Starting phenix.real_space_refine on Tue Jun 17 23:09:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvx_27020/06_2025/8cvx_27020.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvx_27020/06_2025/8cvx_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_27020/06_2025/8cvx_27020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvx_27020/06_2025/8cvx_27020.map" model { file = "/net/cci-nas-00/data/ceres_data/8cvx_27020/06_2025/8cvx_27020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvx_27020/06_2025/8cvx_27020.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.211 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'ARG:plan': 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: {'GLU:plan': 1, 'ARG: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: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP: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, 'ARG:plan': 1, 'ASP: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: 12.79, per 1000 atoms: 0.63 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: 4.98 Conformation dependent library (CDL) restraints added in 2.9 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: 2.28 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: 6.58 Time building geometry restraints manager: 6.06 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 or resid 70 \ 1)) 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 or res \ id 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 or resid 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 625 or resid 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 48.430 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.034 0.005 TRP F 325 HIS 0.033 0.004 HIS A 610 PHE 0.032 0.004 PHE A 400 TYR 0.029 0.004 TYR B 102 ARG 0.033 0.002 ARG B 582 Details of bonding type rmsd hydrogen bonds : bond 0.26541 ( 843) hydrogen bonds : angle 9.29801 ( 2514) covalent geometry : bond 0.00906 (20981) covalent geometry : angle 1.57834 (28452) *********************** 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 : 2.172 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: 0.3490 time to fit residues: 250.5612 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 : 2.294 ------------------------------------------------------------------------------- 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 212 optimal weight: 0.9980 chunk 191 optimal weight: 7.9990 chunk 105 optimal weight: 0.0470 chunk 65 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 197 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 chunk 228 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN G 340 ASN B 149 ASN B 250 HIS B 253 HIS B 260 GLN B 319 ASN ** 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: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.214504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.182947 restraints weight = 22422.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.182047 restraints weight = 48094.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.181238 restraints weight = 42616.338| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20981 Z= 0.146 Angle : 0.609 12.867 28452 Z= 0.320 Chirality : 0.042 0.153 3064 Planarity : 0.004 0.040 3653 Dihedral : 6.398 58.488 2939 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.71 % Allowed : 18.05 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 2525 helix: -0.69 (0.13), residues: 1283 sheet: -1.24 (0.32), residues: 271 loop : -1.36 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 134 HIS 0.012 0.001 HIS B 240 PHE 0.028 0.002 PHE C 156 TYR 0.025 0.002 TYR A 239 ARG 0.006 0.001 ARG B 588 Details of bonding type rmsd hydrogen bonds : bond 0.05086 ( 843) hydrogen bonds : angle 5.20663 ( 2514) covalent geometry : bond 0.00329 (20981) covalent geometry : angle 0.60885 (28452) *********************** 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 335 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 277 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 THR cc_start: 0.8541 (t) cc_final: 0.8275 (t) REVERT: D 94 MET cc_start: 0.5687 (ttt) cc_final: 0.5091 (mmm) REVERT: D 522 MET cc_start: 0.8183 (mtt) cc_final: 0.7737 (mtt) REVERT: D 603 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6850 (ttm170) REVERT: D 606 MET cc_start: 0.6307 (mtp) cc_final: 0.6077 (mtm) REVERT: C 94 MET cc_start: 0.5849 (tpt) cc_final: 0.5280 (tpt) REVERT: C 113 LEU cc_start: 0.7668 (mp) cc_final: 0.7401 (mt) REVERT: C 294 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.6972 (mt0) REVERT: C 301 LYS cc_start: 0.7703 (tttt) cc_final: 0.7427 (tttm) REVERT: C 351 TYR cc_start: 0.7507 (t80) cc_final: 0.7232 (t80) REVERT: C 383 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: C 402 ARG cc_start: 0.7537 (ptt90) cc_final: 0.7131 (mtm110) REVERT: C 510 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: C 599 LYS cc_start: 0.8506 (mppt) cc_final: 0.8243 (mppt) outliers start: 58 outliers final: 23 residues processed: 326 average time/residue: 0.3812 time to fit residues: 184.6346 Evaluate side-chains 262 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 560 LEU 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 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 103 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 236 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 232 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B 467 ASN B 576 GLN B 577 GLN D 260 GLN D 295 ASN C 178 HIS C 205 HIS C 222 ASN C 305 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.207685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.187406 restraints weight = 22052.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.173131 restraints weight = 55437.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.163293 restraints weight = 38613.867| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20981 Z= 0.149 Angle : 0.545 7.475 28452 Z= 0.288 Chirality : 0.042 0.191 3064 Planarity : 0.004 0.039 3653 Dihedral : 5.641 58.620 2911 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.71 % Allowed : 18.75 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.16), residues: 2525 helix: -0.09 (0.14), residues: 1276 sheet: -1.29 (0.31), residues: 278 loop : -1.28 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 182 HIS 0.030 0.002 HIS D 250 PHE 0.024 0.002 PHE F 338 TYR 0.033 0.001 TYR D 221 ARG 0.008 0.001 ARG B 588 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 843) hydrogen bonds : angle 4.75727 ( 2514) covalent geometry : bond 0.00343 (20981) covalent geometry : angle 0.54492 (28452) *********************** 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 297 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 239 time to evaluate : 2.172 Fit side-chains REVERT: A 260 GLN cc_start: 0.6725 (mp10) cc_final: 0.5933 (mp10) REVERT: B 204 THR cc_start: 0.8778 (t) cc_final: 0.8519 (t) REVERT: B 421 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7162 (m-30) REVERT: B 573 SER cc_start: 0.7886 (t) cc_final: 0.7667 (m) REVERT: D 471 ASP cc_start: 0.7280 (m-30) cc_final: 0.7055 (m-30) REVERT: D 522 MET cc_start: 0.8437 (mtt) cc_final: 0.7892 (mtt) REVERT: D 603 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6767 (ttm170) REVERT: D 606 MET cc_start: 0.6256 (mtp) cc_final: 0.5798 (mtm) REVERT: C 113 LEU cc_start: 0.7784 (mp) cc_final: 0.7441 (mt) REVERT: C 244 MET cc_start: 0.8652 (mmm) cc_final: 0.8291 (mtp) REVERT: C 301 LYS cc_start: 0.7901 (tttt) cc_final: 0.7554 (ttpp) REVERT: C 351 TYR cc_start: 0.8051 (t80) cc_final: 0.7399 (t80) REVERT: C 383 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8265 (mp10) REVERT: C 419 MET cc_start: 0.7943 (mmp) cc_final: 0.7682 (mmp) REVERT: C 540 GLU cc_start: 0.6662 (mp0) cc_final: 0.6450 (mp0) REVERT: C 599 LYS cc_start: 0.8731 (mppt) cc_final: 0.8465 (mppt) outliers start: 58 outliers final: 30 residues processed: 287 average time/residue: 0.3508 time to fit residues: 151.3275 Evaluate side-chains 248 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU 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 214 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 413 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 29 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 111 optimal weight: 0.0570 chunk 155 optimal weight: 0.8980 chunk 44 optimal weight: 0.0870 chunk 77 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 226 optimal weight: 0.5980 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 B 95 ASN B 291 HIS B 383 GLN C 205 HIS C 222 ASN ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.204183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3693 r_free = 0.3693 target = 0.160036 restraints weight = 22180.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.156914 restraints weight = 36401.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.157442 restraints weight = 27939.849| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20981 Z= 0.137 Angle : 0.523 8.932 28452 Z= 0.273 Chirality : 0.041 0.238 3064 Planarity : 0.004 0.040 3653 Dihedral : 4.947 58.348 2898 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.26 % Allowed : 18.33 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2525 helix: 0.24 (0.14), residues: 1282 sheet: -1.44 (0.31), residues: 287 loop : -1.17 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 182 HIS 0.016 0.001 HIS B 240 PHE 0.023 0.001 PHE E 338 TYR 0.015 0.001 TYR C 102 ARG 0.006 0.000 ARG B 588 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 843) hydrogen bonds : angle 4.59606 ( 2514) covalent geometry : bond 0.00311 (20981) covalent geometry : angle 0.52264 (28452) *********************** 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 