Starting phenix.real_space_refine on Mon Dec 30 15:34:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ltn_0975/12_2024/6ltn_0975.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ltn_0975/12_2024/6ltn_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_0975/12_2024/6ltn_0975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ltn_0975/12_2024/6ltn_0975.map" model { file = "/net/cci-nas-00/data/ceres_data/6ltn_0975/12_2024/6ltn_0975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ltn_0975/12_2024/6ltn_0975.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13615 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 4.76, per 1000 atoms: 0.35 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 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: 3.03 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.01 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: 3.68 Time building geometry restraints manager: 3.58 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: 7154 15.54 - 31.07: 703 31.07 - 46.61: 287 46.61 - 62.15: 49 62.15 - 77.69: 42 Dihedral angle restraints: 8235 sinusoidal: 3132 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 8232 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: 2.03 - 2.61: 90 2.61 - 3.18: 11128 3.18 - 3.75: 20013 3.75 - 4.33: 27480 4.33 - 4.90: 43947 Nonbonded interactions: 102658 Sorted by model distance: nonbonded pdb=" SG CYS B 66 " pdb=" SG CYS B 265 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS G 66 " pdb=" SG CYS G 265 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS C 66 " pdb=" SG CYS C 265 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS A 66 " pdb=" SG CYS A 265 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS F 66 " pdb=" SG CYS F 265 " model vdw 2.033 3.760 ... (remaining 102653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 26.850 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- 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 13937 Z= 0.388 Angle : 0.949 12.903 18963 Z= 0.484 Chirality : 0.052 0.164 2289 Planarity : 0.010 0.071 2268 Dihedral : 16.291 77.685 4900 Min Nonbonded Distance : 2.033 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.002 TRP E 85 HIS 0.003 0.001 HIS E 106 PHE 0.030 0.002 PHE B 72 TYR 0.008 0.001 TYR F 199 ARG 0.002 0.000 ARG G 75 *********************** 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 : 2.001 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: 0.2327 time to fit residues: 143.4170 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 : 1.642 ------------------------------------------------------------------------------- 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 141 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 255 ASN E 280 ASN A 76 GLN A 205 ASN A 255 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 255 ASN F 280 ASN G 76 GLN G 205 ASN G 280 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13937 Z= 0.211 Angle : 0.651 7.160 18963 Z= 0.331 Chirality : 0.040 0.141 2289 Planarity : 0.007 0.069 2268 Dihedral : 5.874 92.026 1828 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.06 % Allowed : 17.43 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.18), residues: 1652 helix: -1.59 (0.14), residues: 1148 sheet: -2.24 (0.63), residues: 91 loop : -2.40 (0.26), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 127 HIS 0.002 0.001 HIS G 134 PHE 0.014 0.001 PHE D 72 TYR 0.017 0.001 TYR G 150 ARG 0.003 0.000 ARG B 254 *********************** 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 397 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 335 time to evaluate : 1.665 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: E 121 TYR cc_start: 0.8132 (t80) cc_final: 0.7929 (t80) REVERT: E 138 ASP cc_start: 0.7302 (m-30) cc_final: 0.7088 (t0) REVERT: A 37 MET cc_start: 0.8696 (ppp) cc_final: 0.8484 (ppp) REVERT: A 56 GLN cc_start: 0.8560 (tp40) cc_final: 0.8231 (mm-40) REVERT: A 63 GLN cc_start: 0.8471 (mp10) cc_final: 0.8074 (mp10) REVERT: A 124 PRO cc_start: 0.8395 (Cg_exo) cc_final: 0.8044 (Cg_endo) REVERT: A 142 ILE cc_start: 0.7911 (mm) cc_final: 0.7652 (mt) REVERT: A 197 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7243 (tp30) REVERT: B 37 MET cc_start: 0.8556 (ppp) cc_final: 0.8314 (ppp) REVERT: B 56 GLN cc_start: 0.8590 (tp40) cc_final: 0.8303 (mm-40) REVERT: B 63 GLN cc_start: 0.8558 (mp10) cc_final: 0.7991 (mp10) REVERT: B 124 PRO cc_start: 0.8306 (Cg_exo) cc_final: 0.8038 (Cg_endo) REVERT: B 197 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7141 (tp30) REVERT: C 111 TYR cc_start: 0.8763 (m-80) cc_final: 0.8243 (m-80) REVERT: C 121 TYR cc_start: 0.8425 (t80) cc_final: 0.8031 (t80) REVERT: C 124 PRO cc_start: 0.8358 (Cg_exo) cc_final: 0.8055 (Cg_endo) REVERT: C 197 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7533 (tp30) REVERT: C 237 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7647 (pp) REVERT: C 299 PHE cc_start: 0.8212 (t80) cc_final: 0.7935 (t80) REVERT: C 331 TYR cc_start: 0.7099 (t80) cc_final: 0.6799 (t80) REVERT: D 101 LEU cc_start: 0.8595 (tp) cc_final: 0.8391 (mp) REVERT: D 124 PRO cc_start: 0.8367 (Cg_exo) cc_final: 0.8069 (Cg_endo) REVERT: F 36 LYS cc_start: 0.7971 (mmtp) cc_final: 0.6962 (mptt) REVERT: F 56 GLN cc_start: 0.8601 (tp40) cc_final: 0.8190 (mm-40) REVERT: F 63 GLN cc_start: 0.8308 (mp10) cc_final: 0.7835 (mp10) REVERT: F 111 TYR cc_start: 0.8776 (m-80) cc_final: 0.8565 (m-80) REVERT: F 124 PRO cc_start: 0.8564 (Cg_exo) cc_final: 0.8270 (Cg_endo) REVERT: F 138 ASP cc_start: 0.8031 (m-30) cc_final: 0.7556 (t0) REVERT: F 197 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7084 (tp30) REVERT: F 237 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7789 (pp) REVERT: F 280 ASN cc_start: 0.9363 (OUTLIER) cc_final: 0.9122 (t0) REVERT: F 299 PHE cc_start: 0.8077 (t80) cc_final: 0.7785 (t80) REVERT: F 331 TYR cc_start: 0.7140 (t80) cc_final: 0.6073 (t80) REVERT: G 63 GLN cc_start: 0.8359 (mp10) cc_final: 0.7712 (mp10) REVERT: G 121 TYR cc_start: 0.7972 (t80) cc_final: 0.7656 (t80) REVERT: G 146 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5827 (mm) REVERT: G 197 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7040 (tp30) outliers start: 62 outliers final: 33 residues processed: 386 average time/residue: 0.2049 time to fit residues: 123.1660 Evaluate side-chains 325 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 297 VAL 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 218 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 218 LEU 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 120 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 280 ASN Chi-restraints excluded: chain F residue 297 VAL 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 84 optimal weight: 7.9990 chunk 47 optimal weight: 30.0000 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN C 255 ASN D 280 ASN F 205 ASN ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13937 Z= 0.251 Angle : 0.676 12.649 18963 Z= 0.325 Chirality : 0.041 0.179 2289 Planarity : 0.006 0.069 2268 Dihedral : 4.299 17.358 1807 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.91 % Allowed : 19.86 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.21), residues: 1652 helix: -0.40 (0.16), residues: 1134 sheet: -1.93 (0.64), residues: 91 loop : -2.25 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 85 HIS 0.002 0.001 HIS B 106 PHE 0.016 0.001 PHE D 299 TYR 0.011 0.001 TYR D 111 ARG 0.002 0.000 ARG B 254 *********************** 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 377 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 302 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 MET cc_start: 0.8486 (ppp) cc_final: 0.8240 (ppp) REVERT: E 56 GLN cc_start: 0.8390 (tp40) cc_final: 0.8062 (mm-40) REVERT: E 121 TYR cc_start: 0.8155 (t80) cc_final: 0.7938 (t80) REVERT: A 56 GLN cc_start: 0.8575 (tp40) cc_final: 0.8326 (pp30) REVERT: A 63 GLN cc_start: 0.8471 (mp10) cc_final: 0.7969 (mp10) REVERT: A 124 PRO cc_start: 0.8264 (Cg_exo) cc_final: 0.7930 (Cg_endo) REVERT: A 146 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6245 (mm) REVERT: A 197 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7187 (tp30) REVERT: A 331 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7402 (t80) REVERT: B 63 GLN cc_start: 0.8511 (mp10) cc_final: 0.7939 (mp10) REVERT: B 124 PRO cc_start: 0.8212 (Cg_exo) cc_final: 0.7963 (Cg_endo) REVERT: B 146 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6550 (mm) REVERT: B 197 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7066 (tp30) REVERT: C 56 GLN cc_start: 0.8485 (tp40) cc_final: 0.8042 (pp30) REVERT: C 121 TYR cc_start: 0.8323 (t80) cc_final: 0.8009 (t80) REVERT: C 124 PRO cc_start: 0.8244 (Cg_exo) cc_final: 0.7962 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6191 (mm) REVERT: C 197 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7547 (tp30) REVERT: C 237 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7736 (pp) REVERT: C 299 PHE cc_start: 0.8232 (t80) cc_final: 0.7910 (t80) REVERT: D 90 GLN cc_start: 0.8032 (mp10) cc_final: 0.7482 (mt0) REVERT: D 124 PRO cc_start: 0.8253 (Cg_exo) cc_final: 0.7981 (Cg_endo) REVERT: D 146 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6801 (mm) REVERT: F 63 GLN cc_start: 0.8308 (mp10) cc_final: 0.7828 (mp10) REVERT: F 121 TYR cc_start: 0.8285 (t80) cc_final: 0.7843 (t80) REVERT: F 124 PRO cc_start: 0.8678 (Cg_exo) cc_final: 0.8423 (Cg_endo) REVERT: F 138 ASP cc_start: 0.8019 (m-30) cc_final: 0.7556 (t0) REVERT: F 146 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6258 (mm) REVERT: F 197 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7099 (tp30) REVERT: F 237 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7846 (pp) REVERT: F 280 ASN cc_start: 0.9324 (t0) cc_final: 0.8940 (t0) REVERT: F 