Starting phenix.real_space_refine on Fri Mar 6 20:07:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ybq_10771/03_2026/6ybq_10771.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ybq_10771/03_2026/6ybq_10771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ybq_10771/03_2026/6ybq_10771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ybq_10771/03_2026/6ybq_10771.map" model { file = "/net/cci-nas-00/data/ceres_data/6ybq_10771/03_2026/6ybq_10771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ybq_10771/03_2026/6ybq_10771.cif" } resolution = 1.96 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= 0.017 sd= 0.182 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 150 5.16 5 C 20917 2.51 5 N 5897 2.21 5 O 7110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 186 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34092 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "B" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "C" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "D" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "E" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "F" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3902 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "G" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1565 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "H" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain: "I" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1549 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain: "J" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain: "K" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1574 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "L" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "B" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 145 Classifications: {'water': 145} Link IDs: {None: 144} Chain: "C" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 134 Classifications: {'water': 134} Link IDs: {None: 133} Chain: "D" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 144 Classifications: {'water': 144} Link IDs: {None: 143} Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Classifications: {'water': 126} Link IDs: {None: 125} Chain: "F" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 128 Classifications: {'water': 128} Link IDs: {None: 127} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 7.87, per 1000 atoms: 0.23 Number of scatterers: 34092 At special positions: 0 Unit cell: (158.323, 149.811, 162.579, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 18 15.00 O 7110 8.00 N 5897 7.00 C 20917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7774 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 48 sheets defined 41.6% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 removed outlier: 3.698A pdb=" N GLU A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 119 removed outlier: 3.554A pdb=" N VAL A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 136 through 154 removed outlier: 3.861A pdb=" N LEU A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.668A pdb=" N MET A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.656A pdb=" N PHE A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 282 through 291 removed outlier: 3.859A pdb=" N LEU A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.582A pdb=" N PHE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 374 through 389 removed outlier: 4.068A pdb=" N LEU A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.554A pdb=" N ILE A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 431 through 440 Processing helix chain 'A' and resid 441 through 444 removed outlier: 3.907A pdb=" N ILE A 444 " --> pdb=" O ARG A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 446 through 462 Processing helix chain 'A' and resid 464 through 470 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 481 through 494 Processing helix chain 'B' and resid 6 through 16 Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 132 through 135 Processing helix chain 'B' and resid 136 through 154 removed outlier: 3.847A pdb=" N LEU B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 230 through 243 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 282 through 291 removed outlier: 3.979A pdb=" N LEU B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 334 through 351 removed outlier: 3.570A pdb=" N PHE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 373 Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.670A pdb=" N ALA B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU B 382 " --> pdb=" O HIS B 378 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 431 through 440 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 464 through 470 Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'B' and resid 481 through 494 Processing helix chain 'C' and resid 6 through 16 Processing helix chain 'C' and resid 20 through 30 Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 136 through 154 removed outlier: 3.791A pdb=" N LEU C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.527A pdb=" N MET C 177 " --> pdb=" O TYR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 203 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 213 through 220 Processing helix chain 'C' and resid 230 through 243 removed outlier: 3.651A pdb=" N ASP C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 282 through 291 removed outlier: 3.893A pdb=" N LEU C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 295 Processing helix chain 'C' and resid 328 through 332 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'C' and resid 374 through 389 removed outlier: 4.032A pdb=" N LEU C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.519A pdb=" N ILE C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 431 through 440 Processing helix chain 'C' and resid 441 through 444 removed outlier: 3.752A pdb=" N ILE C 444 " --> pdb=" O ARG C 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 464 through 470 Processing helix chain 'C' and resid 478 through 480 No H-bonds generated for 'chain 'C' and resid 478 through 480' Processing helix chain 'C' and resid 481 through 494 Processing helix chain 'D' and resid 6 through 16 Processing helix chain 'D' and resid 20 through 30 Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 60 through 67 removed outlier: 4.409A pdb=" N GLY D 63 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLU D 65 " --> pdb=" O PHE D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 101 through 119 removed outlier: 3.565A pdb=" N VAL D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 135 Processing helix chain 'D' and resid 136 through 154 removed outlier: 3.826A pdb=" N LEU D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 removed outlier: 3.702A pdb=" N MET D 177 " --> pdb=" O TYR D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 203 Processing helix chain 'D' and resid 207 through 213 Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 230 through 245 removed outlier: 3.637A pdb=" N ASP D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 245 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 removed outlier: 3.524A pdb=" N LEU D 272 " --> pdb=" O LEU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 291 removed outlier: 3.911A pdb=" N LEU D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 295 Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 334 through 351 removed outlier: 3.552A pdb=" N PHE D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 373 Processing helix chain 'D' and resid 374 through 389 removed outlier: 3.679A pdb=" N ALA D 380 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU D 382 " --> pdb=" O HIS D 378 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 383 " --> pdb=" O GLY D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 409 removed outlier: 3.503A pdb=" N ILE D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 431 through 440 Processing helix chain 'D' and resid 441 through 444 removed outlier: 3.836A pdb=" N ILE D 444 " --> pdb=" O ARG D 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 441 through 444' Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.516A pdb=" N ALA D 451 " --> pdb=" O ALA D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'D' and resid 481 through 494 Processing helix chain 'E' and resid 6 through 16 Processing helix chain 'E' and resid 20 through 30 Processing helix chain 'E' and resid 34 through 43 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 101 through 119 removed outlier: 3.572A pdb=" N VAL E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 Processing helix chain 'E' and resid 136 through 154 removed outlier: 3.814A pdb=" N LEU E 140 " --> pdb=" O GLY E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 194 through 203 Processing