293 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 223 time to evaluate : 2.915 Fit side-chains REVERT: A 204 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8169 (t) REVERT: A 244 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6497 (mpp) REVERT: B 106 TRP cc_start: 0.6781 (OUTLIER) cc_final: 0.5623 (t60) REVERT: B 204 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8559 (t) REVERT: B 351 TYR cc_start: 0.7222 (t80) cc_final: 0.6909 (t80) REVERT: B 573 SER cc_start: 0.8084 (t) cc_final: 0.7872 (m) REVERT: D 94 MET cc_start: 0.6159 (ttt) cc_final: 0.5128 (mmm) REVERT: D 491 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8272 (m) REVERT: D 522 MET cc_start: 0.8459 (mtt) cc_final: 0.7846 (mtt) REVERT: D 603 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7045 (ttm170) REVERT: D 606 MET cc_start: 0.6216 (mtp) cc_final: 0.5771 (mtm) REVERT: C 34 TRP cc_start: 0.7478 (t-100) cc_final: 0.7239 (t-100) REVERT: C 113 LEU cc_start: 0.7818 (mp) cc_final: 0.7446 (mt) REVERT: C 244 MET cc_start: 0.8764 (mmm) cc_final: 0.8407 (mtp) REVERT: C 301 LYS cc_start: 0.7991 (tttt) cc_final: 0.7586 (tttm) REVERT: C 419 MET cc_start: 0.7970 (mmp) cc_final: 0.7724 (mmp) REVERT: C 510 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: C 540 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6363 (mp0) outliers start: 70 outliers final: 30 residues processed: 277 average time/residue: 0.3958 time to fit residues: 165.9995 Evaluate side-chains 244 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 3.664 ------------------------------------------------------------------------------- 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 204 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 272 ARG 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 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 316 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 323 THR 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 388 GLN Chi-restraints excluded: chain C residue 412 SER 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 Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 106 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 541 HIS B 48 GLN D 205 HIS D 250 HIS D 280 ASN D 577 GLN D 585 GLN C 205 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.197638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.175702 restraints weight = 22333.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.163579 restraints weight = 59229.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.153396 restraints weight = 41765.664| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20981 Z= 0.214 Angle : 0.591 8.324 28452 Z= 0.305 Chirality : 0.044 0.177 3064 Planarity : 0.004 0.048 3653 Dihedral : 5.012 42.000 2895 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.22 % Allowed : 19.31 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2525 helix: 0.32 (0.15), residues: 1260 sheet: -1.56 (0.30), residues: 295 loop : -1.21 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP C 182 HIS 0.016 0.002 HIS B 240 PHE 0.024 0.002 PHE E 338 TYR 0.040 0.002 TYR D 221 ARG 0.009 0.001 ARG C 128 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 843) hydrogen bonds : angle 4.63096 ( 2514) covalent geometry : bond 0.00509 (20981) covalent geometry : angle 0.59095 (28452) *********************** 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 307 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 238 time to evaluate : 2.232 Fit side-chains revert: symmetry clash REVERT: A 34 TRP cc_start: 0.6800 (t-100) cc_final: 0.6472 (t60) REVERT: A 244 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6544 (mpp) REVERT: A 306 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 106 TRP cc_start: 0.6717 (OUTLIER) cc_final: 0.5570 (t60) REVERT: B 204 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8654 (t) REVERT: B 351 TYR cc_start: 0.7812 (t80) cc_final: 0.7488 (t80) REVERT: B 421 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: B 427 MET cc_start: 0.7676 (ptt) cc_final: 0.7349 (ptt) REVERT: B 573 SER cc_start: 0.8161 (t) cc_final: 0.7850 (m) REVERT: D 94 MET cc_start: 0.6026 (ttt) cc_final: 0.5084 (mmm) REVERT: D 522 MET cc_start: 0.8560 (mtt) cc_final: 0.7833 (mtt) REVERT: D 603 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7169 (ttm170) REVERT: D 606 MET cc_start: 0.6184 (mtp) cc_final: 0.5732 (mtm) REVERT: C 49 THR cc_start: 0.8764 (p) cc_final: 0.8461 (p) REVERT: C 211 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.7347 (mtt-85) REVERT: C 294 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7498 (mt0) REVERT: C 419 MET cc_start: 0.8110 (mmp) cc_final: 0.7788 (mmp) REVERT: C 540 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6463 (mp0) outliers start: 69 outliers final: 38 residues processed: 290 average time/residue: 0.3501 