Starting phenix.real_space_refine on Sat Jul 4 15:49:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dls_46984/07_2026/9dls_46984.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dls_46984/07_2026/9dls_46984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dls_46984/07_2026/9dls_46984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dls_46984/07_2026/9dls_46984.map" model { file = "/net/cci-nas-00/data/ceres_data/9dls_46984/07_2026/9dls_46984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dls_46984/07_2026/9dls_46984.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 6 5.21 5 S 96 5.16 5 C 13134 2.51 5 N 3751 2.21 5 O 4255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21282 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3433 Classifications: {'peptide': 440} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 420} Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3437 Classifications: {'peptide': 441} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 421} Chain: "C" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3444 Classifications: {'peptide': 442} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 421} Chain: "D" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3435 Classifications: {'peptide': 441} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 420} Chain: "E" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3444 Classifications: {'peptide': 442} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 421} Chain: "F" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3444 Classifications: {'peptide': 442} Link IDs: {'CIS': 2, 'PTRANS': 19, 'TRANS': 420} Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 453 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.34, per 1000 atoms: 0.25 Number of scatterers: 21282 At special positions: 0 Unit cell: (129.912, 138.573, 137.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 40 15.00 Mg 6 11.99 O 4255 8.00 N 3751 7.00 C 13134 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: 1.58 Conformation dependent library (CDL) restraints added in 1.5 seconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4962 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 6 sheets defined 61.7% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.668A pdb=" N GLU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 50 removed outlier: 4.063A pdb=" N GLU A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.568A pdb=" N PHE A 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 75 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.768A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.703A pdb=" N TYR A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.684A pdb=" N ILE A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 195 removed outlier: 3.822A pdb=" N ILE A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 261 through 275 removed outlier: 3.505A pdb=" N ILE A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 287 through 305 Processing helix chain 'A' and resid 316 through 332 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.864A pdb=" N THR A 351 " --> pdb=" O PRO A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 373 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.627A pdb=" N ARG A 389 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 399 removed outlier: 4.113A pdb=" N LEU A 399 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.993A pdb=" N ILE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 4.252A pdb=" N TYR A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 41 Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 59 through 75 Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.943A pdb=" N TYR B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 145 removed outlier: 3.642A pdb=" N TYR B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 168 removed outlier: 3.651A pdb=" N ILE B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 166 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 196 removed outlier: 3.533A pdb=" N THR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 233 through 249 Processing helix chain 'B' and resid 261 through 275 removed outlier: 3.608A pdb=" N ILE B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 287 through 305 Processing helix chain 'B' and resid 316 through 332 Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.572A pdb=" N MET B 345 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.718A pdb=" N THR B 351 " --> pdb=" O PRO B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 373 Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.149A pdb=" N GLN B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 389' Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.601A pdb=" N LEU B 399 " --> pdb=" O ASN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 45 through 50 removed outlier: 4.163A pdb=" N GLU C 50 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.580A pdb=" N PHE C 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 75 removed outlier: 3.640A pdb=" N ALA C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 99 through 110 removed outlier: 3.608A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 145 removed outlier: 3.939A pdb=" N TYR C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 168 removed outlier: 4.287A pdb=" N ALA C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 196 removed outlier: 3.730A pdb=" N THR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.800A pdb=" N LYS C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 Processing helix chain 'C' and resid 261 through 275 removed outlier: 3.618A pdb=" N ILE C 265 " --> pdb=" O PRO C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 287 through 305 Processing helix chain 'C' and resid 316 through 332 Processing helix chain 'C' and resid 341 through 345 Processing helix chain 'C' and resid 353 through 373 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.766A pdb=" N ARG C 389 " --> pdb=" O LEU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.869A pdb=" N LEU C 399 " --> pdb=" O ASN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 452 through 455 Processing helix chain 'D' and resid 27 through 41 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 59 through 75 removed outlier: 3.933A pdb=" N ALA D 75 " --> pdb=" O SER D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.547A pdb=" N VAL D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 98' Processing helix chain 'D' and resid 99 through 109 removed outlier: 3.537A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 145 removed outlier: 3.896A pdb=" N TYR D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 169 removed outlier: 3.940A pdb=" N LEU D 155 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 196 removed outlier: 3.810A pdb=" N THR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 216 Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 261 through 275 Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 287 through 305 Processing helix chain 'D' and resid 316 through 332 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 347 through 351 removed outlier: 3.747A pdb=" N THR D 351 " --> pdb=" O PRO D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 373 Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.873A pdb=" N LEU D 386 " --> pdb=" O ASN D 383 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 389 " --> pdb=" O LEU D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 399 Processing helix chain 'D' and resid 402 through 408 Processing helix chain 'D' and resid 417 through 421 removed outlier: 3.786A pdb=" N VAL D 420 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'E' and resid 27 through 41 removed outlier: 3.540A pdb=" N GLU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 59 through 75 removed outlier: 3.950A pdb=" N ALA E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 Processing helix chain 'E' and resid 98 through 110 removed outlier: 4.073A pdb=" N TYR E 102 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 145 removed outlier: 3.825A pdb=" N ALA E 120 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU E 121 " --> pdb=" O ASN E 117 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 169 removed outlier: 3.524A pdb=" N ALA E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG E 169 " --> pdb=" O ILE E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 196 removed outlier: 4.272A pdb=" N ILE E 182 " --> pdb=" O ASN E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 Processing helix chain 'E' and resid 233 through 249 Processing helix chain 'E' and resid 261 through 275 Processing helix chain 'E' and resid 277 through 284 Processing helix chain 'E' and resid 287 through 305 removed outlier: 3.516A pdb=" N TRP E 291 " --> pdb=" O ASP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 332 Processing helix chain 'E' and resid 347 through 351 removed outlier: 3.921A pdb=" N THR E 351 " --> pdb=" O PRO E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 373 Processing helix chain 'E' and resid 383 through 389 removed outlier: 4.048A pdb=" N LEU E 386 " --> pdb=" O ASN E 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 388 " --> pdb=" O SER E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 399 removed outlier: 3.869A pdb=" N LEU E 399 " --> pdb=" O ASN E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 409 removed outlier: 3.941A pdb=" N GLU E 406 " --> pdb=" O SER E 402 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 409 " --> pdb=" O ILE E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 421 removed outlier: 3.577A pdb=" N VAL E 420 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 41 Processing helix chain 'F' and resid 44 through 50 removed outlier: 3.679A pdb=" N GLU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 76 Processing helix chain 'F' and resid 80 through 91 Processing helix chain 'F' and resid 99 through 109 Processing helix chain 'F' and resid 115 through 142 Processing helix chain 'F' and resid 150 through 168 removed outlier: 3.707A pdb=" N ALA F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU F 159 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER F 160 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS F 161 " --> pdb=" O LEU F 157 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 193 Processing helix chain 'F' and resid 208 through 216 Processing helix chain 'F' and resid 233 through 249 Processing helix chain 'F' and resid 261 through 275 removed outlier: 3.544A pdb=" N ILE F 265 " --> pdb=" O PRO F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 284 Processing helix chain 'F' and resid 287 through 305 Processing helix chain 'F' and resid 316 through 332 Processing helix chain 'F' and resid 341 through 345 removed outlier: 3.691A pdb=" N MET F 345 " --> pdb=" O LEU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 351 removed outlier: 3.838A pdb=" N THR F 351 " --> pdb=" O PRO F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 373 Processing helix chain 'F' and resid 383 through 389 removed outlier: 3.767A pdb=" N LEU F 386 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU F 387 " --> pdb=" O ARG F 384 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG F 389 " --> pdb=" O LEU F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 399 removed outlier: 4.035A pdb=" N LEU F 399 " --> pdb=" O ASN F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 408 removed outlier: 3.681A pdb=" N GLU F 406 " --> pdb=" O SER F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 removed outlier: 4.297A pdb=" N TYR F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 455 Processing sheet with id=AA1, first strand: chain 'A' and resid 456 through 458 removed outlier: 3.891A pdb=" N GLY A 444 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 412 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 223 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N MET A 413 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE A 225 " --> pdb=" O MET A 413 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE A 415 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ALA A 227 " --> pdb=" O ILE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 177 through 178 removed outlier: 6.408A pdb=" N LEU C 223 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N MET C 413 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 225 " --> pdb=" O MET C 413 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE C 415 