Starting phenix.real_space_refine on Wed Nov 20 00:01:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/11_2024/8cvx_27020.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/11_2024/8cvx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/11_2024/8cvx_27020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/11_2024/8cvx_27020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/11_2024/8cvx_27020.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/11_2024/8cvx_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 12.82, 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: 4.68 Conformation dependent library (CDL) restraints added in 2.5 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: 2.58 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: 7.31 Time building geometry restraints manager: 5.51 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: 2.000 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: 0.030 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 46.830 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.310 ------------------------------------------------------------------------------- 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= 0.588 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 *********************** 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 : 2.144 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: 0.3619 time to fit residues: 259.3913 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 : 2.312 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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= 0.216 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 *********************** 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 : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 HIS cc_start: 0.8254 (m-70) cc_final: 0.7956 (m-70) REVERT: A 611 MET cc_start: 0.6806 (ttm) cc_final: 0.6153 (mmt) REVERT: B 150 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8166 (t0) REVERT: B 272 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8374 (tpt-90) REVERT: B 560 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7286 (tt) REVERT: B 610 HIS cc_start: 0.6579 (m90) cc_final: 0.6073 (m-70) REVERT: D 58 TRP cc_start: 0.6863 (m-90) cc_final: 0.6432 (m-90) REVERT: D 94 MET cc_start: 0.5456 (ttt) cc_final: 0.4785 (mmm) REVERT: D 102 TYR cc_start: 0.5801 (m-80) cc_final: 0.5288 (m-10) REVERT: D 181 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6170 (pt0) REVERT: D 244 MET cc_start: 0.8466 (mtm) cc_final: 0.8044 (mmm) REVERT: D 268 HIS cc_start: 0.7622 (m-70) cc_final: 0.7239 (m170) REVERT: D 522 MET cc_start: 0.8161 (mtt) cc_final: 0.7708 (mtt) REVERT: D 603 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6745 (ttm170) REVERT: D 606 MET cc_start: 0.6051 (mtp) cc_final: 0.5654 (mtm) REVERT: C 52 LYS cc_start: 0.8066 (tttp) cc_final: 0.7471 (tppt) REVERT: C 94 MET cc_start: 0.5437 (tpt) cc_final: 0.4987 (tpt) REVERT: C 113 LEU cc_start: 0.7336 (mp) cc_final: 0.6845 (mt) REVERT: C 162 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6673 (mt) REVERT: C 235 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7726 (mt-10) REVERT: C 294 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7019 (mt0) REVERT: C 301 LYS cc_start: 0.7775 (tttt) cc_final: 0.7509 (tttm) REVERT: C 351 TYR cc_start: 0.7591 (t80) cc_final: 0.7297 (t80) REVERT: C 383 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8303 (mp10) REVERT: C 402 ARG cc_start: 0.7617 (ptt90) cc_final: 0.7229 (mtm110) REVERT: C 510 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: C 599 LYS cc_start: 0.8648 (mppt) cc_final: 0.8355 (mppt) REVERT: C 611 MET cc_start: 0.6142 (ttm) cc_final: 0.5820 (ttp) outliers start: 58 outliers final: 23 residues processed: 326 average time/residue: 0.3716 time to fit residues: 179.7491 Evaluate side-chains 267 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 2.259 ------------------------------------------------------------------------------- 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 150 ASP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 560 LEU 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 162 LEU 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 127 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 227 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 B 48 GLN ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 530 ASN B 577 GLN D 260 GLN D 295 ASN D 577 GLN D 585 GLN C 178 HIS C 222 ASN C 305 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20981 Z= 0.398 Angle : 0.655 8.204 28452 Z= 0.343 Chirality : 0.046 0.182 3064 Planarity : 0.005 0.039 3653 Dihedral : 6.015 57.886 2915 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.82 % Allowed : 18.38 % Favored : 77.80 % 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: -1.38 (0.16), residues: 2525 helix: -0.30 (0.14), residues: 1271 sheet: -1.66 (0.29), residues: 306 loop : -1.33 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 182 HIS 0.052 0.002 HIS D 250 PHE 0.025 0.002 PHE B 477 TYR 0.025 0.002 TYR C 405 ARG 0.016 0.001 ARG A 241 *********************** 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 336 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 254 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 HIS cc_start: 0.8269 (m-70) cc_final: 0.7952 (m-70) REVERT: A 306 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8034 (mm-30) REVERT: A 609 ARG cc_start: 0.7190 (mtm180) cc_final: 0.6865 (mtt-85) REVERT: A 611 MET cc_start: 0.7072 (ttm) cc_final: 0.6478 (mmt) REVERT: B 47 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8379 (mp) REVERT: B 48 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: B 272 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8615 (tpt-90) REVERT: B 344 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7170 (mt-10) REVERT: B 421 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: B 573 SER cc_start: 0.8489 (t) cc_final: 0.8148 (m) REVERT: B 606 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6581 (ttp) REVERT: D 52 LYS cc_start: 0.7587 (tttp) cc_final: 0.7306 (tptt) REVERT: D 58 TRP cc_start: 0.7012 (m-90) cc_final: 0.6718 (m-90) REVERT: D 102 TYR cc_start: 0.5903 (m-80) cc_final: 0.5187 (m-80) REVERT: D 181 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6238 (pt0) REVERT: D 244 MET cc_start: 0.8538 (mtm) cc_final: 0.8040 (mmm) REVERT: D 294 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8375 (mm110) REVERT: D 522 MET cc_start: 0.8519 (mtt) cc_final: 0.7899 (mtt) REVERT: D 536 CYS cc_start: 0.7466 (OUTLIER) cc_final: 0.7160 (m) REVERT: D 553 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8025 (mp) REVERT: D 603 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6979 (ttm170) REVERT: D 606 MET cc_start: 0.5955 (mtp) cc_final: 0.5341 (mtm) REVERT: C 49 THR cc_start: 0.8615 (p) cc_final: 0.8314 (p) REVERT: C 52 LYS cc_start: 0.8085 (tttp) cc_final: 0.7510 (tppt) REVERT: C 113 LEU cc_start: 0.7490 (mp) cc_final: 0.7048 (mt) REVERT: C 244 MET cc_start: 0.8726 (mmm) cc_final: 0.8496 (mtp) REVERT: C 419 MET cc_start: 0.8132 (mmp) cc_final: 0.7827 (mmp) REVERT: C 494 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7699 (tt0) REVERT: C 510 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7689 (tt0) outliers start: 82 outliers final: 38 residues processed: 320 average time/residue: 0.3798 time to fit residues: 181.6282 Evaluate side-chains 276 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 214 CYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 412 SER 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 568 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 48 GLN 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 272 ARG Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 320 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 214 