time to fit residues: 156.0295 Evaluate side-chains 256 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 2.156 ------------------------------------------------------------------------------- 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 244 MET Chi-restraints excluded: chain A residue 272 ARG 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 568 THR 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 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 316 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 421 ASP 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 250 HIS Chi-restraints excluded: chain D residue 316 LEU 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 45 THR Chi-restraints excluded: chain C residue 129 TRP 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 305 GLN Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 544 ASP Chi-restraints excluded: chain C residue 569 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 105 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 226 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 A 541 HIS B 268 HIS D 388 GLN C 205 HIS C 222 ASN ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.200172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.181248 restraints weight = 22074.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.166827 restraints weight = 52501.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.159967 restraints weight = 47177.046| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4346 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= 0.134 Angle : 0.517 6.853 28452 Z= 0.269 Chirality : 0.041 0.173 3064 Planarity : 0.003 0.041 3653 Dihedral : 4.853 44.815 2895 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.47 % Allowed : 20.62 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 2525 helix: 0.55 (0.15), residues: 1262 sheet: -1.65 (0.30), residues: 301 loop : -1.16 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.001 TRP C 182 HIS 0.020 0.001 HIS D 250 PHE 0.018 0.001 PHE E 338 TYR 0.027 0.001 TYR A 242 ARG 0.006 0.000 ARG C 402 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 843) hydrogen bonds : angle 4.45882 ( 2514) covalent geometry : bond 0.00314 (20981) covalent geometry : angle 0.51702 (28452) *********************** 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 271 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 2.086 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6497 (mpp) REVERT: B 106 TRP cc_start: 0.6691 (OUTLIER) cc_final: 0.5840 (t60) REVERT: B 204 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8587 (t) REVERT: B 351 TYR cc_start: 0.7677 (t80) cc_final: 0.7348 (t80) REVERT: B 421 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.6941 (m-30) REVERT: B 427 MET cc_start: 0.7410 (ptt) cc_final: 0.7054 (ptt) REVERT: B 573 SER cc_start: 0.8524 (t) cc_final: 0.8262 (m) REVERT: D 522 MET cc_start: 0.8528 (mtt) cc_final: 0.7790 (mtt) REVERT: D 590 GLU cc_start: 0.7309 (tm-30) cc_final: 0.7094 (tm-30) REVERT: D 603 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.7065 (ttm170) REVERT: D 606 MET cc_start: 0.6218 (mtp) cc_final: 0.5803 (mtm) REVERT: C 34 TRP cc_start: 0.7643 (t-100) cc_final: 0.7432 (t-100) REVERT: C 49 THR cc_start: 0.8776 (p) cc_final: 0.8472 (p) REVERT: C 211 ARG cc_start: 0.7682 (mtt-85) cc_final: 0.7304 (mtt-85) REVERT: C 294 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7135 (mt0) REVERT: C 540 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: C 599 LYS cc_start: 0.8806 (mppt) cc_final: 0.8560 (mppt) outliers start: 53 outliers final: 35 residues processed: 256 average time/residue: 0.3447 time to fit residues: 135.8480 Evaluate side-chains 248 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 2.101 ------------------------------------------------------------------------------- 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 453 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 606 MET 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 262 THR Chi-restraints excluded: chain B residue 316 LEU 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 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 540 GLU Chi-restraints excluded: chain C residue 544 ASP 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 19 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 179 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 541 HIS D 250 HIS C 205 HIS C 222 ASN C 250 HIS C 268 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.199842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.178625 restraints weight = 22076.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.164815 restraints weight = 60234.