Starting phenix.real_space_refine on Thu Mar 5 07:51:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvx_27020/03_2026/8cvx_27020.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvx_27020/03_2026/8cvx_27020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cvx_27020/03_2026/8cvx_27020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvx_27020/03_2026/8cvx_27020.map" model { file = "/net/cci-nas-00/data/ceres_data/8cvx_27020/03_2026/8cvx_27020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvx_27020/03_2026/8cvx_27020.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.211 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 4 5.49 5 S 104 5.16 5 C 13097 2.51 5 N 3520 2.21 5 O 3723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 227 residue(s): 0.01s 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: 20448 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4830 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 577} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 269 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 32} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 269 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 32} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 262 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 265 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4838 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 578} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4833 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 578} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 4818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4818 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 24, 'TRANS': 578} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.75, per 1000 atoms: 0.23 Number of scatterers: 20448 At special positions: 0 Unit cell: (124.331, 155.414, 156.328, 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 104 16.00 P 4 15.00 O 3723 8.00 N 3520 7.00 C 13097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4762 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 12 sheets defined 52.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 removed outlier: 4.082A pdb=" N THR A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 removed outlier: 3.716A pdb=" N ARG A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 96 Processing helix chain 'A' and resid 121 through 137 removed outlier: 3.581A pdb=" N LEU A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 169 removed outlier: 3.857A pdb=" N ASN A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 194 removed outlier: 4.020A pdb=" N CYS A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 4.031A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.702A pdb=" N ARG A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 249 removed outlier: 4.088A pdb=" N ALA A 247 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 291 through 312 removed outlier: 3.629A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 removed outlier: 3.812A pdb=" N PHE A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 removed outlier: 3.539A pdb=" N ALA A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 396 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 436 removed outlier: 3.606A pdb=" N GLN A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.522A pdb=" N THR A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.751A pdb=" N ARG A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 532 through 541 Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 578 through 591 removed outlier: 3.553A pdb=" N GLU A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'E' and resid 319 through 326 removed outlier: 3.520A pdb=" N GLU E 326 " --> pdb=" O LYS E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 350 Processing helix chain 'H' and resid 319 through 326 removed outlier: 3.705A pdb=" N GLU H 323 " --> pdb=" O GLU H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 329 No H-bonds generated for 'chain 'H' and resid 327 through 329' Processing helix chain 'H' and resid 337 through 348 removed outlier: 3.751A pdb=" N ILE H 341 " --> pdb=" O SER H 337 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR H 348 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 326 removed outlier: 3.816A pdb=" N GLU G 323 " --> pdb=" O GLU G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 329 No H-bonds generated for 'chain 'G' and resid 327 through 329' Processing helix chain 'G' and resid 337 through 348 removed outlier: 3.849A pdb=" N TYR G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 326 Processing helix chain 'F' and resid 327 through 329 No H-bonds generated for 'chain 'F' and resid 327 through 329' Processing helix chain 'F' and resid 337 through 346 Processing helix chain 'B' and resid 42 through 58 removed outlier: 4.080A pdb=" N THR B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 57 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.700A pdb=" N THR B 75 " --> pdb=" O GLN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 96 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 145 through 169 removed outlier: 3.873A pdb=" N ASN B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.850A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLY B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 190 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 217 removed outlier: 4.006A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 236 removed outlier: 3.767A pdb=" N ARG B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 249 removed outlier: 4.089A pdb=" N ALA B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 267 Processing helix chain 'B' and resid 291 through 312 removed outlier: 3.631A pdb=" N ALA B 298 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 removed outlier: 3.813A pdb=" N PHE B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.533A pdb=" N ALA B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 396 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 Processing helix chain 'B' and resid 454 through 464 removed outlier: 3.523A pdb=" N THR B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.751A pdb=" N ARG B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 522 removed outlier: 3.608A pdb=" N CYS B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 541 Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 578 through 591 removed outlier: 3.550A pdb=" N GLU B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B 591 " --> pdb=" O ASN B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 617 removed outlier: 4.961A pdb=" N ARG B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 58 removed outlier: 4.085A pdb=" N THR D 49 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP D 56 " --> pdb=" O LYS D 52 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 76 removed outlier: 3.717A pdb=" N ARG D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR D 75 " --> pdb=" O GLN D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 125 through 135 Processing helix chain 'D' and resid 145 through 169 removed outlier: 3.857A pdb=" N ASN D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 169 " --> pdb=" O PHE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.844A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N