Starting phenix.real_space_refine on Wed Mar 4 16:50:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ysz_10911/03_2026/6ysz_10911.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ysz_10911/03_2026/6ysz_10911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ysz_10911/03_2026/6ysz_10911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ysz_10911/03_2026/6ysz_10911.map" model { file = "/net/cci-nas-00/data/ceres_data/6ysz_10911/03_2026/6ysz_10911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ysz_10911/03_2026/6ysz_10911.cif" } resolution = 3.6 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 9348 2.51 5 N 2742 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15192 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.18, per 1000 atoms: 0.14 Number of scatterers: 15192 At special positions: 0 Unit cell: (101.15, 97.75, 143.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 3042 8.00 N 2742 7.00 C 9348 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: 1.47 Conformation dependent library (CDL) restraints added in 569.2 milliseconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 6 sheets defined 81.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.519A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 154 Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 282' Processing helix chain 'A' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE A 299 " --> pdb=" O GLN A 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 88 removed outlier: 3.722A pdb=" N ASN B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 110 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 154 Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 205 Processing helix chain 'B' and resid 216 through 231 Processing helix chain 'B' and resid 238 through 253 removed outlier: 4.346A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.638A pdb=" N ILE B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 282' Processing helix chain 'B' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA B 325 " --> pdb=" O ASP B 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 65 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 110 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 154 Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 205 Processing helix chain 'C' and resid 216 through 231 Processing helix chain 'C' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE C 299 " --> pdb=" O GLN C 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 302 " --> pdb=" O GLN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP D 65 " --> pdb=" O GLN D 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 154 Processing helix chain 'D' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 205 Processing helix chain 'D' and resid 216 through 231 Processing helix chain 'D' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.709A pdb=" N PHE D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE D 282 " --> pdb=" O TYR D 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 282' Processing helix chain 'D' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP D 302 " --> pdb=" O GLN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 318 removed outlier: 3.640A pdb=" N ASN D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA D 325 " --> pdb=" O ASP D 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA D 371 " --> pdb=" O THR D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN E 88 " --> pdb=" O ARG E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 126 removed outlier: 3.503A pdb=" N MET E 101 " --> pdb=" O ASP E 97 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA E 112 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 154 Processing helix chain 'E' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN E 164 " --> pdb=" O ASP E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL E 200 " --> pdb=" O MET E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 205 Processing helix chain 'E' and resid 216 through 231 Processing helix chain 'E' and resid 238 through 253 removed outlier: 4.346A pdb=" N GLN E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.638A pdb=" N ILE E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 282' Processing helix chain 'E' and resid 283 through 302 removed outlier: 4.530A pdb=" N GLN E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE E 299 " --> pdb=" O GLN E 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA E 325 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU E 327 " --> pdb=" O ARG E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA E 371 " --> pdb=" O THR E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.520A pdb=" N ARG F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 65 " --> pdb=" O GLN F 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN F 88 " --> pdb=" O ARG F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET F 101 " --> pdb=" O ASP F 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG F 110 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA F 112 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU F 126 " --> pdb=" O GLN F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 154 Processing helix chain 'F' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG F 199 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL F 200 " --> pdb=" O MET F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 205 Processing helix chain 'F' and resid 216 through 231 Processing helix chain 'F' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE F 282 " --> pdb=" O TYR F 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 282' Processing helix chain 'F' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE F 299 " --> pdb=" O GLN F 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 302 " --> pdb=" O GLN F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA F 325 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA F 371 " --> pdb=" O THR F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing sheet with id=AA1, first strand: chain 'A' and resid 268 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 270 Processing sheet with id=AA3, first strand: chain 'C' and resid 268 through 270 Processing sheet with id=AA4, first strand: chain 'D' and resid 268 through 270 Processing sheet with id=AA5, first strand: chain 'E' and resid 268 through 270 Processing sheet with id=AA6, first strand: chain 'F' and resid 268 through 270 1021 hydrogen bonds defined for protein. 3045 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: 2.42 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5418 1.34 - 1.46: 1718 1.46 - 1.57: 8158 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 15414 Sorted by residual: bond pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.88e+00 bond pdb=" N GLN F 298 " pdb=" CA GLN F 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.87e+00 bond pdb=" N GLN D 298 " pdb=" CA GLN D 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.83e+00 bond pdb=" N GLN A 298 " pdb=" CA GLN A 298 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.27e-02 6.20e+03 5.70e+00 bond pdb=" N GLN B 298 " pdb=" CA GLN B 298 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.27e-02 6.20e+03 5.69e+00 ... (remaining 15409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 19133 0.95 - 1.90: 1364 1.90 - 2.85: 171 2.85 - 3.80: 80 3.80 - 4.75: 30 Bond angle restraints: 20778 Sorted by residual: angle pdb=" N THR B 276 " pdb=" CA THR B 276 " pdb=" C THR B 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.78e+00 angle pdb=" N THR E 276 " pdb=" CA THR E 276 " pdb=" C THR E 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.77e+00 angle pdb=" N THR C 276 " pdb=" CA THR C 276 " pdb=" C THR C 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.77e+00 