Starting phenix.real_space_refine on Sun Aug 24 09:16:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8own_17240/08_2025/8own_17240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8own_17240/08_2025/8own_17240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8own_17240/08_2025/8own_17240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8own_17240/08_2025/8own_17240.map" model { file = "/net/cci-nas-00/data/ceres_data/8own_17240/08_2025/8own_17240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8own_17240/08_2025/8own_17240.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 96 5.16 5 C 11844 2.51 5 N 3330 2.21 5 O 3528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18804 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3133 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.99, per 1000 atoms: 0.16 Number of scatterers: 18804 At special positions: 0 Unit cell: (116.96, 116.1, 124.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 96 16.00 O 3528 8.00 N 3330 7.00 C 11844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 664.4 milliseconds Enol-peptide restraints added in 1.7 microseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 9 sheets defined 57.6% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 2 through 19 removed outlier: 3.704A pdb=" N ALA A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 76 through 95 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 129 through 132 removed outlier: 3.843A pdb=" N ILE A 132 " --> pdb=" O HIS A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 129 through 132' Processing helix chain 'A' and resid 146 through 162 removed outlier: 3.563A pdb=" N MET A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 4.259A pdb=" N VAL A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 183 through 200 removed outlier: 3.836A pdb=" N TYR A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 229 Processing helix chain 'A' and resid 249 through 261 removed outlier: 3.834A pdb=" N LYS A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 295 through 300 removed outlier: 4.114A pdb=" N GLY A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 327 Processing helix chain 'A' and resid 332 through 337 removed outlier: 3.867A pdb=" N ASN A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 358 through 385 Processing helix chain 'A' and resid 387 through 408 removed outlier: 3.583A pdb=" N GLY A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 19 removed outlier: 4.390A pdb=" N THR B 7 " --> pdb=" O ALA B 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 30 Processing helix chain 'B' and resid 76 through 95 Processing helix chain 'B' and resid 113 through 128 Processing helix chain 'B' and resid 129 through 132 removed outlier: 3.843A pdb=" N ILE B 132 " --> pdb=" O HIS B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 132' Processing helix chain 'B' and resid 146 through 162 removed outlier: 3.562A pdb=" N MET B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.259A pdb=" N VAL B 168 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 183 through 200 removed outlier: 3.836A pdb=" N TYR B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 229 Processing helix chain 'B' and resid 249 through 261 removed outlier: 3.834A pdb=" N LYS B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 295 through 300 removed outlier: 4.114A pdb=" N GLY B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 327 Processing helix chain 'B' and resid 332 through 337 removed outlier: 3.866A pdb=" N ASN B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 358 through 385 Processing helix chain 'B' and resid 387 through 408 removed outlier: 3.583A pdb=" N GLY B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 removed outlier: 4.391A pdb=" N THR C 7 " --> pdb=" O ALA C 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN C 8 " --> pdb=" O LEU C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 Processing helix chain 'C' and resid 76 through 95 Processing helix chain 'C' and resid 113 through 128 Processing helix chain 'C' and resid 129 through 132 removed outlier: 3.843A pdb=" N ILE C 132 " --> pdb=" O HIS C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 129 through 132' Processing helix chain 'C' and resid 146 through 162 removed outlier: 3.564A pdb=" N MET C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 168 removed outlier: 4.259A pdb=" N VAL C 168 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 183 through 200 removed outlier: 3.835A pdb=" N TYR C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 229 Processing helix chain 'C' and resid 249 through 261 removed outlier: 3.834A pdb=" N LYS C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 295 through 300 removed outlier: 4.114A pdb=" N GLY C 300 " --> pdb=" O LYS C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 327 Processing helix chain 'C' and resid 332 through 337 removed outlier: 3.866A pdb=" N ASN C 337 " --> pdb=" O ASP C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 354 Processing helix chain 'C' and resid 358 through 385 Processing helix chain 'C' and resid 387 through 408 removed outlier: 3.583A pdb=" N GLY C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 19 removed outlier: 4.390A pdb=" N THR D 7 " --> pdb=" O ALA D 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN D 8 " --> pdb=" O LEU D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 30 Processing helix chain 'D' and resid 76 through 95 Processing helix chain 'D' and resid 113 through 128 Processing helix chain 'D' and resid 129 through 