CYS Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 443 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 529 THR Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 510 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 230 optimal weight: 0.7980 chunk 243 optimal weight: 0.3980 chunk 120 optimal weight: 0.6980 chunk 218 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 48 GLN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 HIS D 250 HIS D 388 GLN C 222 ASN C 291 HIS C 305 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20981 Z= 0.199 Angle : 0.528 8.086 28452 Z= 0.276 Chirality : 0.041 0.171 3064 Planarity : 0.004 0.040 3653 Dihedral : 5.289 53.533 2904 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.71 % Allowed : 19.78 % Favored : 77.52 % 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: -0.92 (0.16), residues: 2525 helix: 0.19 (0.14), residues: 1272 sheet: -1.59 (0.30), residues: 287 loop : -1.25 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 182 HIS 0.013 0.001 HIS B 240 PHE 0.022 0.001 PHE E 338 TYR 0.041 0.001 TYR D 221 ARG 0.007 0.000 ARG B 588 *********************** 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 299 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 241 time to evaluate : 2.268 Fit side-chains revert: symmetry clash REVERT: A 34 TRP cc_start: 0.6157 (t-100) cc_final: 0.5904 (t60) REVERT: A 205 HIS cc_start: 0.8345 (m-70) cc_final: 0.8017 (m-70) REVERT: A 244 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6550 (mpp) REVERT: A 536 CYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7235 (m) REVERT: A 609 ARG cc_start: 0.7189 (mtm180) cc_final: 0.6876 (mtt-85) REVERT: A 611 MET cc_start: 0.6797 (ttm) cc_final: 0.6256 (mmt) REVERT: B 106 TRP cc_start: 0.6149 (OUTLIER) cc_final: 0.4663 (t60) REVERT: B 126 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.5951 (mt) REVERT: B 272 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8702 (tpt-90) REVERT: B 344 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7076 (mt-10) REVERT: B 351 TYR cc_start: 0.7648 (t80) cc_final: 0.7254 (t80) REVERT: B 359 GLU cc_start: 0.5761 (tt0) cc_final: 0.5341 (tt0) REVERT: B 573 SER cc_start: 0.8344 (t) cc_final: 0.8071 (m) REVERT: D 52 LYS cc_start: 0.7596 (tttp) cc_final: 0.7289 (tptt) REVERT: D 58 TRP cc_start: 0.7006 (m-90) cc_final: 0.6673 (m-90) REVERT: D 94 MET cc_start: 0.5550 (ttt) cc_final: 0.4843 (mmm) REVERT: D 102 TYR cc_start: 0.5873 (m-80) cc_final: 0.5194 (m-80) REVERT: D 181 GLU cc_start: 0.6683 (mm-30) cc_final: 0.6196 (pt0) REVERT: D 244 MET cc_start: 0.8531 (mtm) cc_final: 0.7966 (mmm) REVERT: D 522 MET cc_start: 0.8501 (mtt) cc_final: 0.7800 (mtt) REVERT: D 590 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6884 (tm-30) REVERT: D 603 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6974 (ttm170) REVERT: D 606 MET cc_start: 0.5896 (mtp) cc_final: 0.5389 (mtm) REVERT: C 49 THR cc_start: 0.8520 (p) cc_final: 0.8222 (p) REVERT: C 52 LYS cc_start: 0.8040 (tttp) cc_final: 0.7607 (tptt) REVERT: C 113 LEU cc_start: 0.7581 (mp) cc_final: 0.7190 (mt) REVERT: C 128 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7839 (ptm-80) REVERT: C 244 MET cc_start: 0.8739 (mmm) cc_final: 0.8474 (mtp) REVERT: C 494 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7692 (tt0) REVERT: C 510 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: C 599 LYS cc_start: 0.8768 (mppt) cc_final: 0.8527 (mppt) outliers start: 58 outliers final: 27 residues processed: 282 average time/residue: 0.3786 time to fit residues: 159.6376 Evaluate side-chains 258 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 134 TRP Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 250 HIS Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 544 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 8.9990 chunk 138 optimal weight: 50.0000 chunk 3 optimal weight: 5.9990 chunk 181 optimal weight: 0.0050 chunk 100 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.0040 