Starting phenix.real_space_refine on Thu Sep 18 02:49:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ltn_0975/09_2025/6ltn_0975.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ltn_0975/09_2025/6ltn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ltn_0975/09_2025/6ltn_0975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ltn_0975/09_2025/6ltn_0975.map" model { file = "/net/cci-nas-00/data/ceres_data/6ltn_0975/09_2025/6ltn_0975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ltn_0975/09_2025/6ltn_0975.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/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: 2.21, per 1000 atoms: 0.16 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: 1.04 Conformation dependent library (CDL) restraints added in 646.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.44 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: 2.14 Time building geometry restraints manager: 1.44 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: 0.05 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.010 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.460 ------------------------------------------------------------------------------- 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 aren 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 : 0.664 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 199 TYR cc_start: 0.6817 (t80) cc_final: 0.6617 (t80) 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: 0.6164 (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: 0.7971 (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: 0.5905 (t80) outliers start: 21 outliers final: 11 residues processed: 411 average time/residue: 0.1078 time to fit residues: 67.5732 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 : 0.545 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.164431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114258 restraints weight = 22655.409| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.69 r_work: 0.3291 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13944 Z= 0.119 Angle : 0.632 7.155 18977 Z= 0.319 Chirality : 0.038 0.143 2289 Planarity : 0.007 0.067 2268 Dihedral : 5.765 90.860 1828 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.08 % Allowed : 17.23 % Favored : 79.69 % 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 aren not related in a simple way. whole: -2.94 (0.18), residues: 1652 helix: -1.62 (0.14), residues: 1141 sheet: -2.25 (0.63), residues: 91 loop : -2.20 (0.26), 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 0.00238 (13937) covalent geometry : angle 0.63197 (18963) SS BOND : bond 0.01107 ( 7) SS BOND : angle 0.48776 ( 14) hydrogen bonds : bond 0.04231 ( 651) hydrogen bonds : angle 4.20592 ( 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 386 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 339 time to evaluate : 0.570 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 56 GLN cc_start: 0.8613 (tp40) cc_final: 0.8116 (mm-40) REVERT: E 63 GLN cc_start: 0.8623 (mp10) cc_final: 0.8417 (mp10) REVERT: E 121 TYR cc_start: 0.8352 (t80) cc_final: 0.8140 (t80) REVERT: A 37 MET cc_start: 0.8653 (ppp) cc_final: 0.8351 (ppp) REVERT: A 56 GLN cc_start: 0.8655 (tp40) cc_final: 0.8422 (mm-40) REVERT: A 63 GLN cc_start: 0.8756 (mp10) cc_final: 0.8383 (mp10) REVERT: A 124 PRO cc_start: 0.8421 (Cg_exo) cc_final: 0.8089 (Cg_endo) REVERT: A 142 ILE cc_start: 0.7879 (mm) cc_final: 0.7657 (mt) REVERT: A 197 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7169 (tp30) REVERT: B 37 MET cc_start: 0.8531 (ppp) cc_final: 0.8265 (ppp) REVERT: B 56 GLN cc_start: 0.8775 (tp40) cc_final: 0.7990 (mm-40) REVERT: B 63 GLN cc_start: 0.8875 (mp10) cc_final: 0.8342 (mp10) REVERT: B 124 PRO cc_start: 0.8284 (Cg_exo) cc_final: 0.8038 (Cg_endo) REVERT: B 197 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7013 (tp30) REVERT: C 111 TYR cc_start: 0.9237 (m-80) cc_final: 0.8952 (m-80) REVERT: C 121 TYR cc_start: 0.8707 (t80) cc_final: 0.8334 (t80) REVERT: C 124 PRO cc_start: 0.8247 (Cg_exo) cc_final: 0.7944 (Cg_endo) REVERT: C 197 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7404 (tp30) REVERT: C 237 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7596 (pp) REVERT: C 299 PHE cc_start: 0.8372 (t80) cc_final: 0.8077 (t80) REVERT: D 101 LEU cc_start: 0.8817 (tp) cc_final: 0.8563 (mp) REVERT: D 124 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.8011 (Cg_endo) REVERT: D 233 TYR cc_start: 0.9060 (t80) cc_final: 0.8845 (t80) REVERT: F 36 LYS cc_start: 0.7991 (mmtp) cc_final: 0.6957 (mptt) REVERT: F 37 MET cc_start: 0.8609 (ppp) cc_final: 0.8407 (ppp) REVERT: F 56 GLN cc_start: 0.8651 (tp40) cc_final: 0.8319 (mm-40) REVERT: F 63 GLN cc_start: 0.8760 (mp10) cc_final: 0.8284 (mp10) REVERT: F 124 PRO cc_start: 0.8684 (Cg_exo) cc_final: 0.8413 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7825 (m-30) cc_final: 0.7397 (t0) REVERT: F 197 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7115 (tp30) REVERT: F 237 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7763 (pp) REVERT: F 299 PHE cc_start: 0.8138 (t80) cc_final: 0.7832 (t80) REVERT: F 331 TYR cc_start: 0.7116 (t80) cc_final: 0.6015 (t80) REVERT: G 63 GLN cc_start: 0.8768 (mp10) cc_final: 0.8182 (mp10) REVERT: G 111 TYR cc_start: 0.9137 (m-80) cc_final: 0.8761 (m-80) REVERT: G 121 TYR cc_start: 0.8259 (t80) cc_final: 0.7947 (t80) REVERT: G 146 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5541 (mm) REVERT: G 197 GLU cc_start: 0.7780 (mm-30) cc_final: 0.6885 (tp30) REVERT: G 199 TYR cc_start: 0.6633 (t80) cc_final: 0.6222 (t80) outliers