Starting phenix.real_space_refine on Mon Jun 16 13:18:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8own_17240/06_2025/8own_17240.cif Found real_map, /net/cci-nas-00/data/ceres_data/8own_17240/06_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_17240/06_2025/8own_17240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8own_17240/06_2025/8own_17240.map" model { file = "/net/cci-nas-00/data/ceres_data/8own_17240/06_2025/8own_17240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8own_17240/06_2025/8own_17240.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, F Time building chain proxies: 7.67, per 1000 atoms: 0.41 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: 4.88 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.94 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: 5.78 Time building geometry restraints manager: 5.43 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 37.680 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (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 TRP 0.013 0.001 TRP B 348 HIS 0.003 0.001 HIS D 129 PHE 0.035 0.003 PHE E 11 TYR 0.008 0.001 TYR E 51 ARG 0.005 0.001 ARG C 402 Details of bonding type rmsd hydrogen bonds : bond 0.15412 ( 1086) hydrogen bonds : angle 5.32973 ( 3132) covalent geometry : bond 0.00491 (19176) covalent geometry : angle 0.58970 (25974) *********************** 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 : 2.121 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: 0.6167 (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: 0.7602 (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: 0.7497 (tt0) REVERT: F 243 ARG cc_start: 0.6438 (ttt180) cc_final: 0.6198 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.3747 time to fit residues: 135.0127 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 : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 192 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 143 optimal weight: 0.0670 chunk 223 optimal weight: 1.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.128860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.097316 restraints weight = 25954.169| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.81 r_work: 0.2920 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19176 Z= 0.113 Angle : 0.462 3.953 25974 Z= 0.251 Chirality : 0.041 0.168 2904 Planarity : 0.004 0.034 3396 Dihedral : 3.725 17.493 2616 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.66 % Allowed : 6.43 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2448 helix: 2.65 (0.14), residues: 1230 sheet: 0.28 (0.31), residues: 336 loop : -1.44 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 348 HIS 0.004 0.001 HIS D 280 PHE 0.027 0.001 PHE A 11 TYR 0.011 0.001 TYR A 51 ARG 0.005 0.000 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 1086) hydrogen bonds : angle 4.21494 ( 3132) covalent geometry : bond 0.00248 (19176) covalent geometry : angle 0.46222 (25974) *********************** 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: 13 poor density : 184 time to evaluate : 1.893 Fit side-chains REVERT: A 303 LYS cc_start: 0.6960 (ptpt) cc_final: 0.6328 (pttt) REVERT: B 49 VAL cc_start: 0.8868 (t) cc_final: 0.8654 (p) REVERT: B 303 LYS cc_start: 0.6975 (ptpt) cc_final: 0.6108 (pttt) REVERT: C 49 VAL cc_start: 0.8708 (t) cc_final: 0.8404 (p) REVERT: C 281 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6442 (mm-30) REVERT: C 303 LYS cc_start: 0.7098 (ptpt) cc_final: 0.6068 (pttt) REVERT: C 402 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7712 (ttp80) REVERT: E 283 ASP cc_start: 0.7371 (m-30) cc_final: 0.6248 (m-30) REVERT: F 238 ILE cc_start: 0.7698 (tp) cc_final: 0.7430 (mp) outliers start: 13 outliers final: 9 residues processed: 190 average time/residue: 0.3749 time to fit residues: 105.7993 Evaluate side-chains 170 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 275 ASP Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 7 THR 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 183 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 240 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.089624 restraints weight = 26163.764| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.63 r_work: 0.2774 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19176 Z= 0.163 Angle : 0.495 4.517 25974 Z= 0.269 Chirality : 0.042 0.142 2904 Planarity : 0.004 0.033 3396 Dihedral : 3.836 15.885 2616 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.27 % Allowed : 9.12 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2448 helix: 2.64 (0.14), residues: 1230 sheet: -0.23 (0.32), residues: 330 loop : -1.40 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 348 HIS 0.004 0.001 HIS B 384 PHE 0.014 0.002 PHE A 374 TYR 0.012 0.001 TYR A 51 ARG 0.005 0.001 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.05684 ( 1086) hydrogen bonds : angle 4.16620 ( 3132) covalent geometry : bond 0.00391 (19176) covalent geometry : angle 0.49528 (25974) *********************** 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 202 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 1.966 Fit side-chains REVERT: A 303 LYS cc_start: 0.7116 (ptpt) cc_final: 0.6271 (pttt) REVERT: B 303 LYS cc_start: 0.7013 (ptpt) cc_final: 0.6088 (pttt) REVERT: C 214 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7835 (m-10) REVERT: C 303 LYS cc_start: 0.7179 (ptpt) cc_final: 0.6024 (pttt) REVERT: C 381 CYS