weight = 67071.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.107734 restraints weight = 42127.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.110777 restraints weight = 29168.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.113028 restraints weight = 21459.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.114719 restraints weight = 16550.967| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28096 Z= 0.252 Angle : 0.715 8.695 38312 Z= 0.373 Chirality : 0.048 0.228 4536 Planarity : 0.005 0.051 5000 Dihedral : 6.318 56.053 4448 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.63 % Allowed : 26.99 % Favored : 67.38 % 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: -0.15 (0.14), residues: 3704 helix: 0.02 (0.13), residues: 1472 sheet: -0.36 (0.21), residues: 616 loop : 0.13 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 25 TYR 0.023 0.003 TYR C 366 PHE 0.027 0.002 PHE B 316 TRP 0.019 0.002 TRP E 334 HIS 0.011 0.001 HIS A 456 Details of bonding type rmsd covalent geometry : bond 0.00543 (28096) covalent geometry : angle 0.71523 (38312) hydrogen bonds : bond 0.03828 ( 1160) hydrogen bonds : angle 5.54322 ( 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 972 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 814 time to evaluate : 0.962 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: A 53 MET cc_start: 0.8213 (mmt) cc_final: 0.7373 (mmt) REVERT: A 76 GLN cc_start: 0.8373 (pm20) cc_final: 0.7892 (pm20) REVERT: A 99 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8339 (p) REVERT: A 107 ASP cc_start: 0.8548 (m-30) cc_final: 0.8102 (p0) REVERT: A 111 ASP cc_start: 0.8916 (t0) cc_final: 0.8692 (t0) REVERT: A 118 LYS cc_start: 0.7622 (mmtt) cc_final: 0.7236 (mmtp) REVERT: A 138 GLU cc_start: 0.8726 (mp0) cc_final: 0.8282 (tm-30) REVERT: A 155 LEU cc_start: 0.9137 (mm) cc_final: 0.8924 (mm) REVERT: A 184 MET cc_start: 0.8606 (mmm) cc_final: 0.8303 (mmm) REVERT: A 243 LEU cc_start: 0.9041 (pp) cc_final: 0.8655 (mm) REVERT: A 327 ARG cc_start: 0.9057 (mtp180) cc_final: 0.8770 (mtp180) REVERT: A 343 ARG cc_start: 0.8571 (ptm160) cc_final: 0.7892 (ttt180) REVERT: A 387 MET cc_start: 0.8520 (pmm) cc_final: 0.7944 (pmm) REVERT: A 421 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8719 (t) REVERT: A 446 TYR cc_start: 0.8833 (m-80) cc_final: 0.8197 (m-80) REVERT: A 458 LYS cc_start: 0.9432 (mmmt) cc_final: 0.9119 (mmtm) REVERT: B 4 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8627 (t80) REVERT: B 12 TYR cc_start: 0.4836 (p90) cc_final: 0.3609 (p90) REVERT: B 18 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6014 (t0) REVERT: B 68 ARG cc_start: 0.8076 (mmp80) cc_final: 0.7643 (mmm160) REVERT: B 117 HIS cc_start: 0.9081 (m-70) cc_final: 0.8749 (m-70) REVERT: B 118 LYS cc_start: 0.8996 (tptt) cc_final: 0.8600 (tptt) REVERT: B 119 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8042 (ttm-80) REVERT: B 153 ILE cc_start: 0.9306 (tp) cc_final: 0.9037 (tp) REVERT: B 158 PHE cc_start: 0.8212 (p90) cc_final: 0.7868 (p90) REVERT: B 159 VAL cc_start: 0.8099 (t) cc_final: 0.7826 (m) REVERT: B 184 MET cc_start: 0.8549 (tpp) cc_final: 0.8243 (tpt) REVERT: B 197 ARG cc_start: 0.8984 (mtp180) cc_final: 0.8544 (ptp-110) REVERT: B 231 LYS cc_start: 0.8854 (mttm) cc_final: 0.8469 (mtmm) REVERT: B 252 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8069 (tp40) REVERT: B 302 MET cc_start: 0.7538 (mmp) cc_final: 0.6538 (mmp) REVERT: B 357 MET cc_start: 0.8177 (mmm) cc_final: 0.7970 (mmm) REVERT: B 379 ARG cc_start: 0.8637 (mtm180) cc_final: 0.8259 (mtm110) REVERT: B 408 LYS cc_start: 0.8481 (pttt) cc_final: 0.8175 (pttm) REVERT: B 451 ASN cc_start: 0.8657 (p0) cc_final: 0.8374 (p0) REVERT: B 458 LYS cc_start: 0.8887 (mttt) cc_final: 0.8492 (ptpt) REVERT: B 473 HIS cc_start: 0.8983 (t70) cc_final: 0.8712 (t70) REVERT: C 52 ASN cc_start: 0.7666 (p0) cc_final: 0.7224 (p0) REVERT: C 76 GLN cc_start: 0.8337 (pm20) cc_final: 0.7962 (pm20) REVERT: C 99 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8406 (p) REVERT: C 107 ASP cc_start: 0.8492 (m-30) cc_final: 0.8088 (p0) REVERT: C 111 ASP cc_start: 0.8865 (t0) cc_final: 0.8654 (t0) REVERT: C 155 LEU cc_start: 0.9110 (mm) cc_final: 0.8623 (pp) REVERT: C 184 MET cc_start: 0.8615 (mmm) cc_final: 0.8287 (mmm) REVERT: C 197 ARG cc_start: 0.8973 (ttt90) cc_final: 0.8623 (mtp180) REVERT: C 241 ASP cc_start: 0.7500 (t0) cc_final: 0.6921 (m-30) REVERT: C 243 LEU cc_start: 0.8976 (pp) cc_final: 0.8591 (mm) REVERT: C 313 ARG cc_start: 0.7845 (ttt90) cc_final: 0.7478 (ttt90) REVERT: C 343 ARG cc_start: 0.8588 (ptm160) cc_final: 0.7880 (ttt180) REVERT: C 421 SER cc_start: 0.9004 (m) cc_final: 0.8699 (t) REVERT: C 446 TYR cc_start: 0.8841 (m-80) cc_final: 0.8200 (m-80) REVERT: C 458 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9118 (mmtm) REVERT: D 12 TYR cc_start: 0.4809 (p90) cc_final: 0.3603 (p90) REVERT: D 18 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6044 (t0) REVERT: D 68 ARG cc_start: 0.8068 (mmp80) cc_final: 0.7646 (mmm160) REVERT: D 117 HIS cc_start: 0.9063 (m-70) cc_final: 0.8736 (m-70) REVERT: D 118 LYS cc_start: 0.8986 (tptt) cc_final: 0.8593 (tptt) REVERT: D 119 ARG cc_start: 0.8759 (ttm110) cc_final: 0.8066 (ttm-80) REVERT: D 153 ILE cc_start: 0.9306 (tp) cc_final: 0.9033 (tp) REVERT: D 158 PHE cc_start: 0.8201 (p90) cc_final: 0.7864 (p90) REVERT: D 159 VAL cc_start: 0.8078 (t) cc_final: 0.7815 (m) REVERT: D 184 MET cc_start: 0.8566 (tpp) cc_final: 0.8269 (tpt) REVERT: D 197 ARG cc_start: 0.8986 (mtp180) cc_final: 0.8517 (ptp-110) REVERT: D 231 LYS cc_start: 0.8871 (mttm) cc_final: 0.8503 (mtmm) REVERT: D 302 MET cc_start: 0.7522 (mmp) cc_final: 0.6528 (mmp) REVERT: D 303 CYS cc_start: 0.8554 (t) cc_final: 0.8283 (m) REVERT: D 357 MET cc_start: 0.8168 (mmm) cc_final: 0.7946 (mmm) REVERT: D 379 ARG cc_start: 0.8690 (mtm180) cc_final: 0.8311 (mtm110) REVERT: D 415 ILE cc_start: 0.8374 (mm) cc_final: 0.8076 (mm) REVERT: D 451 ASN cc_start: 0.8649 (p0) cc_final: 0.8366 (p0) REVERT: D 458 LYS cc_start: 0.8901 (mttt) cc_final: 0.8502 (ptpt) REVERT: D 473 HIS cc_start: 0.9005 (t70) cc_final: 0.8710 (t70) REVERT: E 6 ASP cc_start: 0.8989 (t0) cc_final: 0.8742 (t0) REVERT: E 18 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7531 (t0) REVERT: E 61 MET cc_start: 0.8389 (mtt) cc_final: 0.7735 (tpp) REVERT: E 86 THR cc_start: 0.9428 (m) cc_final: 0.9204 (p) REVERT: E 118 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7987 (mmtt) REVERT: E 155 LEU cc_start: 0.8561 (mm) cc_final: 0.7910 (pt) REVERT: E 175 GLU cc_start: 0.7586 (tp30) cc_final: 0.7261 (mm-30) REVERT: E 184 MET cc_start: 0.8063 (mmm) cc_final: 0.7646 (mmm) REVERT: E 233 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7719 (tm-30) REVERT: E 242 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.5400 (tt) REVERT: E 246 ASP cc_start: 0.8680 (t0) cc_final: 0.8375 (t0) REVERT: E 292 ILE cc_start: 0.8973 (mm) cc_final: 0.8548 (mm) REVERT: E 306 ARG cc_start: 0.8521 (mtp-110) cc_final: 0.7725 (mtt90) REVERT: E 327 ARG cc_start: 0.8407 (ppt170) cc_final: 0.8195 (ppt170) REVERT: E 341 HIS cc_start: 0.8229 (m170) cc_final: 0.7875 (m-70) REVERT: E 355 ASN cc_start: 0.8797 (t0) cc_final: 0.8429 (t0) REVERT: E 383 GLU cc_start: 0.8513 (pm20) cc_final: 0.8161 (mp0) REVERT: E 390 LYS cc_start: 0.9203 (mmtm) cc_final: 0.8822 (mtpp) REVERT: E 438 SER cc_start: 0.8853 (t) cc_final: 0.8315 (p) REVERT: E 464 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8192 (tp-100) REVERT: F 63 GLU cc_start: 0.8761 (pt0) cc_final: 0.8545 (pp20) REVERT: F 85 GLU cc_start: 0.8816 (tt0) cc_final: 0.8337 (tm-30) REVERT: F 98 ASP cc_start: 0.8751 (m-30) cc_final: 0.8422 (t0) REVERT: F 118 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8157 (mmtp) REVERT: F 169 GLU cc_start: 0.9140 (mp0) cc_final: 0.8610 (mp0) REVERT: F 225 ASN cc_start: 0.8439 (p0) cc_final: 0.7958 (m-40) REVERT: F 302 MET cc_start: 0.7077 (mmp) cc_final: 0.6270 (mmt) REVERT: F 308 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7532 (mmp) REVERT: F 458 LYS cc_start: 0.9109 (pttt) cc_final: 0.8879 (pttm) REVERT: G 6 ASP cc_start: 0.9015 (t0) cc_final: 0.8773 (t0) REVERT: G 18 ASP cc_start: 0.8342 (m-30) cc_final: 0.7806 (t70) REVERT: G 59 ARG cc_start: 0.8318 (ptm160) cc_final: 0.7937 (ptt-90) REVERT: G 61 MET cc_start: 0.8421 (mtt) cc_final: 0.7737 (tpp) REVERT: G 86 THR cc_start: 0.9425 (m) cc_final: 0.9165 (p) REVERT: G 155 LEU cc_start: 0.8514 (mm) cc_final: 0.8019 (pp) REVERT: G 233 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7711 (tm-30) REVERT: G 242 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.5371 (tt) REVERT: G 246 ASP cc_start: 0.8456 (t0) cc_final: 0.7870 (t0) REVERT: G 306 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.7690 (mtm180) REVERT: G 316 PHE cc_start: 0.8574 (t80) cc_final: 0.7813 (t80) REVERT: G 341 HIS cc_start: 0.8212 (m170) cc_final: 0.7850 (m-70) REVERT: G 383 GLU cc_start: 0.8514 (pm20) cc_final: 0.8165 (mp0) REVERT: G 390 LYS cc_start: 0.9204 (mmtm) cc_final: 0.8846 (mtpp) REVERT: G 438 SER cc_start: 0.8866 (t) cc_final: 0.8317 (p) REVERT: G 464 GLN cc_start: 0.8658 (tp-100) cc_final: 0.7978 (tp-100) REVERT: H 63 GLU cc_start: 0.8708 (pt0) cc_final: 0.8482 (pp20) REVERT: H 85 GLU cc_start: 0.8828 (tt0) cc_final: 0.8341 (tm-30) REVERT: H 98 ASP cc_start: 0.8749 (m-30) cc_final: 0.8398 (t0) REVERT: H 118 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8158 (mmtp) REVERT: H 135 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8103 (mm) REVERT: H 169 GLU cc_start: 0.9156 (mp0) cc_final: 0.8618 (mp0) REVERT: H 233 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8396 (pp30) REVERT: H 260 LYS cc_start: 0.8750 (pttp) cc_final: 0.8274 (pttp) REVERT: H 276 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8380 (p) REVERT: H 302 MET cc_start: 0.7123 (mmp) cc_final: 0.6206 (mmt) REVERT: H 308 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7678 (mmt) REVERT: H 355 ASN cc_start: 0.9065 (t0) cc_final: 0.8681 (m-40) REVERT: H 458 LYS cc_start: 0.9122 (mtmm) cc_final: 0.8789 (mtmt) outliers start: 158 outliers final: 105 residues processed: 897 average time/residue: 0.1916 time to fit residues: 267.0664 Evaluate side-chains 862 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 743 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 99 THR Chi-restraints excluded: chain A residue 104 SER 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 A residue 422 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain B residue 4 PHE 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 125 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 332 HIS Chi-restraints excluded: chain B residue 372 LEU 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 18 ASP 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 252 GLN Chi-restraints excluded: chain C residue 328 GLN Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 56 VAL 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 135 LEU Chi-restraints excluded: chain D residue 196 THR 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 372 LEU 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 56 VAL Chi-restraints excluded: chain E residue 96 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 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 445 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 78 LEU 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 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 308 MET Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 456 HIS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 265 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 376 ARG 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 19 VAL Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 78 LEU 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 242 LEU Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 276 VAL Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 372 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 251 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 321 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 HIS ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3865 r_free = 0.3865 target = 0.126224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105151 restraints weight = 65787.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.109302 restraints weight = 41290.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.112371 restraints weight = 28557.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.114717 restraints weight = 20977.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.116520 restraints weight = 16065.412| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28096 Z= 0.182 Angle : 0.685 11.636 38312 Z= 0.351 Chirality : 0.047 0.228 4536 Planarity : 0.005 0.084 5000 Dihedral : 6.206 57.461 4448 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.77 % Allowed : 29.34 % Favored : 65.88 % 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: -0.25 (0.13), residues: 3704 helix: 0.08 (0.13), residues: 1464 sheet: -0.49 (0.20), residues: 616 loop : -0.05 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 306 TYR 0.030 0.002 TYR H 366 PHE 0.022 0.002 PHE B 403 TRP 0.016 0.001 TRP E 334 HIS 0.009 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00415 (28096) covalent geometry : angle 0.68510 (38312) hydrogen bonds : bond 0.03544 ( 1160) hydrogen bonds : angle 5.46456 ( 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 934 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 800 time to evaluate : 0.882 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: A 53 MET cc_start: 0.8122 (mmt) cc_final: 0.7655 (mmt) REVERT: A 59 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7692 (mtt180) REVERT: A 76 GLN cc_start: 0.8222 (pm20) cc_final: 0.7877 (pm20) REVERT: A 107 ASP cc_start: 0.8570 (m-30) cc_final: 0.8141 (p0) REVERT: A 111 ASP cc_start: 0.8917 (t0) cc_final: 0.8677 (t0) REVERT: A 118 LYS cc_start: 0.7481 (mmtt) cc_final: 0.7176 (mmtp) REVERT: A 138 GLU cc_start: 0.8712 (mp0) cc_final: 0.8418 (tm-30) REVERT: A 141 CYS cc_start: 0.8882 (p) cc_final: 0.8306 (p) REVERT: A 155 LEU cc_start: 0.9144 (mm) cc_final: 0.8702 (mt) REVERT: A 184 MET cc_start: 0.8711 (mmm) cc_final: 0.8427 (mmm) REVERT: A 243 LEU cc_start: 0.9030 (pp) cc_final: 0.8660 (mm) REVERT: A 254 LYS cc_start: 0.8578 (tttp) cc_final: 0.8262 (tttt) REVERT: A 343 ARG cc_start: 0.8346 (ptm160) cc_final: 0.7714 (ttm170) REVERT: A 421 SER cc_start: 0.8949 (m) cc_final: 0.8636 (t) REVERT: A 446 TYR cc_start: 0.8765 (m-80) cc_final: 0.8113 (m-80) REVERT: A 458 LYS cc_start: 0.9434 (mmmt) cc_final: 0.9126 (mmtm) REVERT: B 4 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8554 (t80) REVERT: B 31 ARG cc_start: 0.7031 (mtm180) cc_final: 0.6731 (mtm180) REVERT: B 37 SER cc_start: 0.8722 (m) cc_final: 0.8429 (p) REVERT: B 52 ASN cc_start: 0.7956 (p0) cc_final: 0.7725 (p0) REVERT: B 68 ARG cc_start: 0.8399 (mmp80) cc_final: 0.7611 (mmm160) REVERT: B 117 HIS cc_start: 0.9059 (m-70) cc_final: 0.8784 (m-70) REVERT: B 118 LYS cc_start: 0.8976 (tptt) cc_final: 0.8574 (tptt) REVERT: B 119 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8548 (ttm110) REVERT: B 153 ILE cc_start: 0.9282 (tp) cc_final: 0.8998 (tp) REVERT: B 159 VAL cc_start: 0.8101 (t) cc_final: 0.7898 (m) REVERT: B 184 MET cc_start: 0.8639 (tpp) cc_final: 0.8375 (tpt) REVERT: B 197 ARG cc_start: 0.8971 (mtp180) cc_final: 0.8480 (ptp-110) REVERT: B 231 LYS cc_start: 0.8876 (mttm) cc_final: 0.8482 (mtmm) REVERT: B 302 MET cc_start: 0.7558 (mmp) cc_final: 0.6539 (mmp) REVERT: B 379 ARG cc_start: 0.8652 (mtm180) cc_final: 0.8341 (mtm180) REVERT: B 408 LYS cc_start: 0.8519 (pttt) cc_final: 0.8214 (pttm) REVERT: B 451 ASN cc_start: 0.8600 (p0) cc_final: 0.8288 (p0) REVERT: B 458 LYS cc_start: 0.8914 (mttt) cc_final: 0.8519 (ptpt) REVERT: B 473 HIS cc_start: 0.8985 (t70) cc_final: 0.8705 (t70) REVERT: C 52 ASN cc_start: 0.7550 (p0) cc_final: 0.7129 (p0) REVERT: C 53 MET cc_start: 0.8171 (mmt) cc_final: 0.7687 (mmt) REVERT: C 76 GLN cc_start: 0.8055 (pm20) cc_final: 0.7705 (pm20) REVERT: C 107 ASP cc_start: 0.8492 (m-30) cc_final: 0.8118 (p0) REVERT: C 111 ASP cc_start: 0.8848 (t0) cc_final: 0.8628 (t0) REVERT: C 116 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8941 (tp) REVERT: C 141 CYS cc_start: 0.8830 (p) cc_final: 0.8321 (p) REVERT: C 153 ILE cc_start: 0.9333 (tp) cc_final: 0.9081 (mm) REVERT: C 155 LEU cc_start: 0.9129 (mm) cc_final: 0.8509 (pp) REVERT: C 184 MET cc_start: 0.8688 (mmm) cc_final: 0.8404 (mmm) REVERT: C 243 LEU cc_start: 0.9022 (pp) cc_final: 0.8651 (mm) REVERT: C 254 LYS cc_start: 0.8601 (tttp) cc_final: 0.8280 (tttt) REVERT: C 343 ARG cc_start: 0.8406 (ptm160) cc_final: 0.7739 (ttm170) REVERT: C 374 PHE cc_start: 0.8278 (m-10) cc_final: 0.7969 (m-10) REVERT: C 421 SER cc_start: 0.8925 (m) cc_final: 0.8610 (t) REVERT: C 446 TYR cc_start: 0.8793 (m-80) cc_final: 0.8187 (m-80) REVERT: C 458 LYS cc_start: 0.9435 (mmmt) cc_final: 0.9116 (mmtm) REVERT: D 31 ARG cc_start: 0.7201 (mtm180) cc_final: 0.6881 (mtm180) REVERT: D 37 SER cc_start: 0.8675 (m) cc_final: 0.8382 (p) REVERT: D 68 ARG cc_start: 0.8386 (mmp80) cc_final: 0.7639 (mmm160) REVERT: D 117 HIS cc_start: 0.9061 (m-70) cc_final: 0.8797 (m-70) REVERT: D 118 LYS cc_start: 0.8972 (tptt) cc_final: 0.8566 (tptt) REVERT: D 119 ARG cc_start: 0.8717 (ttm110) cc_final: 0.8515 (ttm110) REVERT: D 153 ILE cc_start: 0.9294 (tp) cc_final: 0.9004 (tp) REVERT: D 184 MET cc_start: 0.8655 (tpp) cc_final: 0.8422 (tpt) REVERT: D 197 ARG cc_start: 0.8958 (mtp180) cc_final: 0.8524 (ptp-110) REVERT: D 231 LYS cc_start: 0.8881 (mttm) cc_final: 0.8485 (mtmm) REVERT: D 302 MET cc_start: 0.7501 (mmp) cc_final: 0.6566 (mmt) REVERT: D 303 CYS cc_start: 0.8600 (t) cc_final: 0.8379 (m) REVERT: D 379 ARG cc_start: 0.8721 (mtm180) cc_final: 0.8362 (mtm180) REVERT: D 408 LYS cc_start: 0.8533 (pttt) cc_final: 0.8248 (pttm) REVERT: D 415 ILE cc_start: 0.8403 (mm) cc_final: 0.8121 (mm) REVERT: D 451 ASN cc_start: 0.8606 (p0) cc_final: 0.8293 (p0) REVERT: D 458 LYS cc_start: 0.8909 (mttt) cc_final: 0.8514 (ptpt) REVERT: D 473 HIS cc_start: 0.8979 (t70) cc_final: 0.8705 (t70) REVERT: E 6 ASP cc_start: 0.8949 (t0) cc_final: 0.8692 (t0) REVERT: E 14 LEU cc_start: 0.8366 (mm) cc_final: 0.7760 (mm) REVERT: E 18 ASP cc_start: 0.8258 (m-30) cc_final: 0.6916 (t0) REVERT: E 61 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7735 (tpp) REVERT: E 86 THR cc_start: 0.9426 (m) cc_final: 0.9189 (p) REVERT: E 135 LEU cc_start: 0.8862 (tp) cc_final: 0.8238 (mt) REVERT: E 155 LEU cc_start: 0.8541 (mm) cc_final: 0.8026 (pp) REVERT: E 175 GLU cc_start: 0.7465 (tp30) cc_final: 