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.156279 restraints weight = 43155.939| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4487 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= 0.143 Angle : 0.515 7.475 28452 Z= 0.267 Chirality : 0.041 0.173 3064 Planarity : 0.003 0.045 3653 Dihedral : 4.809 47.483 2895 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.57 % Allowed : 20.76 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2525 helix: 0.59 (0.15), residues: 1276 sheet: -1.66 (0.30), residues: 301 loop : -1.12 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.001 TRP C 182 HIS 0.014 0.001 HIS B 240 PHE 0.020 0.001 PHE A 537 TYR 0.023 0.001 TYR D 221 ARG 0.007 0.000 ARG C 241 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 843) hydrogen bonds : angle 4.37517 ( 2514) covalent geometry : bond 0.00339 (20981) covalent geometry : angle 0.51501 (28452) *********************** 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 272 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 217 time to evaluate : 2.040 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6544 (mpp) REVERT: B 106 TRP cc_start: 0.6684 (OUTLIER) cc_final: 0.5836 (t60) REVERT: B 204 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8613 (t) REVERT: B 351 TYR cc_start: 0.7636 (t80) cc_final: 0.7347 (t80) REVERT: B 421 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: B 427 MET cc_start: 0.7396 (ptt) cc_final: 0.7051 (ptt) REVERT: B 573 SER cc_start: 0.8103 (t) cc_final: 0.7810 (m) REVERT: D 94 MET cc_start: 0.5780 (ttt) cc_final: 0.4843 (mmm) REVERT: D 337 LYS cc_start: 0.8333 (tppt) cc_final: 0.8101 (tppt) REVERT: D 522 MET cc_start: 0.8527 (mtt) cc_final: 0.7772 (mtt) REVERT: D 603 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7107 (ttm170) REVERT: D 606 MET cc_start: 0.6188 (mtp) cc_final: 0.5769 (mtm) REVERT: C 49 THR cc_start: 0.8757 (p) cc_final: 0.8442 (p) REVERT: C 211 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7290 (mtt-85) REVERT: C 268 HIS cc_start: 0.7433 (m-70) cc_final: 0.7122 (m90) REVERT: C 294 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7214 (mt0) REVERT: C 540 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6358 (mp0) REVERT: C 617 PHE cc_start: 0.7407 (m-80) cc_final: 0.7207 (m-80) outliers start: 55 outliers final: 40 residues processed: 256 average time/residue: 0.3263 time to fit residues: 127.6030 Evaluate side-chains 259 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 1.982 ------------------------------------------------------------------------------- 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 214 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 528 SER Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 606 MET 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 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 250 HIS Chi-restraints excluded: chain D residue 290 MET 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 267 GLN Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 388 GLN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 540 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 250 optimal weight: 3.9990 chunk 251 optimal weight: 0.2980 chunk 178 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 213 optimal weight: 0.0470 chunk 146 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 197 optimal weight: 0.0670 overall best weight: 1.4820 ------------------------------------------------------------------------------- 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 D 250 HIS C 205 HIS C 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.197037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.175083 restraints weight = 22237.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.161638 restraints weight = 58228.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.151948 restraints weight = 42145.619| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20981 Z= 0.198 Angle : 0.563 7.531 28452 Z= 0.292 Chirality : 0.043 0.174 3064 Planarity : 0.004 0.042 3653 Dihedral : 4.964 52.960 2895 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.94 % Allowed : 20.66 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2525 helix: 0.52 (0.15), residues: 1274 sheet: -1.81 (0.29), residues: 299 loop : -1.15 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.002 TRP C 182 HIS 0.014 0.001 HIS B 240 PHE 0.019 0.002 PHE E 338 TYR 0.024 0.001 TYR D 221 ARG 0.009 0.000 ARG C 241 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 843) hydrogen bonds : angle 4.44555 ( 2514) covalent geometry : bond 0.00477 (20981) covalent geometry : angle 0.56333 (28452) *********************** 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 280 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TRP cc_start: 0.6844 (t-100) cc_final: 0.6533 (t60) REVERT: A 244 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6571 (mpp) REVERT: A 306 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7975 (mm-30) REVERT: B 106 