start: 47 outliers final: 27 residues processed: 376 average time/residue: 0.0948 time to fit residues: 56.4374 Evaluate side-chains 322 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 256 ASP 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 216 CYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 256 ASP 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 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: 0.0980 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 119 optimal weight: 0.0570 chunk 29 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 overall best weight: 2.2304 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.163206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111866 restraints weight = 22842.343| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.67 r_work: 0.3253 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2917 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= 0.153 Angle : 0.654 12.830 18977 Z= 0.313 Chirality : 0.040 0.177 2289 Planarity : 0.006 0.066 2268 Dihedral : 4.143 15.584 1807 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.31 % Allowed : 18.68 % Favored : 76.02 % 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 aren not related in a simple way. whole: -1.51 (0.21), residues: 1652 helix: -0.39 (0.16), residues: 1134 sheet: -1.87 (0.64), residues: 91 loop : -2.16 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 254 TYR 0.010 0.001 TYR D 111 PHE 0.017 0.001 PHE D 299 TRP 0.007 0.001 TRP D 127 HIS 0.002 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00341 (13937) covalent geometry : angle 0.65420 (18963) SS BOND : bond 0.00155 ( 7) SS BOND : angle 0.32770 ( 14) hydrogen bonds : bond 0.03473 ( 651) hydrogen bonds : angle 3.73735 ( 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 378 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 297 time to evaluate : 0.548 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: E 37 MET cc_start: 0.8444 (ppp) cc_final: 0.8205 (ppp) REVERT: E 56 GLN cc_start: 0.8537 (tp40) cc_final: 0.8235 (mm-40) REVERT: A 56 GLN cc_start: 0.8615 (tp40) cc_final: 0.8271 (pp30) REVERT: A 63 GLN cc_start: 0.8871 (mp10) cc_final: 0.8410 (mp10) REVERT: A 124 PRO cc_start: 0.8268 (Cg_exo) cc_final: 0.7955 (Cg_endo) REVERT: A 146 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.5999 (mm) REVERT: A 197 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7125 (tp30) REVERT: A 331 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7617 (t80) REVERT: B 63 GLN cc_start: 0.8802 (mp10) cc_final: 0.8278 (mp10) REVERT: B 124 PRO cc_start: 0.8271 (Cg_exo) cc_final: 0.8050 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6417 (mm) REVERT: B 197 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7017 (tp30) REVERT: C 56 GLN cc_start: 0.8574 (tp40) cc_final: 0.7942 (pp30) REVERT: C 121 TYR cc_start: 0.8612 (t80) cc_final: 0.8338 (t80) REVERT: C 124 PRO cc_start: 0.8618 (Cg_exo) cc_final: 0.8390 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6073 (mm) REVERT: C 197 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7462 (tp30) REVERT: C 237 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7619 (pp) REVERT: C 299 PHE cc_start: 0.8346 (t80) cc_final: 0.7997 (t80) REVERT: D 90 GLN cc_start: 0.8254 (mp10) cc_final: 0.7731 (mt0) REVERT: D 124 PRO cc_start: 0.8317 (Cg_exo) cc_final: 0.8074 (Cg_endo) REVERT: D 146 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6676 (mm) REVERT: F 63 GLN cc_start: 0.8664 (mp10) cc_final: 0.8246 (mp10) REVERT: F 121 TYR cc_start: 0.8666 (t80) cc_final: 0.8225 (t80) REVERT: F 124 PRO cc_start: 0.8637 (Cg_exo) cc_final: 0.8384 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7792 (m-30) cc_final: 0.7390 (t0) REVERT: F 146 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6102 (mm) REVERT: F 197 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7122 (tp30) REVERT: F 237 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7794 (pp) REVERT: F 299 PHE cc_start: 0.8245 (t80) cc_final: 0.7904 (t80) REVERT: F 331 TYR cc_start: 0.7334 (t80) cc_final: 0.6319 (t80) REVERT: G 37 MET cc_start: 0.8759 (ppp) cc_final: 0.8550 (ppp) REVERT: G 63 GLN cc_start: 0.8859 (mp10) cc_final: 0.8256 (mp10) REVERT: G 121 TYR cc_start: 0.8373 (t80) cc_final: 0.7988 (t80) REVERT: G 124 PRO cc_start: 0.8508 (Cg_exo) cc_final: 0.8267 (Cg_endo) REVERT: G 197 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6767 (tp30) outliers start: 81 outliers final: 51 residues processed: 357 average time/residue: 0.0918 time to fit residues: 52.4362 Evaluate side-chains 338 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 279 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 297 VAL Chi-restraints excluded: chain E residue 331 TYR 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 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 54 PHE 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 C residue 40 CYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 103 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 297 VAL Chi-restraints excluded: chain D residue 125 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 F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU 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 237 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 254 ARG 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: 6.9990 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 111 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: 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 = 0.4136 r_free = 0.4136 target = 