299 PHE cc_start: 0.8117 (t80) cc_final: 0.7801 (t80) REVERT: F 331 TYR cc_start: 0.7449 (t80) cc_final: 0.6518 (t80) REVERT: G 37 MET cc_start: 0.8838 (ppp) cc_final: 0.8632 (ppp) REVERT: G 63 GLN cc_start: 0.8497 (mp10) cc_final: 0.7843 (mp10) REVERT: G 121 TYR cc_start: 0.8064 (t80) cc_final: 0.7650 (t80) REVERT: G 124 PRO cc_start: 0.8575 (Cg_exo) cc_final: 0.8307 (Cg_endo) REVERT: G 138 ASP cc_start: 0.7342 (t0) cc_final: 0.6792 (t0) REVERT: G 197 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7163 (tp30) REVERT: G 199 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.5905 (t80) outliers start: 75 outliers final: 42 residues processed: 353 average time/residue: 0.2057 time to fit residues: 113.1937 Evaluate side-chains 339 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 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 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 40 CYS 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 237 LEU Chi-restraints excluded: chain C residue 348 LEU 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 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 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 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 199 TYR Chi-restraints excluded: chain G residue 252 ILE 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 151 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 102 optimal weight: 0.3980 chunk 153 optimal weight: 20.0000 chunk 162 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 280 ASN B 205 ASN F 205 ASN F 280 ASN ** G 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13937 Z= 0.130 Angle : 0.627 11.692 18963 Z= 0.288 Chirality : 0.039 0.174 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.794 11.679 1806 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.54 % Allowed : 22.02 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.22), residues: 1652 helix: 0.01 (0.17), residues: 1141 sheet: -1.60 (0.64), residues: 91 loop : -1.77 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 85 HIS 0.002 0.000 HIS G 134 PHE 0.010 0.001 PHE A 244 TYR 0.008 0.001 TYR D 111 ARG 0.002 0.000 ARG B 254 *********************** 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 366 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 312 time to evaluate : 1.612 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: 0.8400 (tp40) cc_final: 0.8143 (mm-40) REVERT: E 121 TYR cc_start: 0.8050 (t80) cc_final: 0.7842 (t80) REVERT: A 56 GLN cc_start: 0.8616 (tp40) cc_final: 0.8316 (pp30) REVERT: A 63 GLN cc_start: 0.8398 (mp10) cc_final: 0.7957 (mp10) REVERT: A 124 PRO cc_start: 0.8202 (Cg_exo) cc_final: 0.7888 (Cg_endo) REVERT: A 146 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6432 (mm) REVERT: A 197 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7229 (tp30) REVERT: A 331 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7429 (t80) REVERT: B 63 GLN cc_start: 0.8463 (mp10) cc_final: 0.7887 (mp10) REVERT: B 124 PRO cc_start: 0.8305 (Cg_exo) cc_final: 0.8082 (Cg_endo) REVERT: B 197 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7262 (tp30) REVERT: C 56 GLN cc_start: 0.8416 (tp40) cc_final: 0.8011 (pp30) REVERT: C 121 TYR cc_start: 0.8093 (t80) cc_final: 0.7828 (t80) REVERT: C 124 PRO cc_start: 0.8457 (Cg_exo) cc_final: 0.8222 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6171 (mm) REVERT: C 197 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7514 (tp30) REVERT: C 299 PHE cc_start: 0.8253 (t80) cc_final: 0.7909 (t80) REVERT: D 90 GLN cc_start: 0.8095 (mp10) cc_final: 0.7484 (mt0) REVERT: D 146 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6776 (mm) REVERT: D 216 CYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7747 (t) REVERT: F 63 GLN cc_start: 0.8215 (mp10) cc_final: 0.7783 (mp10) REVERT: F 101 LEU cc_start: 0.8436 (tt) cc_final: 0.8120 (mt) REVERT: F 121 TYR cc_start: 0.8191 (t80) cc_final: 0.7755 (t80) REVERT: F 124 PRO cc_start: 0.8645 (Cg_exo) cc_final: 0.8405 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7864 (m-30) cc_final: 0.7379 (t0) REVERT: F 146 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6441 (mm) REVERT: F 197 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7266 (tp30) REVERT: F 299 PHE cc_start: 0.8110 (t80) cc_final: 0.7840 (t80) REVERT: F 331 TYR cc_start: 0.7271 (t80) cc_final: 0.6356 (t80) REVERT: G 63 GLN cc_start: 0.8439 (mp10) cc_final: 0.7797 (mp10) REVERT: G 121 TYR cc_start: 0.7963 (t80) cc_final: 0.7546 (t80) REVERT: G 124 PRO cc_start: 0.8585 (Cg_exo) cc_final: 0.8318 (Cg_endo) REVERT: G 146 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5595 (mm) REVERT: G 197 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7113 (tp30) outliers start: 54 outliers final: 32 residues processed: 347 average time/residue: 0.2036 time to fit residues: 110.7378 Evaluate side-chains 331 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 