Starting phenix.real_space_refine on Wed Mar 4 11:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ltn_0975/03_2026/6ltn_0975.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ltn_0975/03_2026/6ltn_0975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ltn_0975/03_2026/6ltn_0975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ltn_0975/03_2026/6ltn_0975.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ltn_0975/03_2026/6ltn_0975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ltn_0975/03_2026/6ltn_0975.map" } resolution = 3.1 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= 0.004 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 70 5.16 5 C 9128 2.51 5 N 2079 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.02s 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: 13615 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1945 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Restraints were copied for chains: A, B, C, D, F, G Time building chain proxies: 1.86, per 1000 atoms: 0.14 Number of scatterers: 13615 At special positions: 0 Unit cell: (110.874, 108.7, 110.874, 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 70 16.00 O 2338 8.00 N 2079 7.00 C 9128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 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: 0.81 Conformation dependent library (CDL) restraints added in 622.5 milliseconds 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 72.1% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'E' and resid 37 through 42 Processing helix chain 'E' and resid 43 through 61 removed outlier: 3.653A pdb=" N ILE E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 87 removed outlier: 3.764A pdb=" N ASP E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE E 108 " --> pdb=" O TRP E 104 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.702A pdb=" N PHE E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 151 removed outlier: 4.290A pdb=" N SER E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP E 138 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 139 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP E 147 " --> pdb=" O MET E 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 removed outlier: 3.866A pdb=" N THR E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 238 removed outlier: 3.890A pdb=" N THR E 220 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 237 " --> pdb=" O TYR E 233 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER E 238 " --> pdb=" O TYR E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.555A pdb=" N LEU E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 287 removed outlier: 3.647A pdb=" N TYR E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 294 removed outlier: 3.527A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU E 333 " --> pdb=" O SER E 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU E 335 " --> pdb=" O TYR E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 341 No H-bonds generated for 'chain 'E' and resid 339 through 341' Processing helix chain 'E' and resid 342 through 351 removed outlier: 3.945A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 351 " --> pdb=" O CYS E 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 43 through 61 removed outlier: 3.653A pdb=" N ILE A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.765A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.702A pdb=" N PHE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 151 removed outlier: 4.290A pdb=" N SER A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP A 138 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.866A pdb=" N THR A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 238 removed outlier: 3.891A pdb=" N THR A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 237 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 removed outlier: 3.647A pdb=" N TYR A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.526A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 335 removed outlier: 4.333A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.946A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 43 through 61 removed outlier: 3.651A pdb=" N ILE B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.765A pdb=" N ASP B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 108 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.702A pdb=" N PHE B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 151 removed outlier: 4.290A pdb=" N SER B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP B 138 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP B 147 " --> pdb=" O MET B 143 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.866A pdb=" N THR B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 238 removed outlier: 3.890A pdb=" N THR B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 removed outlier: 3.646A pdb=" N TYR B 284 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.526A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 335 " --> pdb=" O TYR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 351 removed outlier: 3.946A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 43 through 61 removed outlier: 3.652A pdb=" N ILE C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.764A pdb=" N ASP C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 108 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 121 through 131 removed outlier: 3.702A pdb=" N PHE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 151 removed outlier: 4.290A pdb=" N SER C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP C 138 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP C 147 " --> pdb=" O MET C 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 removed outlier: 3.865A pdb=" N THR C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 238 removed outlier: 3.891A pdb=" N THR C 220 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 237 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER C 238 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 287 removed outlier: 3.647A pdb=" N TYR C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 removed outlier: 3.526A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 342 through 351 removed outlier: 3.945A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 351 " --> pdb=" O CYS C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 42 Processing helix chain 'D' and resid 43 through 61 removed outlier: 3.653A pdb=" N ILE D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.764A pdb=" N ASP D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 108 " --> pdb=" O TRP D 104 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 121 through 131 removed outlier: 3.701A pdb=" N PHE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 151 removed outlier: 4.290A pdb=" N SER D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP D 138 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP D 147 " --> pdb=" O MET D 