helix chain 'E' and resid 207 through 213 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 230 through 245 removed outlier: 3.651A pdb=" N PHE E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 272 Processing helix chain 'E' and resid 282 through 291 removed outlier: 3.919A pdb=" N LEU E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 295 Processing helix chain 'E' and resid 328 through 332 Processing helix chain 'E' and resid 334 through 351 removed outlier: 3.559A pdb=" N PHE E 344 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 373 Processing helix chain 'E' and resid 374 through 389 removed outlier: 4.199A pdb=" N LEU E 382 " --> pdb=" O HIS E 378 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 383 " --> pdb=" O GLY E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 409 removed outlier: 3.533A pdb=" N ILE E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 415 Processing helix chain 'E' and resid 431 through 440 Processing helix chain 'E' and resid 447 through 462 Processing helix chain 'E' and resid 464 through 470 Processing helix chain 'E' and resid 478 through 480 No H-bonds generated for 'chain 'E' and resid 478 through 480' Processing helix chain 'E' and resid 481 through 494 Processing helix chain 'F' and resid 6 through 16 Processing helix chain 'F' and resid 20 through 30 Processing helix chain 'F' and resid 34 through 43 Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 101 through 119 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 135 through 154 removed outlier: 3.837A pdb=" N LEU F 140 " --> pdb=" O GLY F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 removed outlier: 3.531A pdb=" N MET F 177 " --> pdb=" O TYR F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 207 through 213 Processing helix chain 'F' and resid 213 through 220 Processing helix chain 'F' and resid 230 through 243 removed outlier: 3.618A pdb=" N ASP F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 272 Processing helix chain 'F' and resid 282 through 291 removed outlier: 3.922A pdb=" N LEU F 286 " --> pdb=" O ASP F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 295 Processing helix chain 'F' and resid 328 through 332 Processing helix chain 'F' and resid 334 through 351 removed outlier: 3.561A pdb=" N PHE F 344 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 373 Processing helix chain 'F' and resid 374 through 389 removed outlier: 4.038A pdb=" N LEU F 382 " --> pdb=" O HIS F 378 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU F 383 " --> pdb=" O GLY F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 409 removed outlier: 3.641A pdb=" N ILE F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 415 Processing helix chain 'F' and resid 431 through 440 Processing helix chain 'F' and resid 441 through 444 removed outlier: 3.692A pdb=" N ILE F 444 " --> pdb=" O ARG F 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 441 through 444' Processing helix chain 'F' and resid 447 through 462 Processing helix chain 'F' and resid 464 through 470 Processing helix chain 'F' and resid 478 through 480 No H-bonds generated for 'chain 'F' and resid 478 through 480' Processing helix chain 'F' and resid 481 through 494 Processing helix chain 'G' and resid 461 through 483 Processing helix chain 'G' and resid 579 through 588 removed outlier: 3.640A pdb=" N LEU G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 483 Processing helix chain 'H' and resid 491 through 495 Processing helix chain 'H' and resid 579 through 587 Processing helix chain 'I' and resid 462 through 483 Processing helix chain 'I' and resid 491 through 495 Processing helix chain 'I' and resid 579 through 587 Processing helix chain 'J' and resid 461 through 483 Processing helix chain 'J' and resid 491 through 495 Processing helix chain 'J' and resid 579 through 587 Processing helix chain 'K' and resid 461 through 483 Processing helix chain 'K' and resid 491 through 495 Processing helix chain 'K' and resid 579 through 587 Processing helix chain 'L' and resid 461 through 483 Processing helix chain 'L' and resid 579 through 587 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.491A pdb=" N THR A 76 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ILE A 123 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 87 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ILE A 125 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A 89 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 180 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 226 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 6.535A pdb=" N CYS A 167 " --> pdb=" O PHE A 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 297 through 299 removed outlier: 4.546A pdb=" N THR A 309 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N VAL A 356 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY A 320 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE A 358 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 322 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ASP A 360 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASN A 324 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 355 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE A 396 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 357 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR A 398 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL A 359 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS A 400 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN A 426 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG A 399 " --> pdb=" O GLN A 426 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA A 428 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA A 401 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 299 removed outlier: 4.546A pdb=" N THR A 309 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N VAL A 356 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY A 320 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N PHE A 358 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 322 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ASP A 360 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASN A 324 " --> pdb=" O ASP A 360 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE A 355 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE A 396 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 357 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR A 398 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL A 359 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYS A 400 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A 393 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N TYR A 420 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR A 395 " --> pdb=" O TYR A 420 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A 475 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.474A pdb=" N THR B 76 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ILE B 123 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE B 87 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ILE B 125 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE B 89 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 180 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 226 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 166 through 168 removed outlier: 6.612A pdb=" N CYS B 167 " --> pdb=" O PHE B 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 297 through 298 removed outlier: 8.522A pdb=" N VAL B 356 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY B 320 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE B 358 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 322 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASP B 360 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASN B 324 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N VAL B 361 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LYS B 400 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA B 428 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ALA B 401 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 297 through 298 removed outlier: 8.522A pdb=" N VAL B 356 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY B 320 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE B 358 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 322 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASP B 360 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASN B 324 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N VAL B 361 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LYS B 400 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU B 393 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N TYR B 420 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B 395 " --> pdb=" O