132 removed outlier: 3.843A pdb=" N ILE D 132 " --> pdb=" O HIS D 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 129 through 132' Processing helix chain 'D' and resid 146 through 162 removed outlier: 3.563A pdb=" N MET D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 168 removed outlier: 4.257A pdb=" N VAL D 168 " --> pdb=" O PRO D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 183 through 200 removed outlier: 3.836A pdb=" N TYR D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 229 Processing helix chain 'D' and resid 249 through 261 removed outlier: 3.834A pdb=" N LYS D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 280 Processing helix chain 'D' and resid 295 through 300 removed outlier: 4.114A pdb=" N GLY D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 327 Processing helix chain 'D' and resid 332 through 337 removed outlier: 3.867A pdb=" N ASN D 337 " --> pdb=" O ASP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 354 Processing helix chain 'D' and resid 358 through 385 Processing helix chain 'D' and resid 387 through 408 removed outlier: 3.584A pdb=" N GLY D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 19 removed outlier: 4.390A pdb=" N THR E 7 " --> pdb=" O ALA E 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN E 8 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 30 Processing helix chain 'E' and resid 76 through 95 Processing helix chain 'E' and resid 113 through 128 Processing helix chain 'E' and resid 129 through 132 removed outlier: 3.843A pdb=" N ILE E 132 " --> pdb=" O HIS E 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 129 through 132' Processing helix chain 'E' and resid 146 through 162 removed outlier: 3.563A pdb=" N MET E 150 " --> pdb=" O ASN E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 168 removed outlier: 4.259A pdb=" N VAL E 168 " --> pdb=" O PRO E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 183 through 200 removed outlier: 3.837A pdb=" N TYR E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 229 Processing helix chain 'E' and resid 249 through 261 removed outlier: 3.835A pdb=" N LYS E 255 " --> pdb=" O ASN E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 Processing helix chain 'E' and resid 295 through 300 removed outlier: 4.114A pdb=" N GLY E 300 " --> pdb=" O LYS E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 327 Processing helix chain 'E' and resid 332 through 337 removed outlier: 3.866A pdb=" N ASN E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 354 Processing helix chain 'E' and resid 358 through 385 Processing helix chain 'E' and resid 387 through 408 removed outlier: 3.583A pdb=" N GLY E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 19 removed outlier: 4.390A pdb=" N THR F 7 " --> pdb=" O ALA F 3 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 30 Processing helix chain 'F' and resid 76 through 95 Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 129 through 132 removed outlier: 3.842A pdb=" N ILE F 132 " --> pdb=" O HIS F 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 129 through 132' Processing helix chain 'F' and resid 146 through 162 removed outlier: 3.563A pdb=" N MET F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 168 removed outlier: 4.258A pdb=" N VAL F 168 " --> pdb=" O PRO F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 183 through 200 removed outlier: 3.836A pdb=" N TYR F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 229 Processing helix chain 'F' and resid 249 through 261 removed outlier: 3.834A pdb=" N LYS F 255 " --> pdb=" O ASN F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 280 Processing helix chain 'F' and resid 295 through 300 removed outlier: 4.115A pdb=" N GLY F 300 " --> pdb=" O LYS F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 327 Processing helix chain 'F' and resid 332 through 337 removed outlier: 3.866A pdb=" N ASN F 337 " --> pdb=" O ASP F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 354 Processing helix chain 'F' and resid 358 through 385 Processing helix chain 'F' and resid 387 through 408 removed outlier: 3.583A pdb=" N GLY F 408 " --> pdb=" O THR F 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 137 through 141 removed outlier: 6.691A pdb=" N MET A 65 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA A 140 " --> pdb=" O MET A 65 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 67 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS A 66 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY A 103 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY A 68 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE A 105 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG A 70 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY A 100 " --> pdb=" O HIS A 58 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY D 100 " --> pdb=" O HIS D 58 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS D 66 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY D 103 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLY D 68 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE D 105 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG D 70 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET D 65 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA D 140 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY D 67 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE A 209 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 235 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE A 211 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR A 208 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE A 286 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 210 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE A 307 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 137 through 141 removed outlier: 6.692A pdb=" N MET B 65 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA B 140 " --> pdb=" O MET B 65 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY B 67 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS B 66 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY B 103 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY B 68 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE B 105 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG B 70 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY B 100 " --> pdb=" O HIS B 58 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY E 100 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS E 66 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLY E 103 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY E 68 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE E 105 " --> pdb=" O GLY E 68 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG E 70 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET E 65 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA E 140 " --> pdb=" O MET E 65 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY E 67 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE B 209 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 235 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE B 211 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR B 208 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE B 286 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 210 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 307 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 137 through 141 removed outlier: 6.691A pdb=" N MET C 65 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA C 140 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY C 67 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS C 66 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY C 103 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLY C 68 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE C 105 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG C 70 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY C 100 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLY F 100 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LYS F 66 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY F 103 " --> pdb=" O LYS F 66 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLY F 68 " --> pdb=" O GLY F 103 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ILE F 105 " --> pdb=" O GLY F 68 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG F 70 " --> pdb=" O ILE F 105 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET F 65 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ALA F 140 " --> pdb=" O MET F 65 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY F 67 " --> pdb=" O ALA F 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE C 209 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 235 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE C 211 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR C 208 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE C 286 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 210 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE C 307 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE D 209 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL D 235 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE D 211 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR D 208 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE D 286 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 210 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE D 307 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE E 209 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 235 " --> pdb=" O PHE E 209 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE E 211 " --> pdb=" O VAL E 235 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR E 208 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE E 286 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL E 210 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE E 307 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 270 through 271 removed outlier: 7.798A pdb=" N PHE F 209 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 235 " --> pdb=" O PHE F 209 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE F 211 " --> pdb=" O VAL F 235 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR F 208 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE F 286 " --> pdb=" O THR F 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL F 210 " --> pdb=" O ILE F 286 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE F 307 " --> pdb=" O LEU F 331 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3132 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: 3.48 Time building geometry restraints manager: 2.11 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: 6365 1.34 - 1.45: 2297 1.45 - 1.57: 10358 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 19176 Sorted by residual: bond pdb=" CB THR E 91 " pdb=" CG2 THR E 91 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.15e-01 bond pdb=" CB THR D 91 " pdb=" CG2 THR D 91 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.96e-01 bond