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA C 227 " --> pdb=" O ILE C 415 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 412 " --> pdb=" O GLY C 436 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 307 through 310 removed outlier: 6.550A pdb=" N ILE B 337 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU B 379 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL B 339 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 223 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N MET B 413 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE B 225 " --> pdb=" O MET B 413 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE B 415 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ALA B 227 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N ARG B 417 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 412 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY B 444 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 451 " --> pdb=" O ARG B 456 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 177 through 178 removed outlier: 6.273A pdb=" N VAL D 253 " --> pdb=" O TYR D 308 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP D 310 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE D 255 " --> pdb=" O ASP D 310 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE D 337 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU D 379 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL D 339 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE D 224 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N SER D 380 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL D 226 " --> pdb=" O SER D 380 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 223 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N MET D 413 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE D 225 " --> pdb=" O MET D 413 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE D 415 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA D 227 " --> pdb=" O ILE D 415 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 412 " --> pdb=" O GLY D 436 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 444 " --> pdb=" O ILE D 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 177 through 178 removed outlier: 6.655A pdb=" N ILE E 337 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE E 224 " --> pdb=" O ALA E 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE E 412 " --> pdb=" O GLY E 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 307 through 310 removed outlier: 6.530A pdb=" N ILE F 337 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU F 379 " --> pdb=" O ILE F 337 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL F 339 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU F 223 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N MET F 413 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE F 225 " --> pdb=" O MET F 413 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE F 415 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ALA F 227 " --> pdb=" O ILE F 415 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE F 412 " --> pdb=" O GLY F 436 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY F 444 " --> pdb=" O ILE F 435 " (cutoff:3.500A) 1215 hydrogen bonds defined for protein. 3483 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: 3.56 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7368 1.36 - 1.51: 5236 1.51 - 1.66: 8861 1.66 - 1.80: 152 1.80 - 1.95: 28 Bond restraints: 21645 Sorted by residual: bond pdb=" O3B AGS D 501 " pdb=" PB AGS D 501 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" O3B AGS A 501 " pdb=" PB AGS A 501 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" O3B AGS C 501 " pdb=" PB AGS C 501 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" O3B AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.02e+01 ... (remaining 21640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 29065 2.02 - 4.04: 263 4.04 - 6.07: 39 6.07 - 8.09: 18 8.09 - 10.11: 23 Bond angle restraints: 29408 Sorted by residual: angle pdb=" N3 DT G 7 " pdb=" C4 DT G 7 " pdb=" O4 DT G 7 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT G 1 " pdb=" C4 DT G 1 " pdb=" O4 DT G 1 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" O4 DT G 7 " pdb=" C4 DT G 7 " pdb=" C5 DT G 7 " ideal model delta sigma weight residual 124.90 122.31 2.59 7.00e-01 2.04e+00 1.37e+01 angle pdb=" O4 DT G 1 " pdb=" C4 DT G 1 " pdb=" C5 DT G 1 " ideal model delta sigma weight residual 124.90 122.32 2.58 7.00e-01 2.04e+00 1.36e+01 angle pdb=" O3A AGS F 501 " pdb=" PB AGS F 501 " pdb=" O3B AGS F 501 " ideal model delta sigma weight residual 100.38 110.49 -10.11 3.00e+00 1.11e-01 1.14e+01 ... (remaining 29403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 13219 35.68 - 71.37: 257 71.37 - 107.05: 20 107.05 - 142.73: 1 142.73 - 178.41: 2 Dihedral angle restraints: 13499 sinusoidal: 5823 harmonic: 7676 Sorted by residual: dihedral pdb=" CA GLU B 401 " pdb=" C GLU B 401 " pdb=" N SER B 402 " pdb=" CA SER B 402 " ideal model delta harmonic sigma weight residual -180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA GLU C 401 " pdb=" C GLU C 401 " pdb=" N SER C 402 " pdb=" CA SER C 402 " ideal model delta harmonic sigma weight residual -180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA GLU E 401 " pdb=" C GLU E 401 " pdb=" N SER E 402 " pdb=" CA SER E 402 " ideal model delta harmonic sigma weight residual -180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 13496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2928 0.057 - 0.114: 391 0.114 - 0.171: 24 0.171 - 0.228: 0 0.228 - 0.286: 6 Chirality restraints: 3349 Sorted by residual: chirality pdb=" C3' AGS A 501 " pdb=" C2' AGS A 501 " pdb=" C4' AGS A 501 " pdb=" O3' AGS A 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C3' AGS E 501 " pdb=" C2' AGS E 501 " pdb=" C4' AGS E 501 " pdb=" O3' AGS E 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C3' AGS B 501 " pdb=" C2' AGS B 501 " pdb=" C4' AGS B 501 " pdb=" O3' AGS B 501 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3346 not shown) Planarity restraints: 3772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 145 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO D 146 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 260 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO D 261 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 261 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 261 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 260 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO C 261 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 261 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 261 " 0.016 5.00e-02 4.00e+02 ... (remaining 3769 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 162 2.54 - 3.13: 16244 3.13 - 3.72: 32282 3.72 - 4.31: 42661 4.31 - 4.90: 74494 Nonbonded interactions: 165843 Sorted by model distance: nonbonded pdb=" OE2 GLU D 259 " pdb="MG MG D 502 " model vdw 1.956 2.170 nonbonded pdb=" OG1 THR B 235 " pdb="MG MG B 502 " model vdw 2.002 2.170 nonbonded pdb=" OD2 ASP B 340 " pdb="MG MG B 502 " model vdw 2.008 2.170 nonbonded pdb=" OE2 GLU C 259 " pdb="MG MG C 502 " model vdw 2.011 2.170 nonbonded pdb=" OG1 THR C 235 " pdb="MG MG C 502 " model vdw 2.066 2.170 ... (remaining 165838 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 23 through 502) selection = (chain 'B' and (resid 23 through 461 or resid 501 through 502)) selection = (chain 'C' and (resid 23 through 461 or resid 501 through 502)) selection = (chain 'D' and (resid 23 through 461 or resid 501 through 502)) selection = (chain 'E' and (resid 23 through 461 or resid 501 through 502)) selection = (chain 'F' and (resid 23 through 461 or resid 501 through 502)) } 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 individual isotropic 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.300 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.040 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 0.091 21645 Z= 0.200 Angle : 0.574 10.111 29408 Z= 0.291 Chirality : 0.040 0.286 3349 Planarity : 0.003 0.035 3772 Dihedral : 12.944 178.414 8537 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.00 % Allowed : 4.14 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 2.43 (0.17), residues: 2636 helix: 3.02 (0.14), residues: 1396 sheet: 0.49 (0.30), residues: 365 loop : -0.26 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 321 TYR 0.008 0.001 TYR E 194 PHE 0.010 0.001 PHE A 457 TRP 0.004 0.001 TRP A 45 HIS 0.003 0.000 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.20 (21645) covalent geometry : angle 0.57446 / 0.29 (29408) hydrogen bonds : bond 0.15610 / 10.59 ( 1215) hydrogen bonds : angle 5.33192 / 3.82 ( 3483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 641 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 VAL cc_start: 0.8572 (m) cc_final: 0.8274 (t) REVERT: A 70 LYS cc_start: 0.8071 (tttt) cc_final: 0.7562 (ttpp) REVERT: A 89 GLU cc_start: 0.8070 (tp30) cc_final: 0.7392 (tm-30) REVERT: A 135 VAL cc_start: 0.8199 (t) cc_final: 0.7913 (p) REVERT: A 139 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.7910 (tp) REVERT: A 161 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8178 (mmmm) REVERT: A 219 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7250 (mm-40) REVERT: A 239 MET cc_start: 0.7891 (mmm) cc_final: 0.7436 (mmm) REVERT: A 261 PRO cc_start: 0.7809 (Cg_exo) cc_final: 0.7353 (Cg_endo) REVERT: A 266 MET cc_start: 0.7852 (mmm) cc_final: 0.7617 (tpt) REVERT: A 272 SER cc_start: 0.8698 (t) cc_final: 0.8317 (p) REVERT: A 280 LYS cc_start: 0.7679 (mttt) cc_final: 0.7403 (mtpp) REVERT: A 363 ARG cc_start: 0.7474 (ttp-170) cc_final: 0.7210 (ttp80) REVERT: A 374 VAL cc_start: 0.7096 (t) cc_final: 0.6862 (m) REVERT: A 393 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7722 (mtt90) REVERT: A 418 ASP cc_start: 0.7856 (t70) cc_final: 0.7162 (t0) REVERT: A 428 LYS cc_start: 0.7570 (mttt) cc_final: 0.7346 (mttt) REVERT: A 453 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7655 (p90) REVERT: B 29 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6935 (tm-30) REVERT: B 58 TYR cc_start: 0.7237 (t80) cc_final: 0.6876 (t80) REVERT: B 102 TYR cc_start: 0.7907 (t80) cc_final: 0.7571 (t80) REVERT: B 122 ILE cc_start: 0.8717 (mm) cc_final: 0.8483 (mm) REVERT: B 145 ASP cc_start: 0.7990 (t0) cc_final: 0.7733 (t0) REVERT: B 177 LYS cc_start: 0.8066 (mtpp) cc_final: 0.7598 (mtpp) REVERT: B 210 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: B 269 MET cc_start: 0.6419 (ttm) cc_final: 0.6020 (mtp) REVERT: B 272 SER cc_start: 0.8215 (t) cc_final: 0.7931 (p) REVERT: B 298 MET cc_start: 0.7632 (tmm) cc_final: 0.7020 (tmm) REVERT: B 300 ILE cc_start: 0.7992 (mt) cc_final: 0.7708 (mt) REVERT: B 302 MET cc_start: 0.8003 (mmm) cc_final: 0.7577 (mmp) REVERT: B 316 THR cc_start: 0.7548 (p) cc_final: 0.7222 (t) REVERT: B 334 LEU cc_start: 0.8518 (mt) cc_final: 0.8309 (mp) REVERT: B 363 ARG cc_start: 0.7000 (ttp-170) cc_final: 0.6726 (ttp-170) REVERT: B 432 GLU cc_start: 0.6695 (tt0) cc_final: 0.6462 (tt0) REVERT: B 451 GLN cc_start: 0.5788 (mm-40) cc_final: 0.5382 (mm-40) REVERT: B 454 TYR cc_start: 0.7409 (m-80) cc_final: 0.6850 (m-80) REVERT: B 455 SER cc_start: 0.7061 (m) cc_final: 0.6587 (p) REVERT: C 44 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7090 (mmt90) REVERT: C 70 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7800 (ttpt) REVERT: C 86 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6625 (mm-30) REVERT: C 214 LYS cc_start: 0.8031 (mttp) cc_final: 0.7697 (mttp) REVERT: C 232 MET cc_start: 0.8745 (mmt) cc_final: 0.8401 (mmt) REVERT: C 251 LYS cc_start: 0.8278 (mmmt) cc_final: 0.8062 (mmtm) REVERT: C 311 ASP cc_start: 0.8007 (p0) cc_final: 0.7453 (t0) REVERT: C 321 ARG cc_start: 0.7252 (ttt-90) cc_final: 0.6975 (ttt-90) REVERT: C 336 LEU cc_start: 0.8621 (mp) cc_final: 0.8387 (mp) REVERT: C 346 ARG cc_start: 0.8636 (ptt90) cc_final: 0.8368 (ptt-90) REVERT: C 350 LEU cc_start: 0.8169 (mp) cc_final: 0.7966 (mt) REVERT: C 389 ARG cc_start: 0.8347 (mtp180) cc_final: 0.8033 (ptp90) REVERT: C 395 VAL cc_start: 0.7731 (m) cc_final: 0.7456 (t) REVERT: C 458 ASP cc_start: 0.7814 (m-30) cc_final: 0.7504 (t70) REVERT: D 31 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7675 (mm-30) REVERT: D 32 GLN cc_start: 0.8453 (mt0) cc_final: 0.8108 (mt0) REVERT: D 33 SER cc_start: 0.8376 (m) cc_final: 0.8084 (t) REVERT: D 52 VAL cc_start: 0.8224 (t) cc_final: 0.7899 (p) REVERT: D 102 TYR