0.7084 (mm-30) REVERT: E 184 MET cc_start: 0.8139 (mmm) cc_final: 0.7662 (mmm) REVERT: E 195 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8800 (tt) REVERT: E 246 ASP cc_start: 0.8703 (t0) cc_final: 0.8311 (t0) REVERT: E 292 ILE cc_start: 0.8975 (mm) cc_final: 0.8588 (mm) REVERT: E 306 ARG cc_start: 0.8515 (mtp-110) cc_final: 0.7696 (mtt90) REVERT: E 341 HIS cc_start: 0.8236 (m170) cc_final: 0.7902 (m-70) REVERT: E 355 ASN cc_start: 0.8836 (t0) cc_final: 0.8508 (t0) REVERT: E 357 MET cc_start: 0.7653 (mmm) cc_final: 0.7422 (tpp) REVERT: E 383 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: E 390 LYS cc_start: 0.9187 (mmtm) cc_final: 0.8799 (mtpp) REVERT: E 422 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8095 (mt) REVERT: E 438 SER cc_start: 0.8842 (t) cc_final: 0.8321 (p) REVERT: E 464 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8015 (tp-100) REVERT: F 76 GLN cc_start: 0.6562 (OUTLIER) cc_final: 0.6343 (tp40) REVERT: F 85 GLU cc_start: 0.8822 (tt0) cc_final: 0.8326 (tm-30) REVERT: F 118 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8172 (mmtp) REVERT: F 169 GLU cc_start: 0.9115 (mp0) cc_final: 0.8598 (mp0) REVERT: F 225 ASN cc_start: 0.8332 (p0) cc_final: 0.8076 (p0) REVERT: F 233 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8354 (pp30) REVERT: F 260 LYS cc_start: 0.8773 (pttp) cc_final: 0.8280 (pttp) REVERT: F 276 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8055 (p) REVERT: F 302 MET cc_start: 0.6999 (mmp) cc_final: 0.6209 (mmt) REVERT: F 304 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8335 (m) REVERT: F 308 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7622 (mmt) REVERT: F 328 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7929 (pp30) REVERT: F 458 LYS cc_start: 0.9129 (pttt) cc_final: 0.8888 (pttm) REVERT: G 6 ASP cc_start: 0.8944 (t0) cc_final: 0.8686 (t0) REVERT: G 14 LEU cc_start: 0.8398 (mm) cc_final: 0.7790 (mm) REVERT: G 18 ASP cc_start: 0.8259 (m-30) cc_final: 0.6969 (t0) REVERT: G 61 MET cc_start: 0.8359 (mtt) cc_final: 0.7719 (tpp) REVERT: G 86 THR cc_start: 0.9431 (m) cc_final: 0.9196 (p) REVERT: G 135 LEU cc_start: 0.8837 (tp) cc_final: 0.8208 (mt) REVERT: G 155 LEU cc_start: 0.8510 (mm) cc_final: 0.8006 (pp) REVERT: G 195 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8586 (tt) REVERT: G 246 ASP cc_start: 0.8459 (t0) cc_final: 0.8247 (t0) REVERT: G 306 ARG cc_start: 0.8396 (mtp-110) cc_final: 0.8079 (mmm160) REVERT: G 316 PHE cc_start: 0.8557 (t80) cc_final: 0.7853 (t80) REVERT: G 327 ARG cc_start: 0.8374 (ppt170) cc_final: 0.8164 (ppt170) REVERT: G 341 HIS cc_start: 0.8299 (m170) cc_final: 0.7952 (m-70) REVERT: G 357 MET cc_start: 0.7708 (mmm) cc_final: 0.7477 (tpp) REVERT: G 383 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: G 390 LYS cc_start: 0.9196 (mmtm) cc_final: 0.8846 (mtpp) REVERT: G 438 SER cc_start: 0.8837 (t) cc_final: 0.8300 (p) REVERT: G 471 GLU cc_start: 0.7922 (pt0) cc_final: 0.7650 (tt0) REVERT: H 61 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8292 (ttm) REVERT: H 76 GLN cc_start: 0.6667 (OUTLIER) cc_final: 0.6337 (tp40) REVERT: H 85 GLU cc_start: 0.8824 (tt0) cc_final: 0.8331 (tm-30) REVERT: H 98 ASP cc_start: 0.8720 (m-30) cc_final: 0.8516 (t0) REVERT: H 118 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8233 (mmmt) REVERT: H 169 GLU cc_start: 0.9120 (mp0) cc_final: 0.8602 (mp0) REVERT: H 233 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8354 (pp30) REVERT: H 260 LYS cc_start: 0.8724 (pttp) cc_final: 0.8277 (pttp) REVERT: H 276 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8391 (p) REVERT: H 302 MET cc_start: 0.7016 (mmp) cc_final: 0.6136 (mmt) REVERT: H 304 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8201 (m) REVERT: H 308 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7531 (mmp) REVERT: H 458 LYS cc_start: 0.9124 (mtmm) cc_final: 0.8788 (mtmt) outliers start: 134 outliers final: 92 residues processed: 873 average time/residue: 0.1847 time to fit residues: 249.5111 Evaluate side-chains 870 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 761 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 422 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 SER 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 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 393 VAL Chi-restraints excluded: chain B residue 417 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 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 422 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 170 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 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 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 307 MET Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 383 GLU 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 19 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 76 GLN 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 275 ASN Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 308 MET 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 46 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 196 THR 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 383 GLU 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 19 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 76 GLN 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 276 VAL 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 Chi-restraints excluded: chain H residue 456 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 175 optimal weight: 0.9980 chunk 312 optimal weight: 2.9990 chunk 358 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 chunk 350 optimal weight: 6.9990 chunk 335 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** C 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 17 ASN ** 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** ** H 355 ASN ** 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 = 0.3875 r_free = 0.3875 target = 0.126965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105733 restraints weight = 65925.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.109849 restraints weight = 41711.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.112873 restraints weight = 29016.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.115204 restraints weight = 21508.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.116955 restraints weight = 16570.445| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28096 Z= 0.171 Angle : 0.699 11.029 38312 Z= 0.356 Chirality : 0.047 0.264 4536 Planarity : 0.005 0.080 5000 Dihedral : 6.234 57.751 4448 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.91 % Allowed : 30.31 % Favored : 64.78 % 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: -0.37 (0.13), residues: 3704 helix: -0.02 (0.13), residues: 1472 sheet: -0.62 (0.20), residues: 616 loop : -0.09 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 327 TYR 0.031 0.002 TYR H 366 PHE 0.023 0.002 PHE B 403 TRP 0.018 0.001 TRP E 334 HIS 0.016 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00397 (28096) covalent geometry : angle 0.69851 (38312) hydrogen bonds : bond 0.03578 ( 1160) hydrogen bonds : angle 5.53304 ( 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 930 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 792 time to evaluate : 0.838 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: 0.7224 (p0) cc_final: 0.6864 (p0) REVERT: A 59 ARG cc_start: 0.8079 (mtt-85) cc_final: 0.7789 (mtt-85) REVERT: A 76 GLN cc_start: 0.8133 (pm20) cc_final: 0.7780 (pm20) REVERT: A 107 ASP cc_start: 0.8604 (m-30) cc_final: 0.8189 (p0) REVERT: A 111 ASP cc_start: 0.8926 (t0) cc_final: 0.8682 (t0) REVERT: A 138 GLU cc_start: 0.8714 (mp0) cc_final: 0.8433 (tm-30) REVERT: A 141 CYS cc_start: 0.8802 (p) cc_final: 0.8274 (p) REVERT: A 155 LEU cc_start: 0.9150 (mm) cc_final: 0.8853 (mm) REVERT: A 184 MET cc_start: 0.8738 (mmm) cc_final: 0.8448 (mmm) REVERT: A 217 ARG cc_start: 0.7707 (mmm-85) cc_final: 0.7231 (mmm-85) REVERT: A 243 LEU cc_start: 0.9028 (pp) cc_final: 0.8686 (mm) REVERT: A 254 LYS cc_start: 0.8584 (tttp) cc_final: 0.8250 (tttt) REVERT: A 313 ARG cc_start: 0.7785 (tpt-90) cc_final: 0.7499 (tpt-90) REVERT: A 343 ARG cc_start: 0.8346 (ptm160) cc_final: 0.7786 (ttt180) REVERT: A 357 MET cc_start: 0.6263 (tpp) cc_final: 0.5615 (tpp) REVERT: A 374 PHE cc_start: 0.8286 (m-10) cc_final: 0.8017 (m-10) REVERT: A 421 SER cc_start: 0.8903 (m) cc_final: 0.8637 (t) REVERT: A 446 TYR cc_start: 0.8783 (m-80) cc_final: 0.8144 (m-80) REVERT: A 458 LYS cc_start: 0.9436 (mmmt) cc_final: 0.9127 (mmtm) REVERT: B 4 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8525 (t80) REVERT: B 37 SER cc_start: 0.8722 (m) cc_final: 0.8422 (p) REVERT: B 52 ASN cc_start: 0.8033 (p0) cc_final: 0.7800 (p0) REVERT: B 68 ARG cc_start: 0.8402 (mmp80) cc_final: 0.7608 (mmm160) REVERT: B 117 HIS cc_start: 0.9056 (m-70) cc_final: 0.8791 (m-70) REVERT: B 118 LYS cc_start: 0.8998 (tptt) cc_final: 0.8588 (tptt) REVERT: B 119 ARG cc_start: 0.8773 (ttm110) cc_final: 0.8565 (ttm110) REVERT: B 153 ILE cc_start: 0.9291 (tp) cc_final: 0.8993 (tp) REVERT: B 158 PHE cc_start: 0.8109 (p90) cc_final: 0.7738 (p90) REVERT: B 159 VAL cc_start: 0.8186 (t) cc_final: 0.7647 (m) REVERT: B 197 ARG cc_start: 0.8956 (mtp180) cc_final: 0.8471 (ptp-110) REVERT: B 231 LYS cc_start: 