chunk 218 optimal weight: 0.9990 chunk 61 optimal weight: 30.0000 overall best weight: 1.0012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 95 ASN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 GLN C 205 HIS C 222 ASN ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20981 Z= 0.242 Angle : 0.529 6.861 28452 Z= 0.275 Chirality : 0.041 0.169 3064 Planarity : 0.004 0.041 3653 Dihedral : 5.186 54.330 2902 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.22 % Allowed : 19.59 % Favored : 77.19 % 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: -0.77 (0.16), residues: 2525 helix: 0.37 (0.14), residues: 1265 sheet: -1.69 (0.30), residues: 299 loop : -1.17 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP C 182 HIS 0.013 0.001 HIS B 240 PHE 0.027 0.002 PHE C 103 TYR 0.023 0.001 TYR A 242 ARG 0.008 0.000 ARG B 588 *********************** 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 305 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 236 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: A 205 HIS cc_start: 0.8334 (m-70) cc_final: 0.7989 (m-70) REVERT: A 244 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.6701 (mpp) REVERT: A 260 GLN cc_start: 0.6890 (mp10) cc_final: 0.6094 (mp10) REVERT: A 609 ARG cc_start: 0.7189 (mtm180) cc_final: 0.6880 (mtt-85) REVERT: A 611 MET cc_start: 0.6828 (ttm) cc_final: 0.6352 (mmt) REVERT: B 44 TYR cc_start: 0.8496 (t80) cc_final: 0.8214 (t80) REVERT: B 106 TRP cc_start: 0.6261 (OUTLIER) cc_final: 0.4995 (t60) REVERT: B 126 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.5939 (mp) REVERT: B 272 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8723 (tpt-90) REVERT: B 344 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7004 (mt-10) REVERT: B 359 GLU cc_start: 0.5835 (tt0) cc_final: 0.5506 (tt0) REVERT: B 421 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7014 (m-30) REVERT: B 573 SER cc_start: 0.8437 (t) cc_final: 0.8105 (m) REVERT: D 52 LYS cc_start: 0.7627 (tttp) cc_final: 0.7313 (tptt) REVERT: D 58 TRP cc_start: 0.6993 (m-90) cc_final: 0.6650 (m-90) REVERT: D 94 MET cc_start: 0.5549 (ttt) cc_final: 0.4845 (mmm) REVERT: D 102 TYR cc_start: 0.5868 (m-80) cc_final: 0.5199 (m-80) REVERT: D 181 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6152 (pt0) REVERT: D 244 MET cc_start: 0.8506 (mtm) cc_final: 0.7929 (mmm) REVERT: D 522 MET cc_start: 0.8528 (mtt) cc_final: 0.7793 (mtt) REVERT: D 536 CYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7131 (m) REVERT: D 590 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7062 (tm-30) REVERT: D 603 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6986 (ttm170) REVERT: D 606 MET cc_start: 0.5893 (mtp) cc_final: 0.5377 (mtm) REVERT: C 49 THR cc_start: 0.8537 (p) cc_final: 0.8229 (p) REVERT: C 52 LYS cc_start: 0.8047 (tttp) cc_final: 0.7627 (tptt) REVERT: C 113 LEU cc_start: 0.7735 (mp) cc_final: 0.7404 (mt) REVERT: C 128 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7852 (ptm-80) REVERT: C 494 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7684 (tt0) REVERT: C 540 GLU cc_start: 0.6709 (mp0) cc_final: 0.6494 (mp0) outliers start: 69 outliers final: 37 residues processed: 286 average time/residue: 0.3710 time to fit residues: 158.5499 Evaluate side-chains 264 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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 127 GLU 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 396 VAL Chi-restraints excluded: chain A residue 453 SER 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 542 ILE 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 126 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 272 ARG 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 214 CYS Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 443 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 536 CYS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 522 