0.161864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110974 restraints weight = 22871.786| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.65 r_work: 0.3258 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3280 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= 0.239 Angle : 0.706 11.216 18977 Z= 0.340 Chirality : 0.042 0.129 2289 Planarity : 0.006 0.065 2268 Dihedral : 4.328 17.598 1806 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.83 % Allowed : 20.45 % Favored : 73.72 % 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 aren not related in a simple way. whole: -0.99 (0.22), residues: 1652 helix: 0.06 (0.17), residues: 1134 sheet: -2.02 (0.62), residues: 91 loop : -2.05 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 254 TYR 0.011 0.001 TYR E 233 PHE 0.015 0.002 PHE E 299 TRP 0.010 0.002 TRP F 85 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00537 (13937) covalent geometry : angle 0.70595 (18963) SS BOND : bond 0.00227 ( 7) SS BOND : angle 0.48484 ( 14) hydrogen bonds : bond 0.03665 ( 651) hydrogen bonds : angle 3.83832 ( 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 369 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 280 time to evaluate : 0.585 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: E 56 GLN cc_start: 0.8547 (tp40) cc_final: 0.8254 (mm-40) REVERT: E 63 GLN cc_start: 0.8608 (mp10) cc_final: 0.8391 (mp10) REVERT: E 240 LEU cc_start: 0.8798 (tp) cc_final: 0.8578 (tp) REVERT: A 63 GLN cc_start: 0.8818 (mp10) cc_final: 0.8399 (mp10) REVERT: A 124 PRO cc_start: 0.8301 (Cg_exo) cc_final: 0.8005 (Cg_endo) REVERT: A 146 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6142 (mm) REVERT: A 147 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7133 (p0) REVERT: A 197 GLU cc_start: 0.7857 (mm-30) cc_final: 0.6961 (tp30) REVERT: A 331 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7388 (t80) REVERT: B 63 GLN cc_start: 0.8810 (mp10) cc_final: 0.8306 (mp10) REVERT: B 124 PRO cc_start: 0.8269 (Cg_exo) cc_final: 0.8057 (Cg_endo) REVERT: B 197 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7041 (tp30) REVERT: C 56 GLN cc_start: 0.8538 (tp40) cc_final: 0.7906 (pp30) REVERT: C 121 TYR cc_start: 0.8602 (t80) cc_final: 0.8279 (t80) REVERT: C 124 PRO cc_start: 0.8247 (Cg_exo) cc_final: 0.7981 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6457 (mm) REVERT: C 197 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7456 (tp30) REVERT: C 237 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7592 (pp) REVERT: D 54 PHE cc_start: 0.8940 (m-10) cc_final: 0.8694 (m-10) REVERT: D 124 PRO cc_start: 0.8319 (Cg_exo) cc_final: 0.8091 (Cg_endo) REVERT: D 146 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6487 (mm) REVERT: F 63 GLN cc_start: 0.8713 (mp10) cc_final: 0.8286 (mp10) REVERT: F 121 TYR cc_start: 0.8668 (t80) cc_final: 0.8224 (t80) REVERT: F 124 PRO cc_start: 0.8656 (Cg_exo) cc_final: 0.8404 (Cg_endo) REVERT: F 146 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6477 (mm) REVERT: F 197 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7060 (tp30) REVERT: F 237 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7571 (pp) REVERT: F 299 PHE cc_start: 0.8313 (t80) cc_final: 0.7980 (t80) REVERT: G 37 MET cc_start: 0.8708 (ppp) cc_final: 0.8490 (ppp) REVERT: G 63 GLN cc_start: 0.8896 (mp10) cc_final: 0.8244 (mp10) REVERT: G 121 TYR cc_start: 0.8459 (t80) cc_final: 0.8018 (t80) REVERT: G 124 PRO cc_start: 0.8609 (Cg_exo) cc_final: 0.8389 (Cg_endo) REVERT: G 138 ASP cc_start: 0.7208 (t0) cc_final: 0.6877 (t0) REVERT: G 146 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5560 (mm) REVERT: G 197 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7029 (tp30) REVERT: G 199 TYR cc_start: 0.6632 (OUTLIER) cc_final: 0.5882 (t80) outliers start: 89 outliers final: 59 residues processed: 345 average time/residue: 0.0894 time to fit residues: 50.0197 Evaluate side-chains 338 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 269 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 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 147 ASP 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 218 LEU 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 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 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 252 ILE 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 348 LEU 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 279 ILE Chi-restraints excluded: chain F residue 294 THR 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 128 ARG Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 199 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 96 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 165 optimal weight: 0.0060 chunk 125 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 83 optimal weight: 0.0020 chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 overall best weight: 0.9406 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.167972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118227 restraints weight = 22429.637| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.57 r_work: 0.3363 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13944 Z= 0.104 Angle : 0.621 10.483 18977 Z= 0.287 Chirality : 0.039 0.183 2289 Planarity : 0.005 0.058 2268 Dihedral : 3.796 13.011 1806 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.06 % Allowed : 22.08 % Favored : 73.85 % 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 aren not related in a simple way. whole: -0.56 (0.22), residues: 1652 helix: 0.35 (0.17), residues: 1134 sheet: -1.72 (0.62), residues: 91 loop : -1.82 