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.865A pdb=" N THR D 202 " --> pdb=" O GLN D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 238 removed outlier: 3.891A pdb=" N THR D 220 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER D 238 " --> pdb=" O TYR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 287 removed outlier: 3.646A pdb=" N TYR D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.527A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU D 335 " --> pdb=" O TYR D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 342 through 351 removed outlier: 3.946A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 351 " --> pdb=" O CYS D 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 42 Processing helix chain 'F' and resid 43 through 61 removed outlier: 3.652A pdb=" N ILE F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 87 removed outlier: 3.764A pdb=" N ASP F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE F 108 " --> pdb=" O TRP F 104 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 121 through 131 removed outlier: 3.701A pdb=" N PHE F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 151 removed outlier: 4.289A pdb=" N SER F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP F 138 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 139 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP F 147 " --> pdb=" O MET F 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS F 148 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.865A pdb=" N THR F 202 " --> pdb=" O GLN F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 238 removed outlier: 3.890A pdb=" N THR F 220 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU F 237 " --> pdb=" O TYR F 233 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER F 238 " --> pdb=" O TYR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 287 removed outlier: 3.647A pdb=" N TYR F 284 " --> pdb=" O ASN F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 294 removed outlier: 3.526A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU F 333 " --> pdb=" O SER F 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE F 334 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU F 335 " --> pdb=" O TYR F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 341 No H-bonds generated for 'chain 'F' and resid 339 through 341' Processing helix chain 'F' and resid 342 through 351 removed outlier: 3.945A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU F 351 " --> pdb=" O CYS F 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 42 Processing helix chain 'G' and resid 43 through 61 removed outlier: 3.652A pdb=" N ILE G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 87 removed outlier: 3.764A pdb=" N ASP G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA G 86 " --> pdb=" O SER G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 119 removed outlier: 3.673A pdb=" N LEU G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE G 108 " --> pdb=" O TRP G 104 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 121 through 131 removed outlier: 3.702A pdb=" N PHE G 129 " --> pdb=" O LEU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 151 removed outlier: 4.289A pdb=" N SER G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP G 138 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 139 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS G 148 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 204 removed outlier: 3.865A pdb=" N THR G 202 " --> pdb=" O GLN G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 238 removed outlier: 3.890A pdb=" N THR G 220 " --> pdb=" O CYS G 216 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 237 " --> pdb=" O TYR G 233 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER G 238 " --> pdb=" O TYR G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 280 removed outlier: 3.556A pdb=" N LEU G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 287 removed outlier: 3.647A pdb=" N TYR G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 294 removed outlier: 3.527A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 335 removed outlier: 4.334A pdb=" N LEU G 333 " --> pdb=" O SER G 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU G 335 " --> pdb=" O TYR G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 341 No H-bonds generated for 'chain 'G' and resid 339 through 341' Processing helix chain 'G' and resid 342 through 351 removed outlier: 3.945A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU G 351 " --> pdb=" O CYS G 347 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 243 through 246 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 246 Processing sheet with id=AA3, first strand: chain 'B' and resid 243 through 246 Processing sheet with id=AA4, first strand: chain 'C' and resid 243 through 246 Processing sheet with id=AA5, first strand: chain 'D' and resid 243 through 246 Processing sheet with id=AA6, first strand: chain 'F' and resid 243 through 246 Processing sheet with id=AA7, first strand: chain 'G' and resid 243 through 246 651 hydrogen bonds defined for protein. 1932 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: 1.83 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3920 1.34 - 1.46: 2959 1.46 - 1.57: 6981 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 13937 Sorted by residual: bond pdb=" CB GLU D 341 " pdb=" CG GLU D 341 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.01e+00 bond pdb=" CB GLU A 341 " pdb=" CG GLU A 341 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.00e+00 bond pdb=" CB GLU C 341 " pdb=" CG GLU C 341 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" CB GLU G 341 " pdb=" CG GLU G 341 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" CB GLU B 341 " pdb=" CG GLU B 341 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 2.95e+00 ... (remaining 13932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 18525 2.58 - 5.16: 319 5.16 - 7.74: 98 7.74 - 10.32: 14 10.32 - 12.90: 7 Bond angle restraints: 18963 Sorted by residual: angle pdb=" N VAL G 297 " pdb=" CA VAL G 297 " pdb=" C VAL G 297 " ideal model delta sigma weight residual 108.88 116.96 -8.08 2.16e+00 2.14e-01 1.40e+01 angle pdb=" N VAL E 297 " pdb=" CA VAL E 297 " pdb=" C VAL E 297 " ideal model delta sigma weight residual 108.88 116.95 -8.07 2.16e+00 2.14e-01 1.40e+01 angle pdb=" N VAL B 297 " pdb=" CA VAL B 297 " pdb=" C VAL B 297 " ideal model delta sigma weight residual 108.88 116.95 -8.07 2.16e+00 2.14e-01 1.40e+01 angle pdb=" N VAL D 297 " pdb=" CA VAL D 297 " pdb=" C VAL D 297 " ideal model delta sigma weight residual 108.88 116.95 -8.07 2.16e+00 2.14e-01 1.40e+01 angle pdb=" N VAL F 297 " pdb=" CA VAL F 297 " pdb=" C VAL F 297 " ideal model delta sigma weight residual 108.88 116.94 -8.06 2.16e+00 2.14e-01 1.39e+01 ... (remaining 18958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.54: 7160 15.54 - 31.07: 715 31.07 - 46.61: 287 46.61 - 62.15: 49 62.15 - 77.69: 42 Dihedral