Starting phenix.real_space_refine on Fri Aug 7 07:45:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptg_17870/08_2026/8ptg_17870.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptg_17870/08_2026/8ptg_17870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ptg_17870/08_2026/8ptg_17870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptg_17870/08_2026/8ptg_17870.map" model { file = "/net/cci-nas-00/data/ceres_data/8ptg_17870/08_2026/8ptg_17870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptg_17870/08_2026/8ptg_17870.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.043 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: 8 Type Number sf(0) Gaussians P 27 5.49 5 Mg 6 5.21 5 S 102 5.16 5 Be 6 3.05 5 C 12645 2.51 5 N 3600 2.21 5 O 3888 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20292 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "B" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "C" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "D" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "E" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "F" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "R" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.33, per 1000 atoms: 0.16 Number of scatterers: 20292 At special positions: 0 Unit cell: (112.347, 149.139, 137.313, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 102 16.00 P 27 15.00 Mg 6 11.99 F 18 9.00 O 3888 8.00 N 3600 7.00 C 12645 6.00 Be 6 4.00 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 805.0 milliseconds 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 23 sheets defined 50.2% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.609A pdb=" N ILE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.977A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.576A pdb=" N HIS A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.511A pdb=" N HIS A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.748A pdb=" N ARG A 299 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.818A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.101A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 391 through 404 Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.751A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 removed outlier: 3.661A pdb=" N ILE B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.608A pdb=" N ARG B 128 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.871A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.616A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 325 through 339 removed outlier: 3.725A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.502A pdb=" N ALA B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.086A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 403 Processing helix chain 'B' and resid 408 through 419 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.575A pdb=" N ILE C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.577A pdb=" N ILE C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.834A pdb=" N ARG C 128 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 3.952A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 256 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.811A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 4.336A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 419 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.701A pdb=" N MET D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.587A pdb=" N ILE D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 126 through 130 removed outlier: 3.579A pdb=" N ASN D 129 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS D 130 " --> pdb=" O ALA D 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 126 through 130' Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 153 through 166 removed outlier: 3.543A pdb=" N LEU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.565A pdb=" N HIS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 removed outlier: 3.689A pdb=" N LEU D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.848A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 404 Processing helix chain 'D' and resid 408 through 419 Processing helix chain 'E' and resid 2 through 9 removed outlier: 3.535A pdb=" N LEU E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 21 removed outlier: 3.543A pdb=" N MET E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.519A pdb=" N ILE E 34 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 123 through 129 removed outlier: 3.915A pdb=" N ASN E 129 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.791A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.661A pdb=" N HIS E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 removed outlier: 3.656A pdb=" N LEU E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.642A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 391 through 404 Processing helix chain 'E' and resid 408 through 419 Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 10 through 21 Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 123 through 129 removed outlier: 3.902A pdb=" N ASN F 129 " --> pdb=" O ASN F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 153 through 166 removed outlier: 3.513A pdb=" N LEU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'F' and resid 212 through 223 Processing helix chain 'F' and resid 235 through 256 Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 294 through 303 removed outlier: 3.569A pdb=" N LYS F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.728A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 Processing