0.8905 (mttm) cc_final: 0.8498 (mtmm) REVERT: B 302 MET cc_start: 0.7528 (mmp) cc_final: 0.6564 (mmp) REVERT: B 379 ARG cc_start: 0.8680 (mtm180) cc_final: 0.8291 (mtm180) REVERT: B 408 LYS cc_start: 0.8554 (pttt) cc_final: 0.8247 (pttm) REVERT: B 451 ASN cc_start: 0.8622 (p0) cc_final: 0.8325 (p0) REVERT: B 458 LYS cc_start: 0.8913 (mttt) cc_final: 0.8528 (ptpt) REVERT: B 473 HIS cc_start: 0.8969 (t70) cc_final: 0.8745 (t70) REVERT: C 52 ASN cc_start: 0.7484 (p0) cc_final: 0.6911 (p0) REVERT: C 76 GLN cc_start: 0.8043 (pm20) cc_final: 0.7581 (pm20) REVERT: C 107 ASP cc_start: 0.8540 (m-30) cc_final: 0.8182 (p0) REVERT: C 111 ASP cc_start: 0.8857 (t0) cc_final: 0.8634 (t0) REVERT: C 116 LEU cc_start: 0.9333 (pp) cc_final: 0.9000 (tp) REVERT: C 141 CYS cc_start: 0.8856 (p) cc_final: 0.8381 (p) REVERT: C 155 LEU cc_start: 0.9164 (mm) cc_final: 0.8626 (pp) REVERT: C 184 MET cc_start: 0.8693 (mmm) cc_final: 0.8438 (mmm) REVERT: C 197 ARG cc_start: 0.8986 (mtp180) cc_final: 0.8551 (mtp180) REVERT: C 217 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.7081 (mmm-85) REVERT: C 241 ASP cc_start: 0.7878 (t0) cc_final: 0.7294 (t0) REVERT: C 243 LEU cc_start: 0.9019 (pp) cc_final: 0.8680 (mm) REVERT: C 254 LYS cc_start: 0.8594 (tttp) cc_final: 0.8263 (tttt) REVERT: C 313 ARG cc_start: 0.7686 (tpt-90) cc_final: 0.7227 (tpt-90) REVERT: C 328 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8584 (tm-30) REVERT: C 343 ARG cc_start: 0.8360 (ptm160) cc_final: 0.7816 (ttt180) REVERT: C 357 MET cc_start: 0.6277 (tpp) cc_final: 0.5786 (tpp) REVERT: C 374 PHE cc_start: 0.8313 (m-10) cc_final: 0.8030 (m-10) REVERT: C 421 SER cc_start: 0.8897 (m) cc_final: 0.8624 (t) REVERT: C 446 TYR cc_start: 0.8821 (m-80) cc_final: 0.8227 (m-80) REVERT: C 458 LYS cc_start: 0.9436 (mmmt) cc_final: 0.9102 (mmtm) REVERT: D 37 SER cc_start: 0.8725 (m) cc_final: 0.8423 (p) REVERT: D 52 ASN cc_start: 0.7744 (p0) cc_final: 0.7517 (p0) REVERT: D 68 ARG cc_start: 0.8383 (mmp80) cc_final: 0.7625 (mmm160) REVERT: D 117 HIS cc_start: 0.9038 (m-70) cc_final: 0.8792 (m-70) REVERT: D 118 LYS cc_start: 0.9000 (tptt) cc_final: 0.8587 (tptt) REVERT: D 153 ILE cc_start: 0.9254 (tp) cc_final: 0.8960 (tp) REVERT: D 158 PHE cc_start: 0.8035 (p90) cc_final: 0.7725 (p90) REVERT: D 197 ARG cc_start: 0.8929 (mtp180) cc_final: 0.8534 (ptp-110) REVERT: D 231 LYS cc_start: 0.8901 (mttm) cc_final: 0.8492 (mtmm) REVERT: D 302 MET cc_start: 0.7477 (mmp) cc_final: 0.6500 (mmp) REVERT: D 329 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6109 (pp) REVERT: D 379 ARG cc_start: 0.8733 (mtm180) cc_final: 0.8334 (mtm180) REVERT: D 387 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8609 (mmp) REVERT: D 408 LYS cc_start: 0.8507 (pttt) cc_final: 0.8228 (pttm) REVERT: D 415 ILE cc_start: 0.8413 (mm) cc_final: 0.8176 (mm) REVERT: D 451 ASN cc_start: 0.8615 (p0) cc_final: 0.8312 (p0) REVERT: D 458 LYS cc_start: 0.8922 (mttt) cc_final: 0.8531 (ptpt) REVERT: D 473 HIS cc_start: 0.8959 (t70) cc_final: 0.8729 (t70) REVERT: E 6 ASP cc_start: 0.8924 (t0) cc_final: 0.8658 (t0) REVERT: E 61 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7738 (tpp) REVERT: E 86 THR cc_start: 0.9420 (m) cc_final: 0.9187 (p) REVERT: E 135 LEU cc_start: 0.8856 (tp) cc_final: 0.8228 (mt) REVERT: E 155 LEU cc_start: 0.8527 (mm) cc_final: 0.8022 (pp) REVERT: E 175 GLU cc_start: 0.7465 (tp30) cc_final: 0.7080 (mm-30) REVERT: E 184 MET cc_start: 0.7952 (mmm) cc_final: 0.7583 (mmm) REVERT: E 195 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8824 (tt) REVERT: E 246 ASP cc_start: 0.8740 (t0) cc_final: 0.8339 (t0) REVERT: E 292 ILE cc_start: 0.8986 (mm) cc_final: 0.8601 (mm) REVERT: E 306 ARG cc_start: 0.8499 (mtp-110) cc_final: 0.7714 (mtt90) REVERT: E 341 HIS cc_start: 0.8206 (m170) cc_final: 0.7870 (m-70) REVERT: E 355 ASN cc_start: 0.8833 (t0) cc_final: 0.8553 (t0) REVERT: E 383 GLU cc_start: 0.8501 (pm20) cc_final: 0.8184 (mp0) REVERT: E 390 LYS cc_start: 0.9174 (mmtm) cc_final: 0.8834 (mtpp) REVERT: E 422 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8109 (mt) REVERT: E 438 SER cc_start: 0.8859 (t) cc_final: 0.8336 (p) REVERT: F 61 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8282 (ttm) REVERT: F 85 GLU cc_start: 0.8835 (tt0) cc_final: 0.8350 (tm-30) REVERT: F 98 ASP cc_start: 0.8356 (t0) cc_final: 0.7476 (t70) REVERT: F 118 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8197 (mmtp) REVERT: F 260 LYS cc_start: 0.8800 (pttp) cc_final: 0.8293 (pttp) REVERT: F 276 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.7952 (p) REVERT: F 302 MET cc_start: 0.7063 (mmp) cc_final: 0.6310 (mmt) REVERT: F 304 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8392 (m) REVERT: F 308 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7488 (mmp) REVERT: F 408 LYS cc_start: 0.8633 (tppt) cc_final: 0.8225 (tptp) REVERT: F 435 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7330 (m-70) REVERT: F 458 LYS cc_start: 0.9133 (pttt) cc_final: 0.8883 (pttm) REVERT: G 6 ASP cc_start: 0.8973 (t0) cc_final: 0.8696 (t0) REVERT: G 61 MET cc_start: 0.8319 (mtt) cc_final: 0.7717 (tpp) REVERT: G 86 THR cc_start: 0.9427 (m) cc_final: 0.9194 (p) REVERT: G 135 LEU cc_start: 0.8847 (tp) cc_final: 0.8269 (mt) REVERT: G 155 LEU cc_start: 0.8507 (mm) cc_final: 0.8009 (pp) REVERT: G 195 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8677 (tt) REVERT: G 233 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7566 (tm-30) REVERT: G 306 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.8069 (mmm160) REVERT: G 316 PHE cc_start: 0.8606 (t80) cc_final: 0.7952 (t80) REVERT: G 341 HIS cc_start: 0.8286 (m170) cc_final: 0.7930 (m-70) REVERT: G 383 GLU cc_start: 0.8480 (pm20) cc_final: 0.8129 (mp0) REVERT: G 390 LYS cc_start: 0.9168 (mmtm) cc_final: 0.8765 (mtpp) REVERT: G 422 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7600 (mt) REVERT: G 438 SER cc_start: 0.8849 (t) cc_final: 0.8305 (p) REVERT: H 61 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8329 (ttm) REVERT: H 76 GLN cc_start: 0.6568 (tp40) cc_final: 0.6351 (tp40) REVERT: H 85 GLU cc_start: 0.8840 (tt0) cc_final: 0.8350 (tm-30) REVERT: H 118 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8190 (mmtp) REVERT: H 260 LYS cc_start: 0.8719 (pttp) cc_final: 0.8222 (pttp) REVERT: H 302 MET cc_start: 0.7046 (mmp) cc_final: 0.6194 (mmt) REVERT: H 304 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8257 (m) REVERT: H 308 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7510 (mmp) REVERT: H 329 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8572 (tt) REVERT: H 408 LYS cc_start: 0.8637 (tppt) cc_final: 0.8326 (tppt) REVERT: H 435 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7295 (m-70) REVERT: H 458 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8818 (mttt) outliers start: 138 outliers final: 96 residues processed: 867 average time/residue: 0.1810 time to fit residues: 242.0130 Evaluate side-chains 875 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 760 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 422 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 22 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 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 387 MET Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 99 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 328 GLN Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain D residue 65 VAL 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 170 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 329 LEU 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 445 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 195 LEU Chi-restraints excluded: chain E residue 196 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 307 MET Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 ILE 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 275 ASN Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 308 MET Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 372 LEU 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 46 ILE Chi-restraints excluded: chain G residue 50 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 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 422 LEU Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 61 MET 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 181 VAL Chi-restraints excluded: chain H residue 224 ILE Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 255 MET 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 339 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 229 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 9 optimal weight: 0.0670 chunk 153 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 344 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN C 17 ASN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 355 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.130685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.109420 restraints weight = 64468.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.113693 restraints weight = 40334.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.116878 restraints weight = 27751.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.119269 restraints weight = 20232.