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 10.0000 chunk 219 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 243 optimal weight: 0.6980 chunk 202 optimal weight: 0.1980 chunk 112 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 B 383 GLN B 446 HIS D 250 HIS C 205 HIS C 250 HIS C 268 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4320 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= 0.188 Angle : 0.500 7.887 28452 Z= 0.260 Chirality : 0.040 0.166 3064 Planarity : 0.003 0.042 3653 Dihedral : 5.050 55.014 2902 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.17 % Allowed : 19.96 % Favored : 76.87 % 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: 0.58 (0.15), residues: 1273 sheet: -1.67 (0.30), residues: 301 loop : -1.10 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.001 TRP C 182 HIS 0.013 0.001 HIS B 240 PHE 0.026 0.001 PHE C 103 TYR 0.021 0.001 TYR D 221 ARG 0.008 0.000 ARG B 588 *********************** 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 297 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 229 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: A 205 HIS cc_start: 0.8415 (m-70) cc_final: 0.8174 (m-70) REVERT: A 244 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6623 (mpp) REVERT: A 536 CYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7289 (m) REVERT: A 611 MET cc_start: 0.6795 (ttm) cc_final: 0.6345 (mmt) REVERT: B 106 TRP cc_start: 0.6193 (OUTLIER) cc_final: 0.4899 (t60) REVERT: B 126 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.5913 (mp) REVERT: B 251 CYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6265 (p) REVERT: B 344 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6965 (mt-10) REVERT: B 359 GLU cc_start: 0.5810 (tt0) cc_final: 0.5494 (tt0) REVERT: B 421 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.6930 (m-30) REVERT: B 573 SER cc_start: 0.8359 (t) cc_final: 0.8051 (m) REVERT: D 52 LYS cc_start: 0.7672 (tttp) cc_final: 0.7386 (tptt) REVERT: D 58 TRP cc_start: 0.6935 (m-90) cc_final: 0.6596 (m-90) REVERT: D 94 MET cc_start: 0.5475 (ttt) cc_final: 0.4828 (mmm) REVERT: D 102 TYR cc_start: 0.5873 (m-80) cc_final: 0.5213 (m-80) REVERT: D 181 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6108 (pt0) REVERT: D 244 MET cc_start: 0.8504 (mtm) cc_final: 0.7947 (mmm) REVERT: D 522 MET cc_start: 0.8540 (mtt) cc_final: 0.7806 (mtt) REVERT: D 536 CYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7131 (m) REVERT: D 590 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7139 (tm-30) REVERT: D 603 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6963 (ttm170) REVERT: D 606 MET cc_start: 0.5880 (mtp) cc_final: 0.5398 (mtm) REVERT: C 49 THR cc_start: 0.8485 (p) cc_final: 0.8175 (p) REVERT: C 52 LYS cc_start: 0.8172 (tttp) cc_final: 0.7752 (tptt) REVERT: C 113 LEU cc_start: 0.7771 (mp) cc_final: 0.7492 (mt) REVERT: C 128 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7875 (ptm-80) REVERT: C 351 TYR cc_start: 0.8013 (t80) cc_final: 0.7742 (t80) REVERT: C 494 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7681 (tt0) REVERT: C 540 GLU cc_start: 0.6580 (mp0) cc_final: 0.6363 (mp0) outliers start: 68 outliers final: 37 residues processed: 275 average time/residue: 0.3750 time to fit residues: 153.5781 Evaluate side-chains 254 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 2.163 ------------------------------------------------------------------------------- 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 127 GLU 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 396 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 443 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 536 CYS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 569 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 chunk 178 optimal weight: 0.3980 chunk 137 optimal weight: 0.0060 chunk 205 optimal weight: 0.9980 chunk 136 optimal weight: 0.0970 chunk 242 