CYS D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 190 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 removed outlier: 4.022A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 236 Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 291 through 312 removed outlier: 3.628A pdb=" N ALA D 298 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG D 303 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D 307 " --> pdb=" O ARG D 303 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 312 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 removed outlier: 3.813A pdb=" N PHE D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 344 " --> pdb=" O ASP D 340 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 409 removed outlier: 3.990A pdb=" N ALA D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL D 396 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS D 397 " --> pdb=" O ALA D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 436 Processing helix chain 'D' and resid 454 through 464 removed outlier: 3.523A pdb=" N THR D 459 " --> pdb=" O PRO D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 500 removed outlier: 3.988A pdb=" N ARG D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 522 removed outlier: 3.608A pdb=" N CYS D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 541 Processing helix chain 'D' and resid 559 through 576 removed outlier: 3.503A pdb=" N SER D 569 " --> pdb=" O SER D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 591 removed outlier: 3.550A pdb=" N GLU D 590 " --> pdb=" O ARG D 586 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 591 " --> pdb=" O ASN D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 617 removed outlier: 4.464A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 58 removed outlier: 3.948A pdb=" N GLU C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 58' Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.715A pdb=" N ARG C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR C 75 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 97 Processing helix chain 'C' and resid 124 through 135 removed outlier: 3.928A pdb=" N LYS C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 169 removed outlier: 3.858A pdb=" N ASN C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 169 " --> pdb=" O PHE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.845A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLY C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N CYS C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 removed outlier: 3.591A pdb=" N ARG C 211 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 236 removed outlier: 3.742A pdb=" N ARG C 236 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 249 removed outlier: 4.087A pdb=" N ALA C 247 " --> pdb=" O CYS C 243 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 291 through 312 removed outlier: 3.629A pdb=" N ALA C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 303 " --> pdb=" O GLN C 299 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 353 removed outlier: 3.817A pdb=" N PHE C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 409 removed outlier: 3.551A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 396 " --> pdb=" O THR C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 Processing helix chain 'C' and resid 454 through 464 removed outlier: 3.521A pdb=" N THR C 459 " --> pdb=" O PRO C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 500 removed outlier: 3.749A pdb=" N ARG C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 522 removed outlier: 3.609A pdb=" N CYS C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 541 Processing helix chain 'C' and resid 559 through 576 Processing helix chain 'C' and resid 578 through 591 removed outlier: 3.552A pdb=" N GLU C 590 " --> pdb=" O ARG C 586 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 591 " --> pdb=" O ASN C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 602 Processing helix chain 'C' and resid 602 through 617 removed outlier: 3.589A pdb=" N SER C 614 " --> pdb=" O HIS C 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 4.013A pdb=" N LEU A 116 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 64 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 117 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 66 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE A 30 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N HIS A 180 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 32 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 175 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE A 201 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA A 177 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR A 203 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE A 179 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N VAL A 254 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR A 200 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR A 256 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE A 202 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 276 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 257 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.417A pdb=" N LEU A 324 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE A 365 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 326 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE A 367 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 328 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N LEU A 502 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N THR A 529 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU A 553 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER A 528 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.787A pdb=" N ASN A 374 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.514A pdb=" N LEU B 64 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU B 117 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY B 66 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE B 30 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N HIS B 180 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 32 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N VAL B 254 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR B 200 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR B 256 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE B 202 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 276 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B 257 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 477 removed outlier: 6.419A pdb=" N LEU B 324 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE B 365 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE B 326 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE B 367 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 328 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LEU B 502 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N THR B 529 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU B 553 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER B 528 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 372 through 375 removed outlier: 3.804A pdb=" N ASN B 374 