292 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR 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 258 THR Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 331 TYR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 216 CYS 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 256 ASP Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 252 ILE 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 146 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 120 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 G 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13937 Z= 0.174 Angle : 0.643 13.673 18963 Z= 0.295 Chirality : 0.039 0.142 2289 Planarity : 0.005 0.067 2268 Dihedral : 3.784 12.872 1806 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.72 % Allowed : 21.82 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1652 helix: 0.34 (0.17), residues: 1134 sheet: -1.63 (0.62), residues: 91 loop : -1.66 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 85 HIS 0.001 0.000 HIS B 106 PHE 0.014 0.001 PHE C 244 TYR 0.008 0.001 TYR F 213 ARG 0.003 0.000 ARG G 254 *********************** 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 368 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 296 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8430 (tp40) cc_final: 0.8057 (mm-40) REVERT: E 116 PHE cc_start: 0.8251 (m-80) cc_final: 0.8017 (m-80) REVERT: A 56 GLN cc_start: 0.8653 (tp40) cc_final: 0.8296 (pp30) REVERT: A 63 GLN cc_start: 0.8447 (mp10) cc_final: 0.8004 (mp10) REVERT: A 124 PRO cc_start: 0.8231 (Cg_exo) cc_final: 0.7930 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6582 (mm) REVERT: A 197 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7328 (tp30) REVERT: A 331 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7267 (t80) REVERT: B 63 GLN cc_start: 0.8507 (mp10) cc_final: 0.7926 (mp10) REVERT: B 124 PRO cc_start: 0.8265 (Cg_exo) cc_final: 0.8049 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6442 (mm) REVERT: B 197 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7220 (tp30) REVERT: C 56 GLN cc_start: 0.8415 (tp40) cc_final: 0.8032 (pp30) REVERT: C 116 PHE cc_start: 0.8213 (m-80) cc_final: 0.7899 (m-80) REVERT: C 121 TYR cc_start: 0.8008 (t80) cc_final: 0.7720 (t80) REVERT: C 124 PRO cc_start: 0.8433 (Cg_exo) cc_final: 0.8199 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6420 (mm) REVERT: C 197 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7441 (tp30) REVERT: C 299 PHE cc_start: 0.8276 (t80) cc_final: 0.7941 (t80) REVERT: D 146 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6719 (mm) REVERT: D 216 CYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7724 (t) REVERT: F 63 GLN cc_start: 0.8263 (mp10) cc_final: 0.7796 (mp10) REVERT: F 121 TYR cc_start: 0.8208 (t80) cc_final: 0.7742 (t80) REVERT: F 124 PRO cc_start: 0.8616 (Cg_exo) cc_final: 0.8378 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7755 (m-30) cc_final: 0.7356 (t0) REVERT: F 146 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6449 (mm) REVERT: F 197 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7182 (tp30) REVERT: F 299 PHE cc_start: 0.8127 (t80) cc_final: 0.7838 (t80) REVERT: F 331 TYR cc_start: 0.7374 (t80) cc_final: 0.6596 (t80) REVERT: G 56 GLN cc_start: 0.8594 (tp-100) cc_final: 0.8053 (pp30) REVERT: G 63 GLN cc_start: 0.8482 (mp10) cc_final: 0.7822 (mp10) REVERT: G 121 TYR cc_start: 0.7997 (t80) cc_final: 0.7544 (t80) REVERT: G 124 PRO cc_start: 0.8647 (Cg_exo) cc_final: 0.8386 (Cg_endo) REVERT: G 146 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6262 (mm) REVERT: G 197 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7301 (tp30) outliers start: 72 outliers final: 47 residues processed: 347 average time/residue: 0.1953 time to fit residues: 107.8467 Evaluate side-chains 341 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 286 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 331 TYR Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 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 101 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 240 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 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 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 147 ASP 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 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 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 252 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13937 Z= 0.324 Angle : 0.711 13.136 18963 Z= 0.338 Chirality : 0.043 0.131 2289 Planarity : 0.006 0.070 2268 Dihedral : 4.224 17.620 1806 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.50 % Allowed : 21.49 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.22), residues: 1652 helix: 0.43 (0.17), residues: 1134 sheet: -1.85 (0.61), residues: 91 loop : -1.80 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 