pdb=" CB THR F 91 " pdb=" CG2 THR F 91 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.89e-01 bond pdb=" CB THR B 91 " pdb=" CG2 THR B 91 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.84e-01 bond pdb=" CB THR C 91 " pdb=" CG2 THR C 91 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.78e-01 ... (remaining 19171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 25287 1.62 - 3.23: 613 3.23 - 4.85: 56 4.85 - 6.46: 12 6.46 - 8.08: 6 Bond angle restraints: 25974 Sorted by residual: angle pdb=" CA GLY E 215 " pdb=" C GLY E 215 " pdb=" O GLY E 215 " ideal model delta sigma weight residual 122.76 119.55 3.21 1.12e+00 7.97e-01 8.21e+00 angle pdb=" CA GLY A 215 " pdb=" C GLY A 215 " pdb=" O GLY A 215 " ideal model delta sigma weight residual 122.76 119.57 3.19 1.12e+00 7.97e-01 8.12e+00 angle pdb=" CA GLY C 215 " pdb=" C GLY C 215 " pdb=" O GLY C 215 " ideal model delta sigma weight residual 122.76 119.62 3.14 1.12e+00 7.97e-01 7.88e+00 angle pdb=" CA GLY D 215 " pdb=" C GLY D 215 " pdb=" O GLY D 215 " ideal model delta sigma weight residual 122.76 119.64 3.12 1.12e+00 7.97e-01 7.76e+00 angle pdb=" CA GLY F 215 " pdb=" C GLY F 215 " pdb=" O GLY F 215 " ideal model delta sigma weight residual 122.76 119.65 3.11 1.12e+00 7.97e-01 7.70e+00 ... (remaining 25969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 10116 17.47 - 34.95: 1110 34.95 - 52.42: 132 52.42 - 69.90: 12 69.90 - 87.37: 24 Dihedral angle restraints: 11394 sinusoidal: 4476 harmonic: 6918 Sorted by residual: dihedral pdb=" CA PHE A 214 " pdb=" C PHE A 214 " pdb=" N GLY A 215 " pdb=" CA GLY A 215 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PHE F 214 " pdb=" C PHE F 214 " pdb=" N GLY F 215 " pdb=" CA GLY F 215 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PHE E 214 " pdb=" C PHE E 214 " pdb=" N GLY E 215 " pdb=" CA GLY E 215 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 11391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1497 0.026 - 0.053: 869 0.053 - 0.079: 326 0.079 - 0.105: 97 0.105 - 0.132: 115 Chirality restraints: 2904 Sorted by residual: chirality pdb=" CA ILE D 69 " pdb=" N ILE D 69 " pdb=" C ILE D 69 " pdb=" CB ILE D 69 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE F 69 " pdb=" N ILE F 69 " pdb=" C ILE F 69 " pdb=" CB ILE F 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE E 69 " pdb=" N ILE E 69 " pdb=" C ILE E 69 " pdb=" CB ILE E 69 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2901 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 11 " -0.015 2.00e-02 2.50e+03 1.54e-02 4.16e+00 pdb=" CG PHE E 11 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE E 11 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE E 11 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 11 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 11 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE E 11 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 11 " 0.015 2.00e-02 2.50e+03 1.53e-02 4.10e+00 pdb=" CG PHE F 11 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE F 11 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE F 11 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 11 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 11 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE F 11 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 11 " -0.015 2.00e-02 2.50e+03 1.53e-02 4.09e+00 pdb=" CG PHE D 11 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE D 11 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE D 11 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 11 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 11 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 11 " 0.002 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5742 2.83 - 3.35: 17129 3.35 - 3.86: 29900 3.86 - 4.38: 33083 4.38 - 4.90: 61723 Nonbonded interactions: 147577 Sorted by model distance: nonbonded pdb=" NZ LYS D 102 " pdb=" OD2 ASP D 142 " model vdw 2.309 3.120 nonbonded pdb=" NZ LYS F 102 " pdb=" OD2 ASP F 142 " model vdw 2.310 3.120 nonbonded pdb=" NZ LYS C 102 " pdb=" OD2 ASP C 142 " model vdw 2.310 3.120 nonbonded pdb=" NZ LYS E 102 " pdb=" OD2 ASP E 142 " model vdw 2.310 3.120 nonbonded pdb=" NZ LYS B 102 " pdb=" OD2 ASP B 142 " model vdw 2.310 3.120 ... (remaining 147572 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.060 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.005 0.030 19176 Z= 0.204 Angle : 0.590 8.077 25974 Z= 0.330 Chirality : 0.043 0.132 2904 Planarity : 0.004 0.045 3396 Dihedral : 14.021 87.372 6978 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.17), residues: 2448 helix: 2.30 (0.14), residues: 1212 sheet: -0.34 (0.27), residues: 426 loop : -1.86 (0.17), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 402 TYR 0.008 0.001 TYR E 51 PHE 0.035 0.003 PHE E 11 TRP 0.013 0.001 TRP B 348 HIS 0.003 0.001 HIS D 129 Details of bonding type rmsd covalent geometry : bond 0.00491 (19176) covalent geometry : angle 0.58970 (25974) hydrogen bonds : bond 0.15412 ( 1086) hydrogen bonds : angle 5.32973 ( 3132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.752 Fit side-chains REVERT: A 303 LYS cc_start: 0.6542 (ptpt) cc_final: 0.5956 (pttt) REVERT: B 87 MET cc_start: 0.8861 (tpp) cc_final: 0.8617 (tpp) REVERT: B 303 LYS cc_start: 0.6756 (ptpt) cc_final: 0.6166 (pttt) REVERT: C 303 LYS cc_start: 0.6873 (ptpt) cc_final: 0.6144 (pttt) REVERT: D 150 MET cc_start: 0.8667 (mmp) cc_final: 0.8449 (mmt) REVERT: D 238 ILE cc_start: 0.7859 (tp) cc_final: 0.7601 (mp) REVERT: D 256 HIS cc_start: 0.7066 (t-170) cc_final: 0.6818 (t-170) REVERT: E 65 MET cc_start: 0.8929 (mtt) cc_final: 0.8703 (mtt) REVERT: E 212 GLN cc_start: 0.7639 (tt0) cc_final: 0.7296 (tt0) REVERT: E 278 LEU cc_start: 0.7243 (mt) cc_final: 0.6940 (tt) REVERT: F 212 GLN cc_start: 0.7762 (tt0) cc_final: 0.7498 (tt0) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1909 time to fit residues: 68.1240 Evaluate side-chains 171 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN B 85 GLN C 85 GLN D 212 GLN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.093585 restraints weight = 26118.379| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.63 r_work: 0.2824 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19176 Z= 0.138 Angle : 0.489 4.366 25974 Z= 0.264 Chirality : 0.042 0.171 2904 Planarity : 0.004 0.035 3396 Dihedral : 3.854 17.025 2616 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.11 % Allowed : 6.64 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.17), residues: 2448 helix: 2.47 (0.14), residues: 1230 sheet: 0.23 (0.31), residues: 336 loop : -1.50 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 110 TYR 0.012 0.001 TYR A 51 PHE 0.027 0.002 PHE A 11 TRP 0.011 0.001 TRP E 348 HIS 0.004 0.001 HIS F 256 Details of bonding type rmsd covalent geometry : bond 0.00325 (19176) covalent geometry : angle 0.48854 (25974) hydrogen bonds : bond 0.04730 ( 1086) hydrogen bonds : angle 4.25398 ( 3132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.707 Fit side-chains REVERT: A 254 ILE cc_start: 0.7516 (mt) cc_final: 0.7229 (mt) REVERT: A 303 LYS cc_start: 0.7065 (ptpt) cc_final: 0.6359 (pttt) REVERT: B 87 MET cc_start: 0.9251 (tpp) cc_final: 0.9032 (tpp) REVERT: B 303 LYS cc_start: 0.7000 (ptpt) cc_final: 0.6091 (pttt) REVERT: C 49 VAL cc_start: 0.8759 (t) cc_final: 0.8435 (p) REVERT: C 303 LYS cc_start: 0.7161 (ptpt) cc_final: 0.6071 (pttt) REVERT: F 238 ILE cc_start: 0.7743 (tp) cc_final: 0.7481 (mp) outliers start: 22 outliers final: 15 residues processed: 188 average time/residue: 0.1674 time to fit residues: 46.7194 Evaluate side-chains 176 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 280 HIS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 280 HIS Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 103 optimal weight: 0.6980 chunk 243 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 223 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 405 GLN D 212 GLN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094294 restraints weight = 26306.706| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.76 r_work: 0.2838 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19176 Z= 0.116 Angle : 0.440 3.936 25974 Z= 0.239 Chirality : 0.040 0.136 2904 Planarity : 0.003 0.033 3396 Dihedral : 3.582 16.175 2616 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.11 % Allowed : 10.28 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.17), residues: 2448 helix: 2.76 (0.14), residues: 1230 sheet: -0.27 (0.31), residues: 342 loop : -1.26 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 110 TYR 0.011 0.001 TYR A 51 PHE 0.012 0.001 PHE C 11 TRP 0.009 0.001 TRP D 348 HIS 0.004 0.001 HIS F 256 Details of bonding type rmsd covalent geometry : bond 0.00267 (19176) covalent geometry : angle 0.43982 (25974) hydrogen bonds : bond 0.04375 ( 1086) hydrogen bonds : angle 3.97270 ( 3132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.824 Fit side-chains REVERT: A 303 LYS cc_start: 0.7030 (ptpt) cc_final: 0.6310 (pttt) REVERT: B 303 LYS cc_start: 0.7021 (ptpt) cc_final: 0.6093 (pttt) REVERT: B 380 MET cc_start: 0.8507 (tpt) cc_final: 0.8293 (tpt) REVERT: C 49 VAL cc_start: 0.8695 (t) cc_final: 0.8360 (p) REVERT: C 143 MET cc_start: 0.8618 (ppp) cc_final: 0.8399 (ptm) REVERT: C 214 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7627 (m-10) REVERT: C 303 LYS cc_start: 0.7181 (ptpt) cc_final: 0.6104 (pttt) REVERT: D 49 VAL cc_start: 0.8612 (t) cc_final: 0.8384 (p) REVERT: F 150 MET cc_start: 0.8828 (mmp) cc_final: 0.8614 (mmt) REVERT: F 238 ILE cc_start: 0.7831 (tp) cc_final: 0.7578 (mp) REVERT: F 280 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6941 (t-90) outliers start: 22 outliers final: 13 residues processed: 199 average time/residue: 0.1646 time to fit residues: 48.6498 Evaluate side-chains 182 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 280 HIS Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 149 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 162 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 GLN ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.118628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.087488 restraints weight = 26498.367| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.66 r_work: 0.2726 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 19176 Z= 0.223 Angle : 0.551 4.904 25974 Z= 0.299 Chirality : 0.044 0.148 2904 Planarity : 0.004 0.042 3396 Dihedral : 4.082 15.297 2616 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.82 % Allowed : 11.60 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.17), residues: 2448 helix: 2.45 (0.14), residues: 1224 sheet: -0.21 (0.32), residues: 324 loop : -1.53 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 110 TYR 0.012 0.001 TYR A 51 PHE 0.018 0.002 PHE A 374 TRP 0.013 0.002 TRP D 348 HIS 0.006 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00556 (19176) covalent geometry : angle 0.55084 (25974) hydrogen bonds : bond 0.06818 ( 1086) hydrogen bonds : angle 4.31043 ( 3132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.844 Fit side-chains REVERT: A 303 LYS cc_start: 0.7046 (ptpt) cc_final: 