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 A 541 HIS D 436 GLN C 205 HIS C 222 ASN C 268 HIS C 587 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20981 Z= 0.155 Angle : 0.485 6.806 28452 Z= 0.253 Chirality : 0.039 0.169 3064 Planarity : 0.003 0.042 3653 Dihedral : 4.876 55.681 2898 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.33 % Allowed : 20.99 % 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: -0.40 (0.17), residues: 2525 helix: 0.77 (0.15), residues: 1278 sheet: -1.68 (0.28), residues: 334 loop : -1.07 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP C 182 HIS 0.014 0.001 HIS B 240 PHE 0.022 0.001 PHE C 103 TYR 0.022 0.001 TYR D 221 ARG 0.008 0.000 ARG B 588 *********************** 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 279 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 HIS cc_start: 0.8403 (m-70) cc_final: 0.8169 (m-70) REVERT: A 244 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6424 (mpp) REVERT: A 606 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.6160 (mtp) REVERT: A 611 MET cc_start: 0.6645 (ttm) cc_final: 0.6284 (mmt) REVERT: B 44 TYR cc_start: 0.8466 (t80) cc_final: 0.8082 (t80) REVERT: B 106 TRP cc_start: 0.6031 (OUTLIER) cc_final: 0.5028 (t60) REVERT: B 126 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.5910 (mp) REVERT: B 251 CYS cc_start: 0.6702 (OUTLIER) cc_final: 0.6372 (p) REVERT: B 344 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6897 (mt-10) REVERT: B 421 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.6880 (m-30) REVERT: B 573 SER cc_start: 0.8309 (t) cc_final: 0.8065 (m) REVERT: D 52 LYS cc_start: 0.7774 (tttp) cc_final: 0.7474 (tptt) REVERT: D 58 TRP cc_start: 0.6976 (m-90) cc_final: 0.6660 (m-90) REVERT: D 94 MET cc_start: 0.5404 (ttt) cc_final: 0.4792 (mmm) REVERT: D 181 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6073 (pt0) REVERT: D 244 MET cc_start: 0.8489 (mtm) cc_final: 0.7928 (mmm) REVERT: D 418 LYS cc_start: 0.7633 (ptpp) cc_final: 0.7119 (pptt) REVERT: D 522 MET cc_start: 0.8513 (mtt) cc_final: 0.7830 (mtt) REVERT: D 590 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7143 (tm-30) REVERT: D 606 MET cc_start: 0.5874 (mtp) cc_final: 0.5343 (mtm) REVERT: C 49 THR cc_start: 0.8460 (p) cc_final: 0.8126 (p) REVERT: C 52 LYS cc_start: 0.8166 (tttp) cc_final: 0.7753 (tptt) REVERT: C 113 LEU cc_start: 0.7777 (mp) cc_final: 0.7489 (mt) REVERT: C 128 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7912 (ptm-80) REVERT: C 211 ARG cc_start: 0.7527 (mtt-85) cc_final: 0.7145 (mtt-85) REVERT: C 351 TYR cc_start: 0.7950 (t80) cc_final: 0.7729 (t80) REVERT: C 448 MET cc_start: 0.8384 (mmm) cc_final: 0.8124 (mmm) REVERT: C 494 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7723 (tt0) REVERT: C 540 GLU cc_start: 0.6556 (mp0) cc_final: 0.6352 (mp0) REVERT: C 546 SER cc_start: 0.8105 (m) cc_final: 0.7825 (t) REVERT: C 599 LYS cc_start: 0.8772 (mppt) cc_final: 0.8511 (mppt) outliers start: 50 outliers final: 30 residues processed: 262 average time/residue: 0.3746 time to fit residues: 146.7467 Evaluate side-chains 248 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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 454 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 541 HIS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 522 MET 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 150 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 165 optimal weight: 0.3980 chunk 120 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A 541 HIS A 576 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 222 ASN C 268 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20981 Z= 0.315 Angle : 0.562 7.105 28452 Z= 0.290 Chirality : 0.043 0.176 3064 Planarity : 0.004 0.042 3653 Dihedral : 4.855 51.550 2895 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.47 % Allowed : 21.04 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.49 (0.16), residues: 2525 helix: 