TRP cc_start: 0.6615 (OUTLIER) cc_final: 0.5703 (t60) REVERT: B 204 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8675 (t) REVERT: B 573 SER cc_start: 0.8482 (t) cc_final: 0.8253 (m) REVERT: D 94 MET cc_start: 0.5840 (ttt) cc_final: 0.4907 (mmm) REVERT: D 337 LYS cc_start: 0.8495 (tppt) cc_final: 0.8217 (tppt) REVERT: D 522 MET cc_start: 0.8509 (mtt) cc_final: 0.7729 (mtt) REVERT: D 603 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7114 (ttm170) REVERT: D 606 MET cc_start: 0.6211 (mtp) cc_final: 0.5787 (mtm) REVERT: C 49 THR cc_start: 0.8802 (p) cc_final: 0.8499 (p) REVERT: C 268 HIS cc_start: 0.7570 (m-70) cc_final: 0.7230 (m90) REVERT: C 294 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7357 (mt0) REVERT: C 351 TYR cc_start: 0.8155 (t80) cc_final: 0.7939 (t80) REVERT: C 540 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: C 597 ASP cc_start: 0.8373 (t0) cc_final: 0.8080 (t0) REVERT: C 599 LYS cc_start: 0.8840 (mppt) cc_final: 0.8370 (mppt) REVERT: C 617 PHE cc_start: 0.7472 (m-80) cc_final: 0.7238 (m-80) outliers start: 63 outliers final: 44 residues processed: 263 average time/residue: 0.3423 time to fit residues: 138.3949 Evaluate side-chains 258 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 214 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 473 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 564 CYS 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 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 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 250 HIS 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 362 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 540 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 218 optimal weight: 4.9990 chunk 49 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 C 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.198376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.176249 restraints weight = 22231.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.161072 restraints weight = 58973.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.151738 restraints weight = 42090.369| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 20981 Z= 0.153 Angle : 0.530 6.779 28452 Z= 0.275 Chirality : 0.041 0.171 3064 Planarity : 0.004 0.043 3653 Dihedral : 4.933 56.682 2895 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.19 % Allowed : 21.18 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2525 helix: 0.58 (0.15), residues: 1280 sheet: -1.81 (0.29), residues: 299 loop : -1.12 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.002 TRP C 182 HIS 0.014 0.001 HIS B 240 PHE 0.019 0.001 PHE D 103 TYR 0.019 0.001 TYR D 221 ARG 0.006 0.000 ARG C 402 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 843) hydrogen bonds : angle 4.36703 ( 2514) covalent geometry : bond 0.00368 (20981) covalent geometry : angle 0.53012 (28452) *********************** 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 263 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TRP cc_start: 0.6744 (t-100) cc_final: 0.6430 (t60) REVERT: A 244 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6544 (mpp) REVERT: A 604 TYR cc_start: 0.7907 (m-80) cc_final: 0.7526 (m-80) REVERT: B 106 TRP cc_start: 0.6620 (OUTLIER) cc_final: 0.5702 (t60) REVERT: B 204 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8634 (t) REVERT: B 573 SER cc_start: 0.8181 (t) cc_final: 0.7754 (m) REVERT: D 94 MET cc_start: 0.5996 (ttt) cc_final: 0.4947 (mmm) REVERT: D 337 LYS cc_start: 0.8519 (tppt) cc_final: 0.8271 (tppt) REVERT: D 603 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7114 (ttm170) REVERT: D 606 MET cc_start: 0.6200 (mtp) cc_final: 0.5770 (mtm) REVERT: C 49 THR cc_start: 0.8728 (p) cc_final: 0.8411 (p) REVERT: C 52 LYS cc_start: 0.8629 (tptp) cc_final: 0.8328 (tppt) REVERT: C 294 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: C 540 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6354 (mp0) REVERT: C 597 ASP cc_start: 0.8439 (t0) cc_final: 0.8113 (t0) REVERT: C 599 LYS cc_start: 0.8802 (mppt) cc_final: 0.8308 (mppt) REVERT: C 617 PHE cc_start: 0.7456 (m-80) cc_final: 0.7213 (m-80) outliers start: 47 outliers final: 33 residues processed: 245 average time/residue: 0.3446 time to fit residues: 128.9043 Evaluate side-chains 248 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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 214 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 528 SER Chi-restraints excluded: chain A residue 542 ILE 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 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 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 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 294 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 540 GLU 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 30 optimal weight: 0.7980 chunk 201 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 17 optimal weight: 0.0030 chunk 76 optimal weight: 0.0570 chunk 130 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 96 optimal weight: 0.0980 chunk 148 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 overall best weight: 0.3508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 376 ASN D 250 HIS 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 = 0.4105 r_free = 0.4105 target = 0.202041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.180576 restraints weight = 22041.