helix chain 'F' and resid 367 through 371 Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 391 through 403 Processing helix chain 'F' and resid 408 through 419 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.652A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS A 115 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS A 100 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL A 116 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER A 98 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU A 118 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR A 96 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE A 49 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.791A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 209 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.791A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 145 removed outlier: 4.525A pdb=" N ILE A 168 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 57 removed outlier: 3.823A pdb=" N ILE B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR B 80 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LYS B 115 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.951A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ASP B 265 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 207 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 204 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.951A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.348A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 57 removed outlier: 3.819A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N TYR C 80 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N LYS C 115 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.674A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 209 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.674A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG C 173 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU C 343 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C 175 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 345 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 177 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N GLU C 342 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ASN C 361 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N HIS C 344 " --> pdb=" O ASP C 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.533A pdb=" N ILE C 168 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.771A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.894A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR D 80 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS D 115 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.659A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.659A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG D 173 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU D 343 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU D 175 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 345 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 177 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLU D 342 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ASN D 361 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS D 344 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.817A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR E 80 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LYS E 115 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.757A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE E 262 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR E 318 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU E 264 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N LEU E 320 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL E 203 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU E 263 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N MET E 205 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.757A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 49 through 57 removed outlier: 3.886A pdb=" N ILE F 79 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR F 80 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LYS F 115 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU F 113 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG F 102 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER F 98 " --> pdb=" O ASN F 117 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL F 119 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR F 96 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.864A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE F 262 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR F 318 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU F 264 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU F 320 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU F 263 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET F 205 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASP F 265 " --> pdb=" O MET F 205 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU F 207 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.864A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 178 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG F 173 " --> pdb=" O MET F 341 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU F 343 " --> pdb=" O ARG F 173 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU F 175 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU F 345 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL F 