cc_start: 0.8585 (t80) cc_final: 0.8018 (t80) REVERT: D 132 LEU cc_start: 0.8766 (tp) cc_final: 0.8540 (tt) REVERT: D 133 ILE cc_start: 0.8426 (mm) cc_final: 0.8023 (mm) REVERT: D 138 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7408 (mm-30) REVERT: D 155 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8174 (tt) REVERT: D 161 LYS cc_start: 0.8088 (tppt) cc_final: 0.7853 (mttp) REVERT: D 177 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8042 (mtpp) REVERT: D 184 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6718 (mm-30) REVERT: D 285 GLN cc_start: 0.8089 (mt0) cc_final: 0.7869 (mt0) REVERT: D 310 ASP cc_start: 0.7829 (t0) cc_final: 0.7604 (t70) REVERT: D 313 SER cc_start: 0.7448 (t) cc_final: 0.7115 (p) REVERT: D 343 GLN cc_start: 0.8368 (mp10) cc_final: 0.8120 (mp10) REVERT: D 346 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7719 (ptm-80) REVERT: D 391 ASP cc_start: 0.7904 (t0) cc_final: 0.7480 (t70) REVERT: D 398 ASP cc_start: 0.7622 (m-30) cc_final: 0.7384 (m-30) REVERT: D 445 SER cc_start: 0.8390 (m) cc_final: 0.8007 (t) REVERT: D 446 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7872 (t) REVERT: E 53 MET cc_start: 0.6362 (ptp) cc_final: 0.5492 (ptp) REVERT: E 89 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7199 (tp30) REVERT: E 131 ASN cc_start: 0.8518 (t0) cc_final: 0.8181 (t0) REVERT: E 189 ARG cc_start: 0.7376 (tpt170) cc_final: 0.7054 (tpt170) REVERT: E 192 LEU cc_start: 0.8267 (tp) cc_final: 0.7753 (tt) REVERT: E 232 MET cc_start: 0.8186 (tpp) cc_final: 0.7884 (mmt) REVERT: E 239 MET cc_start: 0.8053 (mmm) cc_final: 0.7586 (mmm) REVERT: E 241 LEU cc_start: 0.7672 (mt) cc_final: 0.7437 (mt) REVERT: E 311 ASP cc_start: 0.7314 (p0) cc_final: 0.7086 (p0) REVERT: E 312 SER cc_start: 0.7954 (t) cc_final: 0.7577 (m) REVERT: E 346 ARG cc_start: 0.8592 (ptm-80) cc_final: 0.8252 (ptt-90) REVERT: E 373 ASN cc_start: 0.7635 (t0) cc_final: 0.7284 (t0) REVERT: E 387 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7230 (mm-30) REVERT: F 66 PHE cc_start: 0.7984 (t80) cc_final: 0.7740 (t80) REVERT: F 149 ARG cc_start: 0.7820 (mtm110) cc_final: 0.7477 (ptp-170) REVERT: F 213 LYS cc_start: 0.8155 (mmmm) cc_final: 0.7792 (mmmm) REVERT: F 239 MET cc_start: 0.7886 (tpp) cc_final: 0.7612 (mmm) REVERT: F 251 LYS cc_start: 0.7565 (mttp) cc_final: 0.6852 (mmtt) REVERT: F 311 ASP cc_start: 0.7509 (p0) cc_final: 0.7206 (t0) REVERT: F 321 ARG cc_start: 0.7993 (ttt-90) cc_final: 0.7728 (ttt90) REVERT: F 381 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8148 (mm-40) REVERT: F 445 SER cc_start: 0.8214 (p) cc_final: 0.7941 (m) REVERT: F 447 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7322 (tpt170) outliers start: 45 outliers final: 19 residues processed: 674 average time/residue: 0.1848 time to fit residues: 176.5333 Evaluate side-chains 579 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 555 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain B residue 459 ASN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 456 ARG Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 179 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.0470 chunk 111 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 GLN A 249 GLN A 451 GLN B 198 GLN B 381 GLN C 32 GLN C 137 ASN D 178 ASN E 278 GLN E 353 ASN F 62 HIS F 131 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.145285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.121040 restraints weight = 30765.554| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.82 r_work: 0.3417 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21645 Z= 0.155 Angle : 0.549 9.673 29408 Z= 0.285 Chirality : 0.041 0.147 3349 Planarity : 0.004 0.048 3772 Dihedral : 14.375 173.878 3448 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.49 % Allowed : 9.57 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 2.29 (0.17), residues: 2636 helix: 2.82 (0.14), residues: 1416 sheet: 0.48 (0.29), residues: 367 loop : -0.27 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 393 TYR 0.017 0.001 TYR C 87 PHE 0.014 0.002 PHE E 457 TRP 0.006 0.001 TRP A 45 HIS 0.007 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (21645) covalent geometry : angle 0.54910 / 0.29 (29408) hydrogen bonds : bond 0.04309 / 2.92 ( 1215) hydrogen bonds : angle 4.30949 / 3.08 ( 3483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 554 time to evaluate : 0.767 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: A 53 MET cc_start: 0.7743 (mmm) cc_final: 0.7527 (mmm) REVERT: A 70 LYS cc_start: 0.8065 (tttt) cc_final: 0.7680 (ttpp) REVERT: A 71 SER cc_start: 0.7485 (m) cc_final: 0.7191 (p) REVERT: A 89 GLU cc_start: 0.8137 (tp30) cc_final: 0.7476 (tm-30) REVERT: A 139 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8024 (tp) REVERT: A 153 ASP cc_start: 0.8191 (t0) cc_final: 0.7926 (m-30) REVERT: A 161 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8336 (mmmm) REVERT: A 219 GLN cc_start: 0.7747 (mm-40) cc_final: 0.6747 (mm110) REVERT: A 257 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8587 (p) REVERT: A 261 PRO cc_start: 0.7887 (Cg_exo) cc_final: 0.7649 (Cg_endo) REVERT: A 272 SER cc_start: 0.8690 (t) cc_final: 0.8439 (p) REVERT: A 280 LYS cc_start: 0.7797 (mttt) cc_final: 0.7567 (mtpp) REVERT: A 298 MET cc_start: 0.6490 (tmm) cc_final: 0.5909 (tmm) REVERT: A 311 ASP cc_start: 0.7744 (t0) cc_final: 0.7542 (t0) REVERT: A 363 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7541 (ttp80) REVERT: A 387 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7146 (mt-10) REVERT: A 393 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7885 (mtt90) REVERT: A 428 LYS cc_start: 0.7810 (mttt) cc_final: 0.7582 (mttt) REVERT: B 58 TYR cc_start: 0.7287 (t80) cc_final: 0.6971 (t80) REVERT: B 80 ASP cc_start: 0.8227 (p0) cc_final: 0.8026 (p0) REVERT: B 102 TYR cc_start: 0.7845 (t80) cc_final: 0.7542 (t80) REVERT: B 108 LYS cc_start: 0.7836 (ttpp) cc_final: 0.7530 (ttpp) REVERT: B 145 ASP cc_start: 0.7986 (t0) cc_final: 0.7773 (t0) REVERT: B 159 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8010 (tp30) REVERT: B 177 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7441 (mtpp) REVERT: B 189 ARG cc_start: 0.7436 (ttm170) cc_final: 0.7206 (ttm170) REVERT: B 242 CYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7575 (m) REVERT: B 247 MET cc_start: 0.7321 (tpp) cc_final: 0.7086 (tpp) REVERT: B 269 MET cc_start: 0.6429 (ttm) cc_final: 0.5836 (mtp) REVERT: B 272 SER cc_start: 0.8099 (t) cc_final: 0.7826 (p) REVERT: B 298 MET cc_start: 0.7695 (tmm) cc_final: 0.7150 (tmm) REVERT: B 300 ILE cc_start: 0.8076 (mt) cc_final: 0.7823 (mt) REVERT: B 302 MET cc_start: 0.8086 (mmm) cc_final: 0.7840 (mmp) REVERT: B 334 LEU cc_start: 0.8695 (mt) cc_final: 0.8493 (mp) REVERT: B 372 LEU cc_start: 0.7354 (mt) cc_final: 0.7038 (mp) REVERT: B 386 LEU cc_start: 0.8336 (tp) cc_final: 0.7967 (tt) REVERT: B 387 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7774 (mp0) REVERT: B 398 ASP cc_start: 0.7828 (m-30) cc_final: 0.7517 (m-30) REVERT: B 432 GLU cc_start: 0.6846 (tt0) cc_final: 0.6597 (tt0) REVERT: B 451 GLN cc_start: 0.6042 (mm-40) cc_final: 0.5689 (mm-40) REVERT: B 454 TYR cc_start: 0.7518 (m-80) cc_final: 0.7072 (m-80) REVERT: B 455 SER cc_start: 0.7098 (m) cc_final: 0.6851 (p) REVERT: C 44 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.7218 (mmt90) REVERT: C 70 LYS cc_start: 0.8258 (ttpt) cc_final: 0.7957 (ttpt) REVERT: C 250 ASP cc_start: 0.7895 (t0) cc_final: 0.7609 (t0) REVERT: C 311 ASP cc_start: 0.7968 (p0) cc_final: 0.7430 (t0) REVERT: C 321 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.7098 (ttt-90) REVERT: C 326 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7644 (ttp80) REVERT: C 336 LEU cc_start: 0.8532 (mp) cc_final: 0.8265 (mt) REVERT: C 357 GLU cc_start: 0.7273 (tt0) cc_final: 0.7038 (tt0) REVERT: C 389 ARG cc_start: 0.8367 (mtp180) cc_final: 0.8101 (ptp90) REVERT: C 395 VAL cc_start: 0.7778 (m) cc_final: 0.7551 (t) REVERT: D 31 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7805 (mm-30) REVERT: D 33 SER cc_start: 0.8381 (m) cc_final: 0.8063 (t) REVERT: D 52 VAL cc_start: 0.8122 (t) cc_final: 0.7829 (p) REVERT: D 63 ARG cc_start: 0.8527 (tpp80) cc_final: 0.7874 (ttm110) REVERT: D 102 TYR cc_start: 0.8462 (t80) cc_final: 0.8009 (t80) REVERT: D 133 ILE cc_start: 0.8399 (mm) cc_final: 0.8024 (mm) REVERT: D 138 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7481 (mm-30) REVERT: D 161 LYS cc_start: 0.8122 (tppt) cc_final: 0.7888 (mttp) REVERT: D 177 LYS cc_start: 0.8325 (mtpp) cc_final: 0.7986 (mtpp) REVERT: D 184 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7070 (mm-30) REVERT: D 247 MET cc_start: 0.8013 (tpp) cc_final: 0.7703 (mmp) REVERT: D 313 SER cc_start: 0.7457 (t) cc_final: 0.7142 (p) REVERT: D 346 ARG cc_start: 0.8131 (mtm110) cc_final: 0.7901 (ptm-80) REVERT: D 445 SER cc_start: 0.8498 (m) cc_final: 0.8087 (t) REVERT: D 446 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7888 (t) REVERT: E 23 VAL cc_start: 0.8420 (p) cc_final: 0.8113 (m) REVERT: E 53 MET cc_start: 0.6734 (ptp) cc_final: 0.6509 (ptp) REVERT: E 89 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7265 (tp30) REVERT: E 131 ASN cc_start: 0.8496 (t0) cc_final: 0.8213 (t0) REVERT: E 152 GLU cc_start: 0.7933 (mp0) cc_final: 0.7675 (mp0) REVERT: E 192 LEU cc_start: 0.8060 (tp) cc_final: 0.7612 (tt) REVERT: E 232 MET cc_start: 0.8191 (tpp) cc_final: 0.7841 (mmt) REVERT: E 239 MET cc_start: 0.8362 (mmm) cc_final: 0.7852 (mmm) REVERT: E 280 LYS cc_start: 0.8341 (mttm) cc_final: 0.8127 (mtpt) REVERT: E 282 ARG cc_start: 0.7140 (mtp-110) cc_final: 0.6876 (ttp-170) REVERT: E 311 ASP cc_start: 0.7306 (p0) cc_final: 0.7056 (p0) REVERT: E 312 SER cc_start: 0.8047 (t) cc_final: 0.7692 (m) REVERT: E 373 ASN cc_start: 0.7572 (t0) cc_final: 0.7331 (t0) REVERT: E 387 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7235 (mm-30) REVERT: F 66 PHE cc_start: 0.8146 (t80) cc_final: 0.7897 (t80) REVERT: F 193 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7564 (tt) REVERT: F 213 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7715 (mmmm) REVERT: F 232 MET cc_start: 0.8223 (mmt) cc_final: 0.7641 (mmt) REVERT: F 239 MET cc_start: 0.7799 (tpp) cc_final: 0.7555 (mmm) REVERT: F 447 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7336 (tpt170) REVERT: F 456 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.6972 (ttt90) outliers start: 56 outliers final: 30 residues processed: 586 average time/residue: 0.1799 time to fit residues: 149.0591 Evaluate side-chains 568 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 533 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 459 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 67 optimal weight: 0.0060 chunk 259 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 245 optimal weight: 0.5980 chunk 164 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 256 optimal weight: 0.5980 chunk 244 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 249 GLN A 331 HIS B 407 GLN C 331 HIS D 459 ASN E 353 ASN F 62 HIS F 131 ASN F 383 ASN F 407 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120366 restraints weight = 30841.780| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.89 r_work: 0.3404 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21645 Z= 0.138 Angle : 0.520 7.327 29408 Z= 0.268 Chirality : 0.041 0.168 3349 Planarity : 0.004 0.046 3772 Dihedral : 13.624 172.617 3431 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.63 % Allowed : 11.70 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 2.25 (0.17), residues: 2636 helix: 2.83 (0.14), residues: 1416 sheet: 0.31 (0.29), residues: 367 loop : -0.29 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 326 TYR 0.011 0.001 TYR A 454 PHE 0.012 0.001 PHE A 457 TRP 0.005 0.001 TRP A 45 HIS 0.006 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (21645) covalent geometry : angle 0.52041 / 0.27 (29408) hydrogen bonds : bond 0.04070 / 2.74 ( 1215) hydrogen bonds : angle 4.06279 / 2.90 ( 3483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 543 time to evaluate : 0.683 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: A 53 MET cc_start: 0.7790 (mmm) cc_final: 0.7526 (mmm) REVERT: A 70 LYS cc_start: 0.8042 (tttt) cc_final: 0.7667 (ttpp) REVERT: A 71 SER cc_start: 0.7447 (m) cc_final: 0.7100 (p) REVERT: A 89 GLU cc_start: 0.8186 (tp30) cc_final: 0.7759 (tp30) REVERT: A 139 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8040 (tp) REVERT: A 153 ASP cc_start: 0.8242 (t0) cc_final: 0.7953 (m-30) REVERT: A 161 