TYR B 420 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 475 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 51 removed outlier: 4.536A pdb=" N THR C 76 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 180 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 226 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 168 removed outlier: 6.510A pdb=" N CYS C 167 " --> pdb=" O PHE C 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 297 through 299 removed outlier: 4.499A pdb=" N THR C 309 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N VAL C 356 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY C 320 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE C 358 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 322 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASP C 360 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASN C 324 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N VAL C 361 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS C 400 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN C 426 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG C 399 " --> pdb=" O GLN C 426 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA C 428 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA C 401 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 297 through 299 removed outlier: 4.499A pdb=" N THR C 309 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N VAL C 356 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLY C 320 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHE C 358 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 322 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASP C 360 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASN C 324 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N VAL C 361 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS C 400 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU C 393 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N TYR C 420 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 395 " --> pdb=" O TYR C 420 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 475 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 49 through 51 removed outlier: 4.661A pdb=" N THR D 76 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ILE D 123 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE D 87 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ILE D 125 " --> pdb=" O PHE D 87 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE D 89 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 180 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY D 226 " --> pdb=" O ILE D 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 166 through 168 removed outlier: 6.621A pdb=" N CYS D 167 " --> pdb=" O PHE D 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 297 through 298 removed outlier: 8.603A pdb=" N VAL D 356 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY D 320 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE D 358 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 322 " --> pdb=" O PHE D 358 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASP D 360 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN D 324 " --> pdb=" O ASP D 360 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 355 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE D 396 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR D 357 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR D 398 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL D 359 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS D 400 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 297 through 298 removed outlier: 8.603A pdb=" N VAL D 356 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY D 320 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE D 358 " --> pdb=" O GLY D 320 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 322 " --> pdb=" O PHE D 358 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASP D 360 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN D 324 " --> pdb=" O ASP D 360 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 355 " --> pdb=" O VAL D 394 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE D 396 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR D 357 " --> pdb=" O ILE D 396 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR D 398 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL D 359 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS D 400 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU D 393 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR D 420 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR D 395 " --> pdb=" O TYR D 420 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU D 475 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 49 through 51 removed outlier: 4.531A pdb=" N THR E 76 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE E 180 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY E 226 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 166 through 168 removed outlier: 6.581A pdb=" N CYS E 167 " --> pdb=" O PHE E 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 297 through 299 removed outlier: 4.553A pdb=" N THR E 309 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N VAL E 356 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY E 320 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE E 358 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL E 322 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ASP E 360 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASN E 324 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N VAL E 361 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS E 400 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA E 428 " --> pdb=" O ARG E 399 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA E 401 " --> pdb=" O ALA E 428 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 297 through 299 removed outlier: 4.553A pdb=" N THR E 309 " --> pdb=" O ILE E 299 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N VAL E 356 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY E 320 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE E 358 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL E 322 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ASP E 360 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASN E 324 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N VAL E 361 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS E 400 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU E 393 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N TYR E 420 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR E 395 " --> pdb=" O TYR E 420 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU E 475 " --> pdb=" O ASN E 419 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 49 through 51 removed outlier: 4.518A pdb=" N THR F 76 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ILE F 123 " --> pdb=" O THR F 85 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE F 87 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE F 125 " --> pdb=" O PHE F 87 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE F 89 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASP F 127 " --> pdb=" O PHE F 89 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS F 91 " --> pdb=" O ASP F 127 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE F 122 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL F 162 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY F 124 " --> pdb=" O VAL F 162 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET F 164 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE F 126 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA F 168 " --> pdb=" O ALA F 128 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR F 189 " --> pdb=" O GLY F 165 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 49 through 51 removed outlier: 4.518A pdb=" N THR F 76 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ILE F 123 " --> pdb=" O THR F 85 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE F 87 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE F 125 " --> pdb=" O PHE F 87 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE F 89 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ASP F 127 " --> pdb=" O PHE F 89 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS F 91 " --> pdb=" O ASP F 127 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE F 122 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL F 162 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY F 124 " --> pdb=" O VAL F 162 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N MET F 164 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE F 126 