angle pdb=" N THR F 276 " pdb=" CA THR F 276 " pdb=" C THR F 276 " ideal model delta sigma weight residual 108.34 111.48 -3.14 1.31e+00 5.83e-01 5.73e+00 angle pdb=" N THR A 276 " pdb=" CA THR A 276 " pdb=" C THR A 276 " ideal model delta sigma weight residual 108.34 111.47 -3.13 1.31e+00 5.83e-01 5.70e+00 ... (remaining 20773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 8054 15.18 - 30.35: 1084 30.35 - 45.53: 294 45.53 - 60.70: 60 60.70 - 75.88: 36 Dihedral angle restraints: 9528 sinusoidal: 4002 harmonic: 5526 Sorted by residual: dihedral pdb=" CA GLU B 126 " pdb=" C GLU B 126 " pdb=" N GLY B 127 " pdb=" CA GLY B 127 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA GLU D 126 " pdb=" C GLU D 126 " pdb=" N GLY D 127 " pdb=" CA GLY D 127 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLU A 126 " pdb=" C GLU A 126 " pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta harmonic sigma weight residual 180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 9525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1267 0.027 - 0.054: 642 0.054 - 0.081: 193 0.081 - 0.109: 80 0.109 - 0.136: 26 Chirality restraints: 2208 Sorted by residual: chirality pdb=" CB ILE B 171 " pdb=" CA ILE B 171 " pdb=" CG1 ILE B 171 " pdb=" CG2 ILE B 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CB ILE D 171 " pdb=" CA ILE D 171 " pdb=" CG1 ILE D 171 " pdb=" CG2 ILE D 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CB ILE E 171 " pdb=" CA ILE E 171 " pdb=" CG1 ILE E 171 " pdb=" CG2 ILE E 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 2205 not shown) Planarity restraints: 2826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 346 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO C 347 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 347 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 347 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 346 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO E 347 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 347 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 346 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 347 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " 0.025 5.00e-02 4.00e+02 ... (remaining 2823 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4750 2.82 - 3.34: 15895 3.34 - 3.86: 25778 3.86 - 4.38: 27270 4.38 - 4.90: 46431 Nonbonded interactions: 120124 Sorted by model distance: nonbonded pdb=" NE2 GLN B 191 " pdb=" OE1 GLN B 239 " model vdw 2.295 3.120 nonbonded pdb=" NE2 GLN D 191 " pdb=" OE1 GLN D 239 " model vdw 2.295 3.120 nonbonded pdb=" NE2 GLN E 191 " pdb=" OE1 GLN E 239 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN A 191 " pdb=" OE1 GLN A 239 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN C 191 " pdb=" OE1 GLN C 239 " model vdw 2.296 3.120 ... (remaining 120119 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 0.033 15414 Z= 0.193 Angle : 0.562 4.755 20778 Z= 0.338 Chirality : 0.038 0.136 2208 Planarity : 0.003 0.046 2826 Dihedral : 15.540 75.878 5952 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.38 % Allowed : 8.27 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 1884 helix: -0.42 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -2.32 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 139 TYR 0.009 0.001 TYR A 163 PHE 0.009 0.001 PHE D 185 TRP 0.008 0.001 TRP B 366 HIS 0.003 0.001 HIS C 182 Details of bonding type rmsd covalent geometry : bond 0.00420 (15414) covalent geometry : angle 0.56211 (20778) hydrogen bonds : bond 0.12087 ( 1021) hydrogen bonds : angle 4.85719 ( 3045) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 433 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8595 (tppp) cc_final: 0.8106 (tppp) REVERT: A 135 MET cc_start: 0.7875 (tmm) cc_final: 0.7361 (tmm) REVERT: A 152 GLU cc_start: 0.8045 (tp30) cc_final: 0.7645 (tp30) REVERT: A 159 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 243 LEU cc_start: 0.7512 (tp) cc_final: 0.7225 (tp) REVERT: B 82 GLN cc_start: 0.8844 (mt0) cc_final: 0.8581 (mt0) REVERT: B 85 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7810 (tm-30) REVERT: B 121 MET cc_start: 0.7679 (tpt) cc_final: 0.7338 (tmm) REVERT: B 125 LYS cc_start: 0.8451 (tppp) cc_final: 0.7887 (ttmm) REVERT: B 144 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7429 (mm-40) REVERT: B 145 GLU cc_start: 0.8034 (tp30) cc_final: 0.7304 (tp30) REVERT: B 196 MET cc_start: 0.8228 (tpp) cc_final: 0.7959 (tmm) REVERT: B 211 MET cc_start: 0.8295 (tpp) cc_final: 0.7928 (tpt) REVERT: B 286 GLN cc_start: 0.8324 (mm110) cc_final: 0.8122 (mm-40) REVERT: B 335 GLU cc_start: 0.8219 (tp30) cc_final: 0.7799 (tm-30) REVERT: B 344 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8305 (mm110) REVERT: C 68 ASP cc_start: 0.8048 (t70) cc_final: 0.7685 (t70) REVERT: C 94 TYR cc_start: 0.8595 (m-80) cc_final: 0.7711 (m-80) REVERT: C 121 MET cc_start: 0.7725 (tpt) cc_final: 0.7465 (tpp) REVERT: C 125 LYS cc_start: 0.8482 (tppp) cc_final: 0.8000 (tppp) REVERT: C 159 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7203 (tm-30) REVERT: C 211 MET cc_start: 0.8277 (tpp) cc_final: 0.8013 (ttp) REVERT: C 252 SER cc_start: 0.8446 (p) cc_final: 0.8083 (p) REVERT: C 291 MET cc_start: 0.8506 (tpt) cc_final: 0.8247 (tpp) REVERT: C 300 GLU cc_start: 0.8619 (tp30) cc_final: 0.8193 (mm-30) REVERT: D 95 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8570 (tp-100) REVERT: D 125 LYS cc_start: 0.8579 (tppp) cc_final: 0.8071 (tppp) REVERT: D 135 MET cc_start: 0.7809 (tmm) cc_final: 0.7279 (tmm) REVERT: D 152 GLU cc_start: 0.7999 (tp30) cc_final: 0.7550 (tp30) REVERT: D 159 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7347 (tm-30) REVERT: D 196 MET cc_start: 0.8206 (tpp) cc_final: 0.7930 (tmm) REVERT: D 243 LEU cc_start: 0.7516 (tp) cc_final: 0.7267 (tp) REVERT: D 335 GLU cc_start: 0.8309 (tp30) cc_final: 0.7728 (tm-30) REVERT: E 82 GLN cc_start: 0.8852 (mt0) cc_final: 0.8651 (mt0) REVERT: E 95 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8748 (tp40) REVERT: E 125 LYS cc_start: 0.8446 (tppp) cc_final: 0.7959 (ttmm) REVERT: E 144 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7454 (mm-40) REVERT: E 145 GLU cc_start: 0.7975 (tp30) cc_final: 0.7157 (tp30) REVERT: E 196 MET cc_start: 0.8219 (tpp) cc_final: 0.7909 (tmm) REVERT: E 211 MET cc_start: 0.8304 (tpp) cc_final: 0.7807 (tpt) REVERT: E 335 GLU cc_start: 0.8249 (tp30) cc_final: 0.7800 (tm-30) REVERT: F 82 GLN cc_start: 0.8903 (mt0) cc_final: 0.8546 (mt0) REVERT: F 94 TYR cc_start: 0.8618 (m-80) cc_final: 0.7819 (m-80) REVERT: F 117 ASP cc_start: 0.7725 (t0) cc_final: 0.7215 (t0) REVERT: F 125 LYS cc_start: 0.8505 (tppp) cc_final: 0.8042 (tppp) REVERT: F 159 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7194 (tm-30) REVERT: F 211 MET cc_start: 0.8258 (tpp) cc_final: 0.7887 (tpp) REVERT: F 252 SER cc_start: 0.8474 (p) cc_final: 0.8164 (p) REVERT: F 261 LEU cc_start: 0.7925 (mm) cc_final: 0.7664 (mm) REVERT: F 291 MET cc_start: 0.8501 (tpt) cc_final: 0.8253 (tpp) REVERT: F 300 GLU cc_start: 0.8651 (tp30) cc_final: 0.8234 (mm-30) outliers start: 6 outliers final: 2 residues processed: 437 average time/residue: 0.1305 time to fit residues: 82.9311 Evaluate side-chains 361 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain D residue 298 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 203 ASN A 298 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN B 188 GLN B 203 ASN B 286 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN C 203 ASN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN D 144 GLN D 203 ASN D 298 GLN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 203 ASN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN F 203 ASN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.116519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.100424 restraints weight = 25147.