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.510A pdb=" N LEU D 64 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU D 117 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY D 66 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE D 30 " --> pdb=" O HIS D 178 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N HIS D 180 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL D 32 " --> pdb=" O HIS D 180 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL D 175 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE D 201 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA D 177 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR D 203 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE D 179 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N VAL D 254 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR D 200 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR D 256 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE D 202 " --> pdb=" O THR D 256 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE D 276 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR D 257 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 473 through 475 removed outlier: 6.692A pdb=" N VAL D 362 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU D 324 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE D 365 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE D 326 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE D 367 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LEU D 502 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR D 529 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU D 553 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N SER D 528 " --> pdb=" O LEU D 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 374 through 375 removed outlier: 3.771A pdb=" N ASN D 374 " --> pdb=" O ASN D 447 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 77 through 79 removed outlier: 3.619A pdb=" N LEU C 116 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 66 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 28 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N HIS C 178 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE C 30 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N HIS C 180 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 32 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N VAL C 254 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR C 200 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR C 256 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE C 202 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 276 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 257 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 473 through 477 removed outlier: 6.416A pdb=" N LEU C 324 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE C 365 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE C 326 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE C 367 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU C 502 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR C 529 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU C 553 " --> pdb=" O SER C 526 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER C 528 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 372 through 375 removed outlier: 3.798A pdb=" N ASN C 374 " --> pdb=" O ASN C 447 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2514 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3298 1.30 - 1.43: 6025 1.43 - 1.56: 11498 1.56 - 1.69: 4 1.69 - 1.83: 156 Bond restraints: 20981 Sorted by residual: bond pdb=" C ASN B 228 " pdb=" N VAL B 229 " ideal model delta sigma weight residual 1.333 1.227 0.106 1.24e-02 6.50e+03 7.31e+01 bond pdb=" C ASN C 228 " pdb=" N VAL C 229 " ideal model delta sigma weight residual 1.333 1.432 -0.098 1.24e-02 6.50e+03 6.25e+01 bond pdb=" O6 G6P B 701 " pdb=" P G6P B 701 " ideal model delta sigma weight residual 1.722 1.580 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" O6 G6P C 701 " pdb=" P G6P C 701 " ideal model delta sigma weight residual 1.722 1.609 0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" O6 G6P A 701 " pdb=" P G6P A 701 " ideal model delta sigma weight residual 1.722 1.610 0.112 2.00e-02 2.50e+03 3.11e+01 ... (remaining 20976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 24288 2.24 - 4.49: 3850 4.49 - 6.73: 273 6.73 - 8.97: 33 8.97 - 11.22: 8 Bond angle restraints: 28452 Sorted by residual: angle pdb=" N TYR D 514 " pdb=" CA TYR D 514 " pdb=" C TYR D 514 " ideal model delta sigma weight residual 113.55 102.33 11.22 1.26e+00 6.30e-01 7.92e+01 angle pdb=" N TYR C 508 " pdb=" CA TYR C 508 " pdb=" C TYR C 508 " ideal model delta sigma weight residual 113.55 103.69 9.86 1.26e+00 6.30e-01 6.13e+01 angle pdb=" N TYR B 508 " pdb=" CA TYR B 508 " pdb=" C TYR B 508 " ideal model delta sigma weight residual 113.18 103.05 10.13 1.33e+00 5.65e-01 5.80e+01 angle pdb=" N ARG D 603 " pdb=" CA ARG D 603 " pdb=" C ARG D 603 " ideal model delta sigma weight residual 111.36 103.20 8.16 1.09e+00 8.42e-01 5.60e+01 angle pdb=" C PRO C 112 " pdb=" CA PRO C 112 " pdb=" CB PRO C 112 " ideal model delta sigma weight residual 111.46 102.32 9.14 1.29e+00 6.01e-01 5.02e+01 ... (remaining 28447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 10349 14.84 - 29.68: 1356 29.68 - 44.52: 490 44.52 - 59.36: 137 59.36 - 74.20: 42 Dihedral angle restraints: 12374 sinusoidal: 4974 harmonic: 7400 Sorted by residual: dihedral pdb=" C LEU B 488 " pdb=" N LEU B 488 " pdb=" CA LEU B 488 " pdb=" CB LEU B 488 " ideal model delta harmonic sigma weight residual -122.60 -136.32 13.72 0 2.50e+00 1.60e-01 3.01e+01 dihedral pdb=" C PRO C 112 " pdb=" N PRO C 112 " pdb=" CA PRO C 112 " pdb=" CB PRO C 112 " ideal model delta harmonic sigma weight residual -120.70 -107.17 -13.53 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" C PHE A 312 " pdb=" N PHE A 312 " pdb=" CA PHE A 312 " pdb=" CB PHE A 312 " ideal model delta harmonic sigma weight residual -122.60 -109.60 -13.00 0 2.50e+00 1.60e-01 2.70e+01 ... (remaining 12371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2045 0.096 - 0.193: 797 0.193 - 0.289: 184 0.289 - 0.385: 27 0.385 - 0.482: 11 Chirality restraints: 3064 Sorted by residual: chirality pdb=" CA LEU B 488 " pdb=" N LEU B 488 " pdb=" C LEU B 488 " pdb=" CB LEU B 488 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA TYR D 604 " pdb=" N TYR D 604 " pdb=" C TYR D 604 " pdb=" CB TYR D 604 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CG LEU B 126 " pdb=" CB LEU B 126 " pdb=" CD1 LEU B 126 " pdb=" CD2 LEU B 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 3061 not shown) Planarity restraints: 3653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 507 " -0.027 2.00e-02 2.50e+03 5.55e-02 3.09e+01 pdb=" C SER B 507 " 0.096 2.00e-02 2.50e+03 pdb=" O SER B 507 " -0.037 2.00e-02 2.50e+03 pdb=" N TYR B 508 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 399 " 0.026 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C LYS A 399 " -0.094 2.00e-02 2.50e+03 pdb=" O LYS A 399 " 0.036 2.00e-02 2.50e+03 pdb=" N PHE A 400 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 602 " -0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C GLY D 602 " 0.079 2.00e-02 2.50e+03 pdb=" O GLY D 602 " -0.030 2.00e-02 2.50e+03 pdb=" N ARG D 603 " -0.027 2.00e-02 2.50e+03 ... (remaining 3650 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3618 2.80 - 3.32: 19367 3.32 - 3.85: 35354 3.85 - 4.37: 43545 4.37 - 4.90: 71490 Nonbonded interactions: 173374 Sorted by model distance: nonbonded pdb=" OG SER B 259 " pdb=" O PRO B 511 " model vdw 2.272 3.040 nonbonded pdb=" OG SER A 259 " pdb=" O PRO A 511 " model vdw 2.322 3.040 nonbonded pdb=" OG SER D 259 " pdb=" O PRO D 511 " model vdw 2.364 3.040 nonbonded pdb=" OG SER D 407 " pdb=" O SER D 412 " model vdw 2.364 3.040 nonbonded pdb=" OG SER C 259 " pdb=" O PRO C 511 " model vdw 2.403 3.040 ... (remaining 173369 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' and ((resid 24 through 25 and (name N or name CA or name C or name O \ or name CB )) or resid 26 through 94 or (resid 95 and (name N or name CA or name \ C or name O or name CB )) or resid 96 or (resid 97 and (name N or name CA or na \ me C or name O or name CB )) or resid 98 through 108 or (resid 109 and (name N o \ r name CA or name C or name O or name CB )) or resid 110 through 126 or (resid 1 \ 27 through 128 and (name N or name CA or name C or name O or name CB )) or resid \ 129 through 377 or (resid 378 and (name N or name CA or name C or name O or nam \ e CB )) or resid 379 through 422 or (resid 423 and (name N or name CA or name C \ or name O or name CB )) or resid 424 through 437 or (resid 438 and (name N or na \ me CA or name C or name O or name CB )) or resid 439 through 623 or (resid 624 a \ nd (name N or name CA or name C or name O or name CB )) or resid 625 through 701 \ )) selection = (chain 'B' and ((resid 24 through 25 and (name N or name CA or name C or name O \ or name CB )) or resid 26 through 77 or (resid 78 and (name N or name CA or name \ C or name O or name CB )) or resid 79 through 94 or (resid 95 and (name N or na \ me CA or name C or name O or name CB )) or resid 96 or (resid 97 and (name N or \ name CA or name C or name O or name CB )) or resid 98 through 108 or (resid 109 \ and (name N or name CA or name C or name O or name CB )) or resid 110 through 13 \ 4 or (resid 135 and (name N or name CA or name C or name O or name CB )) or resi \ d 136 through 377 or (resid 378 and (name N or name CA or name C or name O or na \ me CB )) or resid 379 through 420 or (resid 421 and (name N or name CA or name C \ or name O or name CB )) or resid 422 or (resid 423 and (name N or name CA or na \ me C or name O or name CB )) or resid 424 through 437 or (resid 438 and (name N \ or name CA or name C or name O or name CB )) or resid 439 through 623 or (resid \ 624 and (name N or name CA or name C or name O or name CB )) or resid 625 throug \ h 701)) selection = (chain 'C' and (resid 24 through 126 or (resid 127 through 128 and (name N or na \ me CA or name C or name O or name CB )) or resid 129 through 420 or (resid 421 a \ nd (name N or name CA or name C or name O or name CB )) or resid 422 through 437 \ or (resid 438 and (name N or name CA or name C or name O or name CB )) or resid \ 439 through 622 or (resid 623 through 624 and (name N or name CA or name C or n \ ame O or name CB )) or resid 625 through 701)) selection = (chain 'D' and ((resid 24 through 25 and (name N or name CA or name C or name O \ or name CB )) or resid 26 through 94 or (resid 95 and (name N or name CA or name \ C or name O or name CB )) or resid 96 or (resid 97 and (name N or name CA or na \ me C or name O or name CB )) or resid 98 through 108 or (resid 109 and (name N o \ r name CA or name C or name O or name CB )) or resid 110 through 126 or (resid 1 \ 27 through 128 and (name N or name CA or name C or name O or name CB )) or resid \ 129 through 377 or (resid 378 and (name N or name CA or name C or name O or nam \ e CB )) or resid 379 through 420 or (resid 421 and (name N or name CA or name C \ or name O or name CB )) or resid 422 or (resid 423 and (name N or name CA or nam \ e C or name O or name CB )) or resid 424 through 701)) } ncs_group { reference = (chain 'E' and (resid 318 through 325 or (resid 326 through 327 and (name N or n \ ame CA or name C or name O or name CB )) or resid 328 through 330 or (resid 331 \ and (name N or name CA or name C or name O or name CB )) or resid 332 through 34 \ 9)) selection = (chain 'F' and (resid 318 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB )) or resid 325 or (resid 326 through 327 and (name N \ or name CA or name C or name O or name CB )) or resid 328 through 330 or (resid \ 331 and (name N or name CA or name C or name O or name CB )) or resid 332 throug \ h 349)) selection = (chain 'G' and (resid 318 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB )) or resid 325 or (resid 326 through 327 and (name N \ or name CA or name C or name O or name CB )) or resid 328 through 349)) selection = (chain 'H' and (resid 318 through 326 or (resid 327 and (name N or name CA or na \ me C or name O or name CB )) or resid 328 through 330 or (resid 331 and (name N \ or name CA or name C or name O or name CB )) or resid 332 through 349)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.410 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 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 : 0.009 0.142 20981 Z= 0.636 Angle : 1.578 11.216 28452 Z= 1.111 Chirality : 0.106 0.482 3064 Planarity : 0.007 0.056 3653 Dihedral : 16.382 74.196 7612 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 5.13 % Allowed : 13.15 % Favored : 81.72 % Cbeta Deviations : 0.67 % 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: -3.03 (0.15), residues: 2525 helix: -2.01 (0.12), residues: 1324 sheet: -1.32 (0.30), residues: 310 loop : -1.95 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG B 582 TYR 0.029 0.004 TYR B 102 PHE 0.032 0.004 PHE A 400 TRP 0.034 0.005 TRP F 325 HIS 0.033 0.004 HIS A 610 Details of bonding type rmsd covalent geometry : bond 0.00906 (20981) covalent geometry : angle 1.57834 (28452) hydrogen bonds : bond 0.26541 ( 843) hydrogen bonds : angle 9.29801 ( 2514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 400 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6542 (tp) REVERT: A 205 HIS cc_start: 0.8224 (m-70) cc_final: 0.7927 (m90) REVERT: A 241 ARG cc_start: 0.7069 (mtt180) cc_final: 0.6674 (mtt180) REVERT: A 244 MET cc_start: 0.7399 (ttm) cc_final: 0.7122 (mtp) REVERT: A 268 HIS cc_start: 0.7716 (m-70) cc_final: 0.7352 (m-70) REVERT: A 611 MET cc_start: 0.7261 (ttm) cc_final: 0.6465 (mmt) REVERT: B 94 MET cc_start: 0.6501 (tpt) cc_final: 0.5906 (ttp) REVERT: B 102 TYR cc_start: 0.6149 (m-80) cc_final: 0.5928 (m-80) REVERT: B 272 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8241 (tpt-90) REVERT: B 606 MET cc_start: 0.6710 (ttt) cc_final: 0.6281 (ttm) REVERT: B 610 HIS cc_start: 0.6519 (m-70) cc_final: 0.5895 (m-70) REVERT: D 58 TRP cc_start: 0.6622 (m-90) cc_final: 0.6146 (m-90) REVERT: D 102 TYR cc_start: 0.6561 (m-80) cc_final: 0.5497 (m-80) REVERT: D 328 ILE cc_start: 0.7490 (tt) cc_final: 0.7264 (tt) REVERT: D 522 MET cc_start: 0.8140 (mtt) cc_final: 0.7834 (mtt) REVERT: C 265 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6511 (mt-10) REVERT: C 352 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8144 (mp) REVERT: C 383 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: C 388 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6501 (pt0) outliers start: 110 outliers final: 17 residues processed: 485 average time/residue: 0.1608 time to fit residues: 116.2878 Evaluate side-chains 259 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 388 GLN Chi-restraints excluded: chain C residue 622 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 222 ASN A 228 ASN A 253 HIS A 291 HIS A 315 HIS A 383 GLN A 576 GLN G 340 ASN B 149 ASN B 250 HIS B 253 HIS B 260 GLN B 319 ASN B 360 GLN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 HIS B 620 HIS D 95 ASN D 178 HIS D 205 HIS D 228 ASN D 250 HIS D 253 HIS D 280 ASN D 291 HIS D 295 ASN D 436 GLN D 610 HIS C 26 ASN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 250 HIS C 253 HIS C 383 GLN C 436 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.215365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.181389 restraints weight = 22511.