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 254 TYR 0.008 0.001 TYR F 213 PHE 0.020 0.001 PHE A 299 TRP 0.005 0.001 TRP F 85 HIS 0.001 0.000 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00224 (13937) covalent geometry : angle 0.62146 (18963) SS BOND : bond 0.00052 ( 7) SS BOND : angle 0.25011 ( 14) hydrogen bonds : bond 0.02684 ( 651) hydrogen bonds : angle 3.52345 ( 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 355 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 293 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8473 (tp40) cc_final: 0.8109 (mm-40) REVERT: E 237 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7644 (pp) REVERT: E 240 LEU cc_start: 0.8697 (tp) cc_final: 0.8494 (tp) REVERT: A 63 GLN cc_start: 0.8792 (mp10) cc_final: 0.8363 (mp10) REVERT: A 124 PRO cc_start: 0.8258 (Cg_exo) cc_final: 0.7965 (Cg_endo) REVERT: A 146 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6385 (mm) REVERT: A 197 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7114 (tp30) REVERT: A 331 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7416 (t80) REVERT: B 63 GLN cc_start: 0.8820 (mp10) cc_final: 0.8319 (mp10) REVERT: B 124 PRO cc_start: 0.8261 (Cg_exo) cc_final: 0.8042 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6318 (mm) REVERT: B 197 GLU cc_start: 0.7697 (mm-30) cc_final: 0.6889 (tp30) REVERT: C 56 GLN cc_start: 0.8372 (tp40) cc_final: 0.7881 (pp30) REVERT: C 121 TYR cc_start: 0.8386 (t80) cc_final: 0.8106 (t80) REVERT: C 124 PRO cc_start: 0.8437 (Cg_exo) cc_final: 0.8195 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.5936 (mm) REVERT: C 197 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7430 (tp30) REVERT: C 237 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.7013 (pp) REVERT: D 124 PRO cc_start: 0.8197 (Cg_exo) cc_final: 0.7952 (Cg_endo) REVERT: D 146 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6541 (mm) REVERT: F 63 GLN cc_start: 0.8600 (mp10) cc_final: 0.8223 (mp10) REVERT: F 121 TYR cc_start: 0.8564 (t80) cc_final: 0.8108 (t80) REVERT: F 124 PRO cc_start: 0.8642 (Cg_exo) cc_final: 0.8396 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7570 (m-30) cc_final: 0.7169 (t0) REVERT: F 146 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6401 (mm) REVERT: F 197 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7165 (tp30) REVERT: F 237 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7071 (pp) REVERT: F 299 PHE cc_start: 0.8282 (t80) cc_final: 0.7962 (t80) REVERT: F 331 TYR cc_start: 0.7444 (t80) cc_final: 0.6504 (t80) REVERT: G 37 MET cc_start: 0.8739 (ppp) cc_final: 0.8457 (ppp) REVERT: G 56 GLN cc_start: 0.8571 (tp40) cc_final: 0.8122 (pp30) REVERT: G 63 GLN cc_start: 0.8866 (mp10) cc_final: 0.8284 (mp10) REVERT: G 121 TYR cc_start: 0.8389 (t80) cc_final: 0.8016 (t80) REVERT: G 146 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.5939 (mm) REVERT: G 197 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7114 (tp30) outliers start: 62 outliers final: 40 residues processed: 341 average time/residue: 0.0893 time to fit residues: 49.3825 Evaluate side-chains 330 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 237 LEU Chi-restraints excluded: chain E residue 331 TYR 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 228 CYS 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 48 LEU 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 294 THR 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 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 294 THR 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 62 THR 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 294 THR 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 128 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 131 optimal weight: 0.0070 chunk 14 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.164890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114295 restraints weight = 22701.478| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.63 r_work: 0.3308 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13944 Z= 0.131 Angle : 0.636 9.414 18977 Z= 0.295 Chirality : 0.040 0.159 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.809 13.767 1806 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.65 % Allowed : 22.48 % Favored : 72.87 % 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 aren not related in a simple way. whole: -0.31 (0.23), residues: 1652 helix: 0.56 (0.17), residues: 1134 sheet: -1.77 (0.60), residues: 91 loop : -1.73 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 254 TYR 0.011 0.001 TYR G 150 PHE 0.015 0.001 PHE E 244 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 0.63570 (18963) SS BOND : bond 0.00105 ( 7) SS BOND : angle 0.31096 ( 14) hydrogen bonds : bond 0.02814 ( 651) hydrogen bonds : angle 3.51541 ( 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 358 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 287 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8538 (tp40) cc_final: 0.8253 (mm-40) REVERT: E 116 PHE cc_start: 0.8476 (m-80) cc_final: 0.8135 (m-80) REVERT: E 237 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7628 (pp) REVERT: E 240 LEU cc_start: 0.8695 (tp) cc_final: 0.8489 (tp) REVERT: A 63 GLN cc_start: 0.8840 (mp10) cc_final: 0.8419 (mp10) REVERT: A 124 PRO cc_start: 0.8178 (Cg_exo) cc_final: 0.7883 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6737 (mm) REVERT: A 197 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7257 (tp30) REVERT: A 331 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7308 (t80) REVERT: B 63 GLN cc_start: 0.8806 (mp10) cc_final: 0.8297 (mp10) REVERT: B 124 PRO cc_start: 0.8225 (Cg_exo) cc_final: 0.8011 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6337 (mm) REVERT: B 197 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7194 (tp30) REVERT: C 56 GLN cc_start: 0.8272 (tp40) cc_final: 0.7841 (tm-30) REVERT: C 121 TYR cc_start: 0.8353 (t80) cc_final: 0.8053 (t80) REVERT: C 124 PRO cc_start: 0.8422 (Cg_exo) cc_final: 0.8188 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6258 (mm) REVERT: C 197 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7410 (tp30) REVERT: C 237 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7119 (pp) REVERT: D 146 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6566 (mm) REVERT: D 197 GLU cc_start: 0.6379 (tp30) cc_final: 0.6158 (tp30) REVERT: D 216 CYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7555 (t) REVERT: F 63 GLN cc_start: 0.8651 (mp10) cc_final: 0.8238 (mp10) REVERT: F 101 LEU cc_start: 0.8519 (tt) cc_final: 0.8194 (mt) REVERT: F 121 TYR cc_start: 0.8575 (t80) cc_final: 0.8096 (t80) REVERT: F 124 PRO cc_start: 0.8611 (Cg_exo) cc_final: 0.8368 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7553 (m-30) cc_final: 0.7195 (t0) REVERT: F 146 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6341 (mm) REVERT: F 197 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7193 (tp30) REVERT: F 237 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7128 (pp) REVERT: F 299 PHE cc_start: 0.8283 (t80) cc_final: 0.7943 (t80) REVERT: F 331 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6442 (t80) REVERT: G 37 MET cc_start: 0.8631 (ppp) cc_final: 0.8418 (ppp) REVERT: G 56 GLN cc_start: 0.8661 (tp40) cc_final: 0.8122 (pp30) REVERT: G 63 GLN cc_start: 0.8880 (mp10) cc_final: 0.8260 (mp10) REVERT: G 121 TYR cc_start: 0.8384 (t80) cc_final: 0.8004 (t80) REVERT: G 197 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7323 (tp30) outliers start: 71 outliers final: 48 residues processed: 341 average time/residue: 0.0867 time to fit residues: 47.6762 Evaluate side-chains 336 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 237 LEU 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 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 228 CYS Chi-restraints excluded: chain A residue 258 THR 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 48 LEU 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 252 ILE 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 48 LEU Chi-restraints excluded: chain C residue 62 THR 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 222 ILE Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 237 LEU 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 294 THR 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 62 THR 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 294 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 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 = 0.4179 r_free = 0.4179 target = 0.165887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.115862 restraints weight = 22687.793| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.66 r_work: 0.3328 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3815 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= 0.113 Angle : 0.633 9.316 18977 Z= 0.293 Chirality : 0.039 0.137 2289 Planarity : 0.005 0.058 2268 Dihedral : 3.711 12.070 1806 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.72 % Allowed : 22.48 % Favored : 72.80 % 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 aren not related in a simple way. whole: -0.14 (0.23), residues: 1652 helix: 0.68 (0.17), residues: 1134 sheet: -1.60 (0.59), residues: 91 loop : -1.69 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 254 TYR 0.010 0.001 TYR E 150 PHE 0.012 0.001 PHE E 244 TRP 0.004 0.001 TRP F 85 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00251 (13937) covalent geometry : angle 0.63339 (18963) SS BOND : bond 0.00094 ( 7) SS BOND : angle 0.27297 ( 14) hydrogen bonds : bond 0.02618 ( 651) hydrogen bonds : angle 3.46897 ( 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 355 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 283 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8625 (tp40) cc_final: 0.8355 (mm-40) REVERT: E 116 PHE cc_start: 0.8428 (m-80) cc_final: 0.8134 (m-80) REVERT: E 146 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7042 (mm) REVERT: E 240 LEU cc_start: 0.8636 (tp) cc_final: 0.8422 (tp) REVERT: A 63 GLN cc_start: 0.8804 (mp10) cc_final: 0.8397 (mp10) REVERT: A 124 PRO cc_start: 0.8140 (Cg_exo) cc_final: 0.7849 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6735 (mm) REVERT: A 197 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7325 (tp30) REVERT: A 331 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7221 (t80) REVERT: B 63 GLN cc_start: 0.8809 (mp10) cc_final: 0.8281 (mp10) REVERT: B 124 PRO cc_start: 0.8249 (Cg_exo) cc_final: 0.8036 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6303 (mm) REVERT: B 197 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7201 (tp30) REVERT: C 56 GLN cc_start: 0.8425 (tp40) cc_final: 0.7908 (tm-30) REVERT: C 124 PRO cc_start: 0.8388 (Cg_exo) cc_final: 0.8148 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6223 (mm) REVERT: C 197 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7254 (tp30) REVERT: C 237 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6772 (pp) REVERT: C 331 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6389 (t80) REVERT: D 90 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: D 146 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6512 (mm) REVERT: F 63 GLN