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.103998 restraints weight = 13198.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.106335 restraints weight = 8082.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107932 restraints weight = 5522.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108964 restraints weight = 4101.645| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15414 Z= 0.117 Angle : 0.517 9.755 20778 Z= 0.259 Chirality : 0.037 0.142 2208 Planarity : 0.004 0.042 2826 Dihedral : 3.775 15.957 2100 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.45 % Allowed : 14.29 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.19), residues: 1884 helix: 0.70 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -1.66 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 142 TYR 0.010 0.001 TYR C 114 PHE 0.009 0.001 PHE E 185 TRP 0.008 0.001 TRP B 366 HIS 0.002 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00250 (15414) covalent geometry : angle 0.51744 (20778) hydrogen bonds : bond 0.04155 ( 1021) hydrogen bonds : angle 3.40078 ( 3045) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 344 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8154 (m-80) cc_final: 0.7769 (m-80) REVERT: A 125 LYS cc_start: 0.8525 (tppp) cc_final: 0.8097 (tppp) REVERT: A 135 MET cc_start: 0.7764 (tmm) cc_final: 0.7311 (tmm) REVERT: A 159 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7168 (tm-30) REVERT: A 211 MET cc_start: 0.8340 (tpp) cc_final: 0.8119 (tpp) REVERT: A 335 GLU cc_start: 0.8301 (tp30) cc_final: 0.7651 (tm-30) REVERT: B 82 GLN cc_start: 0.8712 (mt0) cc_final: 0.8425 (mt0) REVERT: B 85 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 125 LYS cc_start: 0.8413 (tppp) cc_final: 0.7967 (ttpt) REVERT: B 156 ILE cc_start: 0.8173 (mm) cc_final: 0.7830 (tp) REVERT: B 286 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7788 (mm-40) REVERT: B 321 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7271 (p0) REVERT: B 335 GLU cc_start: 0.8117 (tp30) cc_final: 0.7727 (tm-30) REVERT: B 345 MET cc_start: 0.8584 (tpt) cc_final: 0.8373 (tpt) REVERT: C 85 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7698 (tm-30) REVERT: C 125 LYS cc_start: 0.8412 (tppp) cc_final: 0.7923 (ttpt) REVERT: C 135 MET cc_start: 0.7922 (tmm) cc_final: 0.7602 (tmm) REVERT: C 152 GLU cc_start: 0.7884 (tp30) cc_final: 0.7389 (tp30) REVERT: C 159 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7007 (tm-30) REVERT: C 211 MET cc_start: 0.8223 (tpp) cc_final: 0.7733 (tpp) REVERT: C 223 LYS cc_start: 0.7997 (mmmm) cc_final: 0.7571 (tppt) REVERT: C 261 LEU cc_start: 0.7886 (mm) cc_final: 0.7624 (mm) REVERT: C 300 GLU cc_start: 0.8559 (tp30) cc_final: 0.8117 (mm-30) REVERT: C 344 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8318 (mm110) REVERT: C 345 MET cc_start: 0.8874 (tpt) cc_final: 0.8048 (tpt) REVERT: D 85 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7775 (tm-30) REVERT: D 101 MET cc_start: 0.8013 (mmp) cc_final: 0.7363 (mmm) REVERT: D 120 VAL cc_start: 0.7980 (t) cc_final: 0.7740 (p) REVERT: D 125 LYS cc_start: 0.8516 (tppp) cc_final: 0.8045 (tppp) REVERT: D 135 MET cc_start: 0.7741 (tmm) cc_final: 0.7304 (tmm) REVERT: D 211 MET cc_start: 0.8388 (tpp) cc_final: 0.8161 (tpp) REVERT: D 321 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7299 (p0) REVERT: D 335 GLU cc_start: 0.8270 (tp30) cc_final: 0.7649 (tm-30) REVERT: E 82 GLN cc_start: 0.8762 (mt0) cc_final: 0.8477 (mt0) REVERT: E 85 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7818 (tm-30) REVERT: E 101 MET cc_start: 0.7810 (mmp) cc_final: 0.7108 (mmm) REVERT: E 125 LYS cc_start: 0.8424 (tppp) cc_final: 0.7956 (ttpt) REVERT: E 145 GLU cc_start: 0.7912 (tp30) cc_final: 0.7013 (tp30) REVERT: E 196 MET cc_start: 0.8107 (tpp) cc_final: 0.7875 (tmm) REVERT: E 201 GLU cc_start: 0.8593 (tp30) cc_final: 0.8164 (tp30) REVERT: E 321 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7276 (p0) REVERT: E 335 GLU cc_start: 0.8169 (tp30) cc_final: 0.7776 (tm-30) REVERT: E 344 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8326 (mm110) REVERT: E 345 MET cc_start: 0.8613 (tpt) cc_final: 0.8351 (tpt) REVERT: F 82 GLN cc_start: 0.8852 (mt0) cc_final: 0.8547 (mt0) REVERT: F 85 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7720 (tm-30) REVERT: F 117 ASP cc_start: 0.7559 (t0) cc_final: 0.7279 (t0) REVERT: F 125 LYS cc_start: 0.8446 (tppp) cc_final: 0.7974 (ttpt) REVERT: F 135 MET cc_start: 0.7890 (tmm) cc_final: 0.7585 (tmm) REVERT: F 152 GLU cc_start: 0.7728 (tp30) cc_final: 0.7393 (tp30) REVERT: F 159 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6986 (tm-30) REVERT: F 206 LEU cc_start: 0.7905 (mp) cc_final: 0.7595 (mp) REVERT: F 211 MET cc_start: 0.8330 (tpp) cc_final: 0.7936 (ttp) REVERT: F 223 LYS cc_start: 0.8007 (mmmm) cc_final: 0.7551 (mppt) REVERT: F 261 LEU cc_start: 0.7886 (mm) cc_final: 0.7633 (mm) REVERT: F 300 GLU cc_start: 0.8585 (tp30) cc_final: 0.8123 (mm-30) REVERT: F 344 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8287 (mm110) outliers start: 55 outliers final: 39 residues processed: 377 average time/residue: 0.1137 time to fit residues: 65.6319 Evaluate side-chains 360 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 151 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 172 optimal weight: 0.0000 chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 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 = 0.3543 r_free = 0.3543 target = 0.113125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.096683 restraints weight = 25805.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100251 restraints weight = 13734.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102559 restraints weight = 8475.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104114 restraints weight = 5836.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.105129 restraints weight = 4378.794| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15414 Z= 0.173 Angle : 0.517 7.614 20778 Z= 0.264 Chirality : 0.038 0.131 2208 Planarity : 0.004 0.040 2826 Dihedral : 3.708 16.461 2094 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.39 % Allowed : 18.98 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.20), residues: 1884 helix: 1.23 (0.14), residues: 1446 sheet: None (None), residues: 0 loop : -1.43 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.013 0.001 TYR B 278 PHE 0.010 0.001 PHE D 185 TRP 0.008 0.001 TRP B 366 HIS 0.003 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00399 (15414) covalent geometry : angle 0.51657 (20778) hydrogen bonds : bond 0.04383 ( 1021) hydrogen bonds : angle 3.26653 ( 3045) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 338 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7900 (tm-30) REVERT: A 120 VAL cc_start: 0.7918 (t) cc_final: 0.7612 (p) REVERT: A 135 MET cc_start: 0.7842 (tmm) cc_final: 0.7397 (tmm) REVERT: A 211 MET cc_start: 0.8352 (tpp) cc_final: 0.7989 (tpp) REVERT: A 300 GLU cc_start: 0.8513 (tp30) cc_final: 0.8114 (tp30) REVERT: A 335 GLU cc_start: 0.8324 (tp30) cc_final: 0.7685 (tm-30) REVERT: B 82 GLN cc_start: 0.8798 (mt0) cc_final: 0.8562 (mt0) REVERT: B 125 LYS cc_start: 0.8436 (tppp) cc_final: 0.7986 (ttpt) REVERT: B 286 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7869 (mm-40) REVERT: B 321 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7245 (p0) REVERT: B 335 GLU cc_start: 0.8213 (tp30) cc_final: 0.7799 (tm-30) REVERT: C 85 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7641 (tm-30) REVERT: C 117 ASP cc_start: 0.7431 (t0) cc_final: 0.6518 (t0) REVERT: C 125 LYS cc_start: 0.8452 (tppp) cc_final: 0.7954 (ttpt) REVERT: C 159 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6993 (tm-30) REVERT: C 223 LYS cc_start: 0.8031 (mmmm) cc_final: 0.7588 (mppt) REVERT: C 300 GLU cc_start: 0.8517 (tp30) cc_final: 0.7948 (tm-30) REVERT: C 307 GLU cc_start: 0.7292 (tt0) cc_final: 0.6969 (tt0) REVERT: C 345 MET cc_start: 0.8929 (tpt) cc_final: 0.8181 (tpt) REVERT: D 85 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7811 (tm-30) REVERT: D 94 TYR cc_start: 0.8326 (m-80) cc_final: 0.7938 (m-80) REVERT: D 101 MET cc_start: 0.8030 (mmp) cc_final: 0.7415 (mmm) REVERT: D 135 MET cc_start: 0.7811 (tmm) cc_final: 0.7358 (tmm) REVERT: D 159 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7223 (tm-30) REVERT: D 211 MET cc_start: 0.8384 (tpp) cc_final: 0.8047 (tpt) REVERT: D 300 GLU cc_start: 0.8519 (tp30) cc_final: 0.8132 (tp30) REVERT: D 321 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7273 (p0) REVERT: D 335 GLU cc_start: 0.8303 (tp30) cc_final: 0.7644 (tm-30) REVERT: E 82 GLN cc_start: 0.8781 (mt0) cc_final: 0.8538 (mt0) REVERT: E 101 MET cc_start: 0.7905 (mmp) cc_final: 0.7267 (mmm) REVERT: E 125 LYS cc_start: 0.8435 (tppp) cc_final: 0.7970 (ttpt) REVERT: E 201 GLU cc_start: 0.8551 (tp30) cc_final: 0.8107 (tp30) REVERT: E 321 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7288 (p0) REVERT: E 335 GLU cc_start: 0.8289 (tp30) cc_final: 0.7724 (tm-30) REVERT: F 85 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7655 (tm-30) REVERT: F 117 ASP cc_start: 0.7557 (t0) cc_final: 0.7320 (t0) REVERT: F 125 LYS cc_start: 0.8430 (tppp) cc_final: 0.7950 (ttpt) REVERT: F 144 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7262 (mt0) REVERT: F 156 ILE cc_start: 0.8232 (mm) cc_final: 0.7814 (tp) REVERT: F 159 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6986 (tm-30) REVERT: F 206 LEU cc_start: 0.7960 (mp) cc_final: 0.7623 (mp) REVERT: F 211 MET cc_start: 0.8314 (tpp) cc_final: 0.8060 (tpp) REVERT: F 223 LYS cc_start: 0.8075 (mmmm) cc_final: 0.7853 (tppt) REVERT: F 300 GLU cc_start: 0.8534 (tp30) cc_final: 0.7953 (tm-30) REVERT: F 307 GLU cc_start: 0.7354 (tt0) cc_final: 0.7104 (tt0) REVERT: F 335 GLU cc_start: 0.8369 (tp30) cc_final: 0.7989 (tm-30) outliers start: 70 outliers final: 57 residues processed: 368 average time/residue: 0.1060 time to fit residues: 60.6819 Evaluate side-chains 380 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 320 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 49 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.114564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.098197 restraints weight = 25616.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.101731 restraints weight = 13549.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104084 restraints weight = 8374.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105586 restraints weight = 5755.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.106727 restraints weight = 4337.292| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15414 Z= 0.138 Angle : 0.479 6.162 20778 Z= 0.245 Chirality : 0.036 0.134 2208 Planarity : 0.003 0.039 2826 Dihedral : 3.578 15.838 2094 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.39 % Allowed : 20.99 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1884 helix: 1.45 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -1.28 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.011 0.001 TYR C 114 PHE 0.009 0.001 PHE C 185 TRP 0.008 0.001 TRP B 366 HIS 0.002 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00311 (15414) covalent geometry : angle 0.47908 (20778) hydrogen bonds : bond 0.04079 ( 1021) hydrogen bonds : angle 3.13072 ( 3045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 331 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 94 TYR cc_start: 0.8221 (m-80) cc_final: 0.7930 (m-80) REVERT: A 125 LYS cc_start: 0.8542 (tppp) cc_final: 0.8081 (tppp) REVERT: A 135 MET cc_start: 0.7821 (tmm) cc_final: 0.7419 (tmm) REVERT: A 262 MET cc_start: 0.8360 (tpp) cc_final: 0.7310 (tpp) REVERT: A 318 ASN cc_start: 0.9052 (t0) cc_final: 0.7925 (t0) REVERT: A 335 GLU cc_start: 0.8355 (tp30) cc_final: 0.7706 (tm-30) REVERT: B 74 ILE cc_start: 0.8942 (tp) cc_final: 0.8695 (tt) REVERT: B 82 GLN cc_start: 0.8750 (mt0) cc_final: 0.8440 (mt0) REVERT: B 85 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 117 ASP cc_start: 0.7541 (t0) cc_final: 0.6450 (t0) REVERT: B 125 LYS cc_start: 0.8430 (tppp) cc_final: 0.8022 (ttpt) REVERT: B 335 GLU cc_start: 0.8312 (tp30) cc_final: 0.7781 (tm-30) REVERT: B 345 MET cc_start: 0.8742 (tpt) cc_final: 0.8161 (tpt) REVERT: C 85 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 117 ASP cc_start: 0.7451 (t0) cc_final: 0.6783 (t0) REVERT: C 125 LYS cc_start: 0.8422 (tppp) cc_final: 0.7992 (tppp) REVERT: C 159 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6948 (tm-30) REVERT: C 223 LYS cc_start: 0.8078 (mmmm) cc_final: 0.7849 (tppt) REVERT: C 300 GLU cc_start: 0.8488 (tp30) cc_final: 0.7917 (tm-30) REVERT: C 307 GLU cc_start: 0.7310 (tt0) cc_final: 0.7103 (tt0) REVERT: C 318 ASN cc_start: 0.9075 (t0) cc_final: 0.8357 (t0) REVERT: C 345 MET cc_start: 0.8896 (tpt) cc_final: 0.8070 (tpt) REVERT: D 85 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7810 (tm-30) REVERT: D 101 MET cc_start: 0.7933 (mmp) cc_final: 0.7318 (mmm) REVERT: D 125 LYS cc_start: 0.8539 (tppp) cc_final: 0.8066 (tppp) REVERT: D 135 MET cc_start: 0.7812 (tmm) cc_final: 0.7409 (tmm) REVERT: D 152 GLU cc_start: 0.7913 (tp30) cc_final: 0.7494 (tp30) REVERT: D 211 MET cc_start: 0.8376 (tpp) cc_final: 0.8013 (tpt) REVERT: D 307 GLU cc_start: 0.7187 (tt0) cc_final: 0.6962 (tt0) REVERT: D 321 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7301 (p0) REVERT: D 335 GLU cc_start: 0.8309 (tp30) cc_final: 0.7709 (tm-30) REVERT: E 82 GLN cc_start: 0.8735 (mt0) cc_final: 0.8492 (mt0) REVERT: E 101 MET cc_start: 0.7937 (mmp) cc_final: 0.7266 (mmm) REVERT: E 125 LYS cc_start: 0.8458 (tppp) cc_final: 0.8024 (ttpt) REVERT: E 201 GLU cc_start: 0.8510 (tp30) cc_final: 0.8059 (tp30) REVERT: E 214 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7852 (mtp85) REVERT: E 335 GLU cc_start: 0.8287 (tp30) cc_final: 0.7742 (tm-30) REVERT: E 345 MET cc_start: 0.8747 (tpt) cc_final: 0.8217 (tpt) REVERT: F 85 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7614 (tm-30) REVERT: F 125 LYS cc_start: 0.8404 (tppp) cc_final: 0.7926 (tppp) REVERT: F 152 GLU cc_start: 0.7889 (tp30) cc_final: 0.7422 (tp30) REVERT: F 159 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6872 (tm-30) REVERT: F 206 LEU cc_start: 0.7887 (mp) cc_final: 0.7571 (mp) REVERT: F 223 LYS cc_start: 0.8088 (mmmm) cc_final: 0.7863 (tppt) REVERT: F 300 GLU cc_start: 0.8516 (tp30) cc_final: 0.7910 (tm-30) REVERT: F 307 GLU cc_start: 0.7286 (tt0) cc_final: 0.7071 (tt0) REVERT: F 335 GLU cc_start: 0.8383 (tp30) cc_final: 0.7981 (tm-30) outliers start: 70 outliers final: 51 residues processed: 362 average time/residue: 0.1106 time to fit residues: 61.3496 Evaluate side-chains 376 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 108 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 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 = 0.3571 r_free = 0.3571 target = 0.115270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098883 restraints weight = 25397.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.102403 restraints weight = 13412.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104747 restraints weight = 8281.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106305 restraints weight = 5671.