0.6245 (pttt) REVERT: B 303 LYS cc_start: 0.7101 (ptpt) cc_final: 0.6390 (pttt) REVERT: C 214 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7185 (m-10) REVERT: C 303 LYS cc_start: 0.7060 (ptpt) cc_final: 0.6143 (pttt) REVERT: C 381 CYS cc_start: 0.8248 (t) cc_final: 0.7310 (m) outliers start: 36 outliers final: 21 residues processed: 192 average time/residue: 0.1711 time to fit residues: 49.0121 Evaluate side-chains 188 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 96 optimal weight: 0.7980 chunk 194 optimal weight: 0.3980 chunk 172 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS ** B 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS D 212 GLN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 HIS F 212 GLN F 384 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.092901 restraints weight = 26150.962| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.72 r_work: 0.2793 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19176 Z= 0.110 Angle : 0.439 4.537 25974 Z= 0.238 Chirality : 0.040 0.135 2904 Planarity : 0.003 0.031 3396 Dihedral : 3.666 15.394 2616 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.77 % Allowed : 12.31 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.17), residues: 2448 helix: 2.78 (0.14), residues: 1230 sheet: -0.08 (0.32), residues: 330 loop : -1.37 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 110 TYR 0.010 0.001 TYR A 51 PHE 0.012 0.001 PHE A 11 TRP 0.009 0.001 TRP D 348 HIS 0.003 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00251 (19176) covalent geometry : angle 0.43890 (25974) hydrogen bonds : bond 0.04262 ( 1086) hydrogen bonds : angle 3.96180 ( 3132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.766 Fit side-chains REVERT: A 303 LYS cc_start: 0.7083 (ptpt) cc_final: 0.6336 (pttt) REVERT: A 377 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8609 (mt) REVERT: B 303 LYS cc_start: 0.7202 (ptpt) cc_final: 0.6361 (pttt) REVERT: B 377 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8580 (mt) REVERT: C 214 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7378 (m-10) REVERT: C 303 LYS cc_start: 0.7188 (ptpt) cc_final: 0.6252 (pttt) REVERT: C 377 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8665 (mt) REVERT: D 49 VAL cc_start: 0.8678 (t) cc_final: 0.8412 (p) REVERT: D 253 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8003 (tt) REVERT: D 272 MET cc_start: 0.7650 (tpp) cc_final: 0.6828 (mmm) REVERT: D 410 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6861 (mm-30) REVERT: E 377 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8587 (mt) REVERT: F 377 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8546 (mt) outliers start: 35 outliers final: 21 residues processed: 198 average time/residue: 0.1719 time to fit residues: 50.2183 Evaluate side-chains 194 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 280 HIS Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 210 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 103 optimal weight: 0.0670 chunk 234 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 193 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS D 212 GLN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS F 212 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.091289 restraints weight = 26165.438| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.67 r_work: 0.2752 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 19176 Z= 0.187 Angle : 0.508 4.933 25974 Z= 0.275 Chirality : 0.043 0.138 2904 Planarity : 0.004 0.034 3396 Dihedral : 3.862 14.991 2616 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.38 % Allowed : 12.41 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.17), residues: 2448 helix: 2.64 (0.14), residues: 1230 sheet: -0.14 (0.32), residues: 330 loop : -1.43 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 110 TYR 0.010 0.001 TYR A 51 PHE 0.016 0.002 PHE A 374 TRP 0.011 0.001 TRP D 348 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00462 (19176) covalent geometry : angle 0.50844 (25974) hydrogen bonds : bond 0.05904 ( 1086) hydrogen bonds : angle 4.13422 ( 3132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.770 Fit side-chains REVERT: A 303 LYS cc_start: 0.7067 (ptpt) cc_final: 0.6394 (pttt) REVERT: A 377 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8584 (mt) REVERT: B 117 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8884 (mp) REVERT: B 303 LYS cc_start: 0.7057 (ptpt) cc_final: 0.6321 (pttt) REVERT: B 377 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8572 (mt) REVERT: C 117 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8777 (mp) REVERT: C 214 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7214 (m-10) REVERT: C 303 LYS cc_start: 0.7182 (ptpt) cc_final: 0.6207 (pttt) REVERT: C 377 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8636 (mt) REVERT: D 253 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8006 (tt) REVERT: D 410 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6883 (mm-30) REVERT: E 253 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7774 (tt) REVERT: E 377 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8511 (mt) REVERT: F 377 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8568 (mt) outliers start: 47 outliers final: 29 residues processed: 195 average time/residue: 0.1659 time to fit residues: 48.1553 Evaluate side-chains 200 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 39 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS D 212 GLN F 212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.090091 restraints