0.65 (0.15), residues: 1269 sheet: -1.67 (0.30), residues: 298 loop : -1.08 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP C 182 HIS 0.015 0.002 HIS A 541 PHE 0.036 0.002 PHE C 617 TYR 0.024 0.002 TYR D 221 ARG 0.005 0.000 ARG C 241 *********************** 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 285 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5224 (mp) cc_final: 0.4858 (mm) REVERT: A 205 HIS cc_start: 0.8420 (m-70) cc_final: 0.8123 (m-70) REVERT: A 244 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6475 (mpp) REVERT: A 250 HIS cc_start: 0.8263 (t-170) cc_final: 0.8038 (t-170) REVERT: A 268 HIS cc_start: 0.7678 (m-70) cc_final: 0.7204 (m170) REVERT: A 306 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7862 (mm-30) REVERT: A 536 CYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7206 (m) REVERT: A 611 MET cc_start: 0.6686 (ttm) cc_final: 0.6302 (mmt) REVERT: B 106 TRP cc_start: 0.6038 (OUTLIER) cc_final: 0.4855 (t60) REVERT: B 126 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.5975 (mp) REVERT: B 251 CYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6380 (p) REVERT: B 427 MET cc_start: 0.7565 (ptt) cc_final: 0.7268 (ptt) REVERT: B 573 SER cc_start: 0.8641 (t) cc_final: 0.8303 (m) REVERT: D 52 LYS cc_start: 0.7726 (tttp) cc_final: 0.7423 (tptt) REVERT: D 94 MET cc_start: 0.5432 (ttt) cc_final: 0.4831 (mmm) REVERT: D 102 TYR cc_start: 0.5908 (m-80) cc_final: 0.5248 (m-80) REVERT: D 181 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6140 (pt0) REVERT: D 244 MET cc_start: 0.8498 (mtm) cc_final: 0.7919 (mmp) REVERT: D 368 MET cc_start: 0.8607 (mtt) cc_final: 0.8204 (mtt) REVERT: D 418 LYS cc_start: 0.7664 (ptpp) cc_final: 0.7190 (pptt) REVERT: D 522 MET cc_start: 0.8561 (mtt) cc_final: 0.7814 (mtt) REVERT: D 590 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7277 (tm-30) REVERT: D 606 MET cc_start: 0.5945 (mtp) cc_final: 0.5432 (mtm) REVERT: C 49 THR cc_start: 0.8560 (p) cc_final: 0.8245 (p) REVERT: C 52 LYS cc_start: 0.8167 (tttp) cc_final: 0.7697 (tptt) REVERT: C 113 LEU cc_start: 0.7798 (mp) cc_final: 0.7546 (mt) REVERT: C 128 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7896 (ptm-80) REVERT: C 211 ARG cc_start: 0.7612 (mtt-85) cc_final: 0.7140 (mtt-85) REVERT: C 494 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7665 (tt0) REVERT: C 540 GLU cc_start: 0.6602 (mp0) cc_final: 0.6341 (mp0) REVERT: C 597 ASP cc_start: 0.8312 (t0) cc_final: 0.8027 (t0) outliers start: 53 outliers final: 36 residues processed: 269 average time/residue: 0.3619 time to fit residues: 146.2841 Evaluate side-chains 259 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 396 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 536 CYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 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 362 VAL Chi-restraints excluded: chain D residue 443 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 553 LEU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 129 TRP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 544 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.8980 chunk 212 optimal weight: 0.8980 chunk 226 optimal weight: 0.6980 chunk 136 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 177 optimal weight: 0.2980 chunk 69 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A 541 HIS ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 268 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20981 Z= 0.234 Angle : 0.530 7.761 28452 Z= 0.274 Chirality : 0.041 0.190 3064 Planarity : 0.003 0.044 3653 Dihedral : 4.846 56.440 2895 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.15 % Allowed : 21.60 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2525 helix: 0.72 (0.14), residues: 1279 sheet: -1.70 (0.30), residues: 298 loop : -1.11 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.002 TRP C 182 HIS 0.015 0.001 HIS B 240 PHE 0.036 0.001 PHE C 617 TYR 0.028 