angle restraints: 8253 sinusoidal: 3150 harmonic: 5103 Sorted by residual: dihedral pdb=" CA SER A 239 " pdb=" C SER A 239 " pdb=" N LEU A 240 " pdb=" CA LEU A 240 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA SER G 239 " pdb=" C SER G 239 " pdb=" N LEU G 240 " pdb=" CA LEU G 240 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA SER B 239 " pdb=" C SER B 239 " pdb=" N LEU B 240 " pdb=" CA LEU B 240 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 8250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1067 0.033 - 0.066: 814 0.066 - 0.098: 240 0.098 - 0.131: 133 0.131 - 0.164: 35 Chirality restraints: 2289 Sorted by residual: chirality pdb=" CA LEU G 122 " pdb=" N LEU G 122 " pdb=" C LEU G 122 " pdb=" CB LEU G 122 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA LEU E 122 " pdb=" N LEU E 122 " pdb=" C LEU E 122 " pdb=" CB LEU E 122 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA LEU C 122 " pdb=" N LEU C 122 " pdb=" C LEU C 122 " pdb=" CB LEU C 122 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 2286 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 122 " -0.047 5.00e-02 4.00e+02 7.07e-02 7.99e+00 pdb=" N PRO A 123 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 122 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO C 123 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 122 " 0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO E 123 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 123 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 123 " 0.039 5.00e-02 4.00e+02 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3736 2.78 - 3.31: 11937 3.31 - 3.84: 20885 3.84 - 4.37: 24678 4.37 - 4.90: 41404 Nonbonded interactions: 102640 Sorted by model distance: nonbonded pdb=" OG SER B 59 " pdb=" OE2 GLU G 57 " model vdw 2.254 3.040 nonbonded pdb=" OE2 GLU B 57 " pdb=" OG SER D 59 " model vdw 2.291 3.040 nonbonded pdb=" O SER C 65 " pdb=" OG SER C 65 " model vdw 2.342 3.040 nonbonded pdb=" O SER D 65 " pdb=" OG SER D 65 " model vdw 2.343 3.040 nonbonded pdb=" O SER G 65 " pdb=" OG SER G 65 " model vdw 2.343 3.040 ... (remaining 102635 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 'E' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.040 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.006 0.052 13944 Z= 0.274 Angle : 0.949 12.903 18977 Z= 0.484 Chirality : 0.052 0.164 2289 Planarity : 0.010 0.071 2268 Dihedral : 16.291 77.685 4900 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.38 % Allowed : 11.73 % Favored : 86.89 % 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: -6.39 (0.12), residues: 1652 helix: -4.37 (0.06), residues: 1162 sheet: -3.08 (0.57), residues: 91 loop : -2.99 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 75 TYR 0.008 0.001 TYR F 199 PHE 0.030 0.002 PHE B 72 TRP 0.009 0.002 TRP E 85 HIS 0.003 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00616 (13937) covalent geometry : angle 0.94924 (18963) SS BOND : bond 0.00231 ( 7) SS BOND : angle 0.43784 ( 14) hydrogen bonds : bond 0.32546 ( 651) hydrogen bonds : angle 9.36024 ( 1932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 390 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 MET cc_start: 0.8494 (ppp) cc_final: 0.8172 (ppp) REVERT: E 121 TYR cc_start: 0.8448 (t80) cc_final: 0.8180 (t80) REVERT: E 138 ASP cc_start: 0.7988 (m-30) cc_final: 0.7719 (t0) REVERT: E 223 ILE cc_start: 0.9017 (tt) cc_final: 0.8791 (tt) REVERT: A 37 MET cc_start: 0.8794 (ppp) cc_final: 0.8544 (ppp) REVERT: A 56 GLN cc_start: 0.8391 (tp40) cc_final: 0.7904 (mm-40) REVERT: A 57 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6318 (tm-30) REVERT: A 63 GLN cc_start: 0.8368 (mp10) cc_final: 0.8024 (mp10) REVERT: A 138 ASP cc_start: 0.8262 (m-30) cc_final: 0.7903 (t0) REVERT: A 197 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7267 (tp30) REVERT: A 199 TYR cc_start: 0.6542 (t80) cc_final: 0.6165 (t80) REVERT: A 280 ASN cc_start: 0.9184 (t0) cc_final: 0.8842 (t0) REVERT: B 37 MET cc_start: 0.8598 (ppp) cc_final: 0.8302 (ppp) REVERT: B 63 GLN cc_start: 0.8520 (mp10) cc_final: 0.7972 (mp10) REVERT: B 197 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7127 (tp30) REVERT: B 280 ASN cc_start: 0.9231 (t0) cc_final: 0.9018 (t0) REVERT: C 36 LYS cc_start: 0.7886 (mmtp) cc_final: 0.6786 (mptt) REVERT: C 37 MET cc_start: 0.8662 (ppp) cc_final: 0.8334 (ppp) REVERT: C 56 GLN cc_start: 0.8455 (tp40) cc_final: 0.8160 (pp30) REVERT: C 111 TYR cc_start: 0.8861 (m-80) cc_final: 0.8571 (m-80) REVERT: C 121 TYR cc_start: 0.8659 (t80) cc_final: 0.8267 (t80) REVERT: C 126 PHE cc_start: 0.8229 (t80) cc_final: 0.7987 (t80) REVERT: C 197 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7555 (tp30) REVERT: C 299 PHE cc_start: 0.8271 (t80) cc_final: 0.8053 (t80) REVERT: C 331 TYR cc_start: 0.7026 (t80) cc_final: 0.6755 (t80) REVERT: D 36 LYS cc_start: 0.7807 (mmtp) cc_final: 0.7194 (mptt) REVERT: D 101 LEU cc_start: 0.8345 (tp) cc_final: 0.8144 (mp) REVERT: D 299 PHE cc_start: 0.8192 (t80) cc_final: 0.7756 (t80) REVERT: F 36 LYS cc_start: 0.7936 (mmtp) cc_final: 0.6962 (mptt) REVERT: F 37 MET cc_start: 0.8802 (ppp) cc_final: 0.8402 (ppp) REVERT: F 56 GLN cc_start: 0.8509 (tp40) cc_final: 0.8067 (mm-40) REVERT: F 63 GLN cc_start: 0.8286 (mp10) cc_final: 0.7888 (mp10) REVERT: F 124 PRO cc_start: 0.8545 (Cg_exo) cc_final: 0.8278 (Cg_endo) REVERT: F 138 ASP cc_start: 0.8208 (m-30) cc_final: 0.7936 (t0) REVERT: F 197 GLU cc_start: 0.7902 (mm-30) cc_final: 0.6927 (tp30) REVERT: F 299 PHE cc_start: 0.8024 (t80) cc_final: 0.7737 (t80) REVERT: F 331 TYR cc_start: 0.7170 (t80) cc_final: 0.6248 (t80) REVERT: G 63 GLN cc_start: 0.8146 (mp10) cc_final: 0.7592 (mp10) REVERT: G 138 ASP cc_start: 0.7961 (m-30) cc_final: 0.7727 (t0) REVERT: G 197 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6855 (tp30) REVERT: G 199 TYR cc_start: 0.6632 (t80) cc_final: 0.5904 (t80) outliers start: 21 outliers final: 11 residues processed: 411 average time/residue: 0.0966 time to fit residues: 60.8373 Evaluate side-chains 300 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 289 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 341 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN E 205 ASN E 280 ASN A 76 GLN A 205 ASN B 76 GLN B 205 ASN C 76 GLN C 205 ASN C 280 ASN D 76 GLN D 205 ASN D 255 ASN D 280 ASN D 338 ASN F 76 GLN F 205 ASN F 280 ASN G 76 GLN G 205 ASN G 280 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.164443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114268 restraints weight = 22660.566| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.68 r_work: 0.3294 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13944 Z= 0.122 Angle : 0.633 7.034 18977 Z= 0.319 Chirality : 0.038 0.142 2289 Planarity : 0.007 0.067 2268 Dihedral : 5.737 90.868 1828 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.08 % Allowed : 17.30 % Favored : 79.62 % 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: -2.93 (0.18), residues: 1652 helix: -1.62 (0.14), residues: 1141 sheet: -2.25 (0.63), residues: 91 loop : -2.18 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 254 TYR 0.017 0.001 TYR G 150 PHE 0.010 0.001 PHE A 79 TRP 0.007 0.001 TRP D 127 HIS 0.003 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00242 (13937) covalent geometry : angle 0.63262 (18963) SS BOND : bond 0.01026 ( 7) SS BOND : angle 0.48048 ( 14) hydrogen bonds : bond 0.04081 ( 651) hydrogen bonds : angle 4.18441 ( 1932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 341 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8626 (tp40) cc_final: 0.8136 (mm-40) REVERT: E 63 GLN cc_start: 0.8628 (mp10) cc_final: 0.8410 (mp10) REVERT: E 121 TYR cc_start: 0.8328 (t80) cc_final: 0.8114 (t80) REVERT: A 37 MET cc_start: 0.8637 (ppp) cc_final: 0.8336 (ppp) REVERT: A 56 GLN cc_start: 0.8658 (tp40) cc_final: 0.8425 (mm-40) REVERT: A 63 GLN cc_start: 0.8755 (mp10) cc_final: 0.8368 (mp10) REVERT: A 124 PRO cc_start: 0.8406 (Cg_exo) cc_final: 0.8077 (Cg_endo) REVERT: A 142 ILE cc_start: 0.7857 (mm) cc_final: 0.7635 (mt) REVERT: A 147 ASP cc_start: 0.7847 (m-30) cc_final: 0.7646 (p0) REVERT: A 197 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7154 (tp30) REVERT: B 37 MET cc_start: 0.8516 (ppp) cc_final: 0.8251 (ppp) REVERT: B 56 GLN cc_start: 0.8778 (tp40) cc_final: 0.7992 (mm-40) REVERT: B 63 GLN cc_start: 0.8874 (mp10) cc_final: 0.8324 (mp10) REVERT: B 124 PRO cc_start: 0.8272 (Cg_exo) cc_final: 0.8026 (Cg_endo) REVERT: B 197 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7009 (tp30) REVERT: C 111 TYR cc_start: 0.9256 (m-80) cc_final: 0.8981 (m-80) REVERT: C 121 TYR cc_start: 0.8693 (t80) cc_final: 0.8314 (t80) REVERT: C 124 PRO cc_start: 0.8260 (Cg_exo) cc_final: 0.7958 (Cg_endo) REVERT: C 197 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7392 (tp30) REVERT: C 237 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7590 (pp) REVERT: C 299 PHE cc_start: 0.8377 (t80) cc_final: 0.8081 (t80) REVERT: D 101 LEU cc_start: 0.8825 (tp) cc_final: 0.8562 (mp) REVERT: D 124 PRO cc_start: 0.8280 (Cg_exo) cc_final: 0.7995 (Cg_endo) REVERT: D 233 TYR cc_start: 0.9071 (t80) cc_final: 0.8856 (t80) REVERT: F 36 LYS cc_start: 0.7997 (mmtp) cc_final: 0.6967 (mptt) REVERT: F 37 MET cc_start: 0.8597 (ppp) cc_final: 0.8396 (ppp) REVERT: F 56 GLN cc_start: 0.8648 (tp40) cc_final: 0.8328 (mm-40) REVERT: F 63 GLN cc_start: 0.8774 (mp10) cc_final: 0.8284 (mp10) REVERT: F 124 PRO cc_start: 0.8668 (Cg_exo) cc_final: 0.8398 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7800 (m-30) cc_final: 0.7377 (t0) REVERT: F 197 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7106 (tp30) REVERT: F 237 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7771 (pp) REVERT: F 280 ASN cc_start: 0.9450 (OUTLIER) cc_final: 0.9000 (t0) REVERT: F 299 PHE cc_start: 0.8141 (t80) cc_final: 0.7788 (t80) REVERT: F 331 TYR cc_start: 0.7106 (t80) cc_final: 0.6015 (t80) REVERT: G 63 GLN cc_start: 0.8773 (mp10) cc_final: 0.8148 (mp10) REVERT: G 111 TYR cc_start: 0.9161 (m-80) cc_final: 0.8767 (m-80) REVERT: G 121 TYR cc_start: 0.8246 (t80) cc_final: 0.7932 (t80) REVERT: G 146 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5536 (mm) REVERT: G 197 GLU cc_start: 0.7770 (mm-30) cc_final: 0.6871 (tp30) REVERT: G 199 TYR cc_start: 0.6614 (t80) cc_final: 0.6227 (t80) outliers start: 47 outliers final: 25 residues processed: 378 average time/residue: 0.0834 time to fit residues: 50.2341 Evaluate side-chains 323 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 294 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 280 ASN Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 255 ASN A 255 ASN B 205 ASN C 255 ASN D 280 ASN F 205 ASN F 255 ASN F 280 ASN G 255 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.160341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108838 restraints weight = 22915.890| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.66 r_work: 0.3213 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13944 Z= 0.240 Angle : 0.716 12.875 18977 Z= 0.349 Chirality : 0.042 0.181 2289 Planarity : 0.007 0.076 2268 Dihedral : 4.497 18.279 1807 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 6.23 % Allowed : 19.20 % Favored : 74.57 % 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: -1.60 (0.21), residues: 1652 helix: -0.43 (0.16), residues: 1134 sheet: -2.00 (0.64), residues: 91 loop : -2.26 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 254 TYR 0.012 0.001 TYR E 233 PHE 0.018 0.002 PHE A 72 TRP 0.010 0.002 TRP G 85 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00536 (13937) covalent geometry : angle 0.71579 (18963) SS BOND : bond 0.00500 ( 7) SS BOND : angle 0.49525 ( 14) hydrogen bonds : bond 0.03999 ( 651) hydrogen bonds : angle 3.96326 ( 1932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 295 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 MET cc_start: 0.8437 (ppp) cc_final: 0.8163 (ppp) REVERT: E 56 GLN cc_start: 0.8553 (tp40) cc_final: 0.8316 (mm-40) REVERT: E 63 GLN cc_start: 0.8652 (mp10) cc_final: 0.8384 (mp10) REVERT: E 121 TYR cc_start: 0.8481 (t80) cc_final: 0.8263 (t80) REVERT: A 37 MET cc_start: 0.8686 (ppp) cc_final: 0.8427 (ppp) REVERT: A 56 GLN cc_start: 0.8621 (tp40) cc_final: 0.8241 (pp30) REVERT: A 63 GLN cc_start: 0.8862 (mp10) cc_final: 0.8408 (mp10) REVERT: A 124 PRO cc_start: 0.8384 (Cg_exo) cc_final: 0.8066 (Cg_endo) REVERT: A 146 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6090 (mm) REVERT: A 197 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7019 (tp30) REVERT: A 331 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7461 (t80) REVERT: B 63 GLN cc_start: 0.8829 (mp10) cc_final: 0.8313 (mp10) REVERT: B 124 PRO cc_start: 0.8264 (Cg_exo) cc_final: 0.8020 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6287 (mm) REVERT: B 197 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7022 (tp30) REVERT: C 56 GLN cc_start: 0.8606 (tp40) cc_final: 0.7947 (pp30) REVERT: C 121 TYR cc_start: 0.8670 (t80) cc_final: 0.8316 (t80) REVERT: C 124 PRO cc_start: 0.8250 (Cg_exo) cc_final: 0.7966 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6079 (mm) REVERT: C 197 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7443 (tp30) REVERT: C 237 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7927 (pp) REVERT: C 299 PHE cc_start: 0.8359 (t80) cc_final: 0.7986 (t80) REVERT: D 124 PRO cc_start: 0.8258 (Cg_exo) cc_final: 0.7982 (Cg_endo) REVERT: D 146 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6688 (mm) REVERT: D 197 GLU cc_start: 0.6489 (tp30) cc_final: 0.6229 (tp30) REVERT: F 37 MET cc_start: 0.8668 (ppp) cc_final: 0.8448 (ppp) REVERT: F 63 GLN cc_start: 0.8651 (mp10) cc_final: 0.8220 (mp10) REVERT: F 121 TYR cc_start: 0.8694 (t80) cc_final: 0.8207 (t80) REVERT: F 124 PRO cc_start: 0.8693 (Cg_exo) cc_final: 0.8436 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7814 (m-30) cc_final: 0.7381 (t0) REVERT: F 146 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6038 (mm) REVERT: F 197 