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.180241 restraints weight = 47786.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.180032 restraints weight = 44706.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.179262 restraints weight = 26295.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.180155 restraints weight = 21325.796| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20981 Z= 0.146 Angle : 0.609 12.401 28452 Z= 0.323 Chirality : 0.042 0.162 3064 Planarity : 0.004 0.039 3653 Dihedral : 6.378 58.588 2939 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.66 % Allowed : 18.14 % Favored : 79.20 % 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: -1.67 (0.15), residues: 2525 helix: -0.73 (0.13), residues: 1280 sheet: -1.23 (0.32), residues: 271 loop : -1.39 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 462 TYR 0.023 0.002 TYR A 239 PHE 0.032 0.002 PHE C 156 TRP 0.038 0.002 TRP A 134 HIS 0.012 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00323 (20981) covalent geometry : angle 0.60916 (28452) hydrogen bonds : bond 0.05419 ( 843) hydrogen bonds : angle 5.25499 ( 2514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 THR cc_start: 0.8584 (t) cc_final: 0.8336 (t) REVERT: B 294 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7165 (mt0) REVERT: B 473 VAL cc_start: 0.8070 (p) cc_final: 0.7721 (m) REVERT: D 94 MET cc_start: 0.5889 (ttt) cc_final: 0.5137 (mmm) REVERT: D 522 MET cc_start: 0.8156 (mtt) cc_final: 0.7736 (mtt) REVERT: D 603 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6814 (ttm170) REVERT: D 606 MET cc_start: 0.6348 (mtp) cc_final: 0.6086 (mtm) REVERT: C 52 LYS cc_start: 0.8137 (tttp) cc_final: 0.7863 (tppt) REVERT: C 94 MET cc_start: 0.5842 (tpt) cc_final: 0.5240 (tpt) REVERT: C 113 LEU cc_start: 0.7669 (mp) cc_final: 0.7371 (mt) REVERT: C 294 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.6987 (mt0) REVERT: C 301 LYS cc_start: 0.7707 (tttt) cc_final: 0.7395 (tttm) REVERT: C 351 TYR cc_start: 0.7512 (t80) cc_final: 0.7249 (t80) REVERT: C 383 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8247 (mp10) REVERT: C 402 ARG cc_start: 0.7547 (ptt90) cc_final: 0.7115 (mtm110) REVERT: C 510 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: C 599 LYS cc_start: 0.8521 (mppt) cc_final: 0.8255 (mppt) outliers start: 57 outliers final: 21 residues processed: 323 average time/residue: 0.1588 time to fit residues: 76.9751 Evaluate side-chains 259 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 250 HIS Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 388 GLN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 569 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 111 optimal weight: 7.9990 chunk 17 optimal weight: 0.3980 chunk 221 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 186 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 315 HIS ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 577 GLN D 260 GLN D 295 ASN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.206606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.191498 restraints weight = 22268.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 89)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.173090 restraints weight = 52901.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.165107 restraints weight = 44217.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.163463 restraints weight = 32716.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.162855 restraints weight = 28162.727| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20981 Z= 0.140 Angle : 0.542 7.688 28452 Z= 0.286 Chirality : 0.041 0.171 3064 Planarity : 0.004 0.039 3653 Dihedral : 5.771 59.232 2914 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.66 % Allowed : 18.56 % Favored : 78.78 % 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: -1.11 (0.16), residues: 2525 helix: -0.10 (0.14), residues: 1279 sheet: -1.34 (0.31), residues: 284 loop : -1.25 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 371 TYR 0.024 0.001 TYR D 221 PHE 0.024 0.002 PHE F 338 TRP 0.038 0.001 TRP A 182 HIS 0.037 0.002 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00322 (20981) covalent geometry : angle 0.54179 (28452) hydrogen bonds : bond 0.04375 ( 843) hydrogen bonds : angle 4.76842 ( 2514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 245 time to evaluate : 0.748 Fit side-chains REVERT: A 260 GLN cc_start: 0.6676 (mp10) cc_final: 0.6104 (mp10) REVERT: A 360 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.5990 (mp10) REVERT: B 204 THR cc_start: 0.8765 (t) cc_final: 0.8501 (t) REVERT: B 402 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7143 (mtm110) REVERT: B 421 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: D 94 MET cc_start: 0.6150 (ttt) cc_final: 0.5236 (mmm) REVERT: D 471 ASP cc_start: 0.7155 (m-30) cc_final: 0.6924 (m-30) REVERT: D 522 MET cc_start: 0.8373 (mtt) cc_final: 0.7889 (mtt) REVERT: D 603 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6788 (ttm170) REVERT: D 606 MET cc_start: 0.6266 (mtp) cc_final: 0.5819 (mtm) REVERT: C 113 LEU cc_start: 0.7791 (mp) cc_final: 0.7471 (mt) REVERT: C 244 MET cc_start: 0.8646 (mmm) cc_final: 0.8269 (mtp) REVERT: C 301 LYS cc_start: 0.7905 (tttt) cc_final: 0.7576 (ttpp) REVERT: C 351 TYR cc_start: 0.7830 (t80) cc_final: 0.7148 (t80) REVERT: C 383 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8222 (mp10) REVERT: C 419 MET cc_start: 0.7887 (mmp) cc_final: 0.7620 (mmp) REVERT: C 540 GLU cc_start: 0.6620 (mp0) cc_final: 0.6400 (mp0) REVERT: C 599 LYS cc_start: 0.8653 (mppt) cc_final: 0.8374 (mppt) outliers start: 57 outliers final: 25 residues processed: 291 average time/residue: 0.1576 time to fit residues: 68.3606 Evaluate side-chains 246 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 569 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 12 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN A 478 HIS A 576 GLN B 95 ASN B 291 HIS ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS C 205 HIS C 222 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.200051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.179710 restraints weight = 22253.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.169888 restraints weight = 56069.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.162536 restraints weight = 41473.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.159596 restraints weight = 29546.