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA F 168 " --> pdb=" O ALA F 128 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE F 180 " --> pdb=" O GLN F 159 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY F 165 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY F 226 " --> pdb=" O ILE F 181 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 297 through 299 removed outlier: 4.526A pdb=" N THR F 309 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N VAL F 356 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY F 320 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE F 358 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL F 322 " --> pdb=" O PHE F 358 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP F 360 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASN F 324 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL F 361 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LYS F 400 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN F 426 " --> pdb=" O ARG F 399 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 297 through 299 removed outlier: 4.526A pdb=" N THR F 309 " --> pdb=" O ILE F 299 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N VAL F 356 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY F 320 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE F 358 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL F 322 " --> pdb=" O PHE F 358 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP F 360 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASN F 324 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL F 361 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LYS F 400 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU F 393 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N TYR F 420 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR F 395 " --> pdb=" O TYR F 420 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU F 475 " --> pdb=" O ASN F 419 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 500 through 505 Processing sheet with id=AC8, first strand: chain 'G' and resid 600 through 602 removed outlier: 3.794A pdb=" N LYS G 648 " --> pdb=" O GLU G 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 637 through 639 removed outlier: 6.863A pdb=" N LEU G 638 " --> pdb=" O LEU G 626 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU G 626 " --> pdb=" O ILE G 612 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE G 612 " --> pdb=" O LEU G 626 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE G 628 " --> pdb=" O LYS G 610 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 619 through 620 removed outlier: 3.991A pdb=" N VAL G 620 " --> pdb=" O GLY G 644 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY G 644 " --> pdb=" O VAL G 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 500 through 505 Processing sheet with id=AD3, first strand: chain 'H' and resid 600 through 602 removed outlier: 3.812A pdb=" N LEU H 664 " --> pdb=" O LEU H 601 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 637 through 639 removed outlier: 3.721A pdb=" N ALA H 627 " --> pdb=" O LEU H 638 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N LEU H 626 " --> pdb=" O ILE H 612 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE H 612 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE H 628 " --> pdb=" O LYS H 610 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY H 607 " --> pdb=" O LEU H 657 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 619 through 620 Processing sheet with id=AD6, first strand: chain 'I' and resid 500 through 505 Processing sheet with id=AD7, first strand: chain 'I' and resid 600 through 602 removed outlier: 6.740A pdb=" N LEU I 601 " --> pdb=" O ILE I 663 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS I 648 " --> pdb=" O GLU I 665 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 635 through 639 removed outlier: 6.252A pdb=" N ASN I 636 " --> pdb=" O ILE I 628 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE I 628 " --> pdb=" O ASN I 636 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU I 638 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU I 626 " --> pdb=" O ILE I 612 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE I 612 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE I 628 " --> pdb=" O LYS I 610 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 619 through 620 Processing sheet with id=AE1, first strand: chain 'J' and resid 500 through 505 Processing sheet with id=AE2, first strand: chain 'J' and resid 600 through 602 removed outlier: 3.879A pdb=" N LEU J 664 " --> pdb=" O LEU J 601 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS J 648 " --> pdb=" O GLU J 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 635 through 639 removed outlier: 3.656A pdb=" N ALA J 627 " --> pdb=" O LEU J 638 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU J 626 " --> pdb=" O ILE J 612 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE J 612 " --> pdb=" O LEU J 626 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE J 628 " --> pdb=" O LYS J 610 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY J 607 " --> pdb=" O LEU J 657 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 619 through 620 Processing sheet with id=AE5, first strand: chain 'K' and resid 500 through 505 Processing sheet with id=AE6, first strand: chain 'K' and resid 601 through 603 removed outlier: 6.945A pdb=" N LEU K 601 " --> pdb=" O ILE K 663 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA K 661 " --> pdb=" O CYS K 603 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS K 648 " --> pdb=" O GLU K 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 635 through 639 removed outlier: 6.180A pdb=" N ASN K 636 " --> pdb=" O ILE K 628 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE K 628 " --> pdb=" O ASN K 636 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU K 638 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU K 626 " --> pdb=" O ILE K 612 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE K 612 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE K 628 " --> pdb=" O LYS K 610 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 619 through 620 Processing sheet with id=AE9, first strand: chain 'L' and resid 500 through 505 Processing sheet with id=AF1, first strand: chain 'L' and resid 600 through 603 removed outlier: 6.875A pdb=" N LEU L 601 " --> pdb=" O ILE L 663 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA L 661 " --> pdb=" O CYS L 603 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 608 through 612 removed outlier: 6.573A pdb=" N ILE L 628 " --> pdb=" O LYS L 610 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE L 612 " --> pdb=" O LEU L 626 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LEU L 626 " --> pdb=" O ILE L 612 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA L 627 " --> pdb=" O LEU L 638 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 619 through 620 1662 hydrogen bonds defined for protein. 4512 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: 8.62 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5789 1.32 - 1.45: 8330 1.45 - 1.57: 19409 1.57 - 1.70: 25 1.70 - 1.83: 276 Bond restraints: 33829 Sorted by residual: bond pdb=" O3B COA D 601 " pdb=" P3B COA D 601 " ideal model delta sigma weight residual 1.683 1.554 0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" O7A COA B 601 " pdb=" P3B COA B 601 " ideal model delta sigma weight residual 1.541 1.415 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" CE1 HIS B 143 " pdb=" NE2 HIS B 143 " ideal model delta sigma weight residual 1.321 1.260 0.061 1.00e-02 1.00e+04 3.72e+01 bond pdb=" CE1 HIS A 143 " pdb=" NE2 HIS A 143 " ideal model delta sigma weight residual 1.321 1.266 0.055 1.00e-02 1.00e+04 2.99e+01 bond pdb=" O7A COA E 601 " pdb=" P3B COA E 601 " ideal model delta sigma weight residual 1.541 1.434 0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 33824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 45371 3.38 - 6.76: 336 6.76 - 10.14: 39 10.14 - 13.52: 3 13.52 - 16.90: 3 Bond angle restraints: 45752 Sorted by residual: angle pdb=" CA ASP B 171 " pdb=" CB ASP B 171 " pdb=" CG ASP B 171 " ideal model delta sigma weight residual 112.60 119.59 -6.99 1.00e+00 1.00e+00 4.89e+01 angle pdb=" CA ASP C 171 " pdb=" CB ASP C 171 " pdb=" CG ASP C 171 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" C ALA B 168 " pdb=" N GLY B 169 " pdb=" CA GLY B 169 " ideal model delta sigma weight residual 120.00 129.77 -9.77 1.63e+00 3.76e-01 3.59e+01 angle pdb=" C5B COA C 601 " pdb=" O5B COA C 601 " pdb=" P1A COA C 601 " ideal model delta sigma weight residual 120.98 137.88 -16.90 3.00e+00 1.11e-01 3.17e+01 angle pdb=" N ARG C 343 " pdb=" CA ARG C 343 " pdb=" C ARG C 343 " ideal model delta sigma