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.167503 restraints weight = 59317.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.157891 restraints weight = 41656.019| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 20981 Z= 0.109 Angle : 0.500 6.604 28452 Z= 0.260 Chirality : 0.040 0.240 3064 Planarity : 0.003 0.045 3653 Dihedral : 4.800 58.850 2895 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.73 % Allowed : 21.83 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2525 helix: 0.79 (0.15), residues: 1281 sheet: -1.68 (0.30), residues: 297 loop : -1.10 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.002 TRP C 182 HIS 0.015 0.001 HIS B 240 PHE 0.020 0.001 PHE D 103 TYR 0.018 0.001 TYR A 242 ARG 0.005 0.000 ARG A 246 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 843) hydrogen bonds : angle 4.23366 ( 2514) covalent geometry : bond 0.00253 (20981) covalent geometry : angle 0.49955 (28452) ********************** 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 254 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6341 (mpp) REVERT: A 604 TYR cc_start: 0.7755 (m-80) cc_final: 0.7367 (m-80) REVERT: B 31 GLU cc_start: 0.6176 (mt-10) cc_final: 0.5795 (mt-10) REVERT: B 106 TRP cc_start: 0.6510 (OUTLIER) cc_final: 0.5657 (t60) REVERT: B 117 LEU cc_start: 0.6983 (mp) cc_final: 0.6521 (tt) REVERT: B 204 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8524 (t) REVERT: B 573 SER cc_start: 0.8184 (t) cc_final: 0.7962 (m) REVERT: D 94 MET cc_start: 0.5929 (ttt) cc_final: 0.5048 (mmm) REVERT: D 337 LYS cc_start: 0.8403 (tppt) cc_final: 0.8193 (tppt) REVERT: D 522 MET cc_start: 0.8481 (mtt) cc_final: 0.7710 (mtt) REVERT: D 599 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7759 (mttt) REVERT: D 603 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7110 (ttm170) REVERT: D 606 MET cc_start: 0.6100 (mtp) cc_final: 0.5688 (mtm) REVERT: C 49 THR cc_start: 0.8718 (p) cc_final: 0.8375 (p) REVERT: C 52 LYS cc_start: 0.8623 (tptp) cc_final: 0.8327 (tppt) REVERT: C 294 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: C 522 MET cc_start: 0.8376 (mtt) cc_final: 0.8102 (ptp) REVERT: C 540 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: C 599 LYS cc_start: 0.8786 (mppt) cc_final: 0.8482 (mppt) outliers start: 37 outliers final: 23 residues processed: 241 average time/residue: 0.3571 time to fit residues: 131.0017 Evaluate side-chains 229 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 2.184 ------------------------------------------------------------------------------- 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 214 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 542 ILE 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 262 THR Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain D residue 176 VAL 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 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 540 GLU 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 12 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 205 HIS A 222 ASN A 250 HIS D 283 ASN C 222 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.198986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.176212 restraints weight = 22092.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.162447 restraints weight = 58217.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.153385 restraints weight = 41419.176| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20981 Z= 0.153 Angle : 0.531 9.276 28452 Z= 0.274 Chirality : 0.041 0.179 3064 Planarity : 0.004 0.043 3653 Dihedral : 4.854 59.853 2895 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.63 % Allowed : 21.92 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2525 helix: 0.74 (0.15), residues: 1287 sheet: -1.67 (0.30), residues: 295 loop : -1.10 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP A 182 HIS 0.015 0.001 HIS B 240 PHE 0.019 0.001 PHE D 103 TYR 0.026 0.001 TYR B 405 ARG 0.004 0.000 ARG D 331 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 843) hydrogen bonds : angle 4.27398 ( 2514) covalent geometry : bond 0.00367 (20981) covalent geometry : angle 0.53080 (28452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7007.65 seconds wall clock time: 124 minutes 10.24 seconds (7450.24 seconds total)