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107392 restraints weight = 4243.533| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15414 Z= 0.127 Angle : 0.461 5.949 20778 Z= 0.237 Chirality : 0.036 0.136 2208 Planarity : 0.003 0.037 2826 Dihedral : 3.498 15.564 2094 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.51 % Allowed : 21.12 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1884 helix: 1.63 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -1.14 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.012 0.001 TYR E 94 PHE 0.009 0.001 PHE B 185 TRP 0.007 0.001 TRP B 366 HIS 0.002 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00283 (15414) covalent geometry : angle 0.46076 (20778) hydrogen bonds : bond 0.03977 ( 1021) hydrogen bonds : angle 3.02891 ( 3045) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 334 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7925 (tm-30) REVERT: A 94 TYR cc_start: 0.8201 (m-80) cc_final: 0.7852 (m-80) REVERT: A 135 MET cc_start: 0.7849 (tmm) cc_final: 0.7444 (tmm) REVERT: A 152 GLU cc_start: 0.7893 (tp30) cc_final: 0.7458 (tp30) REVERT: A 211 MET cc_start: 0.8369 (tpp) cc_final: 0.8062 (tpp) REVERT: A 298 GLN cc_start: 0.8475 (mt0) cc_final: 0.8250 (mt0) REVERT: A 318 ASN cc_start: 0.9018 (t0) cc_final: 0.7882 (t0) REVERT: A 335 GLU cc_start: 0.8387 (tp30) cc_final: 0.7704 (tm-30) REVERT: B 82 GLN cc_start: 0.8735 (mt0) cc_final: 0.8412 (mt0) REVERT: B 85 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 117 ASP cc_start: 0.7575 (t0) cc_final: 0.6519 (t0) REVERT: B 125 LYS cc_start: 0.8421 (tppp) cc_final: 0.8054 (ttpt) REVERT: B 318 ASN cc_start: 0.9144 (t0) cc_final: 0.8096 (t0) REVERT: B 335 GLU cc_start: 0.8362 (tp30) cc_final: 0.7785 (tm-30) REVERT: B 345 MET cc_start: 0.8772 (tpt) cc_final: 0.8213 (tpt) REVERT: C 85 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7582 (tm-30) REVERT: C 117 ASP cc_start: 0.7451 (t0) cc_final: 0.6908 (t0) REVERT: C 125 LYS cc_start: 0.8417 (tppp) cc_final: 0.7965 (tppp) REVERT: C 152 GLU cc_start: 0.7904 (tp30) cc_final: 0.7394 (tp30) REVERT: C 223 LYS cc_start: 0.8085 (mmmm) cc_final: 0.7862 (tppt) REVERT: C 300 GLU cc_start: 0.8486 (tp30) cc_final: 0.7872 (tm-30) REVERT: C 307 GLU cc_start: 0.7303 (tt0) cc_final: 0.7001 (tt0) REVERT: C 318 ASN cc_start: 0.9075 (t0) cc_final: 0.8403 (t0) REVERT: C 335 GLU cc_start: 0.8447 (tp30) cc_final: 0.7998 (tm-30) REVERT: D 85 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7833 (tm-30) REVERT: D 94 TYR cc_start: 0.8207 (m-80) cc_final: 0.7789 (m-80) REVERT: D 101 MET cc_start: 0.7866 (mmp) cc_final: 0.7329 (mmm) REVERT: D 120 VAL cc_start: 0.7978 (t) cc_final: 0.7628 (p) REVERT: D 135 MET cc_start: 0.7816 (tmm) cc_final: 0.7436 (tmm) REVERT: D 152 GLU cc_start: 0.7897 (tp30) cc_final: 0.7446 (tp30) REVERT: D 211 MET cc_start: 0.8359 (tpp) cc_final: 0.7993 (tpt) REVERT: D 318 ASN cc_start: 0.9026 (t0) cc_final: 0.8629 (t0) REVERT: D 321 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7322 (p0) REVERT: D 335 GLU cc_start: 0.8305 (tp30) cc_final: 0.7727 (tm-30) REVERT: E 82 GLN cc_start: 0.8723 (mt0) cc_final: 0.8394 (mt0) REVERT: E 85 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7861 (tm-30) REVERT: E 101 MET cc_start: 0.7913 (mmp) cc_final: 0.7326 (mmm) REVERT: E 125 LYS cc_start: 0.8459 (tppp) cc_final: 0.8058 (ttpt) REVERT: E 214 ARG cc_start: 0.8054 (mtp85) cc_final: 0.7776 (mtp85) REVERT: E 318 ASN cc_start: 0.9143 (t0) cc_final: 0.8077 (t0) REVERT: E 335 GLU cc_start: 0.8306 (tp30) cc_final: 0.7751 (tm-30) REVERT: E 345 MET cc_start: 0.8740 (tpt) cc_final: 0.8164 (tpt) REVERT: F 85 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7590 (tm-30) REVERT: F 125 LYS cc_start: 0.8383 (tppp) cc_final: 0.7867 (tppp) REVERT: F 223 LYS cc_start: 0.8080 (mmmm) cc_final: 0.7865 (tppt) REVERT: F 300 GLU cc_start: 0.8491 (tp30) cc_final: 0.7862 (tm-30) REVERT: F 307 GLU cc_start: 0.7268 (tt0) cc_final: 0.7064 (tt0) REVERT: F 318 ASN cc_start: 0.9058 (t0) cc_final: 0.8378 (t0) outliers start: 72 outliers final: 59 residues processed: 363 average time/residue: 0.1078 time to fit residues: 60.2500 Evaluate side-chains 381 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 321 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.100159 restraints weight = 25203.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.103731 restraints weight = 13251.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106066 restraints weight = 8127.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107649 restraints weight = 5561.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108652 restraints weight = 4154.079| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15414 Z= 0.115 Angle : 0.462 6.734 20778 Z= 0.234 Chirality : 0.035 0.132 2208 Planarity : 0.003 0.036 2826 Dihedral : 3.403 15.413 2094 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.14 % Allowed : 22.12 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.20), residues: 1884 helix: 1.91 (0.14), residues: 1452 sheet: None (None), residues: 0 loop : -1.06 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.013 0.001 TYR E 94 PHE 0.009 0.001 PHE B 185 TRP 0.007 0.001 TRP E 287 HIS 0.002 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00253 (15414) covalent geometry : angle 0.46165 (20778) hydrogen bonds : bond 0.03845 ( 1021) hydrogen bonds : angle 2.96401 ( 3045) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 329 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 94 TYR cc_start: 0.8196 (m-80) cc_final: 0.7831 (m-80) REVERT: A 135 MET cc_start: 0.7800 (tmm) cc_final: 0.7426 (tmm) REVERT: A 152 GLU cc_start: 0.7871 (tp30) cc_final: 0.7380 (tp30) REVERT: A 211 MET cc_start: 0.8359 (tpp) cc_final: 0.8137 (tpp) REVERT: A 298 GLN cc_start: 0.8458 (mt0) cc_final: 0.8200 (mt0) REVERT: A 318 ASN cc_start: 0.8993 (t0) cc_final: 0.8667 (t0) REVERT: A 335 GLU cc_start: 0.8385 (tp30) cc_final: 0.7723 (tm-30) REVERT: B 82 GLN cc_start: 0.8713 (mt0) cc_final: 0.8382 (mt0) REVERT: B 85 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7850 (tm-30) REVERT: B 117 ASP cc_start: 0.7564 (t0) cc_final: 0.6560 (t0) REVERT: B 125 LYS cc_start: 0.8410 (tppp) cc_final: 0.8026 (ttpt) REVERT: B 318 ASN cc_start: 0.9116 (t0) cc_final: 0.8056 (t0) REVERT: B 335 GLU cc_start: 0.8334 (tp30) cc_final: 0.7769 (tm-30) REVERT: B 345 MET cc_start: 0.8763 (tpt) cc_final: 0.8239 (tpt) REVERT: C 85 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7578 (tm-30) REVERT: C 117 ASP cc_start: 0.7433 (t0) cc_final: 0.6849 (t0) REVERT: C 125 LYS cc_start: 0.8396 (tppp) cc_final: 0.7972 (tppp) REVERT: C 152 GLU cc_start: 0.7908 (tp30) cc_final: 0.7352 (tp30) REVERT: C 223 LYS cc_start: 0.8059 (mmmm) cc_final: 0.7837 (tppt) REVERT: C 307 GLU cc_start: 0.7296 (tt0) cc_final: 0.6994 (tt0) REVERT: C 318 ASN cc_start: 0.9050 (t0) cc_final: 0.8420 (t0) REVERT: C 345 MET cc_start: 0.8853 (tpt) cc_final: 0.8240 (tpt) REVERT: D 85 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7812 (tm-30) REVERT: D 94 TYR cc_start: 0.8187 (m-80) cc_final: 0.7709 (m-80) REVERT: D 101 MET cc_start: 0.7803 (mmp) cc_final: 0.7324 (mmm) REVERT: D 120 VAL cc_start: 0.7916 (t) cc_final: 0.7622 (p) REVERT: D 135 MET cc_start: 0.7754 (tmm) cc_final: 0.7418 (tmm) REVERT: D 152 GLU cc_start: 0.7866 (tp30) cc_final: 0.7371 (tp30) REVERT: D 211 MET cc_start: 0.8338 (tpp) cc_final: 0.7592 (tpt) REVERT: D 318 ASN cc_start: 0.8945 (t0) cc_final: 0.7801 (t0) REVERT: D 335 GLU cc_start: 0.8303 (tp30) cc_final: 0.7729 (tm-30) REVERT: E 82 GLN cc_start: 0.8728 (mt0) cc_final: 0.8403 (mt0) REVERT: E 85 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7848 (tm-30) REVERT: E 125 LYS cc_start: 0.8449 (tppp) cc_final: 0.8051 (ttpt) REVERT: E 145 GLU cc_start: 0.7793 (tp30) cc_final: 0.6963 (tp30) REVERT: E 160 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7320 (t0) REVERT: E 214 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7677 (ttm-80) REVERT: E 318 ASN cc_start: 0.9125 (t0) cc_final: 0.8048 (t0) REVERT: E 335 GLU cc_start: 0.8334 (tp30) cc_final: 0.7780 (tm-30) REVERT: E 345 MET cc_start: 0.8804 (tpt) cc_final: 0.8240 (tpt) REVERT: F 85 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7604 (tm-30) REVERT: F 152 GLU cc_start: 0.7875 (tp30) cc_final: 0.7357 (tp30) REVERT: F 223 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7854 (tppt) REVERT: F 307 GLU cc_start: 0.7230 (tt0) cc_final: 0.6928 (tt0) REVERT: F 318 ASN cc_start: 0.9059 (t0) cc_final: 0.8353 (t0) REVERT: F 337 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.6927 (t70) outliers start: 66 outliers final: 55 residues processed: 364 average time/residue: 0.1044 time to fit residues: 59.1367 Evaluate side-chains 377 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 320 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 318 ASN ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN D 298 GLN D 318 ASN E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.100381 restraints weight = 25071.