85 HIS 0.002 0.001 HIS B 106 PHE 0.018 0.002 PHE E 244 TYR 0.011 0.001 TYR E 233 ARG 0.003 0.000 ARG G 254 *********************** 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 357 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 273 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8501 (tp40) cc_final: 0.8211 (mm-40) REVERT: A 63 GLN cc_start: 0.8465 (mp10) cc_final: 0.8021 (mp10) REVERT: A 124 PRO cc_start: 0.8246 (Cg_exo) cc_final: 0.7944 (Cg_endo) REVERT: A 146 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6497 (mm) REVERT: A 197 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7330 (tp30) REVERT: A 331 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.6993 (t80) REVERT: B 63 GLN cc_start: 0.8506 (mp10) cc_final: 0.7956 (mp10) REVERT: B 124 PRO cc_start: 0.8235 (Cg_exo) cc_final: 0.8016 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6478 (mm) REVERT: B 197 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7257 (tp30) REVERT: C 56 GLN cc_start: 0.8439 (tp40) cc_final: 0.8049 (tm-30) REVERT: C 121 TYR cc_start: 0.8192 (t80) cc_final: 0.7905 (t80) REVERT: C 124 PRO cc_start: 0.8369 (Cg_exo) cc_final: 0.8127 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6544 (mm) REVERT: C 197 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7582 (tp30) REVERT: C 331 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.6865 (t80) REVERT: D 146 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6632 (mm) REVERT: D 197 GLU cc_start: 0.6312 (tp30) cc_final: 0.6094 (tp30) REVERT: F 63 GLN cc_start: 0.8274 (mp10) cc_final: 0.7821 (mp10) REVERT: F 101 LEU cc_start: 0.8411 (tt) cc_final: 0.8038 (mt) REVERT: F 121 TYR cc_start: 0.8289 (t80) cc_final: 0.7819 (t80) REVERT: F 124 PRO cc_start: 0.8592 (Cg_exo) cc_final: 0.8348 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7762 (m-30) cc_final: 0.7361 (t0) REVERT: F 146 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6578 (mm) REVERT: F 197 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7154 (tp30) REVERT: F 299 PHE cc_start: 0.8215 (t80) cc_final: 0.7960 (t80) REVERT: F 331 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.7003 (t80) REVERT: G 56 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8071 (pp30) REVERT: G 63 GLN cc_start: 0.8515 (mp10) cc_final: 0.7802 (mp10) REVERT: G 121 TYR cc_start: 0.8137 (t80) cc_final: 0.7712 (t80) REVERT: G 146 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6088 (mm) REVERT: G 197 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7401 (tp30) outliers start: 84 outliers final: 62 residues processed: 330 average time/residue: 0.1979 time to fit residues: 104.0288 Evaluate side-chains 340 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 125 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 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 216 CYS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 39 THR 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 125 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 240 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 118 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 331 TYR Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 118 ILE 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 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 331 TYR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 331 TYR Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 114 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 252 ILE Chi-restraints excluded: chain G residue 279 ILE 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 156 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13937 Z= 0.266 Angle : 0.681 12.806 18963 Z= 0.321 Chirality : 0.041 0.196 2289 Planarity : 0.006 0.060 2268 Dihedral : 4.107 16.310 1806 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.31 % Allowed : 22.48 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1652 helix: 0.55 (0.17), residues: 1134 sheet: -1.90 (0.60), residues: 91 loop : -1.84 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 85 HIS 0.002 0.000 HIS B 106 PHE 0.015 0.001 PHE E 244 TYR 0.011 0.001 TYR F 213 ARG 0.007 0.000 ARG G 254 *********************** 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 362 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 281 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8487 (tp40) cc_final: 0.8191 (mm-40) REVERT: A 63 GLN cc_start: 0.8449 (mp10) cc_final: 0.8025 (mp10) REVERT: A 124 PRO cc_start: 0.8217 (Cg_exo) cc_final: 0.7921 (Cg_endo) REVERT: A 146 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6501 (mm) REVERT: A 197 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7307 (tp30) REVERT: A 331 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7110 (t80) REVERT: B 63 GLN cc_start: 0.8518 (mp10) cc_final: 0.7960 (mp10) REVERT: B 124 PRO cc_start: 0.8232 (Cg_exo) cc_final: 0.8014 