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.121110 restraints weight = 15412.345| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28096 Z= 0.132 Angle : 0.708 11.329 38312 Z= 0.355 Chirality : 0.047 0.277 4536 Planarity : 0.005 0.079 5000 Dihedral : 6.114 58.993 4448 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.92 % Allowed : 31.05 % Favored : 65.03 % 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: -0.21 (0.14), residues: 3704 helix: 0.13 (0.14), residues: 1416 sheet: -0.72 (0.20), residues: 616 loop : 0.07 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 327 TYR 0.029 0.002 TYR H 366 PHE 0.027 0.002 PHE E 316 TRP 0.019 0.001 TRP E 334 HIS 0.017 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00313 (28096) covalent geometry : angle 0.70763 (38312) hydrogen bonds : bond 0.03450 ( 1160) hydrogen bonds : angle 5.49495 ( 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 912 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 802 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.7098 (p0) cc_final: 0.6667 (p0) REVERT: A 53 MET cc_start: 0.8096 (mmt) cc_final: 0.7488 (mmt) REVERT: A 59 ARG cc_start: 0.8108 (mtt-85) cc_final: 0.7771 (mtt-85) REVERT: A 76 GLN cc_start: 0.8095 (pm20) cc_final: 0.7588 (pm20) REVERT: A 107 ASP cc_start: 0.8593 (m-30) cc_final: 0.8257 (p0) REVERT: A 111 ASP cc_start: 0.8904 (t0) cc_final: 0.8639 (t0) REVERT: A 138 GLU cc_start: 0.8742 (mp0) cc_final: 0.8431 (tm-30) REVERT: A 141 CYS cc_start: 0.8797 (p) cc_final: 0.8325 (p) REVERT: A 155 LEU cc_start: 0.9199 (mm) cc_final: 0.8966 (mm) REVERT: A 184 MET cc_start: 0.8720 (mmm) cc_final: 0.8400 (mmm) REVERT: A 197 ARG cc_start: 0.8991 (ttt90) cc_final: 0.8626 (mtp180) REVERT: A 217 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7244 (mmm-85) REVERT: A 277 VAL cc_start: 0.7884 (m) cc_final: 0.6591 (p) REVERT: A 313 ARG cc_start: 0.7780 (tpt-90) cc_final: 0.7571 (tpt-90) REVERT: A 343 ARG cc_start: 0.8335 (ptm160) cc_final: 0.7752 (ttt180) REVERT: A 446 TYR cc_start: 0.8729 (m-80) cc_final: 0.8137 (m-80) REVERT: A 458 LYS cc_start: 0.9420 (mmmt) cc_final: 0.9113 (mmtm) REVERT: B 4 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8524 (t80) REVERT: B 31 ARG cc_start: 0.6967 (mtm180) cc_final: 0.6741 (mtm180) REVERT: B 37 SER cc_start: 0.8706 (m) cc_final: 0.8397 (p) REVERT: B 52 ASN cc_start: 0.7988 (p0) cc_final: 0.7762 (p0) REVERT: B 68 ARG cc_start: 0.8345 (mmp80) cc_final: 0.7636 (mmm160) REVERT: B 117 HIS cc_start: 0.9069 (m-70) cc_final: 0.8773 (m-70) REVERT: B 118 LYS cc_start: 0.8993 (tptt) cc_final: 0.8627 (tptt) REVERT: B 119 ARG cc_start: 0.8743 (ttm110) cc_final: 0.8211 (ttm110) REVERT: B 153 ILE cc_start: 0.9208 (tp) cc_final: 0.8873 (tp) REVERT: B 197 ARG cc_start: 0.8956 (mtp180) cc_final: 0.8553 (ptp-110) REVERT: B 231 LYS cc_start: 0.8924 (mttm) cc_final: 0.8517 (pttm) REVERT: B 267 LEU cc_start: 0.9236 (mt) cc_final: 0.8950 (tp) REVERT: B 302 MET cc_start: 0.7443 (mmp) cc_final: 0.6520 (mmp) REVERT: B 303 CYS cc_start: 0.7642 (m) cc_final: 0.7178 (m) REVERT: B 332 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6358 (p-80) REVERT: B 379 ARG cc_start: 0.8724 (mtm180) cc_final: 0.8370 (mtm180) REVERT: B 451 ASN cc_start: 0.8640 (p0) cc_final: 0.8318 (p0) REVERT: B 458 LYS cc_start: 0.8901 (mttt) cc_final: 0.8563 (ptpt) REVERT: C 52 ASN cc_start: 0.7324 (p0) cc_final: 0.6683 (p0) REVERT: C 59 ARG cc_start: 0.8331 (ptm160) cc_final: 0.8085 (mtt180) REVERT: C 76 GLN cc_start: 0.7913 (pm20) cc_final: 0.7361 (pm20) REVERT: C 107 ASP cc_start: 0.8536 (m-30) cc_final: 0.8176 (p0) REVERT: C 111 ASP cc_start: 0.8839 (t0) cc_final: 0.8586 (t0) REVERT: C 116 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8940 (tp) REVERT: C 141 CYS cc_start: 0.8782 (p) cc_final: 0.8287 (p) REVERT: C 146 ARG cc_start: 0.8901 (mtm-85) cc_final: 0.8643 (ptp90) REVERT: C 153 ILE cc_start: 0.9206 (tp) cc_final: 0.8986 (mm) REVERT: C 155 LEU cc_start: 0.9109 (mm) cc_final: 0.8533 (pp) REVERT: C 184 MET cc_start: 0.8683 (mmm) cc_final: 0.8391 (mmm) REVERT: C 197 ARG cc_start: 0.9005 (mtp180) cc_final: 0.8604 (mmm160) REVERT: C 243 LEU cc_start: 0.9012 (pp) cc_final: 0.8691 (mm) REVERT: C 313 ARG cc_start: 0.7563 (tpt-90) cc_final: 0.7144 (tpt-90) REVERT: C 343 ARG cc_start: 0.8299 (ptm160) cc_final: 0.7639 (ttm170) REVERT: C 374 PHE cc_start: 0.8205 (m-10) cc_final: 0.7944 (m-10) REVERT: C 446 TYR cc_start: 0.8775 (m-80) cc_final: 0.8221 (m-80) REVERT: C 458 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9096 (mmtm) REVERT: D 31 ARG cc_start: 0.6920 (mtm180) cc_final: 0.6439 (mtm180) REVERT: D 52 ASN cc_start: 0.7735 (p0) cc_final: 0.7531 (p0) REVERT: D 68 ARG cc_start: 0.8332 (mmp80) cc_final: 0.7566 (mmm160) REVERT: D 117 HIS cc_start: 0.9052 (m-70) cc_final: 0.8793 (m-70) REVERT: D 118 LYS cc_start: 0.8956 (tptt) cc_final: 0.8608 (tptt) REVERT: D 153 ILE cc_start: 0.9193 (tp) cc_final: 0.8861 (tp) REVERT: D 158 PHE cc_start: 0.7968 (p90) cc_final: 0.7713 (p90) REVERT: D 184 MET cc_start: 0.8579 (tpp) cc_final: 0.8376 (tpt) REVERT: D 197 ARG cc_start: 0.8952 (mtp180) cc_final: 0.8503 (ptp-110) REVERT: D 231 LYS cc_start: 0.8920 (mttm) cc_final: 0.8530 (mtmm) REVERT: D 267 LEU cc_start: 0.9227 (mt) cc_final: 0.8953 (tp) REVERT: D 302 MET cc_start: 0.7347 (mmp) cc_final: 0.6446 (mmp) REVERT: D 306 ARG cc_start: 0.7785 (mtt180) cc_final: 0.6872 (mtt180) REVERT: D 332 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6346 (p-80) REVERT: D 379 ARG cc_start: 0.8721 (mtm180) cc_final: 0.8370 (mtm180) REVERT: D 387 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8556 (mmp) REVERT: D 408 LYS cc_start: 0.8508 (pttt) cc_final: 0.8268 (pttm) REVERT: D 451 ASN cc_start: 0.8630 (p0) cc_final: 0.8297 (p0) REVERT: D 458 LYS cc_start: 0.8900 (mttt) cc_final: 0.8557 (ptpt) REVERT: D 473 HIS cc_start: 0.8946 (t70) cc_final: 0.8724 (t70) REVERT: E 61 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7622 (tpp) REVERT: E 86 THR cc_start: 0.9419 (m) cc_final: 0.9189 (p) REVERT: E 135 LEU cc_start: 0.8880 (tp) cc_final: 0.8310 (mt) REVERT: E 155 LEU cc_start: 0.8491 (mm) cc_final: 0.7970 (pp) REVERT: E 184 MET cc_start: 0.8005 (mmm) cc_final: 0.7624 (mmm) REVERT: E 195 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8815 (tt) REVERT: E 246 ASP cc_start: 0.8687 (t0) cc_final: 0.8288 (t0) REVERT: E 292 ILE cc_start: 0.8951 (mm) cc_final: 0.8584 (mm) REVERT: E 302 MET cc_start: 0.7781 (mmp) cc_final: 0.6113 (mmp) REVERT: E 306 ARG cc_start: 0.8552 (mtp-110) cc_final: 0.7650 (mtt90) REVERT: E 341 HIS cc_start: 0.8267 (m170) cc_final: 0.7938 (m-70) REVERT: E 355 ASN cc_start: 0.8777 (t0) cc_final: 0.8381 (t0) REVERT: E 383 GLU cc_start: 0.8536 (pm20) cc_final: 0.8177 (mp0) REVERT: E 390 LYS cc_start: 0.9154 (mmtm) cc_final: 0.8751 (mtpp) REVERT: E 438 SER cc_start: 0.8825 (t) cc_final: 0.8313 (p) REVERT: E 471 GLU cc_start: 0.7854 (pt0) cc_final: 0.7626 (tt0) REVERT: F 85 GLU cc_start: 0.8838 (tt0) cc_final: 0.8333 (tm-30) REVERT: F 98 ASP cc_start: 0.8053 (t0) cc_final: 0.7482 (t0) REVERT: F 118 LYS cc_start: 0.8676 (mmtt) cc_final: 0.8221 (mmtp) REVERT: F 169 GLU cc_start: 0.9107 (mp0) cc_final: 0.8601 (mp0) REVERT: F 233 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8357 (pp30) REVERT: F 260 LYS cc_start: 0.8750 (pttp) cc_final: 0.8245 (pttp) REVERT: F 276 VAL cc_start: 0.8204 (OUTLIER) cc_final: 0.7783 (p) REVERT: F 302 MET cc_start: 0.7029 (mmp) cc_final: 0.6298 (mmt) REVERT: F 328 GLN cc_start: 0.8236 (pp30) cc_final: 0.7766 (pp30) REVERT: F 329 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8630 (mt) REVERT: F 367 GLU cc_start: 0.7531 (mp0) cc_final: 0.7306 (mp0) REVERT: F 458 LYS cc_start: 0.9140 (pttt) cc_final: 0.8868 (pttm) REVERT: G 61 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7667 (tpp) REVERT: G 77 ASP cc_start: 0.8059 (m-30) cc_final: 0.7676 (m-30) REVERT: G 86 THR cc_start: 0.9417 (m) cc_final: 0.9184 (p) REVERT: G 135 LEU cc_start: 0.8830 (tp) cc_final: 0.8326 (mt) REVERT: G 155 LEU cc_start: 0.8470 (mm) cc_final: 0.7972 (pp) REVERT: G 158 PHE cc_start: 0.7863 (p90) cc_final: 0.7069 (p90) REVERT: G 195 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8665 (tt) REVERT: G 246 ASP cc_start: 0.8275 (t0) cc_final: 0.7917 (t0) REVERT: G 302 MET cc_start: 0.7841 (mmp) cc_final: 0.6439 (mmp) REVERT: G 306 ARG cc_start: 0.8356 (mtp-110) cc_final: 0.7750 (mtm180) REVERT: G 316 PHE cc_start: 0.8612 (t80) cc_final: 0.7919 (t80) REVERT: G 341 HIS cc_start: 0.8260 (m170) cc_final: 0.7934 (m-70) REVERT: G 355 ASN cc_start: 0.8566 (t0) cc_final: 0.8246 (t0) REVERT: G 383 GLU cc_start: 0.8472 (pm20) cc_final: 0.8090 (mp0) REVERT: G 387 MET cc_start: 0.8712 (pmm) cc_final: 0.8423 (ppp) REVERT: G 438 SER cc_start: 0.8820 (t) cc_final: 0.8303 (p) REVERT: G 471 GLU cc_start: 0.7880 (pt0) cc_final: 0.7498 (tt0) REVERT: H 85 GLU cc_start: 0.8827 (tt0) cc_final: 0.8327 (tm-30) REVERT: H 98 ASP cc_start: 0.8290 (t0) cc_final: 0.7572 (t70) REVERT: H 118 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8171 (mmtp) REVERT: H 169 GLU cc_start: 0.9102 (mp0) cc_final: 0.8667 (mp0) REVERT: H 233 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8363 (pp30) REVERT: H 255 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8444 (tpt) REVERT: H 302 MET cc_start: 0.7043 (mmp) cc_final: 0.6244 (mmt) REVERT: H 304 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8284 (m) REVERT: H 308 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7518 (mmp) REVERT: H 329 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8548 (tt) REVERT: H 408 LYS cc_start: 0.8623 (tppt) cc_final: 0.8289 (tppt) REVERT: H 422 LEU cc_start: 0.8887 (mt) cc_final: 0.8601 (mt) REVERT: H 458 LYS cc_start: 0.9145 (mtmm) cc_final: 0.8799 (mtmt) outliers start: 110 outliers final: 78 residues processed: 853 average time/residue: 0.1922 time to fit residues: 252.5349 Evaluate side-chains 843 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 750 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 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 422 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 LEU 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 393 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 104 SER 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 422 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 196 THR 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 D residue 445 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 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 307 MET Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 385 TYR 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 19 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 102 THR 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 332 HIS 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 17 ASN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 61 MET 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 455 LEU 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 255 MET 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 355 ASN 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: 10.0000 chunk 55 optimal weight: 8.9990 chunk 189 optimal weight: 7.9990 chunk 359 optimal weight: 0.4980 chunk 183 optimal weight: 7.9990 chunk 205 optimal weight: 20.0000 chunk 363 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 chunk 289 optimal weight: 8.9990 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** C 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN G 252 GLN ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.124961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.103902 restraints weight = 66479.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.107991 restraints weight = 41830.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111051 restraints weight = 28982.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.113301 restraints weight = 21303.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.115041 restraints weight = 16415.910| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.6062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28096 Z= 0.249 Angle : 0.779 11.825 38312 Z= 0.400 Chirality : 0.048 0.291 4536 Planarity : 0.006 0.087 5000 Dihedral : 6.314 57.532 4448 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.42 % Allowed : 31.48 % 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: -0.43 (0.14), residues: 3704 helix: 0.00 (0.14), residues: 1360 sheet: -1.16 (0.19), residues: 656 loop : 0.08 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 426 TYR 0.028 0.003 TYR E 12 PHE 0.031 0.002 PHE H 469 TRP 0.023 0.002 TRP E 334 HIS 0.008 0.001 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00547 (28096) covalent geometry : angle 0.77884 (38312) hydrogen bonds : bond 0.03797 ( 1160) hydrogen bonds : angle 5.66734 ( 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 919 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 795 time to evaluate : 0.969 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: 0.7366 (p0) cc_final: 0.7058 (p0) REVERT: A 59 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7703 (mtt180) REVERT: A 76 GLN cc_start: 0.8211 (pm20) cc_final: 0.7669 (pm20) REVERT: A 107 ASP cc_start: 0.8671 (m-30) cc_final: 0.8291 (p0) REVERT: A 111 ASP cc_start: 0.8888 (t0) cc_final: 0.8652 (t0) REVERT: A 138 GLU cc_start: 0.8739 (mp0) cc_final: 0.8518 (tm-30) REVERT: A 141 CYS cc_start: 0.8774 (p) cc_final: 0.8285 (p) REVERT: A 155 LEU cc_start: 0.9182 (mm) cc_final: 0.8907 (pp) REVERT: A 184 MET cc_start: 0.8650 (mmm) cc_final: 0.8410 (mmm) REVERT: A 217 ARG cc_start: 0.7807 (mmm-85) cc_final: 0.7440 (mmm-85) REVERT: A 243 LEU cc_start: 0.8989 (pp) cc_final: 0.8741 (mm) REVERT: A 254 LYS cc_start: 0.8617 (tttp) cc_final: 0.8278 (tttt) REVERT: A 313 ARG cc_start: 0.7832 (tpt-90) cc_final: 0.6894 (tpt170) REVERT: A 343 ARG cc_start: 0.8425 (ptm160) cc_final: 0.7854 (ttt180) REVERT: A 357 MET cc_start: 0.6471 (tpp) cc_final: 0.5585 (tpp) REVERT: A 446 TYR cc_start: 0.8871 (m-80) cc_final: 0.8283 (m-80) REVERT: A 455 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8110 (tt) REVERT: A 458 LYS cc_start: 0.9447 (mmmt) cc_final: 0.9151 (mmtm) REVERT: B 4 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8527 (t80) REVERT: B 31 ARG cc_start: 0.7027 (mtm180) cc_final: 0.6744 (mtm180) REVERT: B 37 SER cc_start: 0.8845 (m) cc_final: 0.8555 (p) REVERT: B 54 THR cc_start: 0.8232 (p) cc_final: 0.7998 (p) REVERT: B 68 ARG cc_start: 0.8390 (mmp80) cc_final: 0.7589 (mmm160) REVERT: B 91 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8335 (mmmt) REVERT: B 99 THR cc_start: 0.9227 (t) cc_final: 0.8955 (t) REVERT: B 117 HIS cc_start: 0.9005 (m-70) cc_final: 0.8742 (m-70) REVERT: B 118 LYS cc_start: 0.9008 (tptt) cc_final: 0.8663 (tptt) REVERT: B 153 ILE cc_start: 0.9138 (tp) cc_final: 0.8865 (tp) REVERT: B 158 PHE cc_start: 0.8094 (p90) cc_final: 0.7670 (p90) REVERT: B 184 MET cc_start: 0.7987 (tpt) cc_final: 0.7667 (tpp) REVERT: B 197 ARG cc_start: 0.8960 (mtp180) cc_final: 0.8372 (ptp-110) REVERT: B 231 LYS cc_start: 0.9024 (mttm) cc_final: 0.8662 (mtmm) REVERT: B 302 MET cc_start: 0.7581 (mmp) cc_final: 0.6785 (mmp) REVERT: B 332 HIS cc_start: 0.7438 (OUTLIER) cc_final: 0.6334 (p-80) REVERT: B 379 ARG cc_start: 0.8628 (mtm180) cc_final: 0.8226 (mtm110) REVERT: B 387 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8458 (mmp) REVERT: B 408 LYS cc_start: 0.8583 (pttt) cc_final: 0.8256 (pttm) REVERT: B 443 THR cc_start: 0.8972 (m) cc_final: 0.8740 (p) REVERT: B 451 ASN cc_start: 0.8597 (p0) cc_final: 0.8377 (p0) REVERT: B 458 LYS cc_start: 0.8935 (mttt) cc_final: 0.8538 (mttt) REVERT: C 52 ASN cc_start: 0.7631 (p0) cc_final: 0.7159 (p0) REVERT: C 53 MET cc_start: 0.8321 (mmt) cc_final: 0.7405 (mmt) REVERT: C 59 ARG cc_start: 0.8281 (ptm160) cc_final: 0.7645 (ptp-110) REVERT: C 76 GLN cc_start: 0.8076 (pm20) cc_final: 0.7424 (pm20) REVERT: C 107 ASP cc_start: 0.8641 (m-30) cc_final: 0.8252 (p0) REVERT: C 111 ASP cc_start: 0.8847 (t0) cc_final: 0.8628 (t0) REVERT: C 116 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9038 (tp) REVERT: C 141 CYS cc_start: 0.8802 (p) cc_final: 0.8332 (p) REVERT: C 146 ARG cc_start: 0.8928 (mtm-85) cc_final: 0.8680 (ptp90) REVERT: C 155 LEU cc_start: 0.9137 (mm) cc_final: 0.8844 (mm) REVERT: C 197 ARG cc_start: 0.8978 (mtp180) cc_final: 0.8532 (mtp180) REVERT: C 217 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7250 (mmm-85) REVERT: C 243 LEU cc_start: 0.8965 (pp) cc_final: 0.8720 (mm) REVERT: C 254 LYS cc_start: 0.8637 (tttp) cc_final: 0.8300 (tttt) REVERT: C 313 ARG cc_start: 0.7728 (tpt-90) cc_final: 0.7347 (tpt-90) REVERT: C 343 ARG cc_start: 0.8412 (ptm160) cc_final: 0.7865 (ttt180) REVERT: C 357 MET cc_start: 0.6395 (tpp) cc_final: 0.5519 (tpp) REVERT: C 387 MET cc_start: 0.8641 (pmm) cc_final: 0.7666 (pmm) REVERT: C 446 TYR cc_start: 0.8887 (m-80) cc_final: 0.8293 (m-80) REVERT: C 458 LYS cc_start: 0.9455 (mmmt) cc_final: 0.9132 (mmtm) REVERT: D 31 ARG cc_start: 0.7033 (mtm180) cc_final: 0.6704 (mtm180) REVERT: D 68 ARG cc_start: 0.8412 (mmp80) cc_final: 0.7562 (mmm160) REVERT: D 91 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8331 (mmmt) REVERT: D 117 HIS cc_start: 0.9030 (m-70) cc_final: 0.8802 (m-70) REVERT: D 118 LYS cc_start: 0.8963 (tptt) cc_final: 0.8604 (tptt) REVERT: D 153 ILE cc_start: 0.9169 (tp) cc_final: 0.8898 (tp) REVERT: D 158 PHE cc_start: 0.8061 (p90) cc_final: 0.7780 (p90) REVERT: D 197 ARG cc_start: 0.8930 (mtp180) cc_final: 0.8452 (ptp-110) REVERT: D 231 LYS cc_start: 0.9017 (mttm) cc_final: 0.8640 (mttp) REVERT: D 302 MET cc_start: 0.7628 (mmp) cc_final: 0.6375 (mmp) REVERT: D 332 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.6359 (p-80) REVERT: D 379 ARG cc_start: 0.8651 (mtm180) cc_final: 0.8253 (mtm110) REVERT: D 408 LYS cc_start: 0.8541 (pttt) cc_final: 0.8261 (pttm) REVERT: D 458 LYS cc_start: 0.8924 (mttt) cc_final: 0.8527 (mttt) REVERT: E 6 ASP cc_start: 0.8970 (t0) cc_final: 0.8710 (t0) REVERT: E 61 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7742 (tpp) REVERT: E 86 THR cc_start: 0.9436 (m) cc_final: 0.9215 (p) REVERT: E 138 GLU cc_start: 0.8595 (mp0) cc_final: 0.8356 (mm-30) REVERT: E 155 LEU cc_start: 0.8574 (mm) cc_final: 0.7934 (pt) REVERT: E 158 PHE cc_start: 0.7866 (p90) cc_final: 0.7624 (p90) REVERT: E 184 MET cc_start: 0.7970 (mmm) cc_final: 0.7623 (mmm) REVERT: E 195 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8913 (tt) REVERT: E 246 ASP cc_start: 0.8856 (t0) cc_final: 0.8492 (t0) REVERT: E 292 ILE cc_start: 0.9054 (mm) cc_final: 0.8672 (mm) REVERT: E 306 ARG cc_start: 0.8543 (mtp-110) cc_final: 0.7904 (mtt90) REVERT: E 341 HIS cc_start: 0.8187 (m170) cc_final: 0.7833 (m-70) REVERT: E 355 ASN cc_start: 0.8911 (t0) cc_final: 0.8489 (t0) REVERT: E 383 GLU cc_start: 0.8546 (pm20) cc_final: 0.8165 (mp0) REVERT: E 390 LYS cc_start: 0.9203 (mmtm) cc_final: 0.8886 (mtpp) REVERT: E 422 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8198 (mt) REVERT: E 438 SER cc_start: 0.8856 (t) cc_final: 0.8297 (p) REVERT: F 85 GLU cc_start: 0.8838 (tt0) cc_final: 0.8372 (tm-30) REVERT: F 98 ASP cc_start: 0.8195 (t0) cc_final: 0.7660 (t0) REVERT: F 118 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8212 (mmtp) REVERT: F 169 GLU cc_start: 0.9122 (mp0) cc_final: 0.8626 (mp0) REVERT: F 233 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8363 (pp30) REVERT: F 260 LYS cc_start: 0.8857 (pttp) cc_final: 0.8399 (pttp) REVERT: F 276 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.7960 (p) REVERT: F 302 MET cc_start: 0.7097 (mmp) cc_final: 0.6419 (mmt) REVERT: F 328 GLN cc_start: 0.8302 (pp30) cc_final: 0.7887 (pp30) REVERT: F 355 ASN cc_start: 0.9013 (t0) cc_final: 0.8327 (m-40) REVERT: F 422 LEU cc_start: 0.9006 (mt) cc_final: 0.8756 (mt) REVERT: F 435 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7452 (m-70) REVERT: F 452 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6370 (mt) REVERT: F 458 LYS cc_start: 0.9150 (pttt) cc_final: 0.8908 (pttm) REVERT: G 6 ASP cc_start: 0.9000 (t0) cc_final: 0.8752 (t0) REVERT: G 61 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7774 (tpp) REVERT: G 86 THR cc_start: 0.9431 (m) cc_final: 0.9210 (p) REVERT: G 135 LEU cc_start: 0.8895 (tp) cc_final: 0.8223 (mt) REVERT: G 155 LEU cc_start: 0.8566 (mm) cc_final: 0.7943 (pt) REVERT: G 195 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8775 (tt) REVERT: G 306 ARG cc_start: 0.8405 (mtp-110) cc_final: 0.7797 (mtm180) REVERT: G 316 PHE cc_start: 0.8628 (t80) cc_final: 0.7997 (t80) REVERT: G 341 HIS cc_start: 0.8188 (m170) cc_final: 0.7853 (m-70) REVERT: G 379 ARG cc_start: 0.8354 (mtm180) cc_final: 0.8148 (mtm180) REVERT: G 383 GLU cc_start: 0.8470 (pm20) cc_final: 0.8070 (mp0) REVERT: G 422 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8206 (mt) REVERT: G 438 SER cc_start: 0.8849 (t) cc_final: 0.8297 (p) REVERT: H 61 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8372 (ttm) REVERT: H 85 GLU cc_start: 0.8831 (tt0) cc_final: 0.8360 (tm-30) REVERT: H 98 ASP cc_start: 0.8330 (t0) cc_final: 0.7585 (t70) REVERT: H 118 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8203 (mmtp) REVERT: H 233 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8345 (pp30) REVERT: H 260 LYS cc_start: 0.8745 (pttp) cc_final: 0.8309 (pttp) REVERT: H 302 MET cc_start: 0.7185 (mmp) cc_final: 0.6299 (mmt) REVERT: H 304 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8398 (m) REVERT: H 308 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7592 (mmp) REVERT: H 329 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8565 (tt) REVERT: H 408 LYS cc_start: 0.8704 (tppt) cc_final: 0.8427 (tppt) REVERT: H 435 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7393 (m-70) REVERT: H 452 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6466 (mt) REVERT: H 458 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8839 (mtmt) REVERT: H 473 HIS cc_start: 0.8813 (t70) cc_final: 0.8432 (t70) outliers start: 124 outliers final: 88 residues processed: 852 average time/residue: 0.1856 time to fit residues: 244.0810 Evaluate side-chains 873 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 764 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 247 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 174 LEU 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 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 104 SER 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 328 GLN Chi-restraints excluded: chain C residue 422 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 170 VAL Chi-restraints excluded: chain D residue 196 THR 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 385 TYR Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 456 HIS Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 76 GLN 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 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 384 SER Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 102 THR 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 332 HIS Chi-restraints excluded: chain F residue 421 SER 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 65 VAL 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 196 THR 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 422 LEU Chi-restraints excluded: chain G residue 455 LEU Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 102 THR 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 242 LEU 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 355 ASN Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 421 SER Chi-restraints excluded: chain H residue 435 HIS Chi-restraints excluded: chain H residue 452 LEU 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: 4.9990 chunk 144 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 chunk 207 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 281 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN C 328 GLN ** C 456 HIS ** 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 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 355 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.129087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.107689 restraints weight = 64767.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.111940 restraints weight = 40845.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.115092 restraints weight = 28212.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.117364 restraints weight = 20676.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.119200 restraints weight = 15937.790| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28096 Z= 0.154 Angle : 0.785 12.368 38312 Z= 0.395 Chirality : 0.049 0.262 4536 Planarity : 0.005 0.098 5000 Dihedral : 6.217 59.907 4448 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.28 % Allowed : 33.30 % Favored : 63.43 % 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: -0.43 (0.13), residues: 3704 helix: 0.00 (0.14), residues: 1368 sheet: -0.97 (0.20), residues: 608 loop : -0.07 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 327 TYR 0.029 0.002 TYR C 12 PHE 0.027 0.002 PHE B 403 TRP 0.018 0.002 TRP E 334 HIS 0.008 0.001 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00362 (28096) covalent geometry : angle 0.78544 (38312) hydrogen bonds : bond 0.03622 ( 1160) hydrogen bonds : angle 5.61695 ( 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 870 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 778 time to evaluate : 0.907 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: A 52 ASN cc_start: 0.7219 (p0) cc_final: 0.6886 (p0) REVERT: A 53 MET cc_start: 0.8215 (mmt) cc_final: 0.7589 (mmt) REVERT: A 59 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7739 (mtt-85) REVERT: A 76 GLN cc_start: 0.8085 (pm20) cc_final: 0.7597 (pm20) REVERT: A 107 ASP cc_start: 0.8677 (m-30) cc_final: 0.8299 (p0) REVERT: A 111 ASP cc_start: 0.8870 (t0) cc_final: 0.8602 (t0) REVERT: A 138 GLU cc_start: 0.8758 (mp0) cc_final: 0.8485 (tm-30) REVERT: A 141 CYS cc_start: 0.8797 (p) cc_final: 0.8291 (p) REVERT: A 155 LEU cc_start: 0.9150 (mm) cc_final: 0.8895 (pp) REVERT: A 197 ARG cc_start: 0.8969 (ttt90) cc_final: 0.8763 (mtp180) REVERT: A 217 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7328 (mmm-85) REVERT: A 254 LYS cc_start: 0.8512 (tttp) cc_final: 0.8191 (tttt) REVERT: A 313 ARG cc_start: 0.7832 (tpt-90) cc_final: 0.7352 (tpt-90) REVERT: A 343 ARG cc_start: 0.8367 (ptm160) cc_final: 0.7718 (ttm170) REVERT: A 357 MET cc_start: 0.6243 (tpp) cc_final: 0.5554 (tpp) REVERT: A 446 TYR cc_start: 0.8789 (m-80) cc_final: 0.8182 (m-80) REVERT: A 458 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9129 (mmtm) REVERT: B 4 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8522 (t80) REVERT: B 37 SER cc_start: 0.8879 (m) cc_final: 0.8601 (p) REVERT: B 68 ARG cc_start: 0.8363 (mmp80) cc_final: 0.7596 (mmm160) REVERT: B 91 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8317 (mmmt) REVERT: B 117 HIS cc_start: 0.8993 (m-70) cc_final: 0.8732 (m-70) REVERT: B 118 LYS cc_start: 0.8960 (tptt) cc_final: 0.8606 (tptt) REVERT: B 128 PHE cc_start: 0.9305 (t80) cc_final: 0.9103 (t80) REVERT: B 153 ILE cc_start: 0.9006 (tp) cc_final: 0.8720 (tp) REVERT: B 158 PHE cc_start: 0.8206 (p90) cc_final: 0.7795 (p90) REVERT: B 184 MET cc_start: 0.7839 (tpt) cc_final: 0.7477 (tpp) REVERT: B 197 ARG cc_start: 0.8973 (mtp180) cc_final: 0.8517 (ptp-110) REVERT: B 231 LYS cc_start: 0.9010 (mttm) cc_final: 0.8625 (pttm) REVERT: B 302 MET cc_start: 0.7483 (mmp) cc_final: 0.6574 (mmp) REVERT: B 306 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6627 (mtt180) REVERT: B 332 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.6192 (p-80) REVERT: B 379 ARG cc_start: 0.8710 (mtm180) cc_final: 0.8351 (mtm180) REVERT: B 408 LYS cc_start: 0.8544 (pttt) cc_final: 0.8241 (pttm) REVERT: B 422 LEU cc_start: 0.8331 (mm) cc_final: 0.7996 (mm) REVERT: B 443 THR cc_start: 0.8852 (m) cc_final: 0.8626 (p) REVERT: B 451 ASN cc_start: 0.8576 (p0) cc_final: 0.8348 (p0) REVERT: B 458 LYS cc_start: 0.8912 (mttt) cc_final: 0.8446 (ptpt) REVERT: C 52 ASN