weight residual 111.36 105.35 6.01 1.09e+00 8.42e-01 3.04e+01 ... (remaining 45747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 19049 17.88 - 35.75: 1283 35.75 - 53.63: 249 53.63 - 71.50: 101 71.50 - 89.38: 42 Dihedral angle restraints: 20724 sinusoidal: 8613 harmonic: 12111 Sorted by residual: dihedral pdb=" CA HIS L 568 " pdb=" C HIS L 568 " pdb=" N ALA L 569 " pdb=" CA ALA L 569 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA GLY K 598 " pdb=" C GLY K 598 " pdb=" N LYS K 599 " pdb=" CA LYS K 599 " ideal model delta harmonic sigma weight residual 180.00 153.35 26.65 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASP C 127 " pdb=" C ASP C 127 " pdb=" N ALA C 128 " pdb=" CA ALA C 128 " ideal model delta harmonic sigma weight residual -180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 20721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 5103 0.209 - 0.418: 9 0.418 - 0.627: 2 0.627 - 0.836: 1 0.836 - 1.045: 2 Chirality restraints: 5117 Sorted by residual: chirality pdb=" C2 BTI J 701 " pdb=" C4 BTI J 701 " pdb=" C7 BTI J 701 " pdb=" S1 BTI J 701 " both_signs ideal model delta sigma weight residual False 3.11 2.06 1.04 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" C2B COA F 601 " pdb=" C1B COA F 601 " pdb=" C3B COA F 601 " pdb=" O2B COA F 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" CAP COA E 601 " pdb=" C9P COA E 601 " pdb=" CBP COA E 601 " pdb=" OAP COA E 601 " both_signs ideal model delta sigma weight residual False -2.50 -1.68 -0.82 2.00e-01 2.50e+01 1.67e+01 ... (remaining 5114 not shown) Planarity restraints: 6000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTI H 701 " -0.038 2.00e-02 2.50e+03 9.61e-02 1.38e+02 pdb=" C4 BTI H 701 " 0.018 2.00e-02 2.50e+03 pdb=" C5 BTI H 701 " 0.123 2.00e-02 2.50e+03 pdb=" N2 BTI H 701 " -0.070 2.00e-02 2.50e+03 pdb=" N3 BTI H 701 " -0.145 2.00e-02 2.50e+03 pdb=" O3 BTI H 701 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI G 701 " -0.019 2.00e-02 2.50e+03 8.66e-02 1.12e+02 pdb=" C4 BTI G 701 " 0.122 2.00e-02 2.50e+03 pdb=" C5 BTI G 701 " -0.121 2.00e-02 2.50e+03 pdb=" N2 BTI G 701 " -0.082 2.00e-02 2.50e+03 pdb=" N3 BTI G 701 " 0.092 2.00e-02 2.50e+03 pdb=" O3 BTI G 701 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P COA B 601 " -0.108 2.00e-02 2.50e+03 8.91e-02 9.93e+01 pdb=" C9P COA B 601 " 0.065 2.00e-02 2.50e+03 pdb=" CAP COA B 601 " -0.092 2.00e-02 2.50e+03 pdb=" N8P COA B 601 " 0.123 2.00e-02 2.50e+03 pdb=" O9P COA B 601 " 0.012 2.00e-02 2.50e+03 ... (remaining 5997 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 481 2.66 - 3.22: 32340 3.22 - 3.78: 51678 3.78 - 4.34: 75740 4.34 - 4.90: 121048 Nonbonded interactions: 281287 Sorted by model distance: nonbonded pdb=" O1A COA C 601 " pdb=" OAP COA C 601 " model vdw 2.097 3.040 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 222 " model vdw 2.100 3.040 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 222 " model vdw 2.118 3.040 nonbonded pdb=" O SER C 221 " pdb=" OG SER C 222 " model vdw 2.121 3.040 nonbonded pdb=" O SER D 221 " pdb=" OG SER D 222 " model vdw 2.147 3.040 ... (remaining 281282 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' } ncs_group { reference = (chain 'G' and resid 461 through 701) selection = (chain 'H' and resid 461 through 701) selection = chain 'I' selection = (chain 'J' and resid 461 through 701) selection = (chain 'K' and resid 461 through 701) selection = (chain 'L' and resid 461 through 701) } 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.890 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 33835 Z= 0.324 Angle : 0.810 16.899 45752 Z= 0.427 Chirality : 0.056 1.045 5117 Planarity : 0.006 0.096 6000 Dihedral : 13.888 89.379 12950 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.11), residues: 4265 helix: -1.47 (0.11), residues: 1529 sheet: 0.22 (0.16), residues: 803 loop : -1.72 (0.11), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 485 TYR 0.020 0.002 TYR D 386 PHE 0.018 0.002 PHE C 89 TRP 0.011 0.002 TRP L 544 HIS 0.018 0.002 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00605 (33829) covalent geometry : angle 0.81018 (45752) hydrogen bonds : bond 0.16501 ( 1562) hydrogen bonds : angle 6.97867 ( 4512) Misc. bond : bond 0.08346 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8066 (mmm) cc_final: 0.7643 (mmm) REVERT: B 455 LYS cc_start: 0.8107 (tttm) cc_final: 0.7812 (tptm) REVERT: B 459 ASP cc_start: 0.7656 (m-30) cc_final: 0.7387 (m-30) REVERT: C 438 ILE cc_start: 0.8501 (mt) cc_final: 0.8245 (mt) REVERT: D 409 MET cc_start: 0.9120 (mmm) cc_final: 0.8801 (mmm) REVERT: D 453 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7815 (mtt90) REVERT: D 492 MET cc_start: 0.9028 (tmm) cc_final: 0.8520 (tmm) REVERT: E 430 MET cc_start: 0.8202 (ptp) cc_final: 0.7915 (ptm) REVERT: F 257 GLU cc_start: 0.7273 (pm20) cc_final: 0.6923 (pm20) REVERT: F 276 ASN cc_start: 0.8434 (t0) cc_final: 0.8131 (t0) REVERT: F 409 MET cc_start: 0.9071 (mmm) cc_final: 0.8617 (mmm) REVERT: F 433 LYS cc_start: 0.7828 (ptmm) cc_final: 0.7596 (ptmm) REVERT: F 492 MET cc_start: 0.9010 (tmm) cc_final: 0.8674 (tmm) REVERT: L 520 ASP cc_start: 0.6401 (m-30) cc_final: 0.5515 (m-30) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 1.0203 time to fit residues: 640.5324 Evaluate side-chains 458 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.0020 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 40.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.1980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 112 GLN B 57 HIS C 57 HIS C 67 GLN D 56 GLN D 57 HIS E 57 HIS E 112 GLN F 57 HIS G 479 ASN G 551 GLN G 611 GLN G 618 GLN H 465 HIS H 556 GLN I 551 GLN I 556 GLN J 508 GLN J 562 ASN J 636 ASN K 465 HIS K 508 GLN K 511 ASN K 562 ASN K 567 GLN K 568 HIS K 611 GLN K 618 GLN L 562 ASN ** L 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 618 GLN L 636 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.168404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131302 restraints weight = 25750.501| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.47 r_work: 0.3258 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33835 Z= 0.114 Angle : 0.531 8.197 45752 Z= 0.292 Chirality : 0.045 0.154 5117 Planarity : 0.004 0.040 6000 Dihedral : 7.906 77.898 5123 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.64 % Allowed : 6.53 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.12), residues: 4265 helix: 0.75 (0.13), residues: 1554 sheet: 0.63 (0.17), residues: 811 loop : -0.99 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 317 TYR 0.011 0.001 TYR D 386 PHE 0.011 0.001 PHE B 244 TRP 0.012 0.001 TRP L 544 HIS 0.007 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00214 (33829) covalent geometry : angle 0.53111 (45752) hydrogen bonds : bond 0.04864 ( 1562) hydrogen bonds : angle 5.01690 ( 4512) Misc. bond : bond 0.00024 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 476 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8397 (mmm) cc_final: 0.7957 (mmm) REVERT: A 502 ARG cc_start: 0.7725 (tmt170) cc_final: 0.7515 (tmt170) REVERT: B 7 LYS cc_start: 0.5325 (tptp) cc_final: 0.4947 (mtpt) REVERT: B 430 MET cc_start: 0.8712 (ptp) cc_final: 0.8502 (ptp) REVERT: B 455 LYS cc_start: 0.8335 (tttm) cc_final: 0.8084 (tptm) REVERT: D 409 MET cc_start: 0.9241 (mmm) cc_final: 0.8976 (mmm) REVERT: D 453 ARG cc_start: 0.8235 (mtt-85) cc_final: 0.8027 (mtt90) REVERT: D 456 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7697 (tp30) REVERT: D 492 MET cc_start: 0.9230 (tmm) cc_final: 0.8706 (tmm) REVERT: E 261 ASP cc_start: 0.8158 (t70) cc_final: 0.7934 (t70) REVERT: E 263 ASN cc_start: 0.8243 (m-40) cc_final: 0.7989 (m-40) REVERT: F 251 GLU cc_start: 0.8105 (pt0) cc_final: 0.7849 (pt0) REVERT: F 433 LYS cc_start: 0.8343 (ptmm) cc_final: 0.7877 (ptmm) REVERT: G 489 MET cc_start: 0.8381 (ttp) cc_final: 0.8107 (ttm) REVERT: G 589 MET cc_start: 0.8972 (mmp) cc_final: 0.8602 (mmp) REVERT: G 605 MET cc_start: 0.7927 (pmm) cc_final: 0.7688 (pmm) REVERT: I 534 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7222 (mpt-90) REVERT: I 556 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7249 (mp-120) REVERT: J 483 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.8273 (mmp-170) REVERT: K 630 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7680 (tp30) outliers start: 22 outliers final: 7 residues processed: 481 average time/residue: 1.0010 time to fit residues: 545.0736 Evaluate side-chains 450 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 440 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain H residue 659 VAL Chi-restraints excluded: chain I residue 556 GLN Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain K residue 630 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 37 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 278 optimal