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6459 (mm) REVERT: B 197 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7255 (tp30) REVERT: C 56 GLN cc_start: 0.8505 (tp40) cc_final: 0.8116 (tm-30) REVERT: C 121 TYR cc_start: 0.8192 (t80) cc_final: 0.7904 (t80) REVERT: C 124 PRO cc_start: 0.8356 (Cg_exo) cc_final: 0.8115 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6540 (mm) REVERT: C 197 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7538 (tp30) REVERT: C 331 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6836 (t80) REVERT: D 146 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6570 (mm) REVERT: F 63 GLN cc_start: 0.8276 (mp10) cc_final: 0.7844 (mp10) REVERT: F 101 LEU cc_start: 0.8422 (tt) cc_final: 0.8018 (mt) REVERT: F 121 TYR cc_start: 0.8273 (t80) cc_final: 0.7837 (t80) REVERT: F 124 PRO cc_start: 0.8631 (Cg_exo) cc_final: 0.8399 (Cg_endo) REVERT: F 146 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6586 (mm) REVERT: F 197 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7244 (tp30) REVERT: G 56 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8063 (pp30) REVERT: G 63 GLN cc_start: 0.8505 (mp10) cc_final: 0.7806 (mp10) REVERT: G 90 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: G 121 TYR cc_start: 0.8123 (t80) cc_final: 0.7700 (t80) REVERT: G 197 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7367 (tp30) REVERT: G 240 LEU cc_start: 0.8573 (tp) cc_final: 0.8227 (tt) outliers start: 81 outliers final: 61 residues processed: 335 average time/residue: 0.2068 time to fit residues: 109.4902 Evaluate side-chains 341 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 272 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 125 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 E residue 348 LEU Chi-restraints excluded: chain A residue 39 THR 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 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 39 THR 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 125 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 240 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 39 THR 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 101 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 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 118 ILE Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 252 ILE 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 125 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 331 TYR Chi-restraints excluded: chain G residue 348 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13937 Z= 0.209 Angle : 0.664 12.253 18963 Z= 0.309 Chirality : 0.040 0.179 2289 Planarity : 0.006 0.056 2268 Dihedral : 3.961 14.912 1806 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.98 % Allowed : 23.20 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1652 helix: 0.66 (0.17), residues: 1134 sheet: -4.57 (0.50), residues: 49 loop : -1.54 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 85 HIS 0.001 0.000 HIS B 106 PHE 0.033 0.001 PHE C 299 TYR 0.010 0.001 TYR F 213 ARG 0.005 0.000 ARG F 254 *********************** 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 350 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 274 time to evaluate : 1.643 Fit side-chains revert: symmetry clash REVERT: E 56 GLN cc_start: 0.8430 (tp40) cc_final: 0.8113 (mm-40) REVERT: E 345 TYR cc_start: 0.3935 (OUTLIER) cc_final: 0.2874 (m-80) REVERT: A 63 GLN cc_start: 0.8416 (mp10) cc_final: 0.7993 (mp10) REVERT: A 124 PRO cc_start: 0.8189 (Cg_exo) cc_final: 0.7894 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6905 (mm) REVERT: A 197 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7417 (tp30) REVERT: A 331 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7073 (t80) REVERT: B 63 GLN cc_start: 0.8495 (mp10) cc_final: 0.7913 (mp10) REVERT: B 124 PRO cc_start: 0.8242 (Cg_exo) cc_final: 0.8026 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6420 (mm) REVERT: B 197 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7351 (tp30) REVERT: C 56 GLN cc_start: 0.8494 (tp40) cc_final: 0.8116 (tm-30) REVERT: C 116 PHE cc_start: 0.8219 (m-80) cc_final: 0.7937 (m-80) REVERT: C 124 PRO cc_start: 0.8335 (Cg_exo) cc_final: 0.8096 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6510 (mm) REVERT: C 197 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7507 (tp30) REVERT: C 331 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6771 (t80) REVERT: D 146 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6552 (mm) REVERT: F 63 GLN cc_start: 0.8256 (mp10) cc_final: 0.7827 (mp10) REVERT: F 101 LEU cc_start: 0.8443 (tt) cc_final: 0.7993 (mt) REVERT: F 121 TYR cc_start: 0.8285 (t80) cc_final: 0.7788 (t80) REVERT: F 124 PRO cc_start: 0.8615 (Cg_exo) cc_final: 0.8398 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7739 (m-30) cc_final: 0.7364 (t0) REVERT: F 146 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6660 (mm) REVERT: F 197 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7257 (tp30) REVERT: F 216 CYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6779 (t) REVERT: G 56 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8075 (pp30) REVERT: G 63 GLN cc_start: 0.8474 (mp10) cc_final: 0.7790 (mp10) REVERT: G 90 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: G 121 TYR cc_start: 0.8102 (t80) cc_final: 0.7681 (t80) REVERT: G 197 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7417 (tp30) REVERT: G 240 LEU cc_start: 0.8627 (tp) cc_final: 0.8282 (tt) outliers start: 76 outliers final: 58 residues processed: 325 average time/residue: 0.1924 time to fit residues: 100.8441 Evaluate side-chains 336 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 268 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 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 39 THR 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 39 THR 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 125 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 240 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 101 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 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 146 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 252 ILE 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 125 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 252 ILE 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 155 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 159 optimal weight: 0.0020 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13937 Z= 0.181 Angle : 0.655 12.195 18963 Z= 0.303 Chirality : 0.040 0.168 2289 Planarity : 0.006 0.068 2268 Dihedral : 3.857 13.218 1806 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.91 % Allowed : 23.53 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1652 helix: 0.73 (0.17), residues: 1141 sheet: -4.43 (0.50), residues: 49 loop : -1.37 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 85 HIS 0.001 0.000 HIS G 134 PHE 0.019 0.001 PHE F 299 TYR 0.022 0.001 TYR G 150 ARG 0.015 0.000 ARG G 254 *********************** 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 354 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 279 time to evaluate : 1.647 Fit side-chains REVERT: E 56 GLN cc_start: 0.8398 (tp40) cc_final: 0.8096 (mm-40) REVERT: E 345 TYR cc_start: 0.3803 (OUTLIER) cc_final: 0.2801 (m-80) REVERT: A 63 GLN cc_start: 0.8381 (mp10) cc_final: 0.7956 (mp10) REVERT: A 124 PRO cc_start: 0.8157 (Cg_exo) cc_final: 0.7861 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6869 (mm) REVERT: A 197 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7458 (tp30) REVERT: A 331 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.7340 (t80) REVERT: B 63 GLN cc_start: 0.8469 (mp10) cc_final: 0.7894 (mp10) REVERT: B 124 PRO cc_start: 0.8239 (Cg_exo) cc_final: 0.8030 (Cg_endo) REVERT: B 146 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6398 (mm) REVERT: B 197 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7294 (tp30) REVERT: C 56 GLN cc_start: 0.8406 (tp40) cc_final: 0.8076 (tm-30) REVERT: C 124 PRO cc_start: 0.8413 (Cg_exo) cc_final: 0.8169 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6473 (mm) REVERT: C 197 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7415 (tp30) REVERT: C 299 PHE cc_start: 0.8050 (t80) cc_final: 0.7787 (t80) REVERT: C 331 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.6679 (t80) REVERT: D 345 TYR cc_start: 0.2573 (OUTLIER) cc_final: 0.2031 (m-80) REVERT: F 63 GLN cc_start: 0.8248 (mp10) cc_final: 0.7832 (mp10) REVERT: F 101 LEU cc_start: 0.8401 (tt) cc_final: 0.7947 (mt) REVERT: F 121 TYR cc_start: 0.8195 (t80) cc_final: 0.7710 (t80) REVERT: F 124 PRO cc_start: 0.8602 (Cg_exo) cc_final: 0.8382 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7757 (m-30) cc_final: 0.7354 (t0) REVERT: F 146 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6562 (mm) REVERT: F 197 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7279 (tp30) REVERT: F 216 CYS cc_start: 0.7587 (OUTLIER) cc_final: 0.6871 (t) REVERT: G 56 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8059 (pp30) REVERT: G 63 GLN cc_start: 0.8463 (mp10) cc_final: 0.7787 (mp10) REVERT: G 121 TYR cc_start: 0.8074 (t80) cc_final: 0.7643 (t80) REVERT: G 197 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7427 (tp30) outliers start: 75 outliers final: 61 residues processed: 327 average time/residue: 0.1936 time to fit residues: 101.4194 Evaluate side-chains 341 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 271 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 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 39 THR 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 39 THR 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 125 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 240 