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.103917 restraints weight = 13266.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106141 restraints weight = 8177.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107753 restraints weight = 5681.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108819 restraints weight = 4241.245| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15414 Z= 0.120 Angle : 0.480 7.880 20778 Z= 0.245 Chirality : 0.036 0.138 2208 Planarity : 0.003 0.036 2826 Dihedral : 3.415 16.255 2094 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.20 % Allowed : 23.50 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.04 (0.20), residues: 1884 helix: 2.02 (0.14), residues: 1452 sheet: None (None), residues: 0 loop : -0.97 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 64 TYR 0.013 0.001 TYR E 94 PHE 0.010 0.001 PHE B 185 TRP 0.007 0.001 TRP B 287 HIS 0.003 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00265 (15414) covalent geometry : angle 0.47960 (20778) hydrogen bonds : bond 0.03845 ( 1021) hydrogen bonds : angle 2.94613 ( 3045) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 327 time to evaluate : 0.580 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 85 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7898 (tm-30) REVERT: A 135 MET cc_start: 0.7805 (tmm) cc_final: 0.7444 (tmm) REVERT: A 152 GLU cc_start: 0.7850 (tp30) cc_final: 0.7361 (tp30) REVERT: A 211 MET cc_start: 0.8371 (tpp) cc_final: 0.8090 (tpp) REVERT: A 318 ASN cc_start: 0.8981 (t0) cc_final: 0.8729 (t0) REVERT: A 335 GLU cc_start: 0.8394 (tp30) cc_final: 0.7714 (tm-30) REVERT: B 82 GLN cc_start: 0.8706 (mt0) cc_final: 0.8406 (mt0) REVERT: B 85 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7862 (tm-30) REVERT: B 117 ASP cc_start: 0.7580 (t0) cc_final: 0.6583 (t0) REVERT: B 125 LYS cc_start: 0.8381 (tppp) cc_final: 0.8021 (ttpt) REVERT: B 318 ASN cc_start: 0.9047 (t160) cc_final: 0.8067 (t0) REVERT: B 335 GLU cc_start: 0.8332 (tp30) cc_final: 0.7747 (tm-30) REVERT: B 345 MET cc_start: 0.8816 (tpt) cc_final: 0.8371 (tpt) REVERT: C 85 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7582 (tm-30) REVERT: C 117 ASP cc_start: 0.7532 (t0) cc_final: 0.6759 (t0) REVERT: C 125 LYS cc_start: 0.8392 (tppp) cc_final: 0.7956 (tppp) REVERT: C 152 GLU cc_start: 0.7938 (tp30) cc_final: 0.7364 (tp30) REVERT: C 223 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7858 (tppt) REVERT: C 262 MET cc_start: 0.8325 (tpp) cc_final: 0.7981 (tpp) REVERT: C 307 GLU cc_start: 0.7281 (tt0) cc_final: 0.7003 (tt0) REVERT: C 318 ASN cc_start: 0.9051 (t0) cc_final: 0.8434 (t0) REVERT: C 345 MET cc_start: 0.8798 (tpt) cc_final: 0.8224 (tpt) REVERT: D 85 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7832 (tm-30) REVERT: D 95 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8468 (tp40) REVERT: D 120 VAL cc_start: 0.7907 (t) cc_final: 0.7535 (p) REVERT: D 135 MET cc_start: 0.7773 (tmm) cc_final: 0.7443 (tmm) REVERT: D 152 GLU cc_start: 0.7847 (tp30) cc_final: 0.7329 (tp30) REVERT: D 211 MET cc_start: 0.8342 (tpp) cc_final: 0.7968 (tpt) REVERT: D 298 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7902 (mt0) REVERT: D 318 ASN cc_start: 0.8917 (t160) cc_final: 0.7839 (t0) REVERT: D 335 GLU cc_start: 0.8329 (tp30) cc_final: 0.7756 (tm-30) REVERT: E 82 GLN cc_start: 0.8717 (mt0) cc_final: 0.8392 (mt0) REVERT: E 85 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7846 (tm-30) REVERT: E 125 LYS cc_start: 0.8445 (tppp) cc_final: 0.8142 (ttpt) REVERT: E 145 GLU cc_start: 0.7795 (tp30) cc_final: 0.6952 (tp30) REVERT: E 160 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7298 (t0) REVERT: E 214 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7652 (ttm-80) REVERT: E 318 ASN cc_start: 0.9118 (t0) cc_final: 0.8046 (t0) REVERT: E 335 GLU cc_start: 0.8333 (tp30) cc_final: 0.7782 (tm-30) REVERT: E 344 GLN cc_start: 0.8636 (mp10) cc_final: 0.8409 (mp10) REVERT: E 345 MET cc_start: 0.8849 (tpt) cc_final: 0.8361 (tpt) REVERT: F 85 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7597 (tm-30) REVERT: F 125 LYS cc_start: 0.8408 (tppp) cc_final: 0.7840 (tppp) REVERT: F 152 GLU cc_start: 0.7849 (tp30) cc_final: 0.7315 (tp30) REVERT: F 223 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7858 (tppt) REVERT: F 307 GLU cc_start: 0.7277 (tt0) cc_final: 0.7000 (tt0) REVERT: F 318 ASN cc_start: 0.9043 (t0) cc_final: 0.8388 (t0) REVERT: F 335 GLU cc_start: 0.8431 (tp30) cc_final: 0.8021 (tm-30) REVERT: F 337 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.6975 (t70) outliers start: 67 outliers final: 58 residues processed: 365 average time/residue: 0.1046 time to fit residues: 58.8292 Evaluate side-chains 383 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 322 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 298 GLN Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 37 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN A 318 ASN B 188 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN E 188 GLN E 318 ASN E 361 ASN ** F 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 361 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100445 restraints weight = 25312.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.103951 restraints weight = 13343.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106311 restraints weight = 8251.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107875 restraints weight = 5662.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108901 restraints weight = 4228.881| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15414 Z= 0.119 Angle : 0.499 11.038 20778 Z= 0.252 Chirality : 0.036 0.141 2208 Planarity : 0.003 0.035 2826 Dihedral : 3.410 17.261 2094 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 4.14 % Allowed : 23.56 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.12 (0.20), residues: 1884 helix: 2.10 (0.14), residues: 1446 sheet: None (None), residues: 0 loop : -1.03 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.015 0.001 TYR E 94 PHE 0.017 0.001 PHE C 129 TRP 0.006 0.001 TRP B 287 HIS 0.002 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00264 (15414) covalent geometry : angle 0.49868 (20778) hydrogen bonds : bond 0.03799 ( 1021) hydrogen bonds : angle 2.92844 ( 3045) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 327 time to evaluate : 0.586 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 85 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7833 (tm-30) REVERT: A 94 TYR cc_start: 0.8176 (m-80) cc_final: 0.7703 (m-80) REVERT: A 135 MET cc_start: 0.7811 (tmm) cc_final: 0.7429 (tmm) REVERT: A 152 GLU cc_start: 0.7844 (tp30) cc_final: 0.7332 (tp30) REVERT: A 298 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: A 300 GLU cc_start: 0.8480 (tp30) cc_final: 0.8165 (tp30) REVERT: A 307 GLU cc_start: 0.7191 (tt0) cc_final: 0.6929 (tt0) REVERT: A 318 ASN cc_start: 0.8949 (t160) cc_final: 0.7857 (t0) REVERT: A 335 GLU cc_start: 0.8421 (tp30) cc_final: 0.7735 (tm-30) REVERT: B 82 GLN cc_start: 0.8725 (mt0) cc_final: 0.8420 (mt0) REVERT: B 85 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7861 (tm-30) REVERT: B 117 ASP cc_start: 0.7602 (t0) cc_final: 0.7263 (t0) REVERT: B 125 LYS cc_start: 0.8391 (tppp) cc_final: 0.8100 (ttpt) REVERT: B 145 GLU cc_start: 0.7871 (tp30) cc_final: 0.7015 (tp30) REVERT: B 318 ASN cc_start: 0.8991 (t160) cc_final: 0.8012 (t0) REVERT: B 335 GLU cc_start: 0.8352 (tp30) cc_final: 0.7792 (tm-30) REVERT: B 345 MET cc_start: 0.8857 (tpt) cc_final: 0.8311 (tpt) REVERT: C 85 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 117 ASP cc_start: 0.7520 (t0) cc_final: 0.6809 (t0) REVERT: C 125 LYS cc_start: 0.8332 (tppp) cc_final: 0.7904 (tppp) REVERT: C 152 GLU cc_start: 0.7945 (tp30) cc_final: 0.7371 (tp30) REVERT: C 307 GLU cc_start: 0.7263 (tt0) cc_final: 0.6954 (tt0) REVERT: C 318 ASN cc_start: 0.9042 (t0) cc_final: 0.8420 (t0) REVERT: D 85 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7873 (tm-30) REVERT: D 94 TYR cc_start: 0.8032 (m-80) cc_final: 0.7530 (m-80) REVERT: D 95 GLN cc_start: 0.8691 (tp-100) cc_final: 0.8491 (tp40) REVERT: D 120 VAL cc_start: 0.7898 (t) cc_final: 0.7530 (p) REVERT: D 135 MET cc_start: 0.7793 (tmm) cc_final: 0.7442 (tmm) REVERT: D 152 GLU cc_start: 0.7831 (tp30) cc_final: 0.7323 (tp30) REVERT: D 298 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: D 318 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.7760 (t0) REVERT: D 335 GLU cc_start: 0.8300 (tp30) cc_final: 0.7782 (tm-30) REVERT: E 82 GLN cc_start: 0.8732 (mt0) cc_final: 0.8405 (mt0) REVERT: E 85 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7845 (tm-30) REVERT: E 94 TYR cc_start: 0.7994 (m-80) cc_final: 0.7684 (m-80) REVERT: E 101 MET cc_start: 0.7950 (mmp) cc_final: 0.7346 (mmm) REVERT: E 125 LYS cc_start: 0.8487 (tppp) cc_final: 0.8204 (ttpt) REVERT: E 145 GLU cc_start: 0.7764 (tp30) cc_final: 0.6935 (tp30) REVERT: E 160 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7307 (t70) REVERT: E 214 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7710 (ttm-80) REVERT: E 318 ASN cc_start: 0.9054 (t160) cc_final: 0.8033 (t0) REVERT: E 335 GLU cc_start: 0.8327 (tp30) cc_final: 0.7805 (tm-30) REVERT: E 345 MET cc_start: 0.8848 (tpt) cc_final: 0.8419 (tpt) REVERT: F 85 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7580 (tm-30) REVERT: F 152 GLU cc_start: 0.7844 (tp30) cc_final: 0.7287 (tp30) REVERT: F 307 GLU cc_start: 0.7282 (tt0) cc_final: 0.6978 (tt0) REVERT: F 318 ASN cc_start: 0.9039 (t0) cc_final: 0.8393 (t0) REVERT: F 335 GLU cc_start: 0.8479 (tp30) cc_final: 0.7950 (tm-30) REVERT: F 337 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.6931 (t70) REVERT: F 344 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8354 (mp10) outliers start: 66 outliers final: 56 residues processed: 362 average time/residue: 0.1035 time to fit residues: 58.1181 Evaluate side-chains 382 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 321 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 298 GLN Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 120 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 177 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN B 188 GLN B 361 ASN C 298 GLN C 318 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN D 319 GLN E 188 GLN F 314 ASN F 318 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.117052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.100759 restraints weight = 25219.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104261 restraints weight = 13344.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.106616 restraints weight = 8278.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.108117 restraints weight = 5693.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.109251 restraints weight = 4290.404| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15414 Z= 0.120 Angle : 0.498 10.773 20778 Z= 0.252 Chirality : 0.035 0.129 2208 Planarity : 0.003 0.034 2826 Dihedral : 3.408 17.365 2094 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.95 % Allowed : 24.12 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.20), residues: 1884 helix: 2.15 (0.14), residues: 1446 sheet: None (None), residues: 0 loop : -0.94 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.014 0.001 TYR F 94 PHE 0.019 0.001 PHE F 129 TRP 0.006 0.001 TRP B 287 HIS 0.003 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00267 (15414) covalent geometry : angle 0.49760 (20778) hydrogen bonds : bond 0.03779 ( 1021) hydrogen bonds : angle 2.92277 ( 3045) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 321 time to evaluate : 0.630 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 85 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 135 MET cc_start: 0.7808 (tmm) cc_final: 0.7415 (tmm) REVERT: A 152 GLU cc_start: 0.7811 (tp30) cc_final: 0.7308 (tp30) REVERT: A 300 GLU cc_start: 0.8463 (tp30) cc_final: 0.8164 (tp30) REVERT: A 307 GLU cc_start: 0.7201 (tt0) cc_final: 0.6935 (tt0) REVERT: A 318 ASN cc_start: 0.8915 (t160) cc_final: 0.7845 (t0) REVERT: A 335 GLU cc_start: 0.8415 (tp30) cc_final: 0.7736 (tm-30) REVERT: B 82 GLN cc_start: 0.8719 (mt0) cc_final: 0.8430 (mt0) REVERT: B 85 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 117 ASP cc_start: 0.7622 (t0) cc_final: 0.7248 (t0) REVERT: B 125 LYS cc_start: 0.8407 (tppp) cc_final: 0.8181 (ttpt) REVERT: B 160 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7273 (t0) REVERT: B 318 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.7954 (t0) REVERT: B 335 GLU cc_start: 0.8345 (tp30) cc_final: 0.7796 (tm-30) REVERT: B 345 MET cc_start: 0.8879 (tpt) cc_final: 0.8278 (tpt) REVERT: C 85 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7568 (tm-30) REVERT: C 94 TYR cc_start: 0.8057 (m-80) cc_final: 0.7555 (m-80) REVERT: C 117 ASP cc_start: 0.7510 (t0) cc_final: 0.6763 (t0) REVERT: C 125 LYS cc_start: 0.8212 (tppp) cc_final: 0.7836 (tppp) REVERT: C 152 GLU cc_start: 0.7910 (tp30) cc_final: 0.7356 (tp30) REVERT: C 307 GLU cc_start: 0.7254 (tt0) cc_final: 0.6956 (tt0) REVERT: C 318 ASN cc_start: 0.8970 (t160) cc_final: 0.8408 (t0) REVERT: C 335 GLU cc_start: 0.8452 (tp30) cc_final: 0.7911 (tm-30) REVERT: D 85 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7844 (tm-30) REVERT: D 94 TYR cc_start: 0.7746 (m-80) cc_final: 0.7470 (m-80) REVERT: D 120 VAL cc_start: 0.7887 (t) cc_final: 0.7575 (p) REVERT: D 135 MET cc_start: 0.7775 (tmm) cc_final: 0.7426 (tmm) REVERT: D 152 GLU cc_start: 0.7823 (tp30) cc_final: 0.7312 (tp30) REVERT: D 211 MET cc_start: 0.8343 (tpp) cc_final: 0.7987 (tpt) REVERT: D 300 GLU cc_start: 0.8502 (tp30) cc_final: 0.8213 (tp30) REVERT: D 307 GLU cc_start: 0.7180 (tt0) cc_final: 0.6931 (tt0) REVERT: D 318 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.7660 (t0) REVERT: D 335 GLU cc_start: 0.8377 (tp30) cc_final: 0.7813 (tm-30) REVERT: E 82 GLN cc_start: 0.8727 (mt0) cc_final: 0.8413 (mt0) REVERT: E 85 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7861 (tm-30) REVERT: E 94 TYR cc_start: 0.7982 (m-80) cc_final: 0.7681 (m-80) REVERT: E 101 MET cc_start: 0.7982 (mmp) cc_final: 0.7361 (mmm) REVERT: E 125 LYS cc_start: 0.8495 (tppp) cc_final: 0.8243 (ttpt) REVERT: E 145 GLU cc_start: 0.7741 (tp30) cc_final: 0.6922 (tp30) REVERT: E 160 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7294 (t70) REVERT: E 214 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7720 (ttm-80) REVERT: E 318 ASN cc_start: 0.9002 (t160) cc_final: 0.7997 (t0) REVERT: E 335 GLU cc_start: 0.8345 (tp30) cc_final: 0.7797 (tm-30) REVERT: E 345 MET cc_start: 0.8875 (tpt) cc_final: 0.8311 (tpt) REVERT: F 85 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7590 (tm-30) REVERT: F 135 MET cc_start: 0.8062 (tmm) cc_final: 0.7175 (tmm) REVERT: F 152 GLU cc_start: 0.7831 (tp30) cc_final: 0.7277 (tp30) REVERT: F 262 MET cc_start: 0.7813 (ttp) cc_final: 0.7516 (ttp) REVERT: F 307 GLU cc_start: 0.7266 (tt0) cc_final: 0.6955 (tt0) REVERT: F 318 ASN cc_start: 0.8975 (t160) cc_final: 0.8365 (t0) REVERT: F 337 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.6920 (t70) REVERT: F 344 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8320 (mp10) outliers start: 63 outliers final: 54 residues processed: 355 average time/residue: 0.1041 time to fit residues: 57.2969 Evaluate side-chains 374 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 315 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 164 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 chunk 127 optimal weight: 0.0370 chunk 97 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 298 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.120009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103752 restraints weight = 25174.