weight: 0.9980 chunk 384 optimal weight: 7.9990 chunk 400 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 380 optimal weight: 0.1980 chunk 145 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN B 112 GLN C 112 GLN D 112 GLN E 67 GLN F 112 GLN G 562 ASN G 567 GLN H 562 ASN I 556 GLN I 562 ASN I 600 GLN L 479 ASN L 511 ASN ** L 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.162386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123799 restraints weight = 24799.755| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.47 r_work: 0.3134 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work: 0.2895 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33835 Z= 0.182 Angle : 0.636 7.817 45752 Z= 0.356 Chirality : 0.048 0.188 5117 Planarity : 0.005 0.043 6000 Dihedral : 7.608 76.059 5123 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.76 % Allowed : 7.55 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.12), residues: 4265 helix: 1.00 (0.13), residues: 1530 sheet: 1.13 (0.17), residues: 751 loop : -0.81 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 453 TYR 0.015 0.002 TYR D 386 PHE 0.020 0.002 PHE K 578 TRP 0.014 0.002 TRP L 544 HIS 0.012 0.002 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00336 (33829) covalent geometry : angle 0.63599 (45752) hydrogen bonds : bond 0.07632 ( 1562) hydrogen bonds : angle 5.24960 ( 4512) Misc. bond : bond 0.00022 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 467 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8478 (mmm) cc_final: 0.8129 (mmm) REVERT: B 7 LYS cc_start: 0.5611 (tptp) cc_final: 0.5095 (mtpt) REVERT: B 409 MET cc_start: 0.9237 (mmm) cc_final: 0.8989 (mmm) REVERT: D 409 MET cc_start: 0.9405 (mmm) cc_final: 0.9146 (mmm) REVERT: D 453 ARG cc_start: 0.8519 (mtt-85) cc_final: 0.8246 (mtt180) REVERT: D 456 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8173 (tp30) REVERT: D 492 MET cc_start: 0.9402 (tmm) cc_final: 0.8799 (tmm) REVERT: F 22 LYS cc_start: 0.8106 (ptpt) cc_final: 0.7665 (pttp) REVERT: F 251 GLU cc_start: 0.8430 (pt0) cc_final: 0.8040 (pt0) REVERT: F 433 LYS cc_start: 0.8439 (ptmm) cc_final: 0.7962 (ptmm) REVERT: G 489 MET cc_start: 0.8542 (ttp) cc_final: 0.8165 (ttm) REVERT: G 589 MET cc_start: 0.9066 (mmp) cc_final: 0.8638 (mmp) REVERT: I 534 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7532 (mpt-90) REVERT: J 483 ARG cc_start: 0.8745 (mtt-85) cc_final: 0.8436 (mmp-170) REVERT: J 624 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: K 630 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7847 (tp30) REVERT: L 630 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7901 (tp30) outliers start: 26 outliers final: 12 residues processed: 472 average time/residue: 1.0203 time to fit residues: 545.2215 Evaluate side-chains 469 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 453 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain H residue 659 VAL Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 624 GLU Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 580 ARG Chi-restraints excluded: chain L residue 630 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 66 optimal weight: 0.0570 chunk 59 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 354 optimal weight: 0.5980 chunk 386 optimal weight: 10.0000 chunk 268 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 321 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN B 263 ASN E 67 GLN G 567 GLN I 556 GLN J 511 ASN L 479 ASN ** L 568 HIS ** 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 = 0.4009 r_free = 0.4009 target = 0.166950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130130 restraints weight = 25413.678| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.34 r_work: 0.3229 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work: 0.3003 rms_B_bonded: 4.85 restraints_weight: 0.1250 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33835 Z= 0.113 Angle : 0.514 6.245 45752 Z= 0.283 Chirality : 0.044 0.154 5117 Planarity : 0.004 0.038 6000 Dihedral : 7.008 78.363 5123 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.70 % Allowed : 8.19 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.62 (0.13), residues: 4265 helix: 1.41 (0.13), residues: 1554 sheet: 1.30 (0.17), residues: 750 loop : -0.76 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 453 TYR 0.008 0.001 TYR D 386 PHE 0.011 0.001 PHE D 351 TRP 0.013 0.001 TRP L 544 HIS 0.007 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00208 (33829) covalent geometry : angle 0.51371 (45752) hydrogen bonds : bond 0.04926 ( 1562) hydrogen bonds : angle 4.78986 ( 4512) Misc. bond : bond 0.00008 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 470 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8556 (mmm) cc_final: 0.8140 (mmm) REVERT: B 7 LYS cc_start: 0.5435 (tptp) cc_final: 0.5060 (mtpt) REVERT: B 29 LYS cc_start: 0.8827 (tptm) cc_final: 0.8492 (ttpp) REVERT: C 7 LYS cc_start: 0.6302 (tptm) cc_final: 0.6081 (tptp) REVERT: D 409 MET cc_start: 0.9355 (mmm) cc_final: 0.9115 (mmm) REVERT: D 453 ARG cc_start: 0.8527 (mtt-85) cc_final: 0.8280 (mtt180) REVERT: D 456 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8171 (tp30) REVERT: D 492 MET cc_start: 0.9353 (tmm) cc_final: 0.8791 (tmm) REVERT: E 22 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7711 (ttpt) REVERT: E 204 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7642 (mt-10) REVERT: F 22 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7697 (pttp) REVERT: F 251 GLU cc_start: 0.8432 (pt0) cc_final: 0.8000 (pt0) REVERT: F 433 LYS cc_start: 0.8358 (ptmm) cc_final: 0.7882 (ptmm) REVERT: G 489 MET cc_start: 0.8510 (ttp) cc_final: 0.8164 (ttm) REVERT: G 589 MET cc_start: 0.9035 (mmp) cc_final: 0.8628 (mmp) REVERT: I 556 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7344 (mp-120) REVERT: J 483 ARG cc_start: 0.8574 (mtt-85) cc_final: 0.8311 (mmp-170) REVERT: J 624 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: K 630 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: L 630 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7826 (tp30) outliers start: 24 outliers final: 8 residues processed: 476 average time/residue: 0.9918 time to fit residues: 534.8696 Evaluate side-chains 468 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 455 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain H residue 659 VAL Chi-restraints excluded: chain I residue 556 GLN Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 624 GLU Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 630 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 278 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 361 optimal weight: 20.0000 chunk 293 optimal weight: 8.9990 chunk 340 optimal weight: 0.0570 chunk 415 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN G 567 GLN I 556 GLN L 479 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.161223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121660 restraints weight = 24655.686| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.53 r_work: 0.3113 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work: 0.2862 rms_B_bonded: 4.99 restraints_weight: 0.1250 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33835 Z= 0.218 Angle : 0.693 6.772 45752 Z= 0.389 Chirality : 0.050 0.206 5117 Planarity : 0.005 0.056 6000 Dihedral : 7.339 72.556 5123 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.96 % Allowed : 8.63 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.12), residues: 4265 helix: 1.06 (0.13), residues: 1530 sheet: 1.27 (0.17), residues: 751 loop : -0.70 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 502 TYR 0.018 0.003 TYR F 173 PHE 0.023 0.002 PHE C 465 TRP 0.015 0.002 TRP L 544 HIS 0.013 0.002 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00416 (33829) covalent geometry : angle 0.69328 (45752) hydrogen bonds : bond 0.08582 ( 1562) hydrogen bonds : angle 5.33481 ( 4512) Misc. bond : bond 0.00035 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 467 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8561 (mmm) cc_final: 0.8233 (mmm) REVERT: A 251 GLU cc_start: 0.8732 (pt0) cc_final: 0.8427 (pt0) REVERT: B 7 LYS cc_start: 0.5782 (tptp) cc_final: 0.5248 (mtpt) REVERT: D 409 MET cc_start: 0.9421 (mmm) cc_final: 0.9103 (mmm) REVERT: D 453 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.8341 (mtt180) REVERT: D 456 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8299 (tp30) REVERT: D 492 MET cc_start: 0.9395 (tmm) cc_final: 0.8844 (tmm) REVERT: E 143 HIS cc_start: 0.9211 (OUTLIER) cc_final: 0.8969 (m170) REVERT: F 7 LYS cc_start: 0.6239 (tptm) cc_final: 0.5934 (tptp) REVERT: F 22 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7791 (pttp) REVERT: F 251 GLU cc_start: 0.8471 (pt0) cc_final: 0.8035 (pt0) REVERT: F 433 LYS cc_start: 0.8420 (ptmm) cc_final: 0.7962 (ptmm) REVERT: G 489 MET cc_start: 0.8572 (ttp) cc_final: 0.8185 (ttm) REVERT: J 483 ARG cc_start: 0.8718 (mtt-85) cc_final: 0.8415 (mmp-170) REVERT: J 624 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: K 630 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: L 630 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8000 (tp30) outliers start: 33 outliers final: 14 residues processed: 478 average time/residue: 0.9900 time to fit residues: 536.3730 Evaluate side-chains 483 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 463 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 143 HIS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain H residue 659 VAL Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 624 GLU Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 630 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 374 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN G 567 GLN I 556 GLN L 479 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.161825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122420 restraints weight = 24653.200| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.53 r_work: 0.3125 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work: 0.2885 rms_B_bonded: 4.68 restraints_weight: 0.1250 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33835 Z= 0.194 Angle : 0.654 7.599 45752 Z= 0.367 Chirality : 0.049 0.196 5117 Planarity : 0.005 0.044 6000 Dihedral : 7.238 71.121 5123 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.85 % Allowed : 9.24 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.12), residues: 4265 helix: 1.07 (0.13), residues: 1530 sheet: 1.25 (0.17), residues: 751 loop : -0.67 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 453 TYR 0.015 0.002 TYR F 173 PHE 0.019 0.002 PHE D 465 TRP 0.016 0.002 TRP L 544 HIS 0.011 0.002 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00363 (33829) covalent geometry : angle 0.65440 (45752) hydrogen bonds : bond 0.07868 ( 1562) hydrogen bonds : angle 5.25175 ( 4512) Misc. bond : bond 0.00029 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 470 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8540 (mmm) cc_final: 0.8193 (mmm) REVERT: A 251 GLU cc_start: 0.8672 (pt0) cc_final: 0.8406 (pt0) REVERT: A 452 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7400 (tm-30) REVERT: B 7 LYS cc_start: 0.5726 (tptp) cc_final: 0.5194 (mtpt) REVERT: D 453 ARG cc_start: 0.8564 (mtt-85) cc_final: 0.8280 (mtt180) REVERT: D 456 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8202 (tp30) REVERT: D 492 MET cc_start: 0.9396 (tmm) cc_final: 0.8867 (tmm) REVERT: E 22 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7795 (ttpt) REVERT: F 7 LYS cc_start: 0.6158 (tptm) cc_final: 0.5851 (tptp) REVERT: F 22 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7756 (pttp) REVERT: F 251 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: F 433 LYS cc_start: 0.8378 (ptmm) cc_final: 0.7929 (ptmm) REVERT: I 556 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7373 (mp-120) REVERT: J 483 ARG cc_start: 0.8712 (mtt-85) cc_final: 0.8425 (mmp-170) REVERT: J 624 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: K 608 LEU cc_start: 0.8064 (mm) cc_final: 0.7507 (tp) REVERT: K 630 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: L 630 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7973 (tp30) outliers start: 29 outliers final: 15 residues processed: 479 average time/residue: 0.9855 time to fit residues: 535.9515 Evaluate side-chains 478 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 456 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 279 LYS Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 251 GLU Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain H residue 482 LYS Chi-restraints excluded: chain H residue 659 VAL Chi-restraints excluded: chain I residue 556 GLN Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 624 GLU Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 630 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 327 optimal weight: 20.0000 chunk 398 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 194 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 350 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 418 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN G 567 GLN I 556 GLN L 479 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.160792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122304 restraints weight = 24567.470| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.42 r_work: 0.3095 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work: 0.2867 rms_B_bonded: 4.51 restraints_weight: 0.1250 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33835 Z= 0.233 Angle : 0.719 7.563 45752 Z= 0.404 Chirality : 0.051 0.210 5117 Planarity : 0.005 0.064 6000 Dihedral : 7.322 69.169 5123 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.87 % Allowed : 9.59 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.12), residues: 4265 helix: 0.91 (0.13), residues: 1530 sheet: 1.16 (0.17), residues: 763 loop : -0.71 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 534 TYR 0.018 0.003 TYR F 173 PHE 0.024 0.002 PHE E 465 TRP 0.017 0.002 TRP L 544 HIS 0.012 0.002 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00447 (33829) covalent geometry : angle 0.71891 (45752) hydrogen bonds : bond 0.08868 ( 1562) hydrogen bonds : angle 5.39747 ( 4512) Misc. bond : bond 0.00041 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 465 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8527 (mmm) cc_final: 0.8179 (mmm) REVERT: A 251 GLU cc_start: 0.8651 (pt0) cc_final: 0.8404 (pt0) REVERT: B 7 LYS cc_start: 0.5841 (tptp) cc_final: 0.5272 (mtpt) REVERT: C 14 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7299 (tm130) REVERT: D 453 ARG cc_start: 0.8559 (mtt-85) cc_final: 0.8094 (mtt180) REVERT: D 456 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8151 (tp30) REVERT: D 492 MET cc_start: 0.9402 (tmm) cc_final: 0.8863 (tmm) REVERT: E 455 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7928 (ttpp) REVERT: E 458 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: F 7 LYS cc_start: 0.6183 (tptm) cc_final: 0.5868 (tptp) REVERT: F 22 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7778 (pttp) REVERT: F 433 LYS cc_start: 0.8376 (ptmm) cc_final: 0.7924 (ptmm) REVERT: J 483 ARG cc_start: 0.8735 (mtt-85) cc_final: 0.8435 (mmp-170) REVERT: J 624 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: K 608 LEU cc_start: 0.8117 (mm) cc_final: 0.7563 (tp) REVERT: K 630 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: L 630 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7900 (tp30) outliers start: 30 outliers final: 14 residues processed: 477 average time/residue: 0.9983 time to fit residues: 540.2213 Evaluate side-chains 481 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 459 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 53 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 458 GLU Chi-restraints excluded: chain F residue 22 LYS Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain H residue 659 VAL Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain J residue 624 GLU Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 630 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 218 optimal weight: 9.9990 chunk 334 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 292 optimal weight: 0.9980 chunk 401 optimal weight: 40.0000 chunk 256 optimal weight: 0.0570 chunk 390 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 360 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 244 optimal weight: 0.0050 overall best weight: 0.3470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 378 HIS G 567 GLN I 511 ASN L 479 ASN L 511 ASN ** L 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.169088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132213 restraints weight = 25731.805| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.33 r_work: 0.3284 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 33835 Z= 0.101 Angle : 0.509 9.123 45752 Z= 0.276 Chirality : 0.044 0.147 5117 Planarity : 0.004 0.040 6000 Dihedral : 6.575 66.593 5123 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.44 % Allowed : 10.32 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.13), residues: 4265 helix: 1.55 (0.14), residues: 1554 sheet: 1.09 (0.17), residues: 798 loop : -0.55 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 534 TYR 0.006 0.001 TYR D 386 PHE 0.011 0.001 PHE F 351 TRP 0.017 0.001 TRP L 544 HIS 0.008 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00200 (33829) covalent geometry : angle 0.50916 (45752) hydrogen bonds : bond 0.04089 ( 1562) hydrogen bonds : angle 4.69021 ( 4512) Misc. bond : bond 0.00005 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 