cc_start: 0.8226 (t) cc_final: 0.7249 (m) REVERT: F 238 ILE cc_start: 0.7870 (tp) cc_final: 0.7598 (mp) outliers start: 25 outliers final: 18 residues processed: 192 average time/residue: 0.3368 time to fit residues: 96.2843 Evaluate side-chains 183 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 214 PHE 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 D residue 214 PHE Chi-restraints excluded: chain D residue 254 ILE 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 7 THR Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 242 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 114 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 70 optimal weight: 0.0670 chunk 224 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 181 optimal weight: 0.0010 chunk 116 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 overall best weight: 1.8130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 280 HIS B 280 HIS ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 HIS F 212 GLN ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.091754 restraints weight = 26145.498| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.62 r_work: 0.2798 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2355 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= 0.135 Angle : 0.458 4.068 25974 Z= 0.249 Chirality : 0.041 0.137 2904 Planarity : 0.004 0.031 3396 Dihedral : 3.721 15.715 2616 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.42 % Allowed : 10.99 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.17), residues: 2448 helix: 2.75 (0.14), residues: 1230 sheet: -0.33 (0.31), residues: 342 loop : -1.29 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 348 HIS 0.003 0.001 HIS F 161 PHE 0.012 0.002 PHE C 11 TYR 0.011 0.001 TYR A 51 ARG 0.005 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 1086) hydrogen bonds : angle 4.05024 ( 3132) covalent geometry : bond 0.00319 (19176) covalent geometry : angle 0.45849 (25974) *********************** 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 198 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 2.221 Fit side-chains REVERT: A 303 LYS cc_start: 0.7050 (ptpt) cc_final: 0.6311 (pttt) REVERT: B 303 LYS cc_start: 0.7073 (ptpt) cc_final: 0.6298 (pttt) REVERT: C 214 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7662 (m-10) REVERT: C 281 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6451 (mm-30) REVERT: C 303 LYS cc_start: 0.7174 (ptpt) cc_final: 0.6146 (pttt) REVERT: E 143 MET cc_start: 0.8632 (ptm) cc_final: 0.8404 (ptm) outliers start: 28 outliers final: 19 residues processed: 188 average time/residue: 0.3418 time to fit residues: 96.4873 Evaluate side-chains 182 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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 214 PHE Chi-restraints excluded: chain B residue 383 THR 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 D residue 214 PHE Chi-restraints excluded: chain D residue 280 HIS 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 7 THR Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 242 ILE Chi-restraints excluded: chain F residue 280 HIS 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 2 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN 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 = 0.3416 r_free = 0.3416 target = 0.120577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.088998 restraints weight = 26407.547| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.64 r_work: 0.2815 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19176 Z= 0.150 Angle : 0.471 4.246 25974 Z= 0.256 Chirality : 0.041 0.135 2904 Planarity : 0.004 0.031 3396 Dihedral : 3.750 15.328 2616 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.93 % Allowed : 12.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2448 helix: 2.73 (0.14), residues: 1230 sheet: -0.14 (0.32), residues: 330 loop : -1.36 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 348 HIS 0.004 0.001 HIS F 161 PHE 0.014 0.002 PHE A 374 TYR 0.010 0.001 TYR A 51 ARG 0.005 0.000 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.05251 ( 1086) hydrogen bonds : angle 4.07172 ( 3132) covalent geometry : bond 0.00362 (19176) covalent geometry : angle 0.47090 (25974) *********************** 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 202 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 2.209 Fit side-chains REVERT: A 303 LYS cc_start: 0.7119 (ptpt) cc_final: 0.6303 (pttt) REVERT: A 377 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8578 (mt) REVERT: B 87 MET cc_start: 0.9307 (tpp) cc_final: 0.9033 (tpp) REVERT: B 303 LYS cc_start: 0.7229 (ptpt) cc_final: 0.6442 (pttt) REVERT: B 377 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8558 (mt) REVERT: C 214 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7510 (m-10) REVERT: C 303 LYS cc_start: 0.7181 (ptpt) cc_final: 0.6238 (pttt) REVERT: C 377 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8634 (mt) REVERT: D 253 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7987 (tt) REVERT: D 410 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6928 (mm-30) REVERT: E 143 MET cc_start: 0.8593 (ptm) cc_final: 0.8358 (ptm) REVERT: E 377 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8538 (mt) outliers start: 38 outliers final: 21 residues processed: 190 average time/residue: 0.3962 time to fit residues: 111.7837 Evaluate side-chains 186 