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7005 (tp30) REVERT: F 237 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8089 (pp) REVERT: F 299 PHE cc_start: 0.8278 (t80) cc_final: 0.7937 (t80) REVERT: F 331 TYR cc_start: 0.7510 (t80) cc_final: 0.6510 (t80) REVERT: G 37 MET cc_start: 0.8717 (ppp) cc_final: 0.8499 (ppp) REVERT: G 63 GLN cc_start: 0.8892 (mp10) cc_final: 0.8244 (mp10) REVERT: G 121 TYR cc_start: 0.8453 (t80) cc_final: 0.8039 (t80) REVERT: G 124 PRO cc_start: 0.8400 (Cg_exo) cc_final: 0.8148 (Cg_endo) REVERT: G 197 GLU cc_start: 0.7763 (mm-30) cc_final: 0.6886 (tp30) outliers start: 95 outliers final: 57 residues processed: 365 average time/residue: 0.0823 time to fit residues: 48.4590 Evaluate side-chains 349 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 284 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 128 optimal weight: 0.0020 chunk 10 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 280 ASN B 205 ASN F 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.164724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113936 restraints weight = 22719.772| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.62 r_work: 0.3301 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13944 Z= 0.129 Angle : 0.648 11.781 18977 Z= 0.303 Chirality : 0.040 0.179 2289 Planarity : 0.006 0.057 2268 Dihedral : 4.003 13.932 1806 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.39 % Allowed : 22.28 % Favored : 73.33 % 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: -0.99 (0.22), residues: 1652 helix: 0.02 (0.17), residues: 1134 sheet: -1.84 (0.63), residues: 91 loop : -1.98 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 254 TYR 0.009 0.001 TYR D 111 PHE 0.019 0.001 PHE E 299 TRP 0.006 0.001 TRP F 85 HIS 0.001 0.000 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00287 (13937) covalent geometry : angle 0.64862 (18963) SS BOND : bond 0.00110 ( 7) SS BOND : angle 0.32687 ( 14) hydrogen bonds : bond 0.03017 ( 651) hydrogen bonds : angle 3.65508 ( 1932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 292 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8494 (tp40) cc_final: 0.8184 (mm-40) REVERT: E 121 TYR cc_start: 0.8357 (t80) cc_final: 0.8074 (t80) REVERT: E 240 LEU cc_start: 0.8728 (tp) cc_final: 0.8510 (tp) REVERT: A 56 GLN cc_start: 0.8683 (tp40) cc_final: 0.8250 (pp30) REVERT: A 63 GLN cc_start: 0.8788 (mp10) cc_final: 0.8362 (mp10) REVERT: A 124 PRO cc_start: 0.8301 (Cg_exo) cc_final: 0.8012 (Cg_endo) REVERT: A 146 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6096 (mm) REVERT: A 197 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7034 (tp30) REVERT: A 331 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 63 GLN cc_start: 0.8846 (mp10) cc_final: 0.8330 (mp10) REVERT: B 124 PRO cc_start: 0.8273 (Cg_exo) cc_final: 0.8059 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6405 (mm) REVERT: B 197 GLU cc_start: 0.7849 (mm-30) cc_final: 0.6990 (tp30) REVERT: C 56 GLN cc_start: 0.8404 (tp40) cc_final: 0.7864 (pp30) REVERT: C 121 TYR cc_start: 0.8504 (t80) cc_final: 0.8232 (t80) REVERT: C 124 PRO cc_start: 0.8430 (Cg_exo) cc_final: 0.8201 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.5893 (mm) REVERT: C 197 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7466 (tp30) REVERT: C 237 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7741 (pp) REVERT: C 299 PHE cc_start: 0.8319 (t80) cc_final: 0.7928 (t80) REVERT: D 124 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.8068 (Cg_endo) REVERT: D 146 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6657 (mm) REVERT: D 197 GLU cc_start: 0.6590 (tp30) cc_final: 0.6373 (tp30) REVERT: F 63 GLN cc_start: 0.8645 (mp10) cc_final: 0.8245 (mp10) REVERT: F 121 TYR cc_start: 0.8643 (t80) cc_final: 0.8175 (t80) REVERT: F 124 PRO cc_start: 0.8645 (Cg_exo) cc_final: 0.8396 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7771 (m-30) cc_final: 0.7351 (t0) REVERT: F 146 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6166 (mm) REVERT: F 197 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7153 (tp30) REVERT: F 237 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7718 (pp) REVERT: F 299 PHE cc_start: 0.8251 (t80) cc_final: 0.7879 (t80) REVERT: F 331 TYR cc_start: 0.7426 (t80) cc_final: 0.6542 (t80) REVERT: G 37 MET cc_start: 0.8750 (ppp) cc_final: 0.8539 (ppp) REVERT: G 63 GLN cc_start: 0.8884 (mp10) cc_final: 0.8291 (mp10) REVERT: G 121 TYR cc_start: 0.8416 (t80) cc_final: 0.7982 (t80) REVERT: G 124 PRO cc_start: 0.8590 (Cg_exo) cc_final: 0.8343 (Cg_endo) REVERT: G 146 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5236 (mm) REVERT: G 197 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7013 (tp30) outliers start: 67 outliers final: 45 residues processed: 340 average time/residue: 0.0798 time to fit residues: 44.2531 Evaluate side-chains 329 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 275 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 331 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 96 optimal weight: 6.9990 chunk 72 optimal weight: 0.0870 chunk 165 optimal weight: 0.0470 chunk 125 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN F 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.167968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117644 restraints weight = 22651.375| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.68 r_work: 0.3345 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13944 Z= 0.097 Angle : 0.617 10.020 18977 Z= 0.281 Chirality : 0.038 0.140 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.628 10.624 1806 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.47 % Allowed : 23.20 % Favored : 73.33 % 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: -0.43 (0.22), residues: 1652 helix: 0.41 (0.17), residues: 1113 sheet: -1.41 (0.62), residues: 91 loop : -1.59 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 254 TYR 0.016 0.001 TYR G 150 PHE 0.014 0.001 PHE E 299 TRP 0.003 0.000 TRP F 85 HIS 0.001 0.000 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00200 (13937) covalent geometry : angle 0.61669 (18963) SS BOND : bond 0.00049 ( 7) SS BOND : angle 0.28323 ( 14) hydrogen bonds : bond 0.02440 ( 651) hydrogen bonds : angle 3.47897 ( 1932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8518 (tp40) cc_final: 0.8177 (mm-40) REVERT: E 121 TYR cc_start: 0.8233 (t80) cc_final: 0.8015 (t80) REVERT: A 56 GLN cc_start: 0.8733 (tp40) cc_final: 0.8211 (pp30) REVERT: A 63 GLN cc_start: 0.8834 (mp10) cc_final: 0.8379 (mp10) REVERT: A 124 PRO cc_start: 0.8213 (Cg_exo) cc_final: 0.7929 (Cg_endo) REVERT: A 146 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6607 (mm) REVERT: A 197 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7210 (tp30) REVERT: A 331 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7373 (t80) REVERT: B 63 GLN cc_start: 0.8824 (mp10) cc_final: 0.8272 (mp10) REVERT: B 124 PRO cc_start: 0.8205 (Cg_exo) cc_final: 0.7987 (Cg_endo) REVERT: B 197 