465 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8435 (mmm) cc_final: 0.7982 (mmm) REVERT: B 7 LYS cc_start: 0.5499 (tptp) cc_final: 0.5178 (mtpt) REVERT: D 453 ARG cc_start: 0.8374 (mtt-85) cc_final: 0.8104 (mtt180) REVERT: D 456 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7778 (tp30) REVERT: D 492 MET cc_start: 0.9220 (tmm) cc_final: 0.8566 (tmm) REVERT: F 22 LYS cc_start: 0.7978 (ptpt) cc_final: 0.7619 (pttp) REVERT: F 251 GLU cc_start: 0.8079 (pt0) cc_final: 0.7812 (pt0) REVERT: F 433 LYS cc_start: 0.8225 (ptmm) cc_final: 0.7782 (ptmm) REVERT: G 589 MET cc_start: 0.8945 (mmp) cc_final: 0.8588 (mmp) REVERT: I 534 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7737 (mpt-90) REVERT: J 483 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8154 (mmp-170) REVERT: K 630 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: L 630 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7704 (tp30) outliers start: 15 outliers final: 7 residues processed: 473 average time/residue: 0.9852 time to fit residues: 528.4400 Evaluate side-chains 458 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 448 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain H residue 659 VAL Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 630 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 379 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 332 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 393 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 264 optimal weight: 2.9990 chunk 336 optimal weight: 0.4980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN G 567 GLN L 479 ASN ** L 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.162439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124468 restraints weight = 24824.510| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.47 r_work: 0.3114 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work: 0.2930 rms_B_bonded: 4.26 restraints_weight: 0.1250 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33835 Z= 0.149 Angle : 0.588 9.234 45752 Z= 0.324 Chirality : 0.046 0.177 5117 Planarity : 0.004 0.049 6000 Dihedral : 6.652 60.687 5123 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.55 % Allowed : 10.52 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.13), residues: 4265 helix: 1.56 (0.14), residues: 1500 sheet: 1.43 (0.17), residues: 750 loop : -0.46 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 317 TYR 0.011 0.002 TYR D 386 PHE 0.019 0.001 PHE C 465 TRP 0.015 0.001 TRP L 544 HIS 0.010 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00276 (33829) covalent geometry : angle 0.58770 (45752) hydrogen bonds : bond 0.06438 ( 1562) hydrogen bonds : angle 4.94438 ( 4512) Misc. bond : bond 0.00014 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 463 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8608 (mmm) cc_final: 0.8197 (mmm) REVERT: A 251 GLU cc_start: 0.8634 (pt0) cc_final: 0.8406 (pt0) REVERT: B 7 LYS cc_start: 0.5707 (tptp) cc_final: 0.5295 (mtpt) REVERT: D 453 ARG cc_start: 0.8548 (mtt-85) cc_final: 0.8311 (mtt180) REVERT: D 456 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8148 (tp30) REVERT: D 492 MET cc_start: 0.9338 (tmm) cc_final: 0.8707 (tmm) REVERT: E 257 GLU cc_start: 0.8014 (pm20) cc_final: 0.7696 (pm20) REVERT: E 458 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7582 (tp30) REVERT: F 22 LYS cc_start: 0.8130 (ptpt) cc_final: 0.7779 (pttp) REVERT: F 251 GLU cc_start: 0.8406 (pt0) cc_final: 0.8018 (pt0) REVERT: F 433 LYS cc_start: 0.8331 (ptmm) cc_final: 0.7912 (ptmm) REVERT: G 589 MET cc_start: 0.9064 (mmp) cc_final: 0.8614 (mmp) REVERT: J 483 ARG cc_start: 0.8666 (mtt-85) cc_final: 0.8449 (mmp-170) REVERT: K 630 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7845 (tp30) REVERT: L 630 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8004 (tp30) outliers start: 19 outliers final: 7 residues processed: 471 average time/residue: 0.9988 time to fit residues: 532.8741 Evaluate side-chains 462 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 451 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain E residue 458 GLU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 630 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 38 optimal weight: 0.0870 chunk 268 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 339 optimal weight: 0.1980 chunk 399 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 376 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 270 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN L 479 ASN ** L 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.163025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125478 restraints weight = 25101.350| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.43 r_work: 0.3128 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work: 0.2944 rms_B_bonded: 4.34 restraints_weight: 0.1250 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33835 Z= 0.140 Angle : 0.578 9.530 45752 Z= 0.317 Chirality : 0.046 0.172 5117 Planarity : 0.004 0.062 6000 Dihedral : 6.587 57.601 5123 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.35 % Allowed : 10.75 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.13), residues: 4265 helix: 1.56 (0.14), residues: 1500 sheet: 1.43 (0.17), residues: 750 loop : -0.46 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 502 TYR 0.011 0.001 TYR D 386 PHE 0.020 0.001 PHE C 465 TRP 0.015 0.001 TRP L 544 HIS 0.009 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00262 (33829) covalent geometry : angle 0.57810 (45752) hydrogen bonds : bond 0.06063 ( 1562) hydrogen bonds : angle 4.90223 ( 4512) Misc. bond : bond 0.00014 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 458 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8609 (mmm) cc_final: 0.8201 (mmm) REVERT: A 251 GLU cc_start: 0.8640 (pt0) cc_final: 0.8421 (pt0) REVERT: B 7 LYS cc_start: 0.5666 (tptp) cc_final: 0.5275 (mtpt) REVERT: D 453 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.8133 (mtt180) REVERT: D 456 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8148 (tp30) REVERT: D 492 MET cc_start: 0.9329 (tmm) cc_final: 0.8708 (tmm) REVERT: E 29 LYS cc_start: 0.8436 (tmmt) cc_final: 0.8184 (pptt) REVERT: E 257 GLU cc_start: 0.8020 (pm20) cc_final: 0.7718 (pm20) REVERT: E 458 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7578 (tp30) REVERT: F 22 LYS cc_start: 0.8121 (ptpt) cc_final: 0.7772 (pttp) REVERT: F 251 GLU cc_start: 0.8407 (pt0) cc_final: 0.8009 (pt0) REVERT: F 433 LYS cc_start: 0.8329 (ptmm) cc_final: 0.7896 (ptmm) REVERT: G 589 MET cc_start: 0.9063 (mmp) cc_final: 0.8624 (mmp) REVERT: J 483 ARG cc_start: 0.8618 (mtt-85) cc_final: 0.8391 (mmp-170) REVERT: K 630 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7847 (tp30) REVERT: L 630 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7990 (tp30) outliers start: 12 outliers final: 7 residues processed: 465 average time/residue: 0.9762 time to fit residues: 515.8400 Evaluate side-chains 466 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 455 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 456 GLU Chi-restraints excluded: chain E residue 458 GLU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain J residue 547 THR Chi-restraints excluded: chain K residue 630 GLU Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 630 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 270 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 401 optimal weight: 40.0000 chunk 284 optimal weight: 5.9990 chunk 351 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 282 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.160420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.124209 restraints weight = 24618.969| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.28 r_work: 0.3085 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work: 0.2902 rms_B_bonded: 4.31 restraints_weight: 0.1250 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33835 Z= 0.194 Angle : 0.668 9.144 45752 Z= 0.371 Chirality : 0.048 0.196 5117 Planarity : 0.005 0.042 6000 Dihedral : 6.874 58.906 5123 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.44 % Allowed : 10.90 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.12), residues: 4265 helix: 1.20 (0.13), residues: 1530 sheet: 1.39 (0.17), residues: 750 loop : -0.57 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 317 TYR 0.015 0.002 TYR F 173 PHE 0.031 0.002 PHE C 465 TRP 0.014 0.002 TRP L 544 HIS 0.011 0.002 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00365 (33829) covalent geometry : angle 0.66781 (45752) hydrogen bonds : bond 0.07963 ( 1562) hydrogen bonds : angle 5.19788 ( 4512) Misc. bond : bond 0.00030 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21895.40 seconds wall clock time: 370 minutes 1.60 seconds (22201.60 seconds total)