cc_start: 0.8651 (mp10) cc_final: 0.8226 (mp10) REVERT: F 101 LEU cc_start: 0.8512 (tt) cc_final: 0.8148 (mt) REVERT: F 121 TYR cc_start: 0.8558 (t80) cc_final: 0.8042 (t80) REVERT: F 124 PRO cc_start: 0.8595 (Cg_exo) cc_final: 0.8372 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7508 (m-30) cc_final: 0.7141 (t0) REVERT: F 146 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6353 (mm) REVERT: F 197 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7147 (tp30) REVERT: F 216 CYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6591 (t) REVERT: F 237 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6828 (pp) REVERT: F 331 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.6892 (t80) REVERT: G 56 GLN cc_start: 0.8679 (tp40) cc_final: 0.8108 (pp30) REVERT: G 63 GLN cc_start: 0.8879 (mp10) cc_final: 0.8261 (mp10) REVERT: G 121 TYR cc_start: 0.8338 (t80) cc_final: 0.7990 (t80) REVERT: G 197 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7298 (tp30) outliers start: 72 outliers final: 48 residues processed: 334 average time/residue: 0.0870 time to fit residues: 47.3753 Evaluate side-chains 333 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 272 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR 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 216 CYS 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 48 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 ILE 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 48 LEU Chi-restraints excluded: chain C residue 62 THR 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 228 CYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 331 TYR 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 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 62 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 294 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 108 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 139 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 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: 9.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.165998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.116626 restraints weight = 22598.718| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.66 r_work: 0.3332 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13944 Z= 0.114 Angle : 0.644 13.367 18977 Z= 0.296 Chirality : 0.039 0.129 2289 Planarity : 0.005 0.056 2268 Dihedral : 3.679 12.572 1806 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.39 % Allowed : 22.94 % Favored : 72.67 % 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 aren not related in a simple way. whole: -0.01 (0.22), residues: 1652 helix: 0.80 (0.17), residues: 1134 sheet: -4.13 (0.52), residues: 49 loop : -1.39 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 254 TYR 0.008 0.001 TYR G 213 PHE 0.012 0.001 PHE C 299 TRP 0.004 0.001 TRP A 85 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00251 (13937) covalent geometry : angle 0.64378 (18963) SS BOND : bond 0.00083 ( 7) SS BOND : angle 0.27395 ( 14) hydrogen bonds : bond 0.02564 ( 651) hydrogen bonds : angle 3.45000 ( 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 338 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 271 time to evaluate : 0.544 Fit side-chains REVERT: E 56 GLN cc_start: 0.8601 (tp40) cc_final: 0.8265 (mm-40) REVERT: E 116 PHE cc_start: 0.8410 (m-80) cc_final: 0.8152 (m-80) REVERT: E 345 TYR cc_start: 0.3426 (OUTLIER) cc_final: 0.2609 (m-80) REVERT: A 63 GLN cc_start: 0.8791 (mp10) cc_final: 0.8364 (mp10) REVERT: A 124 PRO cc_start: 0.8109 (Cg_exo) cc_final: 0.7831 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6722 (mm) REVERT: A 197 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7332 (tp30) REVERT: A 331 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.7175 (t80) REVERT: B 63 GLN cc_start: 0.8796 (mp10) cc_final: 0.8240 (mp10) REVERT: B 124 PRO cc_start: 0.8240 (Cg_exo) cc_final: 0.8031 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6294 (mm) REVERT: B 197 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7258 (tp30) REVERT: C 56 GLN cc_start: 0.8460 (tp40) cc_final: 0.7922 (pp30) REVERT: C 116 PHE cc_start: 0.8373 (m-80) cc_final: 0.8135 (m-80) REVERT: C 124 PRO cc_start: 0.8502 (Cg_exo) cc_final: 0.8273 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6193 (mm) REVERT: C 197 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7335 (tp30) REVERT: C 331 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6658 (t80) REVERT: D 90 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: D 146 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6548 (mm) REVERT: D 197 GLU cc_start: 0.6319 (tp30) cc_final: 0.5629 (mt-10) REVERT: F 56 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8265 (pp30) REVERT: F 63 GLN cc_start: 0.8686 (mp10) cc_final: 0.8270 (mp10) REVERT: F 101 LEU cc_start: 0.8526 (tt) cc_final: 0.8145 (mt) REVERT: F 121 TYR cc_start: 0.8511 (t80) cc_final: 0.7984 (t80) REVERT: F 124 PRO cc_start: 0.8621 (Cg_exo) cc_final: 0.8396 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7475 (m-30) cc_final: 0.7126 (t0) REVERT: F 146 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6329 (mm) REVERT: F 197 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7204 (tp30) REVERT: F 216 CYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6689 (t) REVERT: F 237 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6798 (pp) REVERT: F 331 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6854 (t80) REVERT: G 56 GLN cc_start: 0.8705 (tp40) cc_final: 0.8091 (pp30) REVERT: G 63 GLN cc_start: 0.8854 (mp10) cc_final: 0.8232 (mp10) REVERT: G 121 TYR cc_start: 0.8299 (t80) cc_final: 0.7912 (t80) REVERT: G 197 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7228 (tp30) outliers start: 67 outliers final: 49 residues processed: 319 average time/residue: 0.0883 time to fit residues: 45.9787 Evaluate side-chains 327 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 266 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 345 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 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 48 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 146 LEU 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 48 LEU Chi-restraints excluded: chain C residue 62 THR 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 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 331 TYR 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 39 THR 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 62 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 294 THR 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 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: 2.9990 chunk 126 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.166617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116600 restraints weight = 22808.776| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.66 r_work: 0.3339 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4064 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= 0.110 Angle : 0.651 13.830 18977 Z= 0.298 Chirality : 0.039 0.127 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.630 12.143 1806 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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 aren not related in a simple way. whole: 0.11 (0.23), residues: 1652 helix: 0.89 (0.17), residues: 1134 sheet: -4.04 (0.53), residues: 49 loop : -1.36 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 254 TYR 0.008 0.001 TYR D 111 PHE 0.011 0.001 PHE E 244 TRP 0.003 0.001 TRP F 85 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00242 (13937) covalent geometry : angle 0.65142 (18963) SS BOND : bond 0.00076 ( 7) SS BOND : angle 0.25919 ( 14) hydrogen bonds : bond 0.02493 ( 651) hydrogen bonds : angle 3.45165 ( 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 339 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8625 (tp40) cc_final: 0.8351 (mm-40) REVERT: E 331 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.7247 (t80) REVERT: E 345 TYR cc_start: 0.3554 (OUTLIER) cc_final: 0.2703 (m-80) REVERT: A 63 GLN cc_start: 0.8772 (mp10) cc_final: 0.8376 (mp10) REVERT: A 124 PRO cc_start: 0.8051 (Cg_exo) cc_final: 0.7792 (Cg_endo) REVERT: A 138 ASP cc_start: 0.7627 (m-30) cc_final: 0.7186 (t0) REVERT: A 146 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6561 (mm) REVERT: A 197 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7259 (tp30) REVERT: A 216 CYS cc_start: 0.7364 (OUTLIER) cc_final: 0.7082 (t) REVERT: B 63 GLN cc_start: 0.8777 (mp10) cc_final: 0.8243 (mp10) REVERT: B 124 PRO cc_start: 0.8207 (Cg_exo) cc_final: 0.7996 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6284 (mm) REVERT: B 197 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7221 (tp30) REVERT: C 56 GLN cc_start: 0.8383 (tp40) cc_final: 0.7885 (pp30) REVERT: C 124 PRO cc_start: 0.8499 (Cg_exo) cc_final: 0.8284 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6266 (mm) REVERT: C 197 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7399 (tp30) REVERT: C 331 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6733 (t80) REVERT: D 90 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: D 146 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6553 (mm) REVERT: D 197 GLU cc_start: 0.6458 (tp30) cc_final: 0.5650 (mt-10) REVERT: F 56 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8273 (pp30) REVERT: F 63 GLN cc_start: 0.8609 (mp10) cc_final: 0.8221 (mp10) REVERT: F 101 LEU cc_start: 0.8537 (tt) cc_final: 0.8128 (mt) REVERT: F 121 TYR cc_start: 0.8478 (t80) cc_final: 0.8036 (t80) REVERT: F 138 ASP cc_start: 0.7447 (m-30) cc_final: 0.7140 (t0) REVERT: F 146 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6258 (mm) REVERT: F 197 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7255 (tp30) REVERT: F 331 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6789 (t80) REVERT: G 56 GLN cc_start: 0.8687 (tp40) cc_final: 0.8102 (pp30) REVERT: G 63 GLN cc_start: 0.8845 (mp10) cc_final: 0.8245 (mp10) REVERT: G 121 TYR cc_start: 0.8294 (t80) cc_final: 0.7910 (t80) REVERT: G 197 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7266 (tp30) outliers start: 63 outliers final: 46 residues processed: 320 average time/residue: 0.0897 time to fit residues: 46.8586 Evaluate side-chains 325 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR 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 345 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 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 48 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 146 LEU 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 62 THR 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 331 TYR 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 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 39 THR 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 62 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 294 THR 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 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: 0.7980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 0.0050 chunk 129 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 