weight = 26204.729| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.65 r_work: 0.2817 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19176 Z= 0.111 Angle : 0.436 5.969 25974 Z= 0.237 Chirality : 0.040 0.133 2904 Planarity : 0.003 0.032 3396 Dihedral : 3.590 14.880 2616 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.77 % Allowed : 13.22 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.17), residues: 2448 helix: 2.88 (0.14), residues: 1230 sheet: -0.10 (0.31), residues: 342 loop : -1.27 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 110 TYR 0.009 0.001 TYR A 51 PHE 0.015 0.001 PHE C 11 TRP 0.009 0.001 TRP D 348 HIS 0.003 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00257 (19176) covalent geometry : angle 0.43638 (25974) hydrogen bonds : bond 0.04188 ( 1086) hydrogen bonds : angle 3.91453 ( 3132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.748 Fit side-chains REVERT: A 303 LYS cc_start: 0.7075 (ptpt) cc_final: 0.6412 (pttt) REVERT: A 377 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8566 (mt) REVERT: B 303 LYS cc_start: 0.7058 (ptpt) cc_final: 0.6205 (pttt) REVERT: B 377 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8539 (mt) REVERT: C 214 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7349 (m-10) REVERT: C 303 LYS cc_start: 0.7147 (ptpt) cc_final: 0.6125 (pttt) REVERT: C 377 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8609 (mt) REVERT: D 253 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7957 (tt) REVERT: D 410 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6798 (mm-30) REVERT: E 253 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7766 (tt) REVERT: E 377 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8554 (mt) REVERT: F 243 ARG cc_start: 0.6831 (tmm-80) cc_final: 0.6390 (ttt90) REVERT: F 377 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8538 (mt) outliers start: 35 outliers final: 20 residues processed: 192 average time/residue: 0.1667 time to fit residues: 47.7021 Evaluate side-chains 191 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 175 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 212 GLN E 212 GLN F 212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.091297 restraints weight = 26177.185| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.63 r_work: 0.2846 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19176 Z= 0.104 Angle : 0.433 10.154 25974 Z= 0.233 Chirality : 0.040 0.132 2904 Planarity : 0.003 0.031 3396 Dihedral : 3.470 14.189 2616 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.67 % Allowed : 13.58 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.17), residues: 2448 helix: 2.98 (0.14), residues: 1230 sheet: 0.03 (0.32), residues: 342 loop : -1.23 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 110 TYR 0.009 0.001 TYR A 51 PHE 0.017 0.001 PHE C 11 TRP 0.008 0.001 TRP A 348 HIS 0.003 0.000 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00238 (19176) covalent geometry : angle 0.43338 (25974) hydrogen bonds : bond 0.03958 ( 1086) hydrogen bonds : angle 3.84956 ( 3132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.791 Fit side-chains REVERT: A 303 LYS cc_start: 0.7095 (ptpt) cc_final: 0.6445 (pttt) REVERT: A 377 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 279 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7494 (mm) REVERT: B 281 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6541 (mm-30) REVERT: B 303 LYS cc_start: 0.7157 (ptpt) cc_final: 0.6429 (pttt) REVERT: B 377 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8566 (mt) REVERT: C 214 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7349 (m-10) REVERT: C 303 LYS cc_start: 0.7166 (ptpt) cc_final: 0.6175 (pttt) REVERT: C 377 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8625 (mt) REVERT: D 49 VAL cc_start: 0.8607 (t) cc_final: 0.8343 (p) REVERT: D 253 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7947 (tt) REVERT: D 410 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6772 (mm-30) REVERT: E 29 MET cc_start: 0.8242 (mmm) cc_final: 0.7809 (mmm) REVERT: E 253 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7707 (tt) REVERT: E 377 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8581 (mt) REVERT: F 243 ARG cc_start: 0.6824 (tmm-80) cc_final: 0.6388 (ttt90) REVERT: F 377 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8535 (mt) outliers start: 33 outliers final: 19 residues processed: 192 average time/residue: 0.1774 time to fit residues: 50.1644 Evaluate side-chains 191 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 377 ILE Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 379 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 22 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 181 optimal weight: 0.0030 chunk 200 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.091362 restraints weight = 26132.185| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.59 r_work: 0.2864 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19176 Z= 0.089 Angle : 0.412 10.625 25974 Z= 0.221 Chirality : 0.039 0.130 2904 Planarity : 0.003 0.030 3396 Dihedral : 3.307 13.808 2616 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.42 % Allowed : 13.83 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.17), residues: 2448 helix: 3.11 (0.14), residues: 1230 sheet: 0.16 (0.32), residues: 342 loop : -1.14 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 110 TYR 0.009 0.001 TYR A 51 PHE 0.018 0.001 PHE B 11 TRP 0.007 0.001 TRP B 348 HIS 0.002 0.000 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00196 (19176) covalent