177 " --> pdb=" O LEU F 345 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N GLU F 342 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ASN F 361 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N HIS F 344 " --> pdb=" O ASP F 359 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.513A pdb=" N ILE F 168 " --> pdb=" O LEU F 145 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2817 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6746 1.34 - 1.46: 3796 1.46 - 1.58: 9833 1.58 - 1.70: 47 1.70 - 1.83: 198 Bond restraints: 20620 Sorted by residual: bond pdb=" F2 BEF E1002 " pdb="BE BEF E1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" F2 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" F2 BEF C1002 " pdb="BE BEF C1002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" F2 BEF F1002 " pdb="BE BEF F1002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" F2 BEF B 503 " pdb="BE BEF B 503 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 20615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 27773 5.15 - 10.30: 75 10.30 - 15.45: 11 15.45 - 20.60: 0 20.60 - 25.75: 3 Bond angle restraints: 27862 Sorted by residual: angle pdb=" OP2 C R 92 " pdb=" P C R 92 " pdb=" O5' C R 92 " ideal model delta sigma weight residual 108.00 82.25 25.75 3.00e+00 1.11e-01 7.37e+01 angle pdb=" OP1 C R 92 " pdb=" P C R 92 " pdb=" O5' C R 92 " ideal model delta sigma weight residual 108.00 83.28 24.72 3.00e+00 1.11e-01 6.79e+01 angle pdb=" OP1 C R 92 " pdb=" P C R 92 " pdb=" OP2 C R 92 " ideal model delta sigma weight residual 119.60 141.04 -21.44 3.00e+00 1.11e-01 5.11e+01 angle pdb=" CA PRO D 76 " pdb=" N PRO D 76 " pdb=" CD PRO D 76 " ideal model delta sigma weight residual 112.00 103.80 8.20 1.40e+00 5.10e-01 3.43e+01 angle pdb=" F2 BEF D1002 " pdb="BE BEF D1002 " pdb=" F3 BEF D1002 " ideal model delta sigma weight residual 119.96 106.69 13.27 3.00e+00 1.11e-01 1.96e+01 ... (remaining 27857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 12316 35.90 - 71.80: 435 71.80 - 107.71: 27 107.71 - 143.61: 2 143.61 - 179.51: 6 Dihedral angle restraints: 12786 sinusoidal: 5556 harmonic: 7230 Sorted by residual: dihedral pdb=" O4' U R 14 " pdb=" C1' U R 14 " pdb=" N1 U R 14 " pdb=" C2 U R 14 " ideal model delta sinusoidal sigma weight residual 200.00 49.45 150.55 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" O4' C R 13 " pdb=" C1' C R 13 " pdb=" N1 C R 13 " pdb=" C2 C R 13 " ideal model delta sinusoidal sigma weight residual -128.00 51.51 -179.51 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C R 99 " pdb=" C1' C R 99 " pdb=" N1 C R 99 " pdb=" C2 C R 99 " ideal model delta sinusoidal sigma weight residual -128.00 51.28 -179.28 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2797 0.070 - 0.140: 378 0.140 - 0.210: 1 0.210 - 0.280: 0 0.280 - 0.350: 1 Chirality restraints: 3177 Sorted by residual: chirality pdb=" P C R 92 " pdb=" OP1 C R 92 " pdb=" OP2 C R 92 " pdb=" O5' C R 92 " both_signs ideal model delta sigma weight residual True 2.41 -2.06 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA GLU C 414 " pdb=" N GLU C 414 " pdb=" C GLU C 414 " pdb=" CB GLU C 414 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" C2' U R 14 " pdb=" C3' U R 14 " pdb=" O2' U R 14 " pdb=" C1' U R 14 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 3174 not shown) Planarity restraints: 3549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 381 " -0.035 2.00e-02 2.50e+03 3.57e-02 3.19e+01 pdb=" CG TRP F 381 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 TRP F 381 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP F 381 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 381 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 381 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 381 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 381 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 381 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 353 " -0.335 9.50e-02 1.11e+02 1.50e-01 1.44e+01 pdb=" NE ARG E 353 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG E 353 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 353 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 353 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 414 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" CD GLU C 414 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU C 414 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU C 414 " -0.021 2.00e-02 2.50e+03 ... (remaining 3546 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 12 2.12 - 2.82: 6089 2.82 - 3.51: 28582 3.51 - 4.21: 48220 4.21 - 4.90: 87892 Nonbonded interactions: 170795 Sorted by model distance: nonbonded pdb=" N LYS E 181 " pdb=" F1 BEF E1002 " model vdw 1.427 3.070 nonbonded pdb=" NH2 ARG C 366 " pdb=" F1 BEF B 503 " model vdw 1.767 3.070 nonbonded pdb=" O2B ADP E1000 " pdb="MG MG E1001 " model vdw 1.969 2.170 nonbonded pdb=" O1B ADP A1000 " pdb="MG MG A1001 " model vdw 2.013 2.170 nonbonded pdb=" OG1 THR C 185 " pdb="MG MG C1001 " model vdw 2.014 2.170 ... (remaining 170790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 6.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 14.990 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 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 : 0.012 0.645 20626 Z= 1.106 Angle : 0.759 25.750 27862 Z= 0.357 Chirality : 0.043 0.350 3177 Planarity : 0.005 0.150 3549 Dihedral : 17.756 179.510 8106 Min Nonbonded Distance : 1.427 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.02 % Allowed : 23.82 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2502 helix: 1.41 (0.16), residues: 1092 sheet: 0.03 (0.26), residues: 441 loop : 0.23 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 418 TYR 0.021 0.001 TYR D 80 PHE 0.017 0.001 PHE A 62 TRP 0.096 0.005 TRP F 381 HIS 0.004 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (20620) covalent geometry : angle 0.75943 / 0.36 (27862) hydrogen bonds : bond 0.15749 / 10.10 ( 990) hydrogen bonds : angle 5.97657 / 4.21 ( 2817) Misc. bond : bond 0.63994 / 33.