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8360 (mmmm) REVERT: A 219 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7045 (mm-40) REVERT: A 257 SER cc_start: 0.8858 (OUTLIER) cc_final: 0.8528 (p) REVERT: A 261 PRO cc_start: 0.8090 (Cg_exo) cc_final: 0.7865 (Cg_endo) REVERT: A 298 MET cc_start: 0.6519 (tmm) cc_final: 0.5948 (tmm) REVERT: A 311 ASP cc_start: 0.7749 (t0) cc_final: 0.7508 (t0) REVERT: A 363 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7532 (ttp80) REVERT: A 370 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8445 (ttmm) REVERT: A 387 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7180 (mt-10) REVERT: A 393 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7887 (mtt90) REVERT: A 428 LYS cc_start: 0.7806 (mttt) cc_final: 0.7599 (mttt) REVERT: B 58 TYR cc_start: 0.7298 (t80) cc_final: 0.6928 (t80) REVERT: B 102 TYR cc_start: 0.7952 (t80) cc_final: 0.7610 (t80) REVERT: B 108 LYS cc_start: 0.7896 (ttpp) cc_final: 0.7647 (ttpp) REVERT: B 121 GLU cc_start: 0.7043 (pp20) cc_final: 0.6558 (pp20) REVERT: B 122 ILE cc_start: 0.8765 (mm) cc_final: 0.8296 (mm) REVERT: B 145 ASP cc_start: 0.8012 (t0) cc_final: 0.7801 (t0) REVERT: B 159 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7952 (tp30) REVERT: B 177 LYS cc_start: 0.7846 (mtpp) cc_final: 0.7423 (mtpp) REVERT: B 184 GLU cc_start: 0.7229 (mm-30) cc_final: 0.7008 (mm-30) REVERT: B 189 ARG cc_start: 0.7450 (ttm170) cc_final: 0.7212 (ttp-170) REVERT: B 242 CYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7510 (m) REVERT: B 247 MET cc_start: 0.7374 (tpp) cc_final: 0.7105 (tpp) REVERT: B 269 MET cc_start: 0.6458 (ttm) cc_final: 0.5990 (mtp) REVERT: B 272 SER cc_start: 0.8098 (t) cc_final: 0.7821 (p) REVERT: B 298 MET cc_start: 0.7721 (tmm) cc_final: 0.7207 (tmm) REVERT: B 300 ILE cc_start: 0.8079 (mt) cc_final: 0.7819 (mt) REVERT: B 302 MET cc_start: 0.8083 (mmm) cc_final: 0.7824 (mmp) REVERT: B 327 ILE cc_start: 0.7262 (mm) cc_final: 0.7037 (mp) REVERT: B 331 HIS cc_start: 0.6468 (m-70) cc_final: 0.6226 (m90) REVERT: B 338 MET cc_start: 0.7747 (ttm) cc_final: 0.7475 (ttm) REVERT: B 372 LEU cc_start: 0.7326 (mt) cc_final: 0.7012 (mp) REVERT: B 386 LEU cc_start: 0.8324 (tp) cc_final: 0.7969 (tt) REVERT: B 387 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7655 (mm-30) REVERT: B 398 ASP cc_start: 0.7829 (m-30) cc_final: 0.7501 (m-30) REVERT: B 407 GLN cc_start: 0.7759 (mt0) cc_final: 0.7386 (mt0) REVERT: B 432 GLU cc_start: 0.6831 (tt0) cc_final: 0.6582 (tt0) REVERT: B 451 GLN cc_start: 0.6115 (mm-40) cc_final: 0.5730 (mm-40) REVERT: B 454 TYR cc_start: 0.7528 (m-80) cc_final: 0.7094 (m-80) REVERT: B 455 SER cc_start: 0.7102 (m) cc_final: 0.6769 (p) REVERT: C 44 ARG cc_start: 0.7687 (mmm-85) cc_final: 0.7223 (mmt90) REVERT: C 70 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7869 (ttpt) REVERT: C 248 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7052 (mp0) REVERT: C 250 ASP cc_start: 0.7823 (t0) cc_final: 0.7570 (t0) REVERT: C 311 ASP cc_start: 0.7990 (p0) cc_final: 0.7387 (t0) REVERT: C 326 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7682 (ttp80) REVERT: C 336 LEU cc_start: 0.8550 (mp) cc_final: 0.8277 (mt) REVERT: C 389 ARG cc_start: 0.8365 (mtp180) cc_final: 0.8124 (ptp90) REVERT: C 395 VAL cc_start: 0.7769 (m) cc_final: 0.7555 (t) REVERT: D 31 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7837 (mm-30) REVERT: D 33 SER cc_start: 0.8326 (m) cc_final: 0.8051 (t) REVERT: D 52 VAL cc_start: 0.8109 (t) cc_final: 0.7814 (p) REVERT: D 63 ARG cc_start: 0.8530 (tpp80) cc_final: 0.7846 (ttm110) REVERT: D 102 TYR cc_start: 0.8475 (t80) cc_final: 0.8114 (t80) REVERT: D 133 ILE cc_start: 0.8452 (mm) cc_final: 0.8051 (mm) REVERT: D 138 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7490 (mm-30) REVERT: D 161 LYS cc_start: 0.8084 (tppt) cc_final: 0.7860 (mttp) REVERT: D 184 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7033 (mm-30) REVERT: D 247 MET cc_start: 0.7992 (tpp) cc_final: 0.7677 (mmp) REVERT: D 251 LYS cc_start: 0.7992 (mmtm) cc_final: 0.7751 (mmtm) REVERT: D 275 ARG cc_start: 0.8578 (mmt-90) cc_final: 0.8360 (mmt-90) REVERT: D 313 SER cc_start: 0.7685 (t) cc_final: 0.7344 (p) REVERT: D 346 ARG cc_start: 0.8161 (mtm110) cc_final: 0.7935 (ptm-80) REVERT: D 445 SER cc_start: 0.8535 (m) cc_final: 0.8120 (t) REVERT: D 446 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7915 (t) REVERT: E 23 VAL cc_start: 0.8426 (p) cc_final: 0.8072 (m) REVERT: E 53 MET cc_start: 0.6797 (ptp) cc_final: 0.6402 (ptp) REVERT: E 89 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7288 (tp30) REVERT: E 131 ASN cc_start: 0.8525 (t0) cc_final: 0.8238 (t0) REVERT: E 169 ARG cc_start: 0.5207 (OUTLIER) cc_final: 0.4964 (ptm160) REVERT: E 187 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7203 (mt) REVERT: E 232 MET cc_start: 0.8210 (tpp) cc_final: 0.7774 (mmt) REVERT: E 239 MET cc_start: 0.8325 (mmm) cc_final: 0.7844 (mmm) REVERT: E 280 LYS cc_start: 0.8280 (mttm) cc_final: 0.8064 (mtpt) REVERT: E 311 ASP cc_start: 0.7281 (p0) cc_final: 0.7057 (p0) REVERT: E 312 SER cc_start: 0.8046 (t) cc_final: 0.7698 (m) REVERT: E 373 ASN cc_start: 0.7610 (t0) cc_final: 0.7329 (t0) REVERT: E 387 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7243 (mm-30) REVERT: E 393 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7821 (mtm-85) REVERT: E 401 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5586 (mt-10) REVERT: F 29 GLU cc_start: 0.7825 (mp0) cc_final: 0.7342 (mp0) REVERT: F 66 PHE cc_start: 0.8159 (t80) cc_final: 0.7880 (t80) REVERT: F 193 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7568 (tt) REVERT: F 239 MET cc_start: 0.7831 (tpp) cc_final: 0.7575 (mmm) REVERT: F 311 ASP cc_start: 0.7558 (t0) cc_final: 0.7267 (t0) REVERT: F 387 GLU cc_start: 0.6980 (pm20) cc_final: 0.6752 (pm20) REVERT: F 419 GLU cc_start: 0.8449 (pt0) cc_final: 0.7797 (pt0) REVERT: F 456 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.6998 (ttt90) outliers start: 59 outliers final: 38 residues processed: 576 average time/residue: 0.1844 time to fit residues: 150.5425 Evaluate side-chains 569 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 523 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 189 ARG Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 459 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 184 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 152 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 200 optimal weight: 0.1980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 440 ASN D 278 GLN E 353 ASN F 62 HIS F 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120011 restraints weight = 30735.918| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.84 r_work: 0.3401 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21645 Z= 0.137 Angle : 0.518 10.176 29408 Z= 0.265 Chirality : 0.040 0.136 3349 Planarity : 0.004 0.049 3772 Dihedral : 13.141 172.018 3430 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.98 % Allowed : 12.24 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 2.19 (0.17), residues: 2636 helix: 2.80 (0.14), residues: 1416 sheet: 0.23 (0.29), residues: 367 loop : -0.33 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 393 TYR 0.015 0.001 TYR A 308 PHE 0.012 0.001 PHE A 457 TRP 0.005 0.001 TRP A 45 HIS 0.005 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (21645) covalent geometry : angle 0.51838 / 0.27 (29408) hydrogen bonds : bond 0.03927 / 2.64 ( 1215) hydrogen bonds : angle 3.99200 / 2.85 ( 3483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 543 time to evaluate : 0.636 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: A 53 MET cc_start: 0.7806 (mmm) cc_final: 0.7511 (mmm) REVERT: A 70 LYS cc_start: 0.8037 (tttt) cc_final: 0.7454 (ttpp) REVERT: A 71 SER cc_start: 0.7406 (m) cc_final: 0.7000 (p) REVERT: A 89 GLU cc_start: 0.8271 (tp30) cc_final: 0.7606 (tm-30) REVERT: A 133 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8682 (mt) REVERT: A 139 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8033 (tp) REVERT: A 149 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7605 (mtm180) REVERT: A 153 ASP cc_start: 0.8275 (t0) cc_final: 0.7972 (m-30) REVERT: A 161 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8325 (mmmm) REVERT: A 219 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7128 (mm-40) REVERT: A 257 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8560 (p) REVERT: A 298 MET cc_start: 0.6507 (tmm) cc_final: 0.5985 (tmm) REVERT: A 311 ASP cc_start: 0.7725 (t0) cc_final: 0.7512 (t0) REVERT: A 363 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.7513 (ttp80) REVERT: A 370 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8470 (ttmm) REVERT: A 387 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7243 (mt-10) REVERT: A 393 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7860 (mtt90) REVERT: A 428 LYS cc_start: 0.7776 (mttt) cc_final: 0.7571 (mttt) REVERT: B 58 TYR cc_start: 0.7275 (t80) cc_final: 0.6946 (t80) REVERT: B 96 ASP cc_start: 0.7788 (m-30) cc_final: 0.7576 (m-30) REVERT: B 102 TYR cc_start: 0.8002 (t80) cc_final: 0.7660 (t80) REVERT: B 108 LYS cc_start: 0.7922 (ttpp) cc_final: 0.7686 (ttpp) REVERT: B 159 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7951 (tp30) REVERT: B 177 LYS cc_start: 0.7875 (mtpp) cc_final: 0.7462 (mtpp) REVERT: B 189 ARG cc_start: 0.7477 (ttm170) cc_final: 0.7242 (ttm170) REVERT: B 242 CYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7486 (m) REVERT: B 247 MET cc_start: 0.7391 (tpp) cc_final: 0.7096 (tpp) REVERT: B 269 MET cc_start: 0.6403 (ttm) cc_final: 0.5948 (mtp) REVERT: B 272 SER cc_start: 0.8099 (t) cc_final: 0.7813 (p) REVERT: B 298 MET cc_start: 0.7722 (tmm) cc_final: 0.7183 (tmm) REVERT: B 300 ILE cc_start: 0.8076 (mt) cc_final: 0.7810 (mt) REVERT: B 302 MET cc_start: 0.8107 (mmm) cc_final: 0.7844 (mmp) REVERT: B 320 VAL cc_start: 0.7829 (OUTLIER) cc_final: 0.7466 (m) REVERT: B 327 ILE cc_start: 0.7163 (mm) cc_final: 0.6931 (mp) REVERT: B 331 HIS cc_start: 0.6466 (m-70) cc_final: 0.6167 (m90) REVERT: B 338 MET cc_start: 0.7741 (ttm) cc_final: 0.7428 (ttm) REVERT: B 386 LEU cc_start: 0.8299 (tp) cc_final: 0.7985 (tt) REVERT: B 387 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7666 (mm-30) REVERT: B 407 GLN cc_start: 0.7816 (mt0) cc_final: 0.7438 (mt0) REVERT: B 432 GLU cc_start: 0.6823 (tt0) cc_final: 0.6560 (tt0) REVERT: B 451 GLN cc_start: 0.6145 (mm-40) cc_final: 0.5771 (mm-40) REVERT: B 454 TYR cc_start: 0.7532 (m-80) cc_final: 0.7081 (m-80) REVERT: B 455 SER cc_start: 0.7114 (m) cc_final: 0.6746 (p) REVERT: C 44 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.7210 (mmt90) REVERT: C 70 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7796 (ttpt) REVERT: C 250 ASP cc_start: 0.7834 (t0) cc_final: 0.7569 (t0) REVERT: C 311 ASP cc_start: 0.8008 (p0) cc_final: 0.7360 (t0) REVERT: C 326 ARG cc_start: 0.8033 (ttm170) cc_final: 0.7682 (ttp80) REVERT: C 336 LEU cc_start: 0.8542 (mp) cc_final: 0.8287 (mp) REVERT: C 389 ARG cc_start: 0.8400 (mtp180) cc_final: 0.8097 (ptp90) REVERT: D 31 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7845 (mm-30) REVERT: D 33 SER cc_start: 0.8336 (m) cc_final: 0.8009 (t) REVERT: D 52 VAL cc_start: 0.8093 (t) cc_final: 0.7796 (p) REVERT: D 63 ARG cc_start: 0.8534 (tpp80) cc_final: 0.7834 (ttm110) REVERT: D 102 TYR cc_start: 0.8443 (t80) cc_final: 0.8135 (t80) REVERT: D 133 ILE cc_start: 0.8459 (mm) cc_final: 0.8073 (mm) REVERT: D 138 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7518 (mm-30) REVERT: D 161 LYS cc_start: 0.8095 (tppt) cc_final: 0.7866 (mttp) REVERT: D 184 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6994 (mm-30) REVERT: D 247 MET cc_start: 0.8000 (tpp) cc_final: 0.7686 (mmp) REVERT: D 251 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7762 (mmtm) REVERT: D 313 SER cc_start: 0.7676 (t) cc_final: 0.7347 (p) REVERT: D 346 ARG cc_start: 0.8165 (mtm110) cc_final: 0.7948 (ptm-80) REVERT: D 445 SER cc_start: 0.8547 (m) cc_final: 0.8096 (t) REVERT: D 446 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7919 (t) REVERT: E 23 VAL cc_start: 0.8416 (p) cc_final: 0.8069 (m) REVERT: E 53 MET cc_start: 0.6782 (ptp) cc_final: 0.6368 (ptp) REVERT: E 89 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7209 (tp30) REVERT: E 125 GLU cc_start: 0.7298 (pp20) cc_final: 0.6986 (pp20) REVERT: E 131 ASN cc_start: 0.8518 (t0) cc_final: 0.8216 (t0) REVERT: E 187 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7102 (mt) REVERT: E 232 MET cc_start: 0.8227 (tpp) cc_final: 0.7750 (mmt) REVERT: E 239 MET cc_start: 