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.158872 restraints weight = 26844.352| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20981 Z= 0.191 Angle : 0.575 10.008 28452 Z= 0.299 Chirality : 0.043 0.173 3064 Planarity : 0.004 0.056 3653 Dihedral : 5.123 57.061 2898 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.50 % Allowed : 18.33 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.94 (0.16), residues: 2525 helix: 0.16 (0.14), residues: 1276 sheet: -1.53 (0.30), residues: 287 loop : -1.26 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 588 TYR 0.040 0.002 TYR D 221 PHE 0.024 0.002 PHE E 338 TRP 0.049 0.002 TRP A 182 HIS 0.016 0.002 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00453 (20981) covalent geometry : angle 0.57511 (28452) hydrogen bonds : bond 0.04108 ( 843) hydrogen bonds : angle 4.66941 ( 2514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 236 time to evaluate : 0.592 Fit side-chains REVERT: A 34 TRP cc_start: 0.6711 (t-100) cc_final: 0.6413 (t60) REVERT: A 244 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6657 (mpp) REVERT: A 306 GLU cc_start: 0.8251 (mm-30) cc_final: 0.6789 (mt-10) REVERT: A 360 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.6228 (mp10) REVERT: B 106 TRP cc_start: 0.6682 (OUTLIER) cc_final: 0.5708 (t60) REVERT: B 166 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7152 (mp) REVERT: B 204 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8621 (t) REVERT: B 359 GLU cc_start: 0.6057 (tt0) cc_final: 0.5645 (tt0) REVERT: B 573 SER cc_start: 0.8303 (t) cc_final: 0.8021 (m) REVERT: D 522 MET cc_start: 0.8470 (mtt) cc_final: 0.7796 (mtt) REVERT: D 603 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7152 (ttm170) REVERT: D 606 MET cc_start: 0.6223 (mtp) cc_final: 0.5804 (mtm) REVERT: C 34 TRP cc_start: 0.7600 (t-100) cc_final: 0.7387 (t-100) REVERT: C 113 LEU cc_start: 0.7917 (mp) cc_final: 0.7602 (mt) REVERT: C 419 MET cc_start: 0.8022 (mmp) cc_final: 0.7755 (mmp) REVERT: C 510 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: C 540 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: C 597 ASP cc_start: 0.8415 (t0) cc_final: 0.8214 (t0) outliers start: 75 outliers final: 33 residues processed: 296 average time/residue: 0.1545 time to fit residues: 69.1189 Evaluate side-chains 254 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 569 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 139 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 206 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 213 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 78 optimal weight: 0.0370 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 315 HIS A 388 GLN A 576 GLN B 383 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN D 388 GLN D 576 GLN C 205 HIS C 222 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.202588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.187438 restraints weight = 22107.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.182903 restraints weight = 48872.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.172128 restraints weight = 59875.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.164300 restraints weight = 46261.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.163194 restraints weight = 41865.682| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20981 Z= 0.120 Angle : 0.511 6.600 28452 Z= 0.266 Chirality : 0.040 0.172 3064 Planarity : 0.004 0.050 3653 Dihedral : 4.780 39.852 2895 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.66 % Allowed : 20.06 % Favored : 77.29 % 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: -0.60 (0.16), residues: 2525 helix: 0.50 (0.15), residues: 1259 sheet: -1.49 (0.31), residues: 277 loop : -1.13 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 588 TYR 0.016 0.001 TYR C 102 PHE 0.023 0.001 PHE E 338 TRP 0.060 0.002 TRP C 182 HIS 0.014 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00279 (20981) covalent geometry : angle 0.51060 (28452) hydrogen bonds : bond 0.03810 ( 843) hydrogen bonds : angle 4.49219 ( 2514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 0.741 Fit side-chains REVERT: A 244 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6550 (mpp) REVERT: A 360 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.6157 (mp10) REVERT: B 106 TRP cc_start: 0.6591 (OUTLIER) cc_final: 0.5837 (t60) REVERT: B 166 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6996 (mp) REVERT: B 204 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8499 (t) REVERT: B 359 GLU cc_start: 0.5998 (tt0) cc_final: 0.5605 (tt0) REVERT: B 573 SER cc_start: 0.8129 (t) cc_final: 0.7912 (m) REVERT: D 94 MET cc_start: 0.5401 (ttt) cc_final: 0.4803 (mmm) REVERT: D 522 MET cc_start: 0.8575 (mtt) cc_final: 0.7822 (mtt) REVERT: D 603 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6983 (ttm170) REVERT: D 606 MET cc_start: 0.6208 (mtp) cc_final: 0.5828 (mtm) REVERT: C 113 LEU cc_start: 0.7880 (mp) cc_final: 0.7675 (mt) REVERT: C 211 ARG cc_start: 0.7566 (mtt-85) cc_final: 0.7323 (mtt-85) REVERT: C 294 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7106 (mt0) REVERT: C 351 TYR cc_start: 0.7939 (t80) cc_final: 0.7578 (t80) REVERT: C 510 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7620 (tt0) outliers start: 57 outliers final: 28 residues processed: 270 average time/residue: 0.1558 time to fit residues: 63.6336 Evaluate side-chains 251 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 510 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 31 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 105 optimal weight: 0.0670 chunk 178 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 315 HIS A 388 GLN A 576 GLN B 268 HIS ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 HIS D 280 ASN D 294 GLN C 205 HIS C 250 HIS ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.202291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.182298 restraints weight = 22075.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.169296 restraints weight = 54720.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.160621 restraints weight = 39029.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.158776 restraints weight = 30599.