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 2.633 ------------------------------------------------------------------------------- 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 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 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 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 254 ILE Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 377 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 242 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 177 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS E 212 GLN F 212 GLN ** 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 = 0.3406 r_free = 0.3406 target = 0.119896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.090673 restraints weight = 26402.210| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.67 r_work: 0.2801 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 19176 Z= 0.195 Angle : 0.521 4.953 25974 Z= 0.281 Chirality : 0.043 0.142 2904 Planarity : 0.004 0.036 3396 Dihedral : 3.946 15.485 2616 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.13 % Allowed : 12.61 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.17), residues: 2448 helix: 2.61 (0.14), residues: 1224 sheet: -0.11 (0.32), residues: 324 loop : -1.48 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 348 HIS 0.005 0.001 HIS A 384 PHE 0.017 0.002 PHE F 214 TYR 0.010 0.001 TYR A 51 ARG 0.006 0.001 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.06139 ( 1086) hydrogen bonds : angle 4.19437 ( 3132) covalent geometry : bond 0.00483 (19176) covalent geometry : angle 0.52119 (25974) *********************** 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 204 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 2.089 Fit side-chains REVERT: A 117 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8776 (mp) REVERT: A 303 LYS cc_start: 0.7123 (ptpt) cc_final: 0.6424 (pttt) REVERT: A 377 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8622 (mt) REVERT: B 117 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8886 (mp) REVERT: B 303 LYS cc_start: 0.7037 (ptpt) cc_final: 0.6313 (pttt) REVERT: B 377 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8608 (mt) REVERT: C 117 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8802 (mp) REVERT: C 214 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: C 303 LYS cc_start: 0.7201 (ptpt) cc_final: 0.6288 (pttt) REVERT: C 377 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8664 (mt) REVERT: D 253 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7958 (tt) REVERT: D 410 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6994 (mm-30) REVERT: E 143 MET cc_start: 0.8651 (ptm) cc_final: 0.8409 (ptm) REVERT: E 253 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7824 (tt) REVERT: E 377 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8568 (mt) REVERT: F 280 HIS cc_start: 0.7583 (OUTLIER) cc_final: 0.7302 (t-90) outliers start: 42 outliers final: 22 residues processed: 190 average time/residue: 0.3487 time to fit residues: 99.8502 Evaluate side-chains 195 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU 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 59 ASP 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 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 383 THR 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 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 280 HIS Chi-restraints excluded: chain F residue 290 LEU 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 244 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 176 optimal weight: 0.0470 chunk 202 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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** C 384 HIS 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 = 0.3437 r_free = 0.3437 target = 0.122170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.090919 restraints weight = 26140.729| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.64 r_work: 0.2830 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2765 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= 0.108 Angle : 0.439 5.928 25974 Z= 0.237 Chirality : 0.040 0.132 2904 Planarity : 0.003 0.032 3396 Dihedral : 3.589 15.337 2616 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.42 % Allowed : 13.48 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.17), residues: 2448 helix: 2.89 (0.14), residues: 1230 sheet: -0.20 (0.31), residues: 342 loop : -1.27 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 348 HIS 0.003 0.001 HIS B 280 PHE 0.016 0.001 PHE B 11 TYR 0.009 0.001 TYR A 51 ARG 0.006 0.000 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 1086) hydrogen bonds : angle 3.93008 ( 3132) covalent geometry : bond 0.00246 (19176) covalent geometry : angle 0.43885 (25974) *********************** 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 200 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 2.125 Fit side-chains REVERT: A 303 LYS cc_start: 0.7109 (ptpt) cc_final: 0.6384 (pttt) REVERT: A 377 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8652 (mt) REVERT: B 280 HIS cc_start: 0.7054 (m-70) cc_final: 0.6774 (m170) REVERT: B 281 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6390 (mm-30) REVERT: B 303 LYS cc_start: 0.7024 (ptpt) cc_final: 0.6192 (pttt) REVERT: B 377 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8657 (mt) REVERT: C 214 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7396 (m-10) REVERT: C 303 LYS cc_start: 0.7184 (ptpt) cc_final: 0.6245 (pttt) REVERT: C 377 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8645 (mt) REVERT: E 143 MET cc_start: 0.8577 (ptm) cc_final: 0.8356 (ptm) REVERT: E 253 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7806 (tt) REVERT: E 377 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8576 (mt) REVERT: F 280 HIS cc_start: 0.7473 (OUTLIER) cc_final: 0.7179 (t-90) outliers start: 28 outliers final: 17 residues processed: 191 average time/residue: 0.3492 time to fit residues: 99.3087 Evaluate side-chains 183 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 2.281 ------------------------------------------------------------------------------- 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 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 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 214 PHE 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 258 ASP 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 280 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 53 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 384 HIS 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 = 0.3420 r_free = 0.3420 target = 0.120792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.087626 restraints weight = 26326.215| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.59 r_work: 0.2832 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19176 Z= 0.132 Angle : 0.462 10.639 25974 Z= 0.248 Chirality : 0.041 0.132 2904 Planarity : 0.003 0.032 3396 Dihedral : 3.614 14.950 2616 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.62 % Allowed : 13.73 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.17), residues: 2448 helix: 2.88 (0.14), residues: 1230 sheet: 0.01 (0.32), residues: 330 loop : -1.34 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 348 HIS 0.003 0.001 HIS F 161 PHE 0.013 0.001 PHE F 214 TYR 0.009 0.001 TYR A 51 ARG 0.006 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 1086) hydrogen bonds : angle 3.97125 ( 3132) covalent geometry : bond 0.00316 (19176) covalent geometry : angle 0.46154 (25974) *********************** 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 195 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.962 Fit side-chains REVERT: A 303 LYS cc_start: 0.7138 (ptpt) cc_final: 0.6474 (pttt) REVERT: A 377 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8665 (mt) REVERT: B 303 LYS cc_start: 0.7079 (ptpt) cc_final: 0.6228 (pttt) REVERT: B 377 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8681 (mt) REVERT: C 16 ARG cc_start: 0.7581 (mmp80) cc_final: 0.7354 (ttm170) REVERT: C 117 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8843 (mp) REVERT: C 214 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7387 (m-10) REVERT: C 303 LYS cc_start: 0.7148 (ptpt) cc_final: 0.6169 (pttt) REVERT: C 377 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8660 (mt) REVERT: D 253 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7947 (tt) REVERT: E 143 MET cc_start: 0.8614 (ptm) cc_final: 0.8401 (ptm) REVERT: E 253 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7818 (tt) REVERT: E 377 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8572 (mt) REVERT: F 280 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.7241 (t-90) outliers start: 32 outliers final: 18 residues processed: 186 average time/residue: 0.3393 time to fit residues: 93.5159 Evaluate side-chains 187 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.962 ------------------------------------------------------------------------------- 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 214 PHE Chi-restraints excluded: chain B residue 377 ILE 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 383 THR Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU 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 377 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 280 HIS Chi-restraints excluded: chain F residue 290 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 102 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 243 optimal weight: 10.0000 chunk 181 optimal weight: 0.0770 chunk 81 optimal weight: 5.9990 chunk 194 optimal weight: 0.0980 chunk 94 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 212 GLN ** F 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.091533 restraints weight = 26337.378| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.76 r_work: 0.2834 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2893 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= 0.102 Angle : 0.430 11.529 25974 Z= 0.231 Chirality : 0.040 0.130 2904 Planarity : 0.003 0.031 3396 Dihedral : 3.443 14.807 2616 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.42 % Allowed : 13.93 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.17), residues: 2448 helix: 3.03 (0.14), residues: 1230 sheet: -0.02 (0.32), residues: 342 loop : -1.19 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 348 HIS 0.003 0.001 HIS D 161 PHE 0.018 0.001 PHE B 11 TYR 0.009 0.001 TYR A 51 ARG 0.007 0.000 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 1086) hydrogen bonds : angle 3.85242 ( 3132) covalent geometry : bond 0.00232 (19176) covalent geometry : angle 0.43007 (25974) *********************** 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 196 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 2.103 Fit