0.8306 (mmm) cc_final: 0.7797 (mmm) REVERT: E 266 MET cc_start: 0.8336 (mmm) cc_final: 0.8043 (tpt) REVERT: E 280 LYS cc_start: 0.8245 (mttm) cc_final: 0.8040 (mtpt) REVERT: E 311 ASP cc_start: 0.7280 (p0) cc_final: 0.7040 (p0) REVERT: E 312 SER cc_start: 0.8059 (t) cc_final: 0.7730 (m) REVERT: E 373 ASN cc_start: 0.7603 (t0) cc_final: 0.7319 (t0) REVERT: E 381 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7921 (mm-40) REVERT: E 393 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7830 (mtm-85) REVERT: E 401 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: F 29 GLU cc_start: 0.7831 (mp0) cc_final: 0.7348 (mp0) REVERT: F 66 PHE cc_start: 0.8161 (t80) cc_final: 0.7893 (t80) REVERT: F 125 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: F 193 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7597 (tt) REVERT: F 232 MET cc_start: 0.8269 (mmt) cc_final: 0.7656 (mmt) REVERT: F 239 MET cc_start: 0.7805 (tpp) cc_final: 0.7528 (mmm) REVERT: F 311 ASP cc_start: 0.7573 (t0) cc_final: 0.7361 (t0) REVERT: F 346 ARG cc_start: 0.7877 (mtp-110) cc_final: 0.7633 (mtp-110) REVERT: F 387 GLU cc_start: 0.6985 (pm20) cc_final: 0.6776 (pm20) REVERT: F 419 GLU cc_start: 0.8426 (pt0) cc_final: 0.7976 (pt0) REVERT: F 456 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.7042 (ttt90) outliers start: 67 outliers final: 37 residues processed: 581 average time/residue: 0.1828 time to fit residues: 149.9491 Evaluate side-chains 577 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 530 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 459 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 247 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 HIS D 219 GLN E 353 ASN F 62 HIS F 131 ASN F 440 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119014 restraints weight = 30671.486| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.97 r_work: 0.3382 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21645 Z= 0.172 Angle : 0.543 9.772 29408 Z= 0.278 Chirality : 0.042 0.159 3349 Planarity : 0.004 0.047 3772 Dihedral : 12.903 171.176 3428 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.29 % Allowed : 12.82 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.03 (0.17), residues: 2636 helix: 2.69 (0.14), residues: 1423 sheet: 0.13 (0.28), residues: 365 loop : -0.45 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 185 TYR 0.015 0.001 TYR C 87 PHE 0.016 0.002 PHE A 457 TRP 0.006 0.001 TRP A 45 HIS 0.006 0.001 HIS E 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (21645) covalent geometry : angle 0.54319 / 0.28 (29408) hydrogen bonds : bond 0.04251 / 2.85 ( 1215) hydrogen bonds : angle 4.00141 / 2.87 ( 3483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 545 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7776 (mmm) cc_final: 0.7457 (mmm) REVERT: A 70 LYS cc_start: 0.8054 (tttt) cc_final: 0.7485 (ttpp) REVERT: A 71 SER cc_start: 0.7429 (m) cc_final: 0.7054 (p) REVERT: A 89 GLU cc_start: 0.8247 (tp30) cc_final: 0.7565 (tm-30) REVERT: A 139 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8137 (tp) REVERT: A 150 ASN cc_start: 0.7476 (p0) cc_final: 0.7228 (p0) REVERT: A 153 ASP cc_start: 0.8275 (t0) cc_final: 0.7851 (m-30) REVERT: A 161 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8354 (mmmm) REVERT: A 219 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7032 (mm-40) REVERT: A 257 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 298 MET cc_start: 0.6613 (tmm) cc_final: 0.6065 (tmm) REVERT: A 311 ASP cc_start: 0.7824 (t0) cc_final: 0.7476 (t0) REVERT: A 326 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7347 (ttp80) REVERT: A 363 ARG cc_start: 0.7828 (ttp-170) cc_final: 0.7552 (ttp80) REVERT: A 387 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7258 (mt-10) REVERT: A 393 ARG cc_start: 0.8175 (mtt90) cc_final: 0.7877 (mtt90) REVERT: A 428 LYS cc_start: 0.7812 (mttt) cc_final: 0.7606 (mttt) REVERT: B 58 TYR cc_start: 0.7325 (t80) cc_final: 0.7024 (t80) REVERT: B 102 TYR cc_start: 0.7980 (t80) cc_final: 0.7674 (t80) REVERT: B 122 ILE cc_start: 0.8770 (mm) cc_final: 0.8371 (mm) REVERT: B 159 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7967 (tp30) REVERT: B 177 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7454 (mtpp) REVERT: B 184 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7030 (mm-30) REVERT: B 189 ARG cc_start: 0.7512 (ttm170) cc_final: 0.7261 (ttm170) REVERT: B 269 MET cc_start: 0.6494 (ttm) cc_final: 0.6031 (mtp) REVERT: B 272 SER cc_start: 0.8131 (t) cc_final: 0.7851 (p) REVERT: B 298 MET cc_start: 0.7735 (tmm) cc_final: 0.7218 (tmm) REVERT: B 300 ILE cc_start: 0.8110 (mt) cc_final: 0.7869 (mt) REVERT: B 302 MET cc_start: 0.8114 (mmm) cc_final: 0.7857 (mmp) REVERT: B 320 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7434 (m) REVERT: B 327 ILE cc_start: 0.7276 (mm) cc_final: 0.7033 (mp) REVERT: B 386 LEU cc_start: 0.8356 (tp) cc_final: 0.8043 (tt) REVERT: B 387 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7701 (mm-30) REVERT: B 407 GLN cc_start: 0.7885 (mt0) cc_final: 0.7500 (mt0) REVERT: B 432 GLU cc_start: 0.6858 (tt0) cc_final: 0.6593 (tt0) REVERT: B 451 GLN cc_start: 0.6208 (mm-40) cc_final: 0.5805 (mm-40) REVERT: B 454 TYR cc_start: 0.7619 (m-80) cc_final: 0.7149 (m-80) REVERT: B 455 SER cc_start: 0.7159 (m) cc_final: 0.6755 (p) REVERT: C 44 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7240 (mmt90) REVERT: C 70 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7824 (ttpt) REVERT: C 248 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7139 (mp0) REVERT: C 250 ASP cc_start: 0.7846 (t0) cc_final: 0.7589 (t0) REVERT: C 290 ASP cc_start: 0.7446 (m-30) cc_final: 0.7164 (m-30) REVERT: C 311 ASP cc_start: 0.8025 (p0) cc_final: 0.7378 (t0) REVERT: C 336 LEU cc_start: 0.8551 (mp) cc_final: 0.8293 (mp) REVERT: D 31 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7813 (mm-30) REVERT: D 32 GLN cc_start: 0.8582 (mt0) cc_final: 0.8187 (mm-40) REVERT: D 33 SER cc_start: 0.8418 (m) cc_final: 0.8097 (t) REVERT: D 52 VAL cc_start: 0.8100 (t) cc_final: 0.7813 (p) REVERT: D 63 ARG cc_start: 0.8525 (tpp80) cc_final: 0.7864 (ttm110) REVERT: D 102 TYR cc_start: 0.8458 (t80) cc_final: 0.8009 (t80) REVERT: D 161 LYS cc_start: 0.8106 (tppt) cc_final: 0.7878 (mttp) REVERT: D 184 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7025 (mm-30) REVERT: D 214 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8294 (ttmt) REVERT: D 247 MET cc_start: 0.8029 (tpp) cc_final: 0.7727 (mmp) REVERT: D 251 LYS cc_start: 0.8017 (mmtm) cc_final: 0.7804 (mmtm) REVERT: D 310 ASP cc_start: 0.7829 (t70) cc_final: 0.7270 (t0) REVERT: D 313 SER cc_start: 0.7699 (t) cc_final: 0.7365 (p) REVERT: D 346 ARG cc_start: 0.8217 (mtm110) cc_final: 0.7976 (ptm-80) REVERT: D 388 GLN cc_start: 0.8097 (mp10) cc_final: 0.7874 (mp10) REVERT: D 445 SER cc_start: 0.8515 (m) cc_final: 0.8128 (t) REVERT: D 459 ASN cc_start: 0.7840 (p0) cc_final: 0.7580 (p0) REVERT: E 23 VAL cc_start: 0.8362 (p) cc_final: 0.7992 (m) REVERT: E 53 MET cc_start: 0.6807 (ptp) cc_final: 0.6389 (ptp) REVERT: E 89 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7227 (tp30) REVERT: E 125 GLU cc_start: 0.7281 (pp20) cc_final: 0.6948 (pp20) REVERT: E 131 ASN cc_start: 0.8506 (t0) cc_final: 0.8216 (t0) REVERT: E 215 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8134 (p) REVERT: E 232 MET cc_start: 0.8212 (tpp) cc_final: 0.7755 (mmt) REVERT: E 239 MET cc_start: 0.8237 (mmm) cc_final: 0.7785 (mmm) REVERT: E 266 MET cc_start: 0.8252 (mmm) cc_final: 0.7988 (tpt) REVERT: E 311 ASP cc_start: 0.7308 (p0) cc_final: 0.7074 (p0) REVERT: E 312 SER cc_start: 0.8095 (t) cc_final: 0.7744 (m) REVERT: E 373 ASN cc_start: 0.7673 (t0) cc_final: 0.7361 (t0) REVERT: E 381 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7855 (mm-40) REVERT: E 393 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7830 (mtm-85) REVERT: F 29 GLU cc_start: 0.7825 (mp0) cc_final: 0.7363 (mp0) REVERT: F 66 PHE cc_start: 0.8191 (t80) cc_final: 0.7876 (t80) REVERT: F 125 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: F 129 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8529 (p) REVERT: F 193 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7676 (tt) REVERT: F 239 MET cc_start: 0.7843 (tpp) cc_final: 0.7625 (mmm) REVERT: F 298 MET cc_start: 0.7863 (mtp) cc_final: 0.7528 (mtm) REVERT: F 346 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7635 (mtp-110) REVERT: F 387 GLU cc_start: 0.6984 (pm20) cc_final: 0.6772 (pm20) REVERT: F 419 GLU cc_start: 0.8397 (pt0) cc_final: 0.7968 (pt0) REVERT: F 456 ARG cc_start: 0.7508 (ttm-80) cc_final: 0.7090 (ttt90) outliers start: 74 outliers final: 53 residues processed: 582 average time/residue: 0.1881 time to fit residues: 155.0066 Evaluate side-chains 599 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 539 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 189 ARG Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 247 MET Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 459 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 211 optimal weight: 0.0770 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 232 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 261 optimal weight: 0.1980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 HIS B 331 HIS E 353 ASN F 62 HIS F 131 ASN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120029 restraints weight = 30555.409| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.92 r_work: 0.3390 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21645 Z= 0.135 Angle : 0.529 10.976 29408 Z= 0.270 Chirality : 0.041 0.155 3349 Planarity : 0.004 0.045 3772 Dihedral : 12.701 171.917 3427 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.20 % Allowed : 14.02 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.06 (0.17), residues: 2636 helix: 2.72 (0.14), residues: 1421 sheet: 0.15 (0.28), residues: 358 loop : -0.44 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 321 TYR 0.019 0.001 TYR C 87 PHE 0.012 0.001 PHE A 457 TRP 0.006 0.001 TRP A 45 HIS 0.011 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (21645) covalent geometry : angle 0.52912 / 0.27 (29408) hydrogen bonds : bond 0.03902 / 2.62 ( 1215) hydrogen bonds : angle 3.91438 / 2.80 ( 3483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 533 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7829 (mmm) cc_final: 0.7532 (mmm) REVERT: A 70 LYS cc_start: 0.8042 (tttt) cc_final: 0.7628 (ttpp) REVERT: A 71 SER cc_start: 0.7437 (m) cc_final: 0.7170 (p) REVERT: A 132 LEU cc_start: 0.8390 (tt) cc_final: 0.8151 (tt) REVERT: A 139 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8120 (tp) REVERT: A 153 ASP cc_start: 0.8269 (t0) cc_final: 0.7874 (m-30) REVERT: A 161 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8310 (mmmm) REVERT: A 219 GLN cc_start: 0.7569 (mm-40) cc_final: 0.7101 (mm-40) REVERT: A 257 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8525 (p) REVERT: A 298 MET cc_start: 0.6577 (tmm) cc_final: 0.6029 (tmm) REVERT: A 311 ASP cc_start: 0.7810 (t0) cc_final: 0.7556 (t0) REVERT: A 326 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7384 (ttp80) REVERT: A 363 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7520 (ttp80) REVERT: A 387 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7446 (mt-10) REVERT: A 393 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7860 (mtt90) REVERT: A 428 LYS cc_start: 0.7758 (mttt) cc_final: 0.7549 (mttt) REVERT: B 58 TYR cc_start: 0.7359 (t80) cc_final: 0.7044 (t80) REVERT: B 102 TYR cc_start: 0.7940 (t80) cc_final: 0.7624 (t80) REVERT: B 122 ILE cc_start: 0.8808 (mm) cc_final: 0.8382 (mm) REVERT: B 159 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7939 (tp30) REVERT: B 177 LYS cc_start: 0.7882 (mtpp) cc_final: 0.7472 (mtpp) REVERT: B 184 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6996 (mm-30) REVERT: B 189 ARG cc_start: 0.7479 (ttm170) cc_final: 0.7249 (ttm170) REVERT: B 213 LYS cc_start: 0.7931 (tttt) cc_final: 0.7671 (tttt) REVERT: B 242 CYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7613 (m) REVERT: B 269 MET cc_start: 0.6418 (ttm) cc_final: 0.5925 (mtp) REVERT: B 272 SER cc_start: 0.8108 (t) cc_final: 0.7808 (p) REVERT: B 298 MET cc_start: 0.7755 (tmm) cc_final: 0.7225 (tmm) REVERT: B 300 ILE cc_start: 0.8111 (mt) cc_final: 0.7870 (mt) REVERT: B 302 MET cc_start: 0.8079 (mmm) cc_final: 0.7833 (mmp) REVERT: B 320 VAL cc_start: 0.7744 (OUTLIER) cc_final: 0.7344 (m) REVERT: B 327 ILE cc_start: 0.7178 (mm) cc_final: 0.6942 (mp) REVERT: B 372 LEU cc_start: 