cc_start: 0.7537 (p0) cc_final: 0.7286 (p0) REVERT: C 53 MET cc_start: 0.8241 (mmt) cc_final: 0.7611 (mmt) REVERT: C 59 ARG cc_start: 0.8190 (ptm160) cc_final: 0.7862 (ptp-170) REVERT: C 107 ASP cc_start: 0.8639 (m-30) cc_final: 0.8222 (p0) REVERT: C 111 ASP cc_start: 0.8858 (t0) cc_final: 0.8607 (t0) REVERT: C 116 LEU cc_start: 0.9263 (pp) cc_final: 0.8981 (tp) REVERT: C 141 CYS cc_start: 0.8802 (p) cc_final: 0.8298 (p) REVERT: C 146 ARG cc_start: 0.8906 (mtm-85) cc_final: 0.8645 (ptp90) REVERT: C 197 ARG cc_start: 0.9024 (mtp180) cc_final: 0.8540 (mtp180) REVERT: C 217 ARG cc_start: 0.7718 (mmm-85) cc_final: 0.7203 (mmm-85) REVERT: C 243 LEU cc_start: 0.8984 (pp) cc_final: 0.8697 (mm) REVERT: C 254 LYS cc_start: 0.8543 (tttp) cc_final: 0.8221 (tttt) REVERT: C 313 ARG cc_start: 0.7695 (tpt-90) cc_final: 0.7134 (tpt-90) REVERT: C 343 ARG cc_start: 0.8363 (ptm160) cc_final: 0.7663 (ttm170) REVERT: C 357 MET cc_start: 0.6130 (tpp) cc_final: 0.5493 (tpp) REVERT: C 374 PHE cc_start: 0.8275 (m-10) cc_final: 0.7924 (m-10) REVERT: C 446 TYR cc_start: 0.8822 (m-80) cc_final: 0.8182 (m-80) REVERT: C 458 LYS cc_start: 0.9450 (mmmt) cc_final: 0.9131 (mmtm) REVERT: D 68 ARG cc_start: 0.8400 (mmp80) cc_final: 0.7640 (mmm160) REVERT: D 91 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8318 (mmmt) REVERT: D 117 HIS cc_start: 0.9008 (m-70) cc_final: 0.8800 (m-70) REVERT: D 118 LYS cc_start: 0.8996 (tptt) cc_final: 0.8605 (tptt) REVERT: D 128 PHE cc_start: 0.9323 (t80) cc_final: 0.9112 (t80) REVERT: D 153 ILE cc_start: 0.9056 (tp) cc_final: 0.8775 (tp) REVERT: D 158 PHE cc_start: 0.8067 (p90) cc_final: 0.7821 (p90) REVERT: D 197 ARG cc_start: 0.8937 (mtp180) cc_final: 0.8523 (ptp-110) REVERT: D 231 LYS cc_start: 0.9005 (mttm) cc_final: 0.8628 (pttm) REVERT: D 302 MET cc_start: 0.7458 (mmp) cc_final: 0.6523 (mmp) REVERT: D 306 ARG cc_start: 0.7883 (mtt180) cc_final: 0.6848 (mtt180) REVERT: D 332 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6201 (p-80) REVERT: D 379 ARG cc_start: 0.8727 (mtm180) cc_final: 0.8309 (mtm180) REVERT: D 387 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8641 (mmp) REVERT: D 408 LYS cc_start: 0.8526 (pttt) cc_final: 0.8162 (pttm) REVERT: D 458 LYS cc_start: 0.8915 (mttt) cc_final: 0.8601 (ptpt) REVERT: E 6 ASP cc_start: 0.8951 (t0) cc_final: 0.8666 (t0) REVERT: E 61 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7637 (tpp) REVERT: E 68 ARG cc_start: 0.7839 (mmp80) cc_final: 0.7450 (mmm160) REVERT: E 86 THR cc_start: 0.9421 (m) cc_final: 0.9183 (p) REVERT: E 138 GLU cc_start: 0.8547 (mp0) cc_final: 0.8316 (mm-30) REVERT: E 155 LEU cc_start: 0.8508 (mm) cc_final: 0.7990 (pp) REVERT: E 195 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8730 (tt) REVERT: E 246 ASP cc_start: 0.8763 (t0) cc_final: 0.8374 (t0) REVERT: E 302 MET cc_start: 0.7764 (mmp) cc_final: 0.6238 (mmp) REVERT: E 306 ARG cc_start: 0.8552 (mtp-110) cc_final: 0.7834 (mtt90) REVERT: E 341 HIS cc_start: 0.8243 (m170) cc_final: 0.7914 (m-70) REVERT: E 355 ASN cc_start: 0.8793 (t0) cc_final: 0.8306 (t0) REVERT: E 383 GLU cc_start: 0.8552 (pm20) cc_final: 0.8266 (pm20) REVERT: E 390 LYS cc_start: 0.9171 (mmtm) cc_final: 0.8762 (mtpp) REVERT: E 438 SER cc_start: 0.8730 (t) cc_final: 0.8280 (p) REVERT: F 85 GLU cc_start: 0.8842 (tt0) cc_final: 0.8359 (tm-30) REVERT: F 98 ASP cc_start: 0.8097 (t0) cc_final: 0.7584 (t0) REVERT: F 118 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8228 (mmtp) REVERT: F 169 GLU cc_start: 0.9093 (mp0) cc_final: 0.8674 (mp0) REVERT: F 233 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8348 (pp30) REVERT: F 260 LYS cc_start: 0.8809 (pttp) cc_final: 0.8259 (pttp) REVERT: F 276 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7557 (p) REVERT: F 302 MET cc_start: 0.7043 (mmp) cc_final: 0.6298 (mmt) REVERT: F 306 ARG cc_start: 0.8796 (mtp-110) cc_final: 0.8321 (mtm180) REVERT: F 328 GLN cc_start: 0.8351 (pp30) cc_final: 0.7796 (pp30) REVERT: F 355 ASN cc_start: 0.8934 (t0) cc_final: 0.8176 (m-40) REVERT: F 422 LEU cc_start: 0.8958 (mt) cc_final: 0.8724 (mt) REVERT: F 458 LYS cc_start: 0.9168 (pttt) cc_final: 0.8896 (pttm) REVERT: G 61 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7622 (tpp) REVERT: G 86 THR cc_start: 0.9434 (m) cc_final: 0.9210 (p) REVERT: G 135 LEU cc_start: 0.8852 (tp) cc_final: 0.8283 (mt) REVERT: G 138 GLU cc_start: 0.8564 (mp0) cc_final: 0.8282 (mm-30) REVERT: G 155 LEU cc_start: 0.8498 (mm) cc_final: 0.7836 (pp) REVERT: G 158 PHE cc_start: 0.7918 (p90) cc_final: 0.7268 (p90) REVERT: G 195 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8718 (tt) REVERT: G 246 ASP cc_start: 0.8416 (t0) cc_final: 0.8157 (t0) REVERT: G 302 MET cc_start: 0.7870 (mmp) cc_final: 0.6514 (mmp) REVERT: G 306 ARG cc_start: 0.8405 (mtp-110) cc_final: 0.7752 (mtm180) REVERT: G 316 PHE cc_start: 0.8626 (t80) cc_final: 0.7980 (t80) REVERT: G 341 HIS cc_start: 0.8249 (m170) cc_final: 0.7952 (m-70) REVERT: G 355 ASN cc_start: 0.8489 (t0) cc_final: 0.8137 (t0) REVERT: G 383 GLU cc_start: 0.8480 (pm20) cc_final: 0.8127 (mp0) REVERT: G 387 MET cc_start: 0.8625 (pmm) cc_final: 0.8377 (ppp) REVERT: G 438 SER cc_start: 0.8820 (t) cc_final: 0.8283 (p) REVERT: G 471 GLU cc_start: 0.7778 (pt0) cc_final: 0.7552 (tt0) REVERT: H 85 GLU cc_start: 0.8843 (tt0) cc_final: 0.8372 (tm-30) REVERT: H 98 ASP cc_start: 0.8150 (t0) cc_final: 0.7597 (t0) REVERT: H 118 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8152 (mmtp) REVERT: H 169 GLU cc_start: 0.9105 (mp0) cc_final: 0.8685 (mp0) REVERT: H 233 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8339 (pp30) REVERT: H 260 LYS cc_start: 0.8709 (pttp) cc_final: 0.8489 (pttm) REVERT: H 302 MET cc_start: 0.7136 (mmp) cc_final: 0.6298 (mmt) REVERT: H 304 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8292 (m) REVERT: H 307 MET cc_start: 0.4881 (ptt) cc_final: 0.4509 (ptt) REVERT: H 308 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7500 (mmp) REVERT: H 329 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8528 (tt) REVERT: H 408 LYS cc_start: 0.8675 (tppt) cc_final: 0.8390 (tppt) REVERT: H 422 LEU cc_start: 0.9010 (mm) cc_final: 0.8673 (mm) REVERT: H 458 LYS cc_start: 0.9134 (mtmm) cc_final: 0.8838 (mttt) REVERT: H 473 HIS cc_start: 0.8794 (t70) cc_final: 0.8343 (t70) outliers start: 92 outliers final: 74 residues processed: 817 average time/residue: 0.1952 time to fit residues: 246.0610 Evaluate side-chains 840 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 754 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 247 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 174 LEU 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 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 C residue 242 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 422 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 311 VAL Chi-restraints excluded: chain D residue 332 HIS Chi-restraints excluded: chain D residue 384 SER Chi-restraints excluded: chain D residue 385 TYR Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 49 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 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 384 SER Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 456 HIS Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 102 THR 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 276 VAL 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 46 ILE Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 76 GLN 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 455 LEU Chi-restraints excluded: chain G residue 456 HIS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 242 LEU 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 355 ASN Chi-restraints excluded: chain H residue 417 THR 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: 0.0980 chunk 363 optimal weight: 8.9990 chunk 192 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 456 HIS ** 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 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.108299 restraints weight = 64452.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.112492 restraints weight = 40482.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.115634 restraints weight = 28111.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.118002 restraints weight = 20649.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.119745 restraints weight = 15827.045| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6237 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= 0.149 Angle : 0.794 13.735 38312 Z= 0.396 Chirality : 0.049 0.306 4536 Planarity : 0.005 0.088 5000 Dihedral : 6.114 58.944 4448 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.35 % Allowed : 32.98 % Favored : 63.68 % 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: 0.05 (0.14), residues: 1360 sheet: -0.93 (0.20), residues: 600 loop : -0.04 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 327 TYR 0.027 0.002 TYR C 12 PHE 0.027 0.002 PHE B 403 TRP 0.023 0.002 TRP F 334 HIS 0.008 0.001 HIS C 456 Details of bonding type rmsd covalent geometry : bond 0.00355 (28096) covalent geometry : angle 0.79413 (38312) hydrogen bonds : bond 0.03576 ( 1160) hydrogen bonds : angle 5.63064 ( 3120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5866.77 seconds wall clock time: 101 minutes 49.40 seconds (6109.40 seconds total)