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7008 (tp30) REVERT: C 56 GLN cc_start: 0.8376 (tp40) cc_final: 0.7826 (pp30) REVERT: C 116 PHE cc_start: 0.8404 (m-80) cc_final: 0.8162 (m-80) REVERT: C 121 TYR cc_start: 0.8297 (t80) cc_final: 0.8022 (t80) REVERT: C 124 PRO cc_start: 0.8405 (Cg_exo) cc_final: 0.8200 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6260 (mm) REVERT: C 197 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7410 (tp30) REVERT: C 216 CYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7417 (t) REVERT: D 146 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6569 (mm) REVERT: D 197 GLU cc_start: 0.6534 (tp30) cc_final: 0.6170 (tp30) REVERT: D 216 CYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7614 (t) REVERT: F 63 GLN cc_start: 0.8592 (mp10) cc_final: 0.8155 (mp10) REVERT: F 101 LEU cc_start: 0.8492 (tt) cc_final: 0.8242 (mt) REVERT: F 121 TYR cc_start: 0.8529 (t80) cc_final: 0.8049 (t80) REVERT: F 124 PRO cc_start: 0.8593 (Cg_exo) cc_final: 0.8354 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7409 (m-30) cc_final: 0.7187 (t0) REVERT: F 146 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6259 (mm) REVERT: F 197 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7155 (tp30) REVERT: F 299 PHE cc_start: 0.8241 (t80) cc_final: 0.7904 (t80) REVERT: F 331 TYR cc_start: 0.7345 (t80) cc_final: 0.6434 (t80) REVERT: G 56 GLN cc_start: 0.8549 (tp40) cc_final: 0.8318 (pp30) REVERT: G 63 GLN cc_start: 0.8838 (mp10) cc_final: 0.8228 (mp10) REVERT: G 121 TYR cc_start: 0.8292 (t80) cc_final: 0.7897 (t80) REVERT: G 197 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7188 (tp30) outliers start: 53 outliers final: 30 residues processed: 336 average time/residue: 0.0749 time to fit residues: 41.7759 Evaluate side-chains 316 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 0.0020 chunk 83 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 131 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 140 optimal weight: 0.0870 overall best weight: 0.4366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.170879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.121716 restraints weight = 22310.179| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.60 r_work: 0.3413 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13944 Z= 0.099 Angle : 0.626 14.006 18977 Z= 0.283 Chirality : 0.038 0.144 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.464 11.726 1806 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.80 % Allowed : 23.20 % Favored : 73.00 % 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: -0.15 (0.22), residues: 1652 helix: 0.68 (0.17), residues: 1106 sheet: -4.06 (0.54), residues: 49 loop : -1.32 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 254 TYR 0.007 0.001 TYR G 150 PHE 0.024 0.001 PHE C 299 TRP 0.002 0.000 TRP A 127 HIS 0.001 0.000 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00203 (13937) covalent geometry : angle 0.62647 (18963) SS BOND : bond 0.00030 ( 7) SS BOND : angle 0.23427 ( 14) hydrogen bonds : bond 0.02295 ( 651) hydrogen bonds : angle 3.41172 ( 1932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 287 time to evaluate : 0.484 Fit side-chains REVERT: E 56 GLN cc_start: 0.8487 (tp40) cc_final: 0.8201 (mm-40) REVERT: E 63 GLN cc_start: 0.8577 (mp10) cc_final: 0.8338 (mp10) REVERT: E 146 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7033 (mm) REVERT: A 56 GLN cc_start: 0.8772 (tp40) cc_final: 0.8272 (pp30) REVERT: A 63 GLN cc_start: 0.8782 (mp10) cc_final: 0.8370 (mp10) REVERT: A 146 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6514 (mm) REVERT: A 197 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7348 (tp30) REVERT: A 331 TYR cc_start: 0.7764 (OUTLIER) cc_final: 0.7362 (t80) REVERT: B 63 GLN cc_start: 0.8777 (mp10) cc_final: 0.8245 (mp10) REVERT: B 124 PRO cc_start: 0.8225 (Cg_exo) cc_final: 0.8003 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6301 (mm) REVERT: B 197 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7085 (tp30) REVERT: C 56 GLN cc_start: 0.8232 (tp40) cc_final: 0.7830 (pp30) REVERT: C 116 PHE cc_start: 0.8303 (m-80) cc_final: 0.8103 (m-80) REVERT: C 121 TYR cc_start: 0.8294 (t80) cc_final: 0.8023 (t80) REVERT: C 124 PRO cc_start: 0.8566 (Cg_exo) cc_final: 0.8365 (Cg_endo) REVERT: C 197 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7349 (tp30) REVERT: D 56 GLN cc_start: 0.8744 (tp40) cc_final: 0.8529 (tp-100) REVERT: D 146 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6574 (mm) REVERT: D 197 GLU cc_start: 0.6624 (tp30) cc_final: 0.6351 (tp30) REVERT: F 63 GLN cc_start: 0.8558 (mp10) cc_final: 0.8153 (mp10) REVERT: F 101 LEU cc_start: 0.8495 (tt) cc_final: 0.8204 (mt) REVERT: F 121 TYR cc_start: 0.8414 (t80) cc_final: 0.8011 (t80) REVERT: F 146 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6601 (mm) REVERT: F 197 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7289 (tp30) REVERT: F 299 PHE cc_start: 0.8204 (t80) cc_final: 0.7890 (t80) REVERT: G 63 GLN cc_start: 0.8842 (mp10) cc_final: 0.8237 (mp10) REVERT: G 121 TYR cc_start: 0.8239 (t80) cc_final: 0.7883 (t80) REVERT: G 146 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6228 (mm) REVERT: G 197 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7249 (tp30) outliers start: 58 outliers final: 33 residues processed: 326 average time/residue: 0.0791 time to fit residues: 42.7376 Evaluate side-chains 316 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 CYS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 121 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN F 56 GLN F 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.166746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116112 restraints weight = 22913.078| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.70 r_work: 0.3323 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13944 Z= 0.120 Angle : 0.639 12.873 18977 Z= 0.294 Chirality : 0.039 0.117 2289 Planarity : 0.005 0.056 2268 Dihedral : 3.616 11.465 1806 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.93 % Allowed : 23.46 % Favored : 72.61 % 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: 0.01 (0.23), residues: 1652 helix: 0.71 (0.17), residues: 1141 sheet: -1.39 (0.59), residues: 91 loop : -1.45 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 254 TYR 0.009 0.001 TYR C 213 PHE 0.015 0.001 PHE D 244 TRP 0.004 0.001 TRP C 85 HIS 0.001 0.000 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00265 (13937) covalent geometry : angle 0.63965 (18963) SS BOND : bond 0.00121 ( 7) SS BOND : angle 0.23010 ( 14) hydrogen bonds : bond 0.02577 ( 651) hydrogen bonds : angle 3.45118 ( 1932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 269 time to evaluate : 0.493 Fit side-chains REVERT: E 56 GLN cc_start: 0.8522 (tp40) cc_final: 0.8267 (mm-40) REVERT: E 63 GLN cc_start: 0.8641 (mp10) cc_final: 0.8369 (mp10) REVERT: A 56 GLN cc_start: 0.8698 (tp40) cc_final: 0.8225 (pp30) REVERT: A 63 GLN cc_start: 0.8802 (mp10) cc_final: 0.8431 (mp10) REVERT: A 146 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6559 (mm) REVERT: A 197 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7248 (tp30) REVERT: A 331 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.7273 (t80) REVERT: B 63 GLN cc_start: 0.8794 (mp10) cc_final: 0.8257 (mp10) REVERT: B 124 PRO cc_start: 0.8236 (Cg_exo) cc_final: 0.8026 (Cg_endo) REVERT: B 197 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7129 (tp30) REVERT: C 56 GLN cc_start: 0.8333 (tp40) cc_final: 0.7856 (tm-30) REVERT: C 124 PRO cc_start: 0.8525 (Cg_exo) cc_final: 0.8293 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6249 (mm) REVERT: C 197 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7255 (tp30) REVERT: C 299 PHE cc_start: 0.8115 (t80) cc_final: 0.7849 (t80) REVERT: D 90 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: D 146 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6563 (mm) REVERT: D 197 GLU cc_start: 0.6636 (tp30) cc_final: 0.6364 (tp30) REVERT: F 56 GLN cc_start: 0.8675 (tp40) cc_final: 0.8062 (pp30) REVERT: F 63 GLN cc_start: 0.8616 (mp10) cc_final: 0.8165 (mp10) REVERT: F 101 LEU cc_start: 0.8538 (tt) cc_final: 0.8182 (mt) REVERT: F 121 TYR cc_start: 0.8494 (t80) cc_final: 0.8052 (t80) REVERT: F 138 ASP cc_start: 0.7357 (m-30) cc_final: 0.7064 (t0) REVERT: F 146 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6205 (mm) REVERT: F 197 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7249 (tp30) REVERT: G 63 GLN cc_start: 0.8872 (mp10) cc_final: 0.8257 (mp10) REVERT: G 121 TYR cc_start: 0.8270 (t80) cc_final: 0.7934 (t80) REVERT: G 197 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7285 (tp30) outliers start: 60 outliers final: 42 residues processed: 317 average time/residue: 0.0754 time to fit residues: 39.6236 Evaluate side-chains 311 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 263 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 108 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.165386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115822 restraints weight = 22714.330| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.68 r_work: 0.3312 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13944 Z= 0.132 Angle : 0.644 12.306 18977 Z= 0.299 Chirality : 0.040 0.150 2289 Planarity : 0.005 0.056 2268 Dihedral : 3.714 12.148 1806 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.06 % Allowed : 23.66 % Favored : 72.28 % 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: 0.11 (0.23), residues: 1652 helix: 0.83 (0.17), residues: 1141 sheet: -1.48 (0.59), residues: 91 loop : -1.49 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 254 TYR 0.012 0.001 TYR G 150 PHE 0.022 0.001 PHE F 299 TRP 0.005 0.001 TRP A 85 HIS 0.001 0.000 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00293 (13937) covalent geometry : angle 0.64432 (18963) SS BOND : bond 0.00137 ( 7) SS BOND : angle 0.26987 ( 14) hydrogen bonds : bond 0.02754 ( 651) hydrogen bonds : angle 3.49698 ( 1932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 270 time to evaluate : 0.375 Fit side-chains REVERT: E 56 GLN cc_start: 0.8593 (tp40) cc_final: 0.8281 (mm-40) REVERT: E 63 GLN cc_start: 0.8664 (mp10) cc_final: 0.8392 (mp10) REVERT: E 146 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6952 (mm) REVERT: A 63 GLN cc_start: 0.8845 (mp10) cc_final: 0.8442 (mp10) REVERT: A 124 PRO cc_start: 0.8091 (Cg_exo) cc_final: 0.7801 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6619 (mm) REVERT: A 197 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7180 (tp30) REVERT: A 331 TYR cc_start: 0.7746 (OUTLIER) cc_final: 0.7173 (t80) REVERT: B 63 GLN cc_start: 0.8841 (mp10) cc_final: 0.8301 (mp10) REVERT: B 124 PRO cc_start: 0.8207 (Cg_exo) cc_final: 0.7986 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6282 (mm) REVERT: B 197 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7129 (tp30) REVERT: C 56 GLN cc_start: 0.8513 (tp40) cc_final: 0.7949 (tm-30) REVERT: C 124 PRO cc_start: 0.8527 (Cg_exo) cc_final: 0.8298 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6227 (mm) REVERT: C 197 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7300 (tp30) REVERT: D 90 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: D 146 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6562 (mm) REVERT: D 197 GLU cc_start: 0.6597 (tp30) cc_final: 0.6320 (tp30) REVERT: F 56 GLN cc_start: 0.8741 (tp40) cc_final: 0.8119 (pp30) REVERT: F 63 GLN cc_start: 0.8633 (mp10) cc_final: 0.8216 (mp10) REVERT: F 101 LEU cc_start: 0.8550 (tt) cc_final: 0.8157 (mt) REVERT: F 121 TYR cc_start: 0.8543 (t80) cc_final: 0.8098 (t80) REVERT: F 138 ASP cc_start: 0.7450 (m-30) cc_final: 0.7101 (t0) REVERT: F 146 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6207 (mm) REVERT: F 197 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7167 (tp30) REVERT: G 63 GLN cc_start: 0.8894 (mp10) cc_final: 0.8266 (mp10) REVERT: G 121 TYR cc_start: 0.8328 (t80) cc_final: 0.7960 (t80) REVERT: G 197 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7214 (tp30) outliers start: 62 outliers final: 49 residues processed: 317 average time/residue: 0.0765 time to fit residues: 39.9297 Evaluate side-chains 327 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 270 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 331 TYR Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 139 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 86 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.167089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.117381 restraints weight = 22900.998| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.70 r_work: 0.3336 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13944 Z= 0.107 Angle : 0.639 12.379 18977 Z= 0.292 Chirality : 0.039 0.133 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.590 11.705 1806 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.67 % Allowed : 24.31 % Favored : 72.02 % 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: 0.19 (0.22), residues: 1652 helix: 0.94 (0.17), residues: 1134 sheet: -3.99 (0.53), residues: 49 loop : -1.29 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 254 TYR 0.008 0.001 TYR D 111 PHE 0.019 0.001 PHE F 299 TRP 0.003 0.001 TRP F 85 HIS 0.001 0.000 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00231 (13937) covalent geometry : angle 0.63871 (18963) SS BOND : bond 0.00075 ( 7) SS BOND : angle 0.24084 ( 14) hydrogen bonds : bond 0.02499 ( 651) hydrogen bonds : angle 3.45087 ( 1932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 0.506 Fit side-chains REVERT: E 56 GLN cc_start: 0.8579 (tp40) cc_final: 0.7868 (pp30) REVERT: E 63 GLN cc_start: 0.8637 (mp10) cc_final: 0.8434 (mp10) REVERT: E 146 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7150 (mm) REVERT: A 63 GLN cc_start: 0.8766 (mp10) cc_final: 0.8385 (mp10) REVERT: A 124 PRO cc_start: 0.8104 (Cg_exo) cc_final: 0.7828 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6642 (mm) REVERT: A 197 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7409 (tp30) REVERT: A 331 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7244 (t80) REVERT: B 63 GLN cc_start: 0.8788 (mp10) cc_final: 0.8212 (mp10) REVERT: B 124 PRO cc_start: 0.8229 (Cg_exo) cc_final: 0.8016 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6336 (mm) REVERT: B 197 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7208 (tp30) REVERT: C 56 GLN cc_start: 0.8514 (tp40) cc_final: 0.7939 (pp30) REVERT: C 124 PRO cc_start: 0.8495 (Cg_exo) cc_final: 0.8261 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6248 (mm) REVERT: C 197 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7348 (tp30) REVERT: D 90 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7313 (mp10) REVERT: D 146 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6587 (mm) REVERT: D 197 GLU cc_start: 0.6614 (tp30) cc_final: 0.5738 (mt-10) REVERT: D 201 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7612 (mptt) REVERT: F 56 GLN cc_start: 0.8751 (tp40) cc_final: 0.8123 (pp30) REVERT: F 63 GLN cc_start: 0.8625 (mp10) cc_final: 0.8175 (mp10) REVERT: F 101 LEU cc_start: 0.8568 (tt) cc_final: 0.8143 (mt) REVERT: F 121 TYR cc_start: 0.8490 (t80) cc_final: 0.8047 (t80) REVERT: F 138 ASP cc_start: 0.7407 (m-30) cc_final: 0.7058 (t0) REVERT: F 146 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6139 (mm) REVERT: F 197 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7112 (tp30) REVERT: G 63 GLN cc_start: 0.8872 (mp10) cc_final: 0.8245 (mp10) REVERT: G 121 TYR cc_start: 0.8256 (t80) cc_final: 0.7917 (t80) REVERT: G 197 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7319 (tp30) outliers start: 56 outliers final: 46 residues processed: 316 average time/residue: 0.0805 time to fit residues: 41.6870 Evaluate side-chains 329 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 275 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 331 TYR Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 44 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 0.0370 chunk 129 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 overall best weight: 3.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 ASN F 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.163068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113636 restraints weight = 22809.204| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.63 r_work: 0.3286 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13944 Z= 0.188 Angle : 0.687 11.634 18977 Z= 0.324 Chirality : 0.041 0.136 2289 Planarity : 0.006 0.056 2268 Dihedral : 3.959 14.434 1806 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.00 % Allowed : 23.85 % Favored : 72.15 % 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: 0.09 (0.22), residues: 1652 helix: 0.85 (0.17), residues: 1141 sheet: -1.66 (0.59), residues: 91 loop : -1.58 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 254 TYR 0.009 0.001 TYR C 233 PHE 0.017 0.001 PHE F 299 TRP 0.007 0.002 TRP A 85 HIS 0.002 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00422 (13937) covalent geometry : angle 0.68685 (18963) SS BOND : bond 0.00220 ( 7) SS BOND : angle 0.37290 ( 14) hydrogen bonds : bond 0.03105 ( 651) hydrogen bonds : angle 3.59860 ( 1932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8563 (tp40) cc_final: 0.8290 (mm-40) REVERT: E 63 GLN cc_start: 0.8729 (mp10) cc_final: 0.8440 (mp10) REVERT: E 146 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7089 (mm) REVERT: A 56 GLN cc_start: 0.8799 (tp-100) cc_final: 0.7945 (pp30) REVERT: A 63 GLN cc_start: 0.8822 (mp10) cc_final: 0.8391 (mp10) REVERT: A 124 PRO cc_start: 0.8111 (Cg_exo) cc_final: 0.7823 (Cg_endo) REVERT: A 138 ASP cc_start: 0.7579 (m-30) cc_final: 0.7170 (t0) REVERT: A 146 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6680 (mm) REVERT: A 197 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7256 (tp30) REVERT: A 331 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6472 (t80) REVERT: B 63 GLN cc_start: 0.8810 (mp10) cc_final: 0.8281 (mp10) REVERT: B 124 PRO cc_start: 0.8188 (Cg_exo) cc_final: 0.7965 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6266 (mm) REVERT: B 197 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7174 (tp30) REVERT: C 56 GLN cc_start: 0.8537 (tp40) cc_final: 0.7959 (tm-30) REVERT: C 124 PRO cc_start: 0.8520 (Cg_exo) cc_final: 0.8290 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6322 (mm) REVERT: C 197 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7318 (tp30) REVERT: D 90 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7372 (mp10) REVERT: D 146 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6425 (mm) REVERT: D 197 GLU cc_start: 0.6601 (tp30) cc_final: 0.6344 (tp30) REVERT: F 56 GLN cc_start: 0.8779 (tp40) cc_final: 0.8139 (pp30) REVERT: F 63 GLN cc_start: 0.8676 (mp10) cc_final: 0.8272 (mp10) REVERT: F 101 LEU cc_start: 0.8605 (tt) cc_final: 0.8160 (mt) REVERT: F 121 TYR cc_start: 0.8623 (t80) cc_final: 0.8123 (t80) REVERT: F 124 PRO cc_start: 0.8621 (Cg_exo) cc_final: 0.8378 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7480 (m-30) cc_final: 0.7179 (t0) REVERT: F 146 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6220 (mm) REVERT: F 197 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7065 (tp30) REVERT: G 63 GLN cc_start: 0.8889 (mp10) cc_final: 0.8219 (mp10) REVERT: G 121 TYR cc_start: 0.8401 (t80) cc_final: 0.7997 (t80) REVERT: G 197 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7315 (tp30) outliers start: 61 outliers final: 47 residues processed: 316 average time/residue: 0.0814 time to fit residues: 41.9489 Evaluate side-chains 321 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 331 TYR Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 36 optimal weight: 0.3980 chunk 125 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.167159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116966 restraints weight = 23151.769| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.64 r_work: 0.3354 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13944 Z= 0.128 Angle : 0.662 12.253 18977 Z= 0.305 Chirality : 0.040 0.130 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.789 12.758 1806 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.13 % Allowed : 23.85 % Favored : 72.02 % 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: 0.13 (0.22), residues: 1652 helix: 0.93 (0.17), residues: 1134 sheet: -4.21 (0.52), residues: 49 loop : -1.40 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 254 TYR 0.008 0.001 TYR D 111 PHE 0.016 0.001 PHE F 299 TRP 0.004 0.001 TRP F 85 HIS 0.001 0.000 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00287 (13937) covalent geometry : angle 0.66178 (18963) SS BOND : bond 0.00112 ( 7) SS BOND : angle 0.25512 ( 14) hydrogen bonds : bond 0.02758 ( 651) hydrogen bonds : angle 3.53286 ( 1932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3549.15 seconds wall clock time: 61 minutes 18.30 seconds (3678.30 seconds total)