0.7250 (mt) cc_final: 0.7038 (mp) REVERT: B 386 LEU cc_start: 0.8326 (tp) cc_final: 0.8057 (tt) REVERT: B 387 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7663 (mm-30) REVERT: B 407 GLN cc_start: 0.7850 (mt0) cc_final: 0.7499 (mt0) REVERT: B 432 GLU cc_start: 0.6876 (tt0) cc_final: 0.6619 (tt0) REVERT: B 451 GLN cc_start: 0.6188 (mm-40) cc_final: 0.5790 (mm-40) REVERT: B 454 TYR cc_start: 0.7670 (m-80) cc_final: 0.7235 (m-80) REVERT: B 455 SER cc_start: 0.7128 (m) cc_final: 0.6712 (p) REVERT: C 44 ARG cc_start: 0.7670 (mmm-85) cc_final: 0.7230 (mmt90) REVERT: C 70 LYS cc_start: 0.8152 (ttpt) cc_final: 0.7833 (ttpt) REVERT: C 248 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7103 (mp0) REVERT: C 250 ASP cc_start: 0.7851 (t0) cc_final: 0.7589 (t0) REVERT: C 311 ASP cc_start: 0.8033 (p0) cc_final: 0.7373 (t0) REVERT: C 321 ARG cc_start: 0.7321 (ttt-90) cc_final: 0.6923 (ttt90) REVERT: C 326 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7715 (ttm170) REVERT: C 336 LEU cc_start: 0.8542 (mp) cc_final: 0.8287 (mp) REVERT: C 345 MET cc_start: 0.8620 (mtt) cc_final: 0.8398 (mtp) REVERT: D 31 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7807 (mm-30) REVERT: D 32 GLN cc_start: 0.8572 (mt0) cc_final: 0.8119 (mm-40) REVERT: D 33 SER cc_start: 0.8399 (m) cc_final: 0.8072 (t) REVERT: D 52 VAL cc_start: 0.8083 (t) cc_final: 0.7774 (p) REVERT: D 63 ARG cc_start: 0.8528 (tpp80) cc_final: 0.7804 (ttm110) REVERT: D 102 TYR cc_start: 0.8465 (t80) cc_final: 0.8012 (t80) REVERT: D 122 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8120 (pt) REVERT: D 161 LYS cc_start: 0.8106 (tppt) cc_final: 0.7870 (mttp) REVERT: D 184 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7005 (mm-30) REVERT: D 214 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8260 (ttmt) REVERT: D 247 MET cc_start: 0.8043 (tpp) cc_final: 0.7746 (mmp) REVERT: D 313 SER cc_start: 0.7681 (t) cc_final: 0.7353 (p) REVERT: D 346 ARG cc_start: 0.8229 (mtm110) cc_final: 0.7992 (ptm-80) REVERT: D 388 GLN cc_start: 0.8074 (mp10) cc_final: 0.7825 (mp10) REVERT: D 445 SER cc_start: 0.8531 (m) cc_final: 0.8120 (t) REVERT: E 23 VAL cc_start: 0.8296 (p) cc_final: 0.7930 (m) REVERT: E 53 MET cc_start: 0.6854 (ptp) cc_final: 0.6405 (ptp) REVERT: E 89 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7218 (tp30) REVERT: E 125 GLU cc_start: 0.7357 (pp20) cc_final: 0.6979 (pp20) REVERT: E 131 ASN cc_start: 0.8502 (t0) cc_final: 0.8182 (t0) REVERT: E 215 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8100 (p) REVERT: E 232 MET cc_start: 0.8233 (tpp) cc_final: 0.7746 (mmt) REVERT: E 239 MET cc_start: 0.8155 (mmm) cc_final: 0.7741 (mmm) REVERT: E 266 MET cc_start: 0.8209 (mmm) cc_final: 0.7980 (tpt) REVERT: E 311 ASP cc_start: 0.7304 (p0) cc_final: 0.7081 (p0) REVERT: E 312 SER cc_start: 0.8091 (t) cc_final: 0.7739 (m) REVERT: E 373 ASN cc_start: 0.7626 (t0) cc_final: 0.7334 (t0) REVERT: E 381 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7869 (mm-40) REVERT: E 393 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7822 (mtm-85) REVERT: F 29 GLU cc_start: 0.7783 (mp0) cc_final: 0.7331 (mp0) REVERT: F 66 PHE cc_start: 0.8186 (t80) cc_final: 0.7903 (t80) REVERT: F 125 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: F 129 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8509 (p) REVERT: F 239 MET cc_start: 0.7797 (tpp) cc_final: 0.7491 (mmm) REVERT: F 251 LYS cc_start: 0.7877 (mttp) cc_final: 0.7076 (mmtt) REVERT: F 346 ARG cc_start: 0.7879 (mtp-110) cc_final: 0.7634 (mtp-110) REVERT: F 387 GLU cc_start: 0.7005 (pm20) cc_final: 0.6790 (pm20) REVERT: F 419 GLU cc_start: 0.8414 (pt0) cc_final: 0.7951 (pt0) REVERT: F 456 ARG cc_start: 0.7491 (ttm-80) cc_final: 0.7096 (ttt90) outliers start: 72 outliers final: 51 residues processed: 572 average time/residue: 0.1788 time to fit residues: 144.8019 Evaluate side-chains 589 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 530 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 189 ARG Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 459 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 156 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 261 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 98 optimal weight: 0.0670 chunk 61 optimal weight: 0.3980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 HIS E 353 ASN F 62 HIS F 131 ASN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.144124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119312 restraints weight = 30626.023| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.91 r_work: 0.3392 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21645 Z= 0.133 Angle : 0.535 13.493 29408 Z= 0.270 Chirality : 0.040 0.151 3349 Planarity : 0.004 0.044 3772 Dihedral : 12.565 171.978 3427 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.56 % Allowed : 13.48 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.07 (0.17), residues: 2636 helix: 2.73 (0.14), residues: 1421 sheet: 0.16 (0.28), residues: 358 loop : -0.45 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 91 TYR 0.011 0.001 TYR E 194 PHE 0.011 0.001 PHE A 457 TRP 0.006 0.001 TRP A 45 HIS 0.018 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (21645) covalent geometry : angle 0.53482 / 0.27 (29408) hydrogen bonds : bond 0.03798 / 2.55 ( 1215) hydrogen bonds : angle 3.87761 / 2.78 ( 3483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 534 time to evaluate : 0.708 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: A 53 MET cc_start: 0.7775 (mmm) cc_final: 0.7490 (mmm) REVERT: A 70 LYS cc_start: 0.8090 (tttt) cc_final: 0.7473 (ttpp) REVERT: A 71 SER cc_start: 0.7430 (m) cc_final: 0.7050 (p) REVERT: A 132 LEU cc_start: 0.8401 (tt) cc_final: 0.8135 (tt) REVERT: A 139 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8115 (tp) REVERT: A 153 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: A 161 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8301 (mmmm) REVERT: A 219 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7102 (mm-40) REVERT: A 257 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8542 (p) REVERT: A 269 MET cc_start: 0.7682 (ttm) cc_final: 0.7443 (ttm) REVERT: A 287 ASP cc_start: 0.7176 (p0) cc_final: 0.6715 (p0) REVERT: A 298 MET cc_start: 0.6597 (tmm) cc_final: 0.6036 (tmm) REVERT: A 326 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7600 (ttp80) REVERT: A 363 ARG cc_start: 0.7812 (ttp-170) cc_final: 0.7536 (ttp80) REVERT: A 387 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7456 (mt-10) REVERT: A 393 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7870 (mtt90) REVERT: A 428 LYS cc_start: 0.7754 (mttt) cc_final: 0.7545 (mttt) REVERT: B 58 TYR cc_start: 0.7369 (t80) cc_final: 0.7033 (t80) REVERT: B 80 ASP cc_start: 0.8219 (p0) cc_final: 0.7947 (p0) REVERT: B 102 TYR cc_start: 0.7930 (t80) cc_final: 0.7607 (t80) REVERT: B 122 ILE cc_start: 0.8745 (mm) cc_final: 0.8344 (mm) REVERT: B 159 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8059 (tp30) REVERT: B 177 LYS cc_start: 0.7880 (mtpp) cc_final: 0.7470 (mtpp) REVERT: B 189 ARG cc_start: 0.7503 (ttm170) cc_final: 0.7270 (ttm170) REVERT: B 213 LYS cc_start: 0.7916 (tttt) cc_final: 0.7608 (tttt) REVERT: B 242 CYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7535 (m) REVERT: B 269 MET cc_start: 0.6422 (ttm) cc_final: 0.5941 (mtp) REVERT: B 272 SER cc_start: 0.8096 (t) cc_final: 0.7819 (p) REVERT: B 298 MET cc_start: 0.7739 (tmm) cc_final: 0.7206 (tmm) REVERT: B 300 ILE cc_start: 0.8115 (mt) cc_final: 0.7874 (mt) REVERT: B 302 MET cc_start: 0.8038 (mmm) cc_final: 0.7790 (mmp) REVERT: B 320 VAL cc_start: 0.7753 (p) cc_final: 0.7339 (m) REVERT: B 327 ILE cc_start: 0.7164 (mm) cc_final: 0.6915 (mp) REVERT: B 338 MET cc_start: 0.7783 (ttm) cc_final: 0.7557 (ttm) REVERT: B 343 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7317 (mt0) REVERT: B 372 LEU cc_start: 0.7222 (mt) cc_final: 0.7012 (mp) REVERT: B 386 LEU cc_start: 0.8313 (tp) cc_final: 0.8005 (tt) REVERT: B 387 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7657 (mm-30) REVERT: B 398 ASP cc_start: 0.7884 (m-30) cc_final: 0.7539 (m-30) REVERT: B 432 GLU cc_start: 0.6925 (tt0) cc_final: 0.6637 (tt0) REVERT: B 451 GLN cc_start: 0.6178 (mm-40) cc_final: 0.5779 (mm-40) REVERT: B 454 TYR cc_start: 0.7564 (m-80) cc_final: 0.7138 (m-80) REVERT: B 455 SER cc_start: 0.7118 (m) cc_final: 0.6695 (p) REVERT: C 44 ARG cc_start: 0.7620 (mmm-85) cc_final: 0.7179 (mmt90) REVERT: C 70 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7850 (ttpt) REVERT: C 91 ARG cc_start: 0.8420 (mtt90) cc_final: 0.8075 (mtm180) REVERT: C 248 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7089 (mp0) REVERT: C 250 ASP cc_start: 0.7807 (t0) cc_final: 0.7535 (t0) REVERT: C 311 ASP cc_start: 0.8035 (p0) cc_final: 0.7378 (t0) REVERT: C 326 ARG cc_start: 0.7978 (ttm170) cc_final: 0.7647 (ttm170) REVERT: C 336 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8307 (mp) REVERT: C 345 MET cc_start: 0.8623 (mtt) cc_final: 0.8420 (mtp) REVERT: D 31 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7835 (mm-30) REVERT: D 33 SER cc_start: 0.8394 (m) cc_final: 0.8071 (t) REVERT: D 52 VAL cc_start: 0.8076 (t) cc_final: 0.7762 (p) REVERT: D 63 ARG cc_start: 0.8515 (tpp80) cc_final: 0.7805 (ttm110) REVERT: D 102 TYR cc_start: 0.8476 (t80) cc_final: 0.8145 (t80) REVERT: D 122 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8087 (pt) REVERT: D 161 LYS cc_start: 0.8082 (tppt) cc_final: 0.7856 (mttp) REVERT: D 184 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7001 (mm-30) REVERT: D 247 MET cc_start: 0.8034 (tpp) cc_final: 0.7730 (mmp) REVERT: D 251 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7768 (mmtm) REVERT: D 313 SER cc_start: 0.7701 (t) cc_final: 0.7378 (p) REVERT: D 327 ILE cc_start: 0.7650 (mm) cc_final: 0.7432 (mm) REVERT: D 346 ARG cc_start: 0.8232 (mtm110) cc_final: 0.7995 (ptm-80) REVERT: D 388 GLN cc_start: 0.8071 (mp10) cc_final: 0.7798 (mp10) REVERT: D 445 SER cc_start: 0.8538 (m) cc_final: 0.8110 (t) REVERT: E 23 VAL cc_start: 0.8272 (p) cc_final: 0.7885 (m) REVERT: E 89 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7214 (tp30) REVERT: E 125 GLU cc_start: 0.7313 (pp20) cc_final: 0.6921 (pp20) REVERT: E 131 ASN cc_start: 0.8479 (t0) cc_final: 0.8150 (t0) REVERT: E 215 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8110 (p) REVERT: E 232 MET cc_start: 0.8242 (tpp) cc_final: 0.7759 (mmt) REVERT: E 239 MET cc_start: 0.8117 (mmm) cc_final: 0.7718 (mmm) REVERT: E 311 ASP cc_start: 0.7312 (p0) cc_final: 0.7075 (p0) REVERT: E 312 SER cc_start: 0.8089 (t) cc_final: 0.7740 (m) REVERT: E 373 ASN cc_start: 0.7613 (t0) cc_final: 0.7309 (t0) REVERT: E 381 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7883 (mm-40) REVERT: E 393 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7820 (mtm-85) REVERT: F 29 GLU cc_start: 0.7797 (mp0) cc_final: 0.7344 (mp0) REVERT: F 66 PHE cc_start: 0.8185 (t80) cc_final: 0.7854 (t80) REVERT: F 129 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8525 (p) REVERT: F 239 MET cc_start: 0.7785 (tpp) cc_final: 0.7485 (mmm) REVERT: F 251 LYS cc_start: 0.7861 (mttp) cc_final: 0.7064 (mmtt) REVERT: F 346 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7645 (mtp-110) REVERT: F 419 GLU cc_start: 0.8405 (pt0) cc_final: 0.7966 (pt0) REVERT: F 456 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.7113 (ttt90) outliers start: 80 outliers final: 58 residues processed: 579 average time/residue: 0.1828 time to fit residues: 149.6374 Evaluate side-chains 595 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 528 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 189 ARG Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 459 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 45 optimal weight: 0.8980 chunk 242 optimal weight: 0.6980 chunk 230 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 175 optimal weight: 0.0770 chunk 76 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 221 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 84 optimal weight: 0.0270 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 331 HIS E 353 ASN F 62 HIS F 131 ASN ** F 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119699 restraints weight = 30729.858| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.84 r_work: 0.3397 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21645 Z= 0.129 Angle : 0.533 12.565 29408 Z= 0.268 Chirality : 0.040 0.145 3349 Planarity : 0.004 0.043 3772 Dihedral : 12.439 172.060 3426 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.07 % Allowed : 14.15 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.09 (0.17), residues: 2636 helix: 2.76 (0.14), residues: 1417 sheet: 0.20 (0.29), residues: 351 loop : -0.47 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 282 TYR 0.011 0.001 TYR E 194 PHE 0.011 0.001 PHE A 457 TRP 0.006 0.001 TRP A 45 HIS 0.005 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (21645) covalent geometry : angle 0.53285 / 0.27 (29408) hydrogen bonds : bond 0.03711 / 2.50 ( 1215) hydrogen bonds : angle 3.84297 / 2.75 ( 3483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 535 time to evaluate : 0.706 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: A 53 MET cc_start: 0.7748 (mmm) cc_final: 0.7448 (mmm) REVERT: A 70 LYS cc_start: 0.8083 (tttt) cc_final: 0.7483 (ttpp) REVERT: A 71 SER cc_start: 0.7416 (m) cc_final: 0.7047 (p) REVERT: A 132 LEU cc_start: 0.8400 (tt) cc_final: 0.8139 (tt) REVERT: A 139 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8115 (tp) REVERT: A 153 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: A 161 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8325 (mmmm) REVERT: A 219 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7102 (mm-40) REVERT: A 257 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8533 (p) REVERT: A 269 MET cc_start: 0.7682 (ttm) cc_final: 0.7450 (ttm) REVERT: A 280 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7525 (ttmm) REVERT: A 287 ASP cc_start: 0.7220 (p0) cc_final: 0.6799 (p0) REVERT: A 298 MET cc_start: 0.6611 (tmm) cc_final: 0.6055 (tmm) REVERT: A 311 ASP cc_start: 0.7803 (t0) cc_final: 0.7553 (t0) REVERT: A 326 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7612 (ttp80) REVERT: A 363 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7536 (ttp80) REVERT: A 387 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7441 (mt-10) REVERT: A 393 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7904 (mtt90) REVERT: A 428 LYS cc_start: 0.7765 (mttt) cc_final: 0.7553 (mttt) REVERT: B 58 TYR cc_start: 0.7346 (t80) cc_final: 0.7023 (t80) REVERT: B 80 ASP cc_start: 0.8194 (p0) cc_final: 0.7923 (p0) REVERT: B 102 TYR cc_start: 0.7936 (t80) cc_final: 0.7612 (t80) REVERT: B 122 ILE cc_start: 0.8735 (mm) cc_final: 0.8343 (mm) REVERT: B 159 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8036 (tp30) REVERT: B 177 LYS cc_start: 0.7879 (mtpp) cc_final: 0.7472 (mtpp) REVERT: B 213 LYS cc_start: 0.7914 (tttt) cc_final: 0.7614 (tttt) REVERT: B 242 CYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7432 (m) REVERT: B 269 MET cc_start: 0.6430 (ttm) cc_final: 0.5948 (mtp) REVERT: B 272 SER cc_start: 0.8100 (t) cc_final: 0.7833 (p) REVERT: B 298 MET cc_start: 0.7744 (tmm) cc_final: 0.7224 (tmm) REVERT: B 300 ILE cc_start: 0.8131 (mt) cc_final: 0.7891 (mt) REVERT: B 302 MET cc_start: 0.8070 (mmm) cc_final: 0.7816 (mmp) REVERT: B 320 VAL cc_start: 0.7789 (p) cc_final: 0.7385 (m) REVERT: B 327 ILE cc_start: 0.7221 (mm) cc_final: 0.6982 (mp) REVERT: B 338 MET cc_start: 0.7751 (ttm) cc_final: 0.7516 (ttm) REVERT: B 343 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7293 (mt0) REVERT: B 386 LEU cc_start: 0.8305 (tp) cc_final: 0.7984 (tt) REVERT: B 387 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7649 (mm-30) REVERT: B 398 ASP cc_start: 0.7907 (m-30) cc_final: 0.7575 (m-30) REVERT: B 432 GLU cc_start: 0.6911 (tt0) cc_final: 0.6629 (tt0) REVERT: B 451 GLN cc_start: 0.6194 (mm-40) cc_final: 0.5802 (mm-40) REVERT: B 454 TYR cc_start: 0.7527 (m-80) cc_final: 0.7103 (m-80) REVERT: B 455 SER cc_start: 0.7093 (m) cc_final: 0.6676 (p) REVERT: C 44 ARG cc_start: 0.7622 (mmm-85) cc_final: 0.7181 (mmt90) REVERT: C 70 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7848 (ttpt) REVERT: C 91 ARG cc_start: 0.8411 (mtt90) cc_final: 0.8104 (mtm180) REVERT: C 248 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7090 (mp0) REVERT: C 250 ASP cc_start: 0.7783 (t0) cc_final: 0.7525 (t0) REVERT: C 298 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7857 (ttm) REVERT: C 321 ARG cc_start: 0.7384 (ttt-90) cc_final: 0.7038 (ttt90) REVERT: C 326 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7662 (ttm170) REVERT: C 336 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8294 (mp) REVERT: C 345 MET cc_start: 0.8631 (mtt) cc_final: 0.8427 (mtp) REVERT: D 31 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7851 (mm-30) REVERT: D 32 GLN cc_start: 0.8564 (mt0) cc_final: 0.8145 (mm-40) REVERT: D 33 SER cc_start: 0.8409 (m) cc_final: 0.8092 (t) REVERT: D 52 VAL cc_start: 0.8077 (t) cc_final: 0.7759 (p) REVERT: D 63 ARG cc_start: 0.8505 (tpp80) cc_final: 0.7806 (ttm110) REVERT: D 102 TYR cc_start: 0.8452 (t80) cc_final: 0.8011 (t80) REVERT: D 161 LYS cc_start: 0.8051 (tppt) cc_final: 0.7832 (mttp) REVERT: D 184 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7107 (mm-30) REVERT: D 247 MET cc_start: 0.8048 (tpp) cc_final: 0.7751 (mmp) REVERT: D 251 LYS cc_start: 0.7997 (mmtm) cc_final: 0.7763 (mmtm) REVERT: D 313 SER cc_start: 0.7701 (t) cc_final: 0.7378 (p) REVERT: D 327 ILE cc_start: 0.7638 (mm) cc_final: 0.7410 (mm) REVERT: D 346 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7991 (ptm-80) REVERT: D 388 GLN cc_start: 0.8071 (mp10) cc_final: 0.7776 (mp10) REVERT: D 445 SER cc_start: 0.8527 (m) cc_final: 0.8083 (t) REVERT: D 446 VAL cc_start: 0.8166 (m) cc_final: 0.7818 (t) REVERT: E 23 VAL cc_start: 0.8286 (p) cc_final: 0.7899 (m) REVERT: E 89 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7219 (tp30) REVERT: E 125 GLU cc_start: 0.7256 (pp20) cc_final: 0.6862 (pp20) REVERT: E 131 ASN cc_start: 0.8484 (t0) cc_final: 0.8147 (t0) REVERT: E 215 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8165 (p) REVERT: E 232 MET cc_start: 0.8241 (tpp) cc_final: 0.7759 (mmt) REVERT: E 239 MET cc_start: 0.8149 (mmm) cc_final: 0.7741 (mmm) REVERT: E 311 ASP cc_start: 0.7311 (p0) cc_final: 0.7087 (p0) REVERT: E 312 SER cc_start: 0.8087 (t) cc_final: 0.7745 (m) REVERT: E 373 ASN cc_start: 0.7603 (t0) cc_final: 0.7305 (t0) REVERT: E 381 GLN cc_start: 0.8088 (mm-40) cc_final: 0.7872 (mm-40) REVERT: E 393 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7838 (mtm-85) REVERT: F 29 GLU cc_start: 0.7704 (mp0) cc_final: 0.7274 (mp0) REVERT: F 66 PHE cc_start: 0.8185 (t80) cc_final: 0.7857 (t80) REVERT: F 129 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8564 (p) REVERT: F 239 MET cc_start: 0.7804 (tpp) cc_final: 0.7488 (mmm) REVERT: F 346 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7648 (mtp-110) REVERT: F 419 GLU cc_start: 0.8393 (pt0) cc_final: 0.7949 (pt0) REVERT: F 456 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7128 (ttt90) outliers start: 69 outliers final: 53 residues processed: 576 average time/residue: 0.1941 time to fit residues: 157.4613 Evaluate side-chains 591 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 529 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 298 MET Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 459 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 127 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 167 optimal weight: 0.0470 chunk 91 optimal weight: 0.0980 chunk 203 optimal weight: 0.8980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 353 ASN F 62 HIS F 131 ASN F 440 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119637 restraints weight = 30751.257| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.92 r_work: 0.3393 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21645 Z= 0.133 Angle : 0.542 12.358 29408 Z= 0.271 Chirality : 0.040 0.171 3349 Planarity : 0.004 0.042 3772 Dihedral : 12.352 171.953 3422 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.94 % Allowed : 14.20 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.09 (0.17), residues: 2636 helix: 2.74 (0.14), residues: 1423 sheet: 0.20 (0.29), residues: 351 loop : -0.44 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 189 TYR 0.011 0.001 TYR E 194 PHE 0.011 0.001 PHE A 457 TRP 0.006 0.001 TRP A 45 HIS 0.004 0.001 HIS E 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (21645) covalent geometry : angle 0.54197 / 0.27 (29408) hydrogen bonds : bond 0.03722 / 2.50 ( 1215) hydrogen bonds : angle 3.82792 / 2.74 ( 3483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 535 time to evaluate : 0.795 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: A 53 MET cc_start: 0.7773 (mmm) cc_final: 0.7460 (mmm) REVERT: A 70 LYS cc_start: 0.8088 (tttt) cc_final: 0.7488 (ttpp) REVERT: A 71 SER cc_start: 0.7440 (m) cc_final: 0.7060 (p) REVERT: A 132 LEU cc_start: 0.8366 (tt) cc_final: 0.8116 (tt) REVERT: A 139 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8090 (tp) REVERT: A 153 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: A 161 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8312 (mmmm) REVERT: A 257 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8537 (p) REVERT: A 269 MET cc_start: 0.7658 (ttm) cc_final: 0.7442 (ttm) REVERT: A 280 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7518 (ttmm) REVERT: A 287 ASP cc_start: 0.7182 (p0) cc_final: 0.6722 (p0) REVERT: A 298 MET cc_start: 0.6608 (tmm) cc_final: 0.6033 (tmm) REVERT: A 311 ASP cc_start: 0.7827 (t0) cc_final: 0.7577 (t0) REVERT: A 326 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7595 (ttp80) REVERT: A 338 MET cc_start: 0.7390 (tmm) cc_final: 0.7188 (tmm) REVERT: A 363 ARG cc_start: 0.7822 (ttp-170) cc_final: 0.7544 (ttp80) REVERT: A 384 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7556 (ptm160) REVERT: A 387 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 393 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7894 (mtt90) REVERT: A 428 LYS cc_start: 0.7754 (mttt) cc_final: 0.7537 (mttt) REVERT: B 58 TYR cc_start: 0.7371 (t80) cc_final: 0.7036 (t80) REVERT: B 59 SER cc_start: 0.7992 (t) cc_final: 0.7750 (t) REVERT: B 80 ASP cc_start: 0.8229 (p0) cc_final: 0.7971 (p0) REVERT: B 102 TYR cc_start: 0.7966 (t80) cc_final: 0.7634 (t80) REVERT: B 122 ILE cc_start: 0.8745 (mm) cc_final: 0.8367 (mm) REVERT: B 159 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8033 (tp30) REVERT: B 177 LYS cc_start: 0.7885 (mtpp) cc_final: 0.7475 (mtpp) REVERT: B 213 LYS cc_start: 0.7933 (tttt) cc_final: 0.7628 (tttt) REVERT: B 242 CYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7405 (m) REVERT: B 269 MET cc_start: 0.6457 (ttm) cc_final: 0.5968 (mtp) REVERT: B 272 SER cc_start: 0.8089 (t) cc_final: 0.7807 (p) REVERT: B 298 MET cc_start: 0.7767 (tmm) cc_final: 0.7251 (tmm) REVERT: B 300 ILE cc_start: 0.8115 (mt) cc_final: 0.7878 (mt) REVERT: B 302 MET cc_start: 0.8082 (mmm) cc_final: 0.7833 (mmp) REVERT: B 310 ASP cc_start: 0.7400 (t0) cc_final: 0.6810 (t0) REVERT: B 311 ASP cc_start: 0.7091 (t0) cc_final: 0.6731 (t70) REVERT: B 320 VAL cc_start: 0.7748 (p) cc_final: 0.7352 (m) REVERT: B 327 ILE cc_start: 0.7192 (mm) cc_final: 0.6966 (mp) REVERT: B 331 HIS cc_start: 0.6292 (m-70) cc_final: 0.6044 (m-70) REVERT: B 338 MET cc_start: 0.7774 (ttm) cc_final: 0.7527 (ttm) REVERT: B 343 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7253 (mt0) REVERT: B 381 GLN cc_start: 0.7836 (mt0) cc_final: 0.7530 (mt0) REVERT: B 385 SER cc_start: 0.8461 (p) cc_final: 0.8146 (p) REVERT: B 386 LEU cc_start: 0.8304 (tp) cc_final: 0.7949 (tt) REVERT: B 387 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7679 (mm-30) REVERT: B 398 ASP cc_start: 0.7912 (m-30) cc_final: 0.7577 (m-30) REVERT: B 400 ARG cc_start: 0.7273 (mtm180) cc_final: 0.7060 (mmm-85) REVERT: B 432 GLU cc_start: 0.6873 (tt0) cc_final: 0.6587 (tt0) REVERT: B 451 GLN cc_start: 0.6195 (mm-40) cc_final: 0.5793 (mm-40) REVERT: B 454 TYR cc_start: 0.7524 (m-80) cc_final: 0.7092 (m-80) REVERT: B 455 SER cc_start: 0.7108 (m) cc_final: 0.6680 (p) REVERT: C 44 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7176 (mmt90) REVERT: C 70 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7842 (ttpt) REVERT: C 91 ARG cc_start: 0.8515 (mtt90) cc_final: 0.8125 (mtm180) REVERT: C 248 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7082 (mp0) REVERT: C 250 ASP cc_start: 0.7804 (t0) cc_final: 0.7529 (t0) REVERT: C 321 ARG cc_start: 0.7377 (ttt-90) cc_final: 0.7021 (ttt90) REVERT: C 326 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7588 (ttm170) REVERT: C 336 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8350 (mp) REVERT: C 346 ARG cc_start: 0.8805 (ptt-90) cc_final: 0.8498 (ptt-90) REVERT: D 31 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7906 (mm-30) REVERT: D 32 GLN cc_start: 0.8572 (mt0) cc_final: 0.8126 (mm-40) REVERT: D 33 SER cc_start: 