side-chains REVERT: A 303 LYS cc_start: 0.7183 (ptpt) cc_final: 0.6517 (pttt) REVERT: A 377 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8672 (mt) REVERT: B 303 LYS cc_start: 0.7115 (ptpt) cc_final: 0.6405 (pttt) REVERT: B 377 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8684 (mt) REVERT: C 214 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7397 (m-10) REVERT: C 303 LYS cc_start: 0.7197 (ptpt) cc_final: 0.6266 (pttt) REVERT: C 377 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8677 (mt) REVERT: D 253 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7921 (tt) REVERT: E 143 MET cc_start: 0.8609 (ptm) cc_final: 0.8398 (ptm) REVERT: E 253 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7743 (tt) REVERT: E 410 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7139 (tm-30) outliers start: 28 outliers final: 15 residues processed: 188 average time/residue: 0.3429 time to fit residues: 95.6656 Evaluate side-chains 182 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 2.282 ------------------------------------------------------------------------------- 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 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 D residue 214 PHE Chi-restraints excluded: chain D residue 253 LEU 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 379 THR Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain F residue 280 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 58 optimal weight: 0.5980 chunk 240 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 234 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 74 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 HIS E 212 GLN F 212 GLN ** 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 = 0.3537 r_free = 0.3537 target = 0.128856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.095655 restraints weight = 25971.145| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.67 r_work: 0.2895 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19176 Z= 0.090 Angle : 0.418 11.905 25974 Z= 0.223 Chirality : 0.039 0.129 2904 Planarity : 0.003 0.030 3396 Dihedral : 3.294 15.175 2616 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.27 % Allowed : 14.13 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.17), residues: 2448 helix: 3.18 (0.14), residues: 1230 sheet: 0.08 (0.32), residues: 342 loop : -1.13 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 89 HIS 0.002 0.000 HIS F 256 PHE 0.019 0.001 PHE B 11 TYR 0.009 0.001 TYR A 51 ARG 0.007 0.000 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 1086) hydrogen bonds : angle 3.74588 ( 3132) covalent geometry : bond 0.00197 (19176) covalent geometry : angle 0.41846 (25974) ********************** 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 196 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.989 Fit side-chains REVERT: A 303 LYS cc_start: 0.7165 (ptpt) cc_final: 0.6500 (pttt) REVERT: A 377 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8586 (mt) REVERT: B 303 LYS cc_start: 0.7191 (ptpt) cc_final: 0.6515 (pttt) REVERT: C 214 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7450 (m-10) REVERT: C 303 LYS cc_start: 0.7139 (ptpt) cc_final: 0.6267 (pttt) REVERT: E 143 MET cc_start: 0.8383 (ptm) cc_final: 0.8174 (ptm) REVERT: E 253 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7714 (tt) REVERT: E 410 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: F 280 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.6985 (t-90) outliers start: 25 outliers final: 15 residues processed: 187 average time/residue: 0.3520 time to fit residues: 96.8688 Evaluate side-chains 176 residues out of total 1974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.981 ------------------------------------------------------------------------------- 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 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 D residue 214 PHE Chi-restraints excluded: chain E residue 7 THR 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 410 GLU Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 280 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 0.0470 chunk 226 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 198 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN F 212 GLN ** 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 = 0.3469 r_free = 0.3469 target = 0.123605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.091094 restraints weight = 26241.169| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.79 r_work: 0.2822 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19176 Z= 0.163 Angle : 0.498 12.102 25974 Z= 0.267 Chirality : 0.042 0.135 2904 Planarity : 0.004 0.032 3396 Dihedral : 3.660 16.158 2616 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.17 % Allowed : 14.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.17), residues: 2448 helix: 2.92 (0.14), residues: 1230 sheet: 0.15 (0.32), residues: 330 loop : -1.26 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 348 HIS 0.005 0.001 HIS F 161 PHE 0.015 0.002 PHE C 374 TYR 0.009 0.001 TYR A 51 ARG 0.006 0.000 ARG D 110 Details of bonding type rmsd hydrogen bonds : bond 0.05411 ( 1086) hydrogen bonds : angle 4.00725 ( 3132) covalent geometry : bond 0.00397 (19176) covalent geometry : angle 0.49829 (25974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9585.18 seconds wall clock time: 168 minutes 19.07 seconds (10099.07 seconds total)