geometry : angle 0.41236 (25974) hydrogen bonds : bond 0.03284 ( 1086) hydrogen bonds : angle 3.73337 ( 3132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.794 Fit side-chains REVERT: A 303 LYS cc_start: 0.7075 (ptpt) cc_final: 0.6392 (pttt) REVERT: A 377 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8476 (mt) REVERT: B 281 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6560 (mm-30) REVERT: B 303 LYS cc_start: 0.7092 (ptpt) cc_final: 0.6346 (pttt) REVERT: B 377 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8505 (mt) REVERT: C 214 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7310 (m-10) REVERT: C 303 LYS cc_start: 0.7088 (ptpt) cc_final: 0.6198 (pttt) REVERT: D 49 VAL cc_start: 0.8521 (t) cc_final: 0.8236 (p) REVERT: D 253 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7881 (tt) REVERT: D 410 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6619 (mm-30) REVERT: E 253 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7647 (tt) REVERT: F 243 ARG cc_start: 0.6746 (tmm-80) cc_final: 0.6264 (ttt90) REVERT: F 410 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7042 (tm-30) outliers start: 28 outliers final: 17 residues processed: 192 average time/residue: 0.1717 time to fit residues: 48.6512 Evaluate side-chains 188 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 410 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 139 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 chunk 156 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN C 280 HIS ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN F 212 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.088702 restraints weight = 26318.459| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.73 r_work: 0.2819 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 19176 Z= 0.239 Angle : 0.572 11.186 25974 Z= 0.306 Chirality : 0.045 0.145 2904 Planarity : 0.004 0.038 3396 Dihedral : 3.941 14.727 2616 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.32 % Allowed : 13.88 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.17), residues: 2448 helix: 2.68 (0.14), residues: 1224 sheet: 0.11 (0.32), residues: 324 loop : -1.43 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 110 TYR 0.010 0.002 TYR A 51 PHE 0.022 0.002 PHE B 11 TRP 0.010 0.002 TRP E 348 HIS 0.007 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00599 (19176) covalent geometry : angle 0.57177 (25974) hydrogen bonds : bond 0.06625 ( 1086) hydrogen bonds : angle 4.17187 ( 3132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.742 Fit side-chains REVERT: A 303 LYS cc_start: 0.7050 (ptpt) cc_final: 0.6460 (pttt) REVERT: A 377 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8570 (mt) REVERT: B 16 ARG cc_start: 0.7707 (mmp80) cc_final: 0.7458 (ttm170) REVERT: B 281 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6641 (mm-30) REVERT: B 303 LYS cc_start: 0.7169 (ptpt) cc_final: 0.6477 (pttt) REVERT: B 377 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8596 (mt) REVERT: C 16 ARG cc_start: 0.7692 (mmp80) cc_final: 0.7434 (ttm170) REVERT: C 214 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7172 (m-10) REVERT: C 281 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6636 (mm-30) REVERT: C 303 LYS cc_start: 0.7012 (ptpt) cc_final: 0.6110 (pttt) REVERT: D 253 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8049 (tt) REVERT: D 410 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6919 (mm-30) REVERT: E 26 ARG cc_start: 0.7786 (tpt-90) cc_final: 0.6974 (ttt-90) REVERT: E 29 MET cc_start: 0.8434 (mmm) cc_final: 0.8101 (mmm) REVERT: E 253 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7812 (tt) REVERT: F 243 ARG cc_start: 0.6987 (tmm-80) cc_final: 0.6555 (ttt90) REVERT: F 410 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7267 (tm-30) outliers start: 26 outliers final: 16 residues processed: 187 average time/residue: 0.1737 time to fit residues: 46.8503 Evaluate side-chains 185 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 214 PHE Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 275 ASP Chi-restraints excluded: chain D residue 410 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 214 PHE Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 410 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 116 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 237 optimal weight: 0.0970 chunk 191 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 136 optimal weight: 0.4980 chunk 65 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 280 HIS ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.094389 restraints weight = 25925.315| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.83 r_work: 0.2855 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19176 Z= 0.105 Angle : 0.450 11.405 25974 Z= 0.240 Chirality : 0.040 0.133 2904 Planarity : 0.003 0.031 3396 Dihedral : 3.535 15.031 2616 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.11 % Allowed : 14.08 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.17), residues: 2448 helix: 2.98 (0.14), residues: 1230 sheet: 0.03 (0.32), residues: 342 loop : -1.22 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 110 TYR 0.009 0.001 TYR A 51 PHE 0.021 0.001 PHE B 11 TRP 0.009 0.001 TRP B 348 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00239 (19176) covalent geometry : angle 0.45013 (25974) hydrogen bonds : bond 0.03949 ( 1086) hydrogen bonds : angle 3.86251 ( 3132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4629.85 seconds wall clock time: 80 minutes 24.89 seconds (4824.89 seconds total)