82 optimal weight: 30.0000 chunk 154 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.165684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.116229 restraints weight = 22732.258| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.66 r_work: 0.3321 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13944 Z= 0.126 Angle : 0.677 14.862 18977 Z= 0.309 Chirality : 0.040 0.133 2289 Planarity : 0.005 0.056 2268 Dihedral : 3.698 12.228 1806 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.93 % Allowed : 24.31 % Favored : 71.76 % 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 aren not related in a simple way. whole: 0.14 (0.23), residues: 1652 helix: 0.92 (0.17), residues: 1134 sheet: -1.53 (0.59), residues: 91 loop : -1.65 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 254 TYR 0.008 0.001 TYR B 213 PHE 0.012 0.001 PHE E 244 TRP 0.004 0.001 TRP A 85 HIS 0.001 0.000 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00282 (13937) covalent geometry : angle 0.67676 (18963) SS BOND : bond 0.00127 ( 7) SS BOND : angle 0.28070 ( 14) hydrogen bonds : bond 0.02667 ( 651) hydrogen bonds : angle 3.52504 ( 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 325 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 265 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8566 (tp40) cc_final: 0.8293 (mm-40) REVERT: E 345 TYR cc_start: 0.3379 (OUTLIER) cc_final: 0.2623 (m-80) REVERT: A 63 GLN cc_start: 0.8799 (mp10) cc_final: 0.8409 (mp10) REVERT: A 124 PRO cc_start: 0.8202 (Cg_exo) cc_final: 0.7975 (Cg_endo) REVERT: A 138 ASP cc_start: 0.7577 (m-30) cc_final: 0.7148 (t0) REVERT: A 146 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6525 (mm) REVERT: A 197 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7297 (tp30) REVERT: B 63 GLN cc_start: 0.8822 (mp10) cc_final: 0.8272 (mp10) REVERT: B 124 PRO cc_start: 0.8352 (Cg_exo) cc_final: 0.8140 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6274 (mm) REVERT: B 197 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7229 (tp30) REVERT: C 56 GLN cc_start: 0.8412 (tp40) cc_final: 0.7906 (tm-30) REVERT: C 124 PRO cc_start: 0.8519 (Cg_exo) cc_final: 0.8291 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6220 (mm) REVERT: C 197 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7362 (tp30) REVERT: C 331 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6723 (t80) REVERT: D 90 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: D 146 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6534 (mm) REVERT: D 197 GLU cc_start: 0.6446 (tp30) cc_final: 0.5557 (mt-10) REVERT: F 56 GLN cc_start: 0.8728 (tp-100) cc_final: 0.8270 (pp30) REVERT: F 63 GLN cc_start: 0.8649 (mp10) cc_final: 0.8257 (mp10) REVERT: F 101 LEU cc_start: 0.8570 (tt) cc_final: 0.8140 (mt) REVERT: F 121 TYR cc_start: 0.8514 (t80) cc_final: 0.8073 (t80) REVERT: F 138 ASP cc_start: 0.7318 (m-30) cc_final: 0.7064 (t0) REVERT: F 146 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6233 (mm) REVERT: F 197 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7134 (tp30) REVERT: F 331 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.6831 (t80) REVERT: G 56 GLN cc_start: 0.8703 (tp40) cc_final: 0.8060 (pp30) REVERT: G 63 GLN cc_start: 0.8850 (mp10) cc_final: 0.8239 (mp10) REVERT: G 121 TYR cc_start: 0.8310 (t80) cc_final: 0.7932 (t80) REVERT: G 197 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7286 (tp30) outliers start: 60 outliers final: 49 residues processed: 307 average time/residue: 0.0853 time to fit residues: 43.1628 Evaluate side-chains 323 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 THR 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 345 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 48 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 114 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 62 THR 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 331 TYR 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 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 39 THR 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 62 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 294 THR 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 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 36 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 82 optimal weight: 9.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.161850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.111603 restraints weight = 23165.327| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.64 r_work: 0.3265 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3974 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= 0.225 Angle : 0.734 14.281 18977 Z= 0.345 Chirality : 0.043 0.138 2289 Planarity : 0.006 0.060 2268 Dihedral : 4.139 17.372 1806 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.19 % Allowed : 24.31 % Favored : 71.49 % 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 aren not related in a simple way. whole: -0.11 (0.22), residues: 1652 helix: 0.78 (0.17), residues: 1134 sheet: -1.88 (0.59), residues: 91 loop : -1.85 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 254 TYR 0.012 0.001 TYR C 233 PHE 0.014 0.001 PHE D 244 TRP 0.009 0.002 TRP C 85 HIS 0.002 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00509 (13937) covalent geometry : angle 0.73370 (18963) SS BOND : bond 0.00238 ( 7) SS BOND : angle 0.41469 ( 14) hydrogen bonds : bond 0.03338 ( 651) hydrogen bonds : angle 3.69945 ( 1932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4052.44 seconds wall clock time: 70 minutes 15.17 seconds (4215.17 seconds total)