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 239 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6747 (pmm) REVERT: A 29 MET cc_start: 0.5696 (tmm) cc_final: 0.4109 (pmm) REVERT: C 244 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8184 (mp0) outliers start: 65 outliers final: 53 residues processed: 294 average time/residue: 0.6223 time to fit residues: 204.0613 Evaluate side-chains 286 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.0770 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 378 GLN C 193 GLN D 117 ASN E 42 HIS E 59 GLN E 193 GLN E 241 GLN F 241 GLN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.102267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073422 restraints weight = 41558.994| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.54 r_work: 0.2998 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20626 Z= 0.129 Angle : 0.623 7.711 27862 Z= 0.307 Chirality : 0.043 0.146 3177 Planarity : 0.005 0.055 3549 Dihedral : 13.182 179.987 3128 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.81 % Allowed : 21.12 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2502 helix: 1.59 (0.16), residues: 1092 sheet: 0.15 (0.27), residues: 381 loop : 0.05 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 87 TYR 0.016 0.001 TYR D 110 PHE 0.012 0.001 PHE D 232 TRP 0.028 0.002 TRP F 381 HIS 0.005 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (20620) covalent geometry : angle 0.62301 / 0.31 (27862) hydrogen bonds : bond 0.04245 / 2.73 ( 990) hydrogen bonds : angle 4.77163 / 3.41 ( 2817) Misc. bond : bond 0.00438 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 255 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8810 (tt0) cc_final: 0.8493 (pt0) REVERT: A 128 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7489 (mtt90) REVERT: A 244 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8594 (mm-30) REVERT: A 392 GLU cc_start: 0.8057 (pt0) cc_final: 0.7760 (pt0) REVERT: B 244 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8687 (mm-30) REVERT: B 285 LEU cc_start: 0.9259 (mp) cc_final: 0.9055 (mp) REVERT: B 334 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 244 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8586 (mp0) REVERT: C 414 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: D 41 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8368 (pp30) REVERT: D 374 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8268 (tm-30) REVERT: E 353 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7942 (ttp-170) REVERT: F 244 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8549 (mm-30) REVERT: F 342 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7853 (pm20) outliers start: 82 outliers final: 39 residues processed: 317 average time/residue: 0.6007 time to fit residues: 211.2936 Evaluate side-chains 283 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 415 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 227 optimal weight: 0.0970 chunk 60 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN A 220 GLN C 193 GLN D 2 ASN E 59 GLN E 193 GLN E 241 GLN F 241 GLN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.101419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072389 restraints weight = 41955.399| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.55 r_work: 0.2981 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20626 Z= 0.152 Angle : 0.614 8.715 27862 Z= 0.298 Chirality : 0.043 0.140 3177 Planarity : 0.004 0.054 3549 Dihedral : 13.058 179.847 3090 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.81 % Allowed : 21.59 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2502 helix: 1.62 (0.16), residues: 1098 sheet: 0.09 (0.27), residues: 393 loop : 0.00 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 238 TYR 0.020 0.001 TYR B 110 PHE 0.012 0.001 PHE B 232 TRP 0.012 0.001 TRP F 381 HIS 0.005 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (20620) covalent geometry : angle 0.61421 / 0.30 (27862) hydrogen bonds : bond 0.03794 / 2.47 ( 990) hydrogen bonds : angle 4.61142 / 3.31 ( 2817) Misc. bond : bond 0.00116 / 0.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 253 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8806 (tt0) cc_final: 0.8447 (pt0) REVERT: A 244 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8558 (mm-30) REVERT: A 392 GLU cc_start: 0.8077 (pt0) cc_final: 0.7786 (pt0) REVERT: B 5 GLU cc_start: 0.9484 (mp0) cc_final: 0.9234 (mp0) REVERT: B 244 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8628 (mm-30) REVERT: C 244 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8483 (mp0) REVERT: C 290 ASP cc_start: 0.8421 (m-30) cc_final: 0.8124 (t0) REVERT: C 374 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8228 (tp-100) REVERT: C 414 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: D 41 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8388 (pp30) REVERT: D 329 GLU cc_start: 0.8588 (tp30) cc_final: 0.8287 (tp30) REVERT: D 374 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8220 (tm-30) REVERT: E 353 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7924 (ttp-110) REVERT: F 60 ASP cc_start: 0.7624 (m-30) cc_final: 