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.157848 restraints weight = 24920.826| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20981 Z= 0.125 Angle : 0.501 6.623 28452 Z= 0.261 Chirality : 0.040 0.171 3064 Planarity : 0.003 0.042 3653 Dihedral : 4.711 40.774 2895 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.61 % Allowed : 20.43 % Favored : 76.96 % 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 (0.16), residues: 2525 helix: 0.62 (0.15), residues: 1267 sheet: -1.42 (0.31), residues: 276 loop : -1.07 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 588 TYR 0.021 0.001 TYR D 221 PHE 0.023 0.001 PHE C 103 TRP 0.068 0.002 TRP C 182 HIS 0.014 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00295 (20981) covalent geometry : angle 0.50145 (28452) hydrogen bonds : bond 0.03690 ( 843) hydrogen bonds : angle 4.40350 ( 2514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6594 (mpp) REVERT: A 360 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6143 (mp10) REVERT: B 106 TRP cc_start: 0.6644 (OUTLIER) cc_final: 0.5787 (t60) REVERT: B 204 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8568 (t) REVERT: B 359 GLU cc_start: 0.6088 (tt0) cc_final: 0.5755 (tt0) REVERT: B 421 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.6999 (m-30) REVERT: B 573 SER cc_start: 0.8263 (t) cc_final: 0.8018 (m) REVERT: D 94 MET cc_start: 0.5908 (ttt) cc_final: 0.4994 (mmm) REVERT: D 522 MET cc_start: 0.8468 (mtt) cc_final: 0.7703 (mtt) REVERT: D 603 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7088 (ttm170) REVERT: D 606 MET cc_start: 0.6219 (mtp) cc_final: 0.5753 (mtm) REVERT: C 49 THR cc_start: 0.8691 (p) cc_final: 0.8375 (p) REVERT: C 113 LEU cc_start: 0.7953 (mp) cc_final: 0.7718 (mt) REVERT: C 211 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7310 (mtt-85) REVERT: C 294 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7136 (mt0) REVERT: C 351 TYR cc_start: 0.7918 (t80) cc_final: 0.7568 (t80) outliers start: 56 outliers final: 33 residues processed: 261 average time/residue: 0.1522 time to fit residues: 60.7384 Evaluate side-chains 250 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 143 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 245 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 576 GLN B 48 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 GLN D 577 GLN D 585 GLN C 205 HIS C 250 HIS ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.198703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3649 r_free = 0.3649 target = 0.156105 restraints weight = 22277.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.153996 restraints weight = 24982.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.153822 restraints weight = 22572.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.153840 restraints weight = 18093.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.153917 restraints weight = 16633.668| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20981 Z= 0.187 Angle : 0.553 7.060 28452 Z= 0.287 Chirality : 0.043 0.179 3064 Planarity : 0.004 0.044 3653 Dihedral : 4.864 46.400 2895 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.71 % Allowed : 20.57 % Favored : 76.73 % 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: -0.58 (0.16), residues: 2525 helix: 0.54 (0.15), residues: 1273 sheet: -1.64 (0.29), residues: 300 loop : -1.12 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 588 TYR 0.031 0.002 TYR D 221 PHE 0.023 0.002 PHE C 103 TRP 0.082 0.002 TRP C 182 HIS 0.014 0.002 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00450 (20981) covalent geometry : angle 0.55339 (28452) hydrogen bonds : bond 0.03775 ( 843) hydrogen bonds : angle 4.42884 ( 2514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6598 (mpp) REVERT: A 306 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 360 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.6238 (mp10) REVERT: A 604 TYR cc_start: 0.7891 (m-80) cc_final: 0.7499 (m-80) REVERT: B 47 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8666 (mp) REVERT: B 106 TRP cc_start: 0.6752 (OUTLIER) cc_final: 0.5785 (t60) REVERT: B 204 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8671 (t) REVERT: B 351 TYR cc_start: 0.7486 (t80) cc_final: 0.7247 (t80) REVERT: B 359 GLU cc_start: 0.5996 (tt0) cc_final: 0.5751 (tt0) REVERT: B 421 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: B 427 MET cc_start: 0.7447 (ptt) cc_final: 0.7108 (ptt) REVERT: B 573 SER cc_start: 0.8471 (t) cc_final: 0.8158 (m) REVERT: D 94 MET cc_start: 0.5914 (ttt) cc_final: 0.5084 (mmm) REVERT: D 522 MET cc_start: 0.8536 (mtt) cc_final: 0.7809 (mtt) REVERT: D 603 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.7065 (ttm170) REVERT: D 606 MET cc_start: 0.6359 (mtp) cc_final: 0.5903 (mtm) REVERT: C 49 THR cc_start: 0.8805 (p) cc_final: 0.8483 (p) REVERT: C 294 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7283 (mt0) outliers start: 58 outliers final: 38 residues processed: 271 average time/residue: 0.1527 time to fit residues: 63.7153 Evaluate side-chains 263 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 217 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 167 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 181 optimal weight: 0.0370 chunk 89 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 230 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 446 HIS B 446 HIS D 388 GLN C 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.200185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.179228 restraints weight = 22057.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.165557 restraints weight = 56799.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.157188 restraints weight = 40500.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.155913 restraints weight = 32921.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.155834 restraints weight = 23876.175| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20981 Z= 0.141 Angle : 0.525 9.254 28452 Z= 0.272 Chirality : 0.041 0.178 3064 Planarity : 0.003 0.045 3653 Dihedral : 4.807 50.541 2895 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.43 % Allowed : 21.08 % Favored : 76.49 % 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: -0.49 (0.16), residues: 2525 helix: 0.66 (0.15), residues: 1279 sheet: -1.67 (0.30), residues: 298 loop : -1.13 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 402 TYR 0.023 0.001 TYR A 242 PHE 0.023 0.001 PHE C 103 TRP 0.085 0.002 TRP C 182 HIS 0.015 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00335 (20981) covalent geometry : angle 0.52497 (28452) hydrogen bonds : bond 0.03644 ( 843) hydrogen bonds : angle 4.33314 ( 2514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6501 (mpp) REVERT: A 360 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.6281 (mp10) REVERT: A 604 TYR cc_start: 0.7891 (m-80) cc_final: 0.7520 (m-80) REVERT: B 106 TRP cc_start: 0.6618 (OUTLIER) cc_final: 0.5713 (t60) REVERT: B 117 LEU cc_start: 0.6966 (mp) cc_final: 0.6459 (tt) REVERT: B 204 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8660 (t) REVERT: B 344 GLU cc_start: 0.7657 (pt0) cc_final: 0.7448 (pt0) REVERT: B 359 GLU cc_start: 0.6102 (tt0) cc_final: 0.5883 (tt0) REVERT: B 421 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: B 573 SER cc_start: 0.8450 (t) cc_final: 0.8198 (m) REVERT: D 94 MET cc_start: 0.5971 (ttt) cc_final: 0.5085 (mmm) REVERT: D 337 LYS cc_start: 0.8352 (tppt) cc_final: 0.8066 (tppt) REVERT: D 603 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.7065 (ttm170) REVERT: D 606 MET cc_start: 0.6303 (mtp) cc_final: 0.5872 (mtm) REVERT: C 34 TRP cc_start: 0.7470 (t-100) cc_final: 0.7265 (t-100) REVERT: C 49 THR cc_start: 0.8736 (p) cc_final: 0.8416 (p) REVERT: C 211 ARG cc_start: 0.7625 (mtt-85) cc_final: 0.7403 (mtt-85) REVERT: C 268 HIS cc_start: 0.7493 (m-70) cc_final: 0.7185 (m90) REVERT: C 294 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: C 522 MET cc_start: 0.8388 (mtt) cc_final: 0.8179 (ptp) REVERT: C 599 LYS cc_start: 0.8779 (mppt) cc_final: 0.8495 (mppt) outliers start: 52 outliers final: 35 residues processed: 259 average time/residue: 0.1476 time to fit residues: 59.2276 Evaluate side-chains 251 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 129 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 184 optimal weight: 0.1980 chunk 157 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN D 283 ASN ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** 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 = 0.4041 r_free = 0.4041 target = 0.194721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.173700 restraints weight = 22194.