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 39 THR 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 101 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 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 103 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 228 CYS Chi-restraints excluded: chain D residue 252 ILE 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 345 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 125 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 331 TYR Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 128 ARG Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 252 ILE 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 97 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 0.3980 chunk 154 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13937 Z= 0.145 Angle : 0.649 12.245 18963 Z= 0.298 Chirality : 0.039 0.160 2289 Planarity : 0.005 0.057 2268 Dihedral : 3.645 12.175 1806 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.34 % Allowed : 25.23 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1652 helix: 0.85 (0.17), residues: 1141 sheet: -4.24 (0.52), residues: 49 loop : -1.23 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 85 HIS 0.002 0.001 HIS G 134 PHE 0.023 0.001 PHE E 299 TYR 0.008 0.001 TYR D 111 ARG 0.013 0.000 ARG G 254 ********************** 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 330 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 1.632 Fit side-chains REVERT: E 56 GLN cc_start: 0.8403 (tp40) cc_final: 0.8072 (mm-40) REVERT: E 345 TYR cc_start: 0.3877 (OUTLIER) cc_final: 0.2940 (m-80) REVERT: A 63 GLN cc_start: 0.8339 (mp10) cc_final: 0.7940 (mp10) REVERT: A 124 PRO cc_start: 0.8081 (Cg_exo) cc_final: 0.7805 (Cg_endo) REVERT: A 146 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6826 (mm) REVERT: A 197 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7531 (tp30) REVERT: B 63 GLN cc_start: 0.8438 (mp10) cc_final: 0.7866 (mp10) REVERT: B 146 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6372 (mm) REVERT: B 197 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7326 (tp30) REVERT: C 56 GLN cc_start: 0.8216 (tp40) cc_final: 0.7990 (tm-30) REVERT: C 124 PRO cc_start: 0.8405 (Cg_exo) cc_final: 0.8166 (Cg_endo) REVERT: C 146 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6356 (mm) REVERT: C 197 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7516 (tp30) REVERT: D 197 GLU cc_start: 0.6350 (tp30) cc_final: 0.5615 (mt-10) REVERT: D 331 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7367 (t80) REVERT: D 345 TYR cc_start: 0.2398 (OUTLIER) cc_final: 0.1942 (m-80) REVERT: F 63 GLN cc_start: 0.8199 (mp10) cc_final: 0.7801 (mp10) REVERT: F 101 LEU cc_start: 0.8340 (tt) cc_final: 0.7884 (mt) REVERT: F 121 TYR cc_start: 0.8108 (t80) cc_final: 0.7619 (t80) REVERT: F 124 PRO cc_start: 0.8579 (Cg_exo) cc_final: 0.8342 (Cg_endo) REVERT: F 138 ASP cc_start: 0.7524 (m-30) cc_final: 0.7174 (t0) REVERT: F 146 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6393 (mm) REVERT: F 197 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7319 (tp30) REVERT: G 56 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8044 (pp30) REVERT: G 63 GLN cc_start: 0.8452 (mp10) cc_final: 0.7801 (mp10) REVERT: G 121 TYR cc_start: 0.7996 (t80) cc_final: 0.7553 (t80) REVERT: G 197 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7499 (tp30) outliers start: 51 outliers final: 35 residues processed: 308 average time/residue: 0.1856 time to fit residues: 92.5601 Evaluate side-chains 315 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 39 THR Chi-restraints excluded: chain A residue 146 LEU 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 39 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 125 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 39 THR 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 146 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 345 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 146 LEU Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.163196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114031 restraints weight = 22790.761| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.62 r_work: 0.3285 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13937 Z= 0.258 Angle : 0.684 11.402 18963 Z= 0.323 Chirality : 0.041 0.170 2289 Planarity : 0.006 0.056 2268 Dihedral : 3.944 14.554 1806 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.00 % Allowed : 24.84 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1652 helix: 0.85 (0.17), residues: 1141 sheet: -1.69 (0.59), residues: 91 loop : -1.60 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 85 HIS 0.001 0.000 HIS B 106 PHE 0.019 0.001 PHE E 299 TYR 0.011 0.001 TYR F 213 ARG 0.013 0.000 ARG G 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2915.51 seconds wall clock time: 54 minutes 31.64 seconds (3271.64 seconds total)