0.7327 (m-30) REVERT: F 244 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8515 (mm-30) REVERT: F 342 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7831 (pm20) outliers start: 82 outliers final: 41 residues processed: 313 average time/residue: 0.6015 time to fit residues: 209.7358 Evaluate side-chains 284 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 103 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 234 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 92 optimal weight: 0.0770 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN B 241 GLN E 59 GLN E 193 GLN E 241 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN F 241 GLN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.102353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.073421 restraints weight = 41940.875| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.56 r_work: 0.2998 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20626 Z= 0.117 Angle : 0.599 9.154 27862 Z= 0.289 Chirality : 0.042 0.137 3177 Planarity : 0.004 0.053 3549 Dihedral : 12.826 179.920 3082 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.62 % Allowed : 21.82 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2502 helix: 1.64 (0.16), residues: 1104 sheet: 0.10 (0.27), residues: 393 loop : -0.03 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 299 TYR 0.014 0.001 TYR C 110 PHE 0.009 0.001 PHE A 62 TRP 0.009 0.001 TRP E 381 HIS 0.005 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (20620) covalent geometry : angle 0.59905 / 0.29 (27862) hydrogen bonds : bond 0.03370 / 2.20 ( 990) hydrogen bonds : angle 4.49951 / 3.24 ( 2817) Misc. bond : bond 0.00061 / 0.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 255 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8775 (tt0) cc_final: 0.8488 (pt0) REVERT: A 244 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8616 (mm-30) REVERT: B 5 GLU cc_start: 0.9478 (mp0) cc_final: 0.9233 (mp0) REVERT: B 42 HIS cc_start: 0.8014 (t-90) cc_final: 0.7781 (t-90) REVERT: B 244 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8604 (mm-30) REVERT: C 244 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8455 (mp0) REVERT: C 290 ASP cc_start: 0.8445 (m-30) cc_final: 0.8187 (t0) REVERT: C 374 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8237 (tp-100) REVERT: C 414 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: D 329 GLU cc_start: 0.8584 (tp30) cc_final: 0.8237 (tp30) REVERT: D 374 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8187 (tm-30) REVERT: E 353 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7948 (ttp-110) REVERT: F 41 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8741 (mp10) REVERT: F 244 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8497 (mm-30) REVERT: F 272 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8387 (mtm-85) REVERT: F 342 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7819 (pm20) outliers start: 78 outliers final: 44 residues processed: 311 average time/residue: 0.6295 time to fit residues: 217.6652 Evaluate side-chains 286 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 131 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 211 optimal weight: 8.9990 chunk 238 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 173 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN B 241 GLN C 275 ASN E 59 GLN E 193 GLN E 241 GLN E 275 ASN F 41 GLN F 241 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.101931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.073038 restraints weight = 41762.501| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.59 r_work: 0.2964 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20626 Z= 0.126 Angle : 0.609 10.179 27862 Z= 0.291 Chirality : 0.042 0.137 3177 Planarity : 0.004 0.053 3549 Dihedral : 12.686 179.736 3079 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.53 % Allowed : 22.24 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2502 helix: 1.67 (0.16), residues: 1104 sheet: 0.07 (0.27), residues: 393 loop : -0.06 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 418 TYR 0.021 0.001 TYR D 110 PHE 0.010 0.001 PHE B 232 TRP 0.009 0.001 TRP E 381 HIS 0.004 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (20620) covalent geometry : angle 0.60884 / 0.29 (27862) hydrogen bonds : bond 0.03294 / 2.15 ( 990) hydrogen bonds : angle 4.46656 / 3.21 ( 2817) Misc. bond : bond 0.00069 / 0.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 252 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.4214 (OUTLIER) cc_final: 0.3930 (pmt-80) REVERT: A 56 GLU cc_start: 0.8629 (tt0) cc_final: 0.8322 (pt0) REVERT: A 193 GLN cc_start: 0.8814 (mt0) cc_final: 0.8600 (mt0) REVERT: A 244 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8329 (mm-30) REVERT: B 5 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9214 (mp0) REVERT: B 42 HIS cc_start: 0.8026 (t-90) cc_final: 0.7764 (t-90) REVERT: B 244 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 298 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8585 (mmmm) REVERT: B 334 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8265 (tm-30) REVERT: C 244 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: C 374 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7962 (tp-100) REVERT: C 414 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: D 329 GLU cc_start: 0.8346 (tp30) cc_final: 0.8021 (tp30) REVERT: D 374 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7956 (tm-30) REVERT: E 226 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: E 244 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8476 (mm-30) REVERT: E 272 ARG cc_start: 0.8636 (mtt-85) cc_final: 0.8383 (mtt-85) REVERT: E 329 GLU cc_start: 0.7914 (mp0) cc_final: 0.7606 (mp0) REVERT: E 353 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7903 (ttp-110) REVERT: F 211 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: F 244 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8295 (mm-30) REVERT: F 272 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.8198 (mtm-85) REVERT: F 342 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7466 (pm20) outliers start: 76 outliers final: 40 residues processed: 306 average time/residue: 0.6488 time to fit residues: 220.5953 Evaluate side-chains 292 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 156 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 145 optimal weight: 0.4980 chunk 179 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 chunk 137 optimal weight: 4.9990 chunk 199 optimal weight: 0.0980 chunk 47 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN B 241 GLN C 275 ASN E 59 GLN E 193 GLN E 241 GLN F 41 GLN F 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.102580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.073758 restraints weight = 41689.042| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.60 r_work: 0.2985 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20626 Z= 0.108 Angle : 0.616 9.963 27862 Z= 0.292 Chirality : 0.041 0.134 3177 Planarity : 0.004 0.052 3549 Dihedral : 12.441 179.791 3073 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.44 % Allowed : 23.17 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2502 helix: 1.73 (0.16), residues: 1101 sheet: 0.08 (0.27), residues: 375 loop : -0.05 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 87 TYR 0.022 0.001 TYR B 332 PHE 0.009 0.001 PHE B 398 TRP 0.009 0.001 TRP E 381 HIS 0.004 0.001 HIS F 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (20620) covalent geometry : angle 0.61555 / 0.29 (27862) hydrogen bonds : bond 0.03036 / 1.98 ( 990) hydrogen bonds : angle 4.39993 / 3.17 ( 2817) Misc. bond : bond 0.00047 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 256 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8584 (tt0) cc_final: 0.8196 (pt0) REVERT: A 193 GLN cc_start: 0.8862 (mt0) cc_final: 0.8653 (mt0) REVERT: A 244 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8326 (mm-30) REVERT: A 274 TYR cc_start: 0.8541 (m-10) cc_final: 0.8321 (m-10) REVERT: B 5 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9213 (mp0) REVERT: B 42 HIS cc_start: 0.8015 (t-90) cc_final: 0.7758 (t-90) REVERT: B 244 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8268 (mm-30) REVERT: B 334 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8260 (tm-30) REVERT: B 342 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7889 (mt-10) REVERT: C 244 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: C 374 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7949 (tp-100) REVERT: C 414 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: D 374 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7968 (tm-30) REVERT: E 226 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: E 244 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8397 (mm-30) REVERT: E 272 ARG cc_start: 0.8621 (mtt-85) cc_final: 0.8418 (mtt-85) REVERT: E 327 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7995 (tpt) REVERT: E 353 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7827 (ttp-110) REVERT: F 244 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8236 (mm-30) REVERT: F 272 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.8151 (mtm-85) REVERT: F 342 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: F 401 ASN cc_start: 0.9160 (t0) cc_final: 0.8778 (t0) outliers start: 74 outliers final: 36 residues processed: 311 average time/residue: 0.6483 time to fit residues: 223.7395 Evaluate side-chains 290 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 201 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN C 2 ASN D 41 GLN E 59 GLN E 193 GLN E 241 GLN F 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.100194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.071021 restraints weight = 41991.232| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.59 r_work: 0.2926 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20626 Z= 0.208 Angle : 0.662 10.257 27862 Z= 0.317 Chirality : 0.044 0.160 3177 Planarity : 0.004 0.052 3549 Dihedral : 12.396 179.800 3068 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.67 % Allowed : 23.07 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.17), residues: 2502 helix: 1.70 (0.16), residues: 1104 sheet: -0.18 (0.27), residues: 390 loop : -0.07 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 87 TYR 0.022 0.001 TYR B 332 PHE 0.017 0.001 PHE B 232 TRP 0.012 0.001 TRP E 381 HIS 0.005 0.001 HIS E 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (20620) covalent geometry : angle 0.66219 / 0.32 (27862) hydrogen bonds : bond 0.03586 / 2.35 ( 990) hydrogen bonds : angle 4.41469 / 3.17 ( 2817) Misc. bond : bond 0.00122 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 243 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.4308 (OUTLIER) cc_final: 0.4056 (pmt-80) REVERT: A 56 GLU cc_start: 0.8756 (tt0) cc_final: 0.8401 (pt0) REVERT: A 128 ARG cc_start: 0.7845 (mtt90) cc_final: 0.7589 (mtm-85) REVERT: A 244 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8561 (mm-30) REVERT: B 5 GLU cc_start: 0.9465 (OUTLIER) cc_final: 0.9228 (mp0) REVERT: B 42 HIS cc_start: 0.8041 (t-90) cc_final: 0.7825 (t-90) REVERT: B 244 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8589 (mm-30) REVERT: B 342 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8259 (mt-10) REVERT: B 374 GLN cc_start: 0.8748 (tp40) cc_final: 0.8497 (tp40) REVERT: C 244 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8587 (mp0) REVERT: C 374 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8274 (tp-100) REVERT: C 414 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: D 374 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8198 (tm-30) REVERT: E 226 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: E 244 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8645 (mm-30) REVERT: E 353 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8006 (ttp-110) REVERT: F 244 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8482 (mm-30) REVERT: F 334 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8713 (tp30) REVERT: F 342 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7841 (pm20) outliers start: 79 outliers final: 45 residues processed: 304 average time/residue: 0.6632 time to fit residues: 224.1292 Evaluate side-chains 290 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 21 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 233 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 222 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 170 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN A 220 GLN E 59 GLN E 193 GLN E 241 GLN F 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.101409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.072461 restraints weight = 41953.237| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.59 r_work: 0.2958 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20626 Z= 0.125 Angle : 0.638 10.879 27862 Z= 0.303 Chirality : 0.042 0.140 3177 Planarity : 0.004 0.057 3549 Dihedral : 12.316 179.643 3068 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.16 % Allowed : 23.96 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2502 helix: 1.74 (0.16), residues: 1104 sheet: -0.11 (0.26), residues: 396 loop : -0.03 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 87 TYR 0.027 0.001 TYR B 332 PHE 0.009 0.001 PHE D 232 TRP 0.010 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (20620) covalent geometry : angle 0.63837 / 0.30 (27862) hydrogen bonds : bond 0.03199 / 2.10 ( 990) hydrogen bonds : angle 4.36297 / 3.14 ( 2817) Misc. bond : bond 0.00054 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 244 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8585 (tt0) cc_final: 0.8209 (pt0) REVERT: A 128 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7557 (mtm-85) REVERT: A 244 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8336 (mm-30) REVERT: A 348 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8396 (ptmm) REVERT: B 5 GLU cc_start: 0.9441 (OUTLIER) cc_final: 0.9220 (mp0) REVERT: B 42 HIS cc_start: 0.8052 (t-90) cc_final: 0.7803 (t-90) REVERT: B 244 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8256 (mm-30) REVERT: C 244 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: C 374 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8049 (tp-100) REVERT: C 414 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: D 374 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7944 (tm-30) REVERT: E 20 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8530 (p0) REVERT: E 226 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: E 244 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8384 (mm-30) REVERT: E 353 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7947 (ttp-110) REVERT: F 244 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8250 (mm-30) REVERT: F 334 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8493 (tp30) REVERT: F 342 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7474 (pm20) outliers start: 68 outliers final: 42 residues processed: 295 average time/residue: 0.6145 time to fit residues: 201.1870 Evaluate side-chains 293 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 242 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 341 MET Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 32 optimal weight: 0.3980 chunk 191 optimal weight: 3.9990 chunk 231 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN A 220 GLN B 378 GLN E 59 GLN E 193 GLN E 241 GLN F 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.101639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072718 restraints weight = 41551.105| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.59 r_work: 0.2963 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20626 Z= 0.127 Angle : 0.647 11.398 27862 Z= 0.307 Chirality : 0.042 0.137 3177 Planarity : 0.004 0.059 3549 Dihedral : 12.235 179.661 3067 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.02 % Allowed : 24.33 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2502 helix: 1.74 (0.16), residues: 1104 sheet: -0.11 (0.26), residues: 396 loop : -0.03 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 418 TYR 0.026 0.001 TYR B 332 PHE 0.016 0.001 PHE A 62 TRP 0.010 0.001 TRP E 381 HIS 0.005 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (20620) covalent geometry : angle 0.64719 / 0.31 (27862) hydrogen bonds : bond 0.03133 / 2.05 ( 990) hydrogen bonds : angle 4.34986 / 3.13 ( 2817) Misc. bond : bond 0.00059 / 0.