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.156291 restraints weight = 59748.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.146862 restraints weight = 39912.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.146566 restraints weight = 28912.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.146358 restraints weight = 25609.006| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 20981 Z= 0.251 Angle : 0.618 7.406 28452 Z= 0.320 Chirality : 0.045 0.240 3064 Planarity : 0.004 0.041 3653 Dihedral : 5.179 58.115 2895 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.38 % Allowed : 21.41 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2525 helix: 0.37 (0.14), residues: 1274 sheet: -1.80 (0.29), residues: 294 loop : -1.28 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 241 TYR 0.025 0.002 TYR D 221 PHE 0.025 0.002 PHE C 103 TRP 0.099 0.002 TRP C 182 HIS 0.014 0.002 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00611 (20981) covalent geometry : angle 0.61768 (28452) hydrogen bonds : bond 0.03974 ( 843) hydrogen bonds : angle 4.55270 ( 2514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6559 (mpp) REVERT: A 250 HIS cc_start: 0.8084 (t-170) cc_final: 0.7872 (t-170) REVERT: A 306 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8030 (mm-30) REVERT: A 360 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.6412 (mp10) REVERT: A 604 TYR cc_start: 0.8082 (m-80) cc_final: 0.7609 (m-80) REVERT: B 47 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8662 (mp) REVERT: B 50 LYS cc_start: 0.8224 (tttp) cc_final: 0.8020 (tttp) REVERT: B 106 TRP cc_start: 0.6653 (OUTLIER) cc_final: 0.5610 (t60) REVERT: B 427 MET cc_start: 0.7937 (ptt) cc_final: 0.7602 (ptt) REVERT: B 573 SER cc_start: 0.8711 (t) cc_final: 0.8372 (m) REVERT: D 260 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7158 (mt0) REVERT: D 273 LYS cc_start: 0.8060 (tmtt) cc_final: 0.7768 (tptp) REVERT: D 337 LYS cc_start: 0.8359 (tppt) cc_final: 0.8094 (tppt) REVERT: D 418 LYS cc_start: 0.7858 (ptpp) cc_final: 0.7363 (pptt) REVERT: D 603 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7132 (ttm170) REVERT: D 606 MET cc_start: 0.6333 (mtp) cc_final: 0.5893 (mtm) REVERT: C 34 TRP cc_start: 0.7524 (t-100) cc_final: 0.7319 (t-100) REVERT: C 49 THR cc_start: 0.8825 (p) cc_final: 0.8506 (p) REVERT: C 294 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7565 (mt0) outliers start: 51 outliers final: 38 residues processed: 262 average time/residue: 0.1527 time to fit residues: 61.4072 Evaluate side-chains 266 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 544 ASP Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 198 optimal weight: 7.9990 chunk 236 optimal weight: 0.6980 chunk 150 optimal weight: 0.2980 chunk 242 optimal weight: 0.7980 chunk 171 optimal weight: 0.2980 chunk 191 optimal weight: 5.9990 chunk 17 optimal weight: 0.0970 chunk 165 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 222 ASN A 250 HIS ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 268 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.201817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.182035 restraints weight = 22111.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.165471 restraints weight = 57702.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.157399 restraints weight = 39906.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.156009 restraints weight = 26477.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.155348 restraints weight = 22715.071| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20981 Z= 0.113 Angle : 0.515 9.160 28452 Z= 0.268 Chirality : 0.040 0.254 3064 Planarity : 0.003 0.046 3653 Dihedral : 4.859 57.065 2895 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.91 % Allowed : 22.11 % Favored : 75.98 % 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: -0.48 (0.16), residues: 2525 helix: 0.73 (0.15), residues: 1273 sheet: -1.68 (0.30), residues: 294 loop : -1.20 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 241 TYR 0.024 0.001 TYR A 242 PHE 0.022 0.001 PHE C 103 TRP 0.091 0.002 TRP A 182 HIS 0.015 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00260 (20981) covalent geometry : angle 0.51480 (28452) hydrogen bonds : bond 0.03567 ( 843) hydrogen bonds : angle 4.29289 ( 2514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6418 (mpp) REVERT: A 604 TYR cc_start: 0.7876 (m-80) cc_final: 0.7548 (m-80) REVERT: B 106 TRP cc_start: 0.6516 (OUTLIER) cc_final: 0.5560 (t60) REVERT: B 117 LEU cc_start: 0.7003 (mp) cc_final: 0.6508 (tt) REVERT: B 204 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8582 (t) REVERT: B 244 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7417 (tpp) REVERT: B 573 SER cc_start: 0.8301 (t) cc_final: 0.8071 (m) REVERT: D 260 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7059 (mt0) REVERT: D 603 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.7068 (ttm170) REVERT: D 606 MET cc_start: 0.6158 (mtp) cc_final: 0.5700 (mtm) REVERT: C 49 THR cc_start: 0.8710 (p) cc_final: 0.8387 (p) REVERT: C 294 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.6877 (mt0) REVERT: C 599 LYS cc_start: 0.8721 (mppt) cc_final: 0.8433 (mppt) outliers start: 41 outliers final: 23 residues processed: 245 average time/residue: 0.1516 time to fit residues: 56.7869 Evaluate side-chains 239 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 237 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 141 optimal weight: 0.0870 chunk 172 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 78 optimal weight: 40.0000 chunk 46 optimal weight: 0.4980 chunk 65 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 222 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.198496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.175623 restraints weight = 22100.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.161124 restraints weight = 59539.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.152685 restraints weight = 42245.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.152646 restraints weight = 37647.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.151457 restraints weight = 30340.505| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20981 Z= 0.161 Angle : 0.547 8.223 28452 Z= 0.283 Chirality : 0.042 0.191 3064 Planarity : 0.004 0.043 3653 Dihedral : 4.867 55.991 2895 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.82 % Allowed : 22.39 % Favored : 75.79 % 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: -0.50 (0.17), residues: 2525 helix: 0.66 (0.15), residues: 1294 sheet: -1.70 (0.30), residues: 294 loop : -1.16 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 303 TYR 0.026 0.001 TYR C 572 PHE 0.023 0.002 PHE C 103 TRP 0.085 0.002 TRP A 182 HIS 0.015 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00388 (20981) covalent geometry : angle 0.54681 (28452) hydrogen bonds : bond 0.03651 ( 843) hydrogen bonds : angle 4.31684 ( 2514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3286.23 seconds wall clock time: 57 minutes 47.30 seconds (3467.30 seconds total)