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107334 restraints weight = 13257.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.109735 restraints weight = 8165.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111271 restraints weight = 5572.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112399 restraints weight = 4169.944| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15414 Z= 0.103 Angle : 0.506 10.807 20778 Z= 0.251 Chirality : 0.035 0.130 2208 Planarity : 0.003 0.038 2826 Dihedral : 3.350 17.750 2094 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.20 % Allowed : 24.81 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.20), residues: 1884 helix: 2.19 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -0.87 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.015 0.001 TYR F 94 PHE 0.008 0.001 PHE F 185 TRP 0.005 0.001 TRP E 287 HIS 0.002 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00221 (15414) covalent geometry : angle 0.50615 (20778) hydrogen bonds : bond 0.03511 ( 1021) hydrogen bonds : angle 2.86733 ( 3045) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 329 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8011 (m-80) cc_final: 0.7686 (m-80) REVERT: A 101 MET cc_start: 0.7795 (mmp) cc_final: 0.7062 (mmm) REVERT: A 125 LYS cc_start: 0.8554 (tppp) cc_final: 0.8038 (tppp) REVERT: A 135 MET cc_start: 0.7691 (tmm) cc_final: 0.7383 (tmm) REVERT: A 152 GLU cc_start: 0.7737 (tp30) cc_final: 0.7219 (tp30) REVERT: A 307 GLU cc_start: 0.7093 (tt0) cc_final: 0.6798 (tt0) REVERT: A 318 ASN cc_start: 0.8806 (t160) cc_final: 0.7773 (t0) REVERT: A 335 GLU cc_start: 0.8378 (tp30) cc_final: 0.7741 (tm-30) REVERT: B 82 GLN cc_start: 0.8709 (mt0) cc_final: 0.8462 (mt0) REVERT: B 94 TYR cc_start: 0.8129 (m-80) cc_final: 0.7800 (m-80) REVERT: B 117 ASP cc_start: 0.7575 (t0) cc_final: 0.7195 (t0) REVERT: B 121 MET cc_start: 0.7753 (tpp) cc_final: 0.7175 (tpp) REVERT: B 125 LYS cc_start: 0.8422 (tppp) cc_final: 0.8191 (ttpt) REVERT: B 160 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7268 (t0) REVERT: B 211 MET cc_start: 0.8235 (tpt) cc_final: 0.7466 (ttp) REVERT: B 318 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.7926 (t0) REVERT: B 335 GLU cc_start: 0.8307 (tp30) cc_final: 0.7803 (tm-30) REVERT: B 345 MET cc_start: 0.8846 (tpt) cc_final: 0.8358 (tpt) REVERT: C 85 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 94 TYR cc_start: 0.7947 (m-80) cc_final: 0.7551 (m-80) REVERT: C 117 ASP cc_start: 0.7488 (t0) cc_final: 0.6747 (t0) REVERT: C 125 LYS cc_start: 0.8164 (tppp) cc_final: 0.7664 (ttpt) REVERT: C 152 GLU cc_start: 0.7859 (tp30) cc_final: 0.7343 (tp30) REVERT: C 307 GLU cc_start: 0.7088 (tt0) cc_final: 0.6818 (tt0) REVERT: C 318 ASN cc_start: 0.8944 (t160) cc_final: 0.8358 (t0) REVERT: C 335 GLU cc_start: 0.8364 (tp30) cc_final: 0.7952 (tm-30) REVERT: D 95 GLN cc_start: 0.8600 (tp40) cc_final: 0.8206 (tp-100) REVERT: D 135 MET cc_start: 0.7724 (tmm) cc_final: 0.7376 (tmm) REVERT: D 152 GLU cc_start: 0.7768 (tp30) cc_final: 0.7199 (tp30) REVERT: D 157 ASP cc_start: 0.8060 (t0) cc_final: 0.7855 (t0) REVERT: D 211 MET cc_start: 0.8325 (tpp) cc_final: 0.7973 (tpt) REVERT: D 302 ASP cc_start: 0.7387 (m-30) cc_final: 0.7004 (t0) REVERT: D 318 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.7626 (t0) REVERT: D 335 GLU cc_start: 0.8323 (tp30) cc_final: 0.7832 (tm-30) REVERT: D 344 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8362 (mp10) REVERT: E 82 GLN cc_start: 0.8706 (mt0) cc_final: 0.8376 (mt0) REVERT: E 85 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7868 (tm-30) REVERT: E 101 MET cc_start: 0.7934 (mmp) cc_final: 0.7326 (mmm) REVERT: E 125 LYS cc_start: 0.8412 (tppp) cc_final: 0.8187 (ttpt) REVERT: E 145 GLU cc_start: 0.7656 (tp30) cc_final: 0.6891 (tp30) REVERT: E 160 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7314 (t70) REVERT: E 201 GLU cc_start: 0.8327 (tp30) cc_final: 0.7875 (tp30) REVERT: E 214 ARG cc_start: 0.7978 (mtp85) cc_final: 0.7663 (ttm-80) REVERT: E 318 ASN cc_start: 0.8935 (t160) cc_final: 0.7971 (t0) REVERT: E 335 GLU cc_start: 0.8322 (tp30) cc_final: 0.7785 (tm-30) REVERT: E 342 ASP cc_start: 0.7665 (t0) cc_final: 0.7231 (t0) REVERT: E 345 MET cc_start: 0.8828 (tpt) cc_final: 0.8396 (tpt) REVERT: F 85 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7547 (tm-30) REVERT: F 94 TYR cc_start: 0.7973 (m-80) cc_final: 0.7596 (m-80) REVERT: F 121 MET cc_start: 0.7511 (tpp) cc_final: 0.7198 (tpp) REVERT: F 152 GLU cc_start: 0.7825 (tp30) cc_final: 0.7274 (tp30) REVERT: F 262 MET cc_start: 0.7764 (ttp) cc_final: 0.7480 (ttp) REVERT: F 307 GLU cc_start: 0.7218 (tt0) cc_final: 0.6940 (tt0) REVERT: F 318 ASN cc_start: 0.8947 (t160) cc_final: 0.8337 (t0) REVERT: F 335 GLU cc_start: 0.8467 (tp30) cc_final: 0.7951 (tm-30) REVERT: F 337 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.6923 (t70) REVERT: F 344 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8247 (mp10) outliers start: 51 outliers final: 41 residues processed: 361 average time/residue: 0.1044 time to fit residues: 58.0994 Evaluate side-chains 363 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 317 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 318 ASN Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 ASP Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 152 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 70 optimal weight: 3.9990 chunk 138 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN D 82 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.102901 restraints weight = 25045.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.106514 restraints weight = 13298.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.108850 restraints weight = 8185.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110366 restraints weight = 5622.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.111474 restraints weight = 4234.477| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15414 Z= 0.111 Angle : 0.518 10.600 20778 Z= 0.259 Chirality : 0.035 0.138 2208 Planarity : 0.003 0.037 2826 Dihedral : 3.352 17.231 2094 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.07 % Allowed : 26.00 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.35 (0.20), residues: 1884 helix: 2.23 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -0.83 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.015 0.001 TYR F 94 PHE 0.009 0.001 PHE F 185 TRP 0.005 0.001 TRP E 287 HIS 0.003 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00244 (15414) covalent geometry : angle 0.51837 (20778) hydrogen bonds : bond 0.03595 ( 1021) hydrogen bonds : angle 2.86101 ( 3045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.80 seconds wall clock time: 38 minutes 19.87 seconds (2299.87 seconds total)