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 246 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8699 (tt0) cc_final: 0.8358 (pt0) REVERT: A 128 ARG cc_start: 0.7823 (mtt90) cc_final: 0.7552 (mtm-85) REVERT: A 244 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8571 (mm-30) REVERT: A 348 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8530 (ptmm) REVERT: B 5 GLU cc_start: 0.9471 (OUTLIER) cc_final: 0.9234 (mp0) REVERT: B 42 HIS cc_start: 0.8069 (t-90) cc_final: 0.7793 (t-90) REVERT: C 244 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8472 (mp0) REVERT: C 374 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8237 (tp-100) REVERT: C 414 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: D 374 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8162 (tm-30) REVERT: E 20 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8609 (p0) REVERT: E 226 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: E 244 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8600 (mm-30) REVERT: E 327 MET cc_start: 0.8509 (tpp) cc_final: 0.8080 (ttt) REVERT: E 353 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7955 (ttp-110) REVERT: F 244 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8435 (mm-30) REVERT: F 334 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8724 (tp30) REVERT: F 342 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7829 (pm20) outliers start: 65 outliers final: 44 residues processed: 295 average time/residue: 0.6347 time to fit residues: 207.2470 Evaluate side-chains 290 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 341 MET Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 245 optimal weight: 0.9980 chunk 166 optimal weight: 0.5980 chunk 168 optimal weight: 10.0000 chunk 177 optimal weight: 0.0470 chunk 143 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 244 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN B 241 GLN E 59 GLN E 193 GLN E 241 GLN F 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.101980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.073030 restraints weight = 41982.523| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.60 r_work: 0.2989 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20626 Z= 0.122 Angle : 0.659 11.858 27862 Z= 0.313 Chirality : 0.042 0.136 3177 Planarity : 0.004 0.060 3549 Dihedral : 12.172 179.666 3067 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.79 % Allowed : 24.74 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2502 helix: 1.74 (0.16), residues: 1104 sheet: -0.14 (0.27), residues: 390 loop : -0.02 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 87 TYR 0.032 0.001 TYR B 332 PHE 0.016 0.001 PHE A 62 TRP 0.011 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (20620) covalent geometry : angle 0.65938 / 0.31 (27862) hydrogen bonds : bond 0.03057 / 1.99 ( 990) hydrogen bonds : angle 4.35098 / 3.13 ( 2817) Misc. bond : bond 0.00047 / 0.02 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8540 (tt0) cc_final: 0.8191 (pt0) REVERT: A 128 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7584 (mtm-85) REVERT: A 193 GLN cc_start: 0.8931 (mt0) cc_final: 0.8730 (mt0) REVERT: A 244 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8346 (mm-30) REVERT: A 348 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8424 (ptmm) REVERT: B 5 GLU cc_start: 0.9437 (OUTLIER) cc_final: 0.9232 (mp0) REVERT: B 42 HIS cc_start: 0.8168 (t-90) cc_final: 0.7880 (t-90) REVERT: B 244 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8233 (mm-30) REVERT: C 244 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: C 374 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8045 (tp-100) REVERT: C 414 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: D 374 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7915 (tm-30) REVERT: E 20 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8542 (p0) REVERT: E 226 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: E 244 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8397 (mm-30) REVERT: E 327 MET cc_start: 0.8522 (tpp) cc_final: 0.8068 (ttt) REVERT: E 353 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7925 (ttp-110) REVERT: F 244 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8262 (mm-30) REVERT: F 342 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7491 (pm20) outliers start: 60 outliers final: 43 residues processed: 288 average time/residue: 0.6463 time to fit residues: 206.4689 Evaluate side-chains 295 residues out of total 2154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 341 MET Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 119 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 163 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 234 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 241 GLN E 193 GLN E 241 GLN F 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.102059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073160 restraints weight = 41909.104| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.59 r_work: 0.2994 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20626 Z= 0.124 Angle : 0.662 12.545 27862 Z= 0.315 Chirality : 0.042 0.172 3177 Planarity : 0.004 0.064 3549 Dihedral : 12.103 179.744 3065 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.74 % Allowed : 24.88 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2502 helix: 1.74 (0.16), residues: 1104 sheet: -0.16 (0.27), residues: 384 loop : -0.07 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 87 TYR 0.025 0.001 TYR B 332 PHE 0.016 0.001 PHE A 62 TRP 0.011 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (20620) covalent geometry : angle 0.66214 / 0.32 (27862) hydrogen bonds : bond 0.03033 / 1.99 ( 990) hydrogen bonds : angle 4.34897 / 3.12 ( 2817) Misc. bond : bond 0.00048 / 0.02 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6864.69 seconds wall clock time: 117 minutes 25.44 seconds (7045.44 seconds total)