0.8401 (m) cc_final: 0.8071 (t) REVERT: D 52 VAL cc_start: 0.8085 (t) cc_final: 0.7755 (p) REVERT: D 63 ARG cc_start: 0.8511 (ttp80) cc_final: 0.7797 (ttm110) REVERT: D 102 TYR cc_start: 0.8494 (t80) cc_final: 0.8045 (t80) REVERT: D 161 LYS cc_start: 0.8040 (tppt) cc_final: 0.7818 (mttp) REVERT: D 184 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7148 (mm-30) REVERT: D 247 MET cc_start: 0.8050 (tpp) cc_final: 0.7746 (mmp) REVERT: D 251 LYS cc_start: 0.7995 (mmtm) cc_final: 0.7764 (mmtm) REVERT: D 327 ILE cc_start: 0.7606 (mm) cc_final: 0.7379 (mm) REVERT: D 346 ARG cc_start: 0.8235 (mtm110) cc_final: 0.7997 (ptm-80) REVERT: D 388 GLN cc_start: 0.8051 (mp10) cc_final: 0.7763 (mp10) REVERT: D 445 SER cc_start: 0.8539 (m) cc_final: 0.8086 (t) REVERT: D 446 VAL cc_start: 0.8176 (m) cc_final: 0.7818 (t) REVERT: E 23 VAL cc_start: 0.8268 (p) cc_final: 0.7878 (m) REVERT: E 89 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7207 (tp30) REVERT: E 131 ASN cc_start: 0.8474 (t0) cc_final: 0.8131 (t0) REVERT: E 215 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8148 (p) REVERT: E 232 MET cc_start: 0.8243 (tpp) cc_final: 0.7771 (mmt) REVERT: E 239 MET cc_start: 0.8132 (mmm) cc_final: 0.7733 (mmm) REVERT: E 311 ASP cc_start: 0.7334 (p0) cc_final: 0.7103 (p0) REVERT: E 312 SER cc_start: 0.8090 (t) cc_final: 0.7754 (m) REVERT: E 373 ASN cc_start: 0.7612 (t0) cc_final: 0.7306 (t0) REVERT: E 381 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7884 (mm-40) REVERT: E 393 ARG cc_start: 0.8065 (mtm-85) cc_final: 0.7827 (mtm-85) REVERT: F 29 GLU cc_start: 0.7720 (mp0) cc_final: 0.7279 (mp0) REVERT: F 66 PHE cc_start: 0.8194 (t80) cc_final: 0.7859 (t80) REVERT: F 129 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8525 (p) REVERT: F 157 LEU cc_start: 0.8570 (tp) cc_final: 0.8233 (tt) REVERT: F 239 MET cc_start: 0.7775 (tpp) cc_final: 0.7457 (mmm) REVERT: F 251 LYS cc_start: 0.7870 (mttp) cc_final: 0.7024 (mmtt) REVERT: F 346 ARG cc_start: 0.7925 (mtp-110) cc_final: 0.7663 (mtp-110) REVERT: F 371 GLU cc_start: 0.8130 (tt0) cc_final: 0.7285 (tt0) REVERT: F 419 GLU cc_start: 0.8397 (pt0) cc_final: 0.7950 (pt0) REVERT: F 456 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7137 (ttt90) outliers start: 66 outliers final: 52 residues processed: 575 average time/residue: 0.1921 time to fit residues: 155.4803 Evaluate side-chains 589 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 529 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 ARG Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 459 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 13 optimal weight: 0.4980 chunk 143 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 243 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 chunk 231 optimal weight: 0.7980 chunk 263 optimal weight: 0.7980 chunk 178 optimal weight: 0.2980 chunk 158 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 353 ASN F 62 HIS F 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119603 restraints weight = 30797.284| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.83 r_work: 0.3393 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21645 Z= 0.145 Angle : 0.563 13.122 29408 Z= 0.279 Chirality : 0.041 0.255 3349 Planarity : 0.004 0.043 3772 Dihedral : 12.336 171.507 3422 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.80 % Allowed : 14.60 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.06 (0.17), residues: 2636 helix: 2.70 (0.14), residues: 1429 sheet: 0.18 (0.29), residues: 351 loop : -0.44 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 185 TYR 0.011 0.001 TYR E 194 PHE 0.012 0.001 PHE A 457 TRP 0.006 0.001 TRP A 45 HIS 0.004 0.001 HIS E 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (21645) covalent geometry : angle 0.56285 / 0.28 (29408) hydrogen bonds : bond 0.03837 / 2.57 ( 1215) hydrogen bonds : angle 3.85401 / 2.76 ( 3483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 532 time to evaluate : 0.804 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: A 53 MET cc_start: 0.7793 (mmm) cc_final: 0.7472 (mmm) REVERT: A 70 LYS cc_start: 0.8093 (tttt) cc_final: 0.7707 (ttpp) REVERT: A 71 SER cc_start: 0.7447 (m) cc_final: 0.7195 (p) REVERT: A 132 LEU cc_start: 0.8363 (tt) cc_final: 0.8098 (tt) REVERT: A 139 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8105 (tp) REVERT: A 153 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7823 (m-30) REVERT: A 161 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8321 (mmmm) REVERT: A 257 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8543 (p) REVERT: A 280 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7507 (ttmm) REVERT: A 287 ASP cc_start: 0.7190 (p0) cc_final: 0.6734 (p0) REVERT: A 298 MET cc_start: 0.6583 (tmm) cc_final: 0.6004 (tmm) REVERT: A 311 ASP cc_start: 0.7822 (t0) cc_final: 0.7577 (t0) REVERT: A 326 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7605 (ttp80) REVERT: A 363 ARG cc_start: 0.7792 (ttp-170) cc_final: 0.7521 (ttp80) REVERT: A 384 ARG cc_start: 0.7856 (ptm160) cc_final: 0.7549 (ptm160) REVERT: A 387 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7495 (mt-10) REVERT: A 393 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7886 (mtt90) REVERT: A 428 LYS cc_start: 0.7767 (mttt) cc_final: 0.7534 (mttt) REVERT: B 58 TYR cc_start: 0.7357 (t80) cc_final: 0.7014 (t80) REVERT: B 59 SER cc_start: 0.7980 (t) cc_final: 0.7740 (t) REVERT: B 80 ASP cc_start: 0.8239 (p0) cc_final: 0.7987 (p0) REVERT: B 102 TYR cc_start: 0.7982 (t80) cc_final: 0.7658 (t80) REVERT: B 122 ILE cc_start: 0.8682 (mm) cc_final: 0.8305 (mm) REVERT: B 159 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8010 (tp30) REVERT: B 177 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7458 (mtpp) REVERT: B 213 LYS cc_start: 0.7940 (tttt) cc_final: 0.7639 (tttt) REVERT: B 242 CYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7374 (m) REVERT: B 269 MET cc_start: 0.6490 (ttm) cc_final: 0.5978 (mtp) REVERT: B 272 SER cc_start: 0.8085 (t) cc_final: 0.7812 (p) REVERT: B 298 MET cc_start: 0.7752 (tmm) cc_final: 0.7245 (tmm) REVERT: B 300 ILE cc_start: 0.8112 (mt) cc_final: 0.7877 (mt) REVERT: B 302 MET cc_start: 0.8043 (mmm) cc_final: 0.7803 (mmp) REVERT: B 310 ASP cc_start: 0.7397 (t0) cc_final: 0.6794 (t0) REVERT: B 311 ASP cc_start: 0.7174 (t0) cc_final: 0.6870 (t70) REVERT: B 320 VAL cc_start: 0.7766 (p) cc_final: 0.7372 (m) REVERT: B 327 ILE cc_start: 0.7187 (mm) cc_final: 0.6944 (mp) REVERT: B 338 MET cc_start: 0.7754 (ttm) cc_final: 0.7500 (ttm) REVERT: B 343 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7242 (mt0) REVERT: B 385 SER cc_start: 0.8474 (p) cc_final: 0.8146 (p) REVERT: B 386 LEU cc_start: 0.8316 (tp) cc_final: 0.7969 (tt) REVERT: B 387 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7649 (mm-30) REVERT: B 398 ASP cc_start: 0.7928 (m-30) cc_final: 0.7599 (m-30) REVERT: B 400 ARG cc_start: 0.7275 (mtm180) cc_final: 0.7061 (mmm-85) REVERT: B 451 GLN cc_start: 0.6192 (mm-40) cc_final: 0.5793 (mm-40) REVERT: B 454 TYR cc_start: 0.7505 (m-80) cc_final: 0.7060 (m-80) REVERT: B 455 SER cc_start: 0.7080 (m) cc_final: 0.6649 (p) REVERT: C 44 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7154 (mmt90) REVERT: C 70 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7821 (ttpt) REVERT: C 248 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7041 (mp0) REVERT: C 250 ASP cc_start: 0.7821 (t0) cc_final: 0.7547 (t0) REVERT: C 326 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7586 (ttm170) REVERT: C 336 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8357 (mp) REVERT: C 360 GLU cc_start: 0.7784 (tp30) cc_final: 0.7538 (tp30) REVERT: D 31 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7899 (mm-30) REVERT: D 32 GLN cc_start: 0.8599 (mt0) cc_final: 0.8155 (mm-40) REVERT: D 33 SER cc_start: 0.8391 (m) cc_final: 0.8083 (t) REVERT: D 52 VAL cc_start: 0.8093 (t) cc_final: 0.7765 (p) REVERT: D 63 ARG cc_start: 0.8512 (ttp80) cc_final: 0.7796 (ttm110) REVERT: D 102 TYR cc_start: 0.8501 (t80) cc_final: 0.8046 (t80) REVERT: D 161 LYS cc_start: 0.8034 (tppt) cc_final: 0.7812 (mttp) REVERT: D 184 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7118 (mm-30) REVERT: D 247 MET cc_start: 0.8049 (tpp) cc_final: 0.7747 (mmp) REVERT: D 251 LYS cc_start: 0.8000 (mmtm) cc_final: 0.7772 (mmtm) REVERT: D 300 ILE cc_start: 0.8170 (mm) cc_final: 0.7914 (mm) REVERT: D 327 ILE cc_start: 0.7622 (mm) cc_final: 0.7395 (mm) REVERT: D 346 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7979 (ptm-80) REVERT: D 387 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7316 (mp0) REVERT: D 388 GLN cc_start: 0.8029 (mp10) cc_final: 0.7753 (mp10) REVERT: D 445 SER cc_start: 0.8533 (m) cc_final: 0.8081 (t) REVERT: D 446 VAL cc_start: 0.8183 (m) cc_final: 0.7813 (t) REVERT: D 459 ASN cc_start: 0.7727 (p0) cc_final: 0.7486 (p0) REVERT: E 23 VAL cc_start: 0.8272 (p) cc_final: 0.7880 (m) REVERT: E 89 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7212 (tp30) REVERT: E 131 ASN cc_start: 0.8503 (t0) cc_final: 0.8163 (t0) REVERT: E 215 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8105 (p) REVERT: E 232 MET cc_start: 0.8232 (tpp) cc_final: 0.7763 (mmt) REVERT: E 239 MET cc_start: 0.8126 (mmm) cc_final: 0.7683 (mmm) REVERT: E 311 ASP cc_start: 0.7357 (p0) cc_final: 0.7135 (p0) REVERT: E 312 SER cc_start: 0.8092 (t) cc_final: 0.7763 (m) REVERT: E 373 ASN cc_start: 0.7615 (t0) cc_final: 0.7310 (t0) REVERT: E 381 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7860 (mm-40) REVERT: E 393 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7828 (mtm-85) REVERT: E 396 ASN cc_start: 0.8169 (m-40) cc_final: 0.7961 (m-40) REVERT: F 29 GLU cc_start: 0.7729 (mp0) cc_final: 0.7290 (mp0) REVERT: F 66 PHE cc_start: 0.8207 (t80) cc_final: 0.7873 (t80) REVERT: F 125 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: F 129 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8539 (p) REVERT: F 157 LEU cc_start: 0.8584 (tp) cc_final: 0.8262 (tt) REVERT: F 239 MET cc_start: 0.7788 (tpp) cc_final: 0.7451 (mmm) REVERT: F 243 GLU cc_start: 0.7661 (tt0) cc_final: 0.7359 (tt0) REVERT: F 251 LYS cc_start: 0.7875 (mttp) cc_final: 0.7058 (mmtt) REVERT: F 346 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.7644 (mtp-110) REVERT: F 371 GLU cc_start: 0.8139 (tt0) cc_final: 0.6865 (tt0) REVERT: F 419 GLU cc_start: 0.8390 (pt0) cc_final: 0.7692 (pt0) REVERT: F 456 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7130 (ttt90) outliers start: 63 outliers final: 51 residues processed: 570 average time/residue: 0.1966 time to fit residues: 157.6039 Evaluate side-chains 591 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 531 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 331 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 453 HIS Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 336 LEU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 44 ARG Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 399 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 459 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 150 optimal weight: 0.5980 chunk 236 optimal weight: 0.7980 chunk 155 optimal weight: 0.3980 chunk 209 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 93 optimal weight: 0.1980 chunk 128 optimal weight: 0.8980 chunk 36 optimal weight: 0.0370 chunk 207 optimal weight: 0.0870 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 381 GLN E 353 ASN F 62 HIS F 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.146342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121761 restraints weight = 30680.157| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.87 r_work: 0.3418 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21645 Z= 0.108 Angle : 0.537 11.998 29408 Z= 0.268 Chirality : 0.040 0.252 3349 Planarity : 0.004 0.048 3772 Dihedral : 12.178 172.673 3422 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.36 % Allowed : 15.31 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: 2.20 (0.17), residues: 2636 helix: 2.83 (0.14), residues: 1417 sheet: 0.28 (0.29), residues: 353 loop : -0.38 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 91 TYR 0.041 0.001 TYR C 87 PHE 0.008 0.001 PHE A 457 TRP 0.007 0.001 TRP F 45 HIS 0.003 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (21645) covalent geometry : angle 0.53716 / 0.27 (29408) hydrogen bonds : bond 0.03316 / 2.24 ( 1215) hydrogen bonds : angle 3.76065 / 2.69 ( 3483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5755.05 seconds wall clock time: 98 minutes 59.39 seconds (5939.39 seconds total)