0.001 TYR C 572 ARG 0.008 0.000 ARG C 241 *********************** 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 262 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5262 (mp) cc_final: 0.4985 (mm) REVERT: A 205 HIS cc_start: 0.8405 (m-70) cc_final: 0.8094 (m-70) REVERT: A 244 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6388 (mpp) REVERT: A 250 HIS cc_start: 0.8164 (t-170) cc_final: 0.7957 (t-170) REVERT: A 268 HIS cc_start: 0.7661 (m-70) cc_final: 0.7142 (m170) REVERT: A 611 MET cc_start: 0.6693 (ttm) cc_final: 0.6352 (mmt) REVERT: B 106 TRP cc_start: 0.6026 (OUTLIER) cc_final: 0.4925 (t60) REVERT: B 126 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6072 (mp) REVERT: B 251 CYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6341 (p) REVERT: B 573 SER cc_start: 0.8554 (t) cc_final: 0.8239 (m) REVERT: D 94 MET cc_start: 0.5404 (ttt) cc_final: 0.4796 (mmm) REVERT: D 102 TYR cc_start: 0.5908 (m-80) cc_final: 0.5264 (m-80) REVERT: D 244 MET cc_start: 0.8488 (mtm) cc_final: 0.7905 (mmp) REVERT: D 418 LYS cc_start: 0.7621 (ptpp) cc_final: 0.7151 (pptt) REVERT: D 522 MET cc_start: 0.8569 (mtt) cc_final: 0.7819 (mtt) REVERT: D 606 MET cc_start: 0.5968 (mtp) cc_final: 0.5459 (mtm) REVERT: C 49 THR cc_start: 0.8535 (p) cc_final: 0.8218 (p) REVERT: C 52 LYS cc_start: 0.8131 (tttp) cc_final: 0.7703 (tptt) REVERT: C 113 LEU cc_start: 0.7854 (mp) cc_final: 0.7628 (mt) REVERT: C 128 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7655 (ptm-80) REVERT: C 494 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7665 (tt0) REVERT: C 540 GLU cc_start: 0.6582 (mp0) cc_final: 0.6325 (mp0) REVERT: C 546 SER cc_start: 0.8311 (m) cc_final: 0.7993 (t) REVERT: C 597 ASP cc_start: 0.8280 (t0) cc_final: 0.8041 (t0) outliers start: 46 outliers final: 33 residues processed: 247 average time/residue: 0.3738 time to fit residues: 138.5968 Evaluate side-chains 246 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 2.228 ------------------------------------------------------------------------------- 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 388 GLN Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 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 443 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 569 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 251 optimal weight: 0.0970 chunk 231 optimal weight: 2.9990 chunk 199 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 268 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20981 Z= 0.227 Angle : 0.534 10.650 28452 Z= 0.275 Chirality : 0.041 0.210 3064 Planarity : 0.004 0.044 3653 Dihedral : 4.850 59.340 2895 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.01 % Allowed : 21.60 % 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: -0.42 (0.16), residues: 2525 helix: 0.75 (0.15), residues: 1279 sheet: -1.73 (0.30), residues: 298 loop : -1.11 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.002 TRP C 182 HIS 0.015 0.001 HIS B 240 PHE 0.039 0.001 PHE C 617 TYR 0.024 0.001 TYR C 572 ARG 0.004 0.000 ARG B 371 ********************** 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 251 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.5314 (mp) cc_final: 0.5051 (mm) REVERT: A 205 HIS cc_start: 0.8400 (m-70) cc_final: 0.8051 (m-70) REVERT: A 244 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6343 (mpp) REVERT: A 250 HIS cc_start: 0.8154 (t-170) cc_final: 0.7921 (t-170) REVERT: A 268 HIS cc_start: 0.7651 (m-70) cc_final: 0.7194 (m170) REVERT: A 611 MET cc_start: 0.6667 (ttm) cc_final: 0.6321 (mmt) REVERT: B 106 TRP cc_start: 0.6028 (OUTLIER) cc_final: 0.4901 (t60) REVERT: B 126 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6060 (mp) REVERT: B 244 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7675 (tpp) REVERT: B 251 CYS cc_start: 0.6856 (OUTLIER) cc_final: 0.6324 (p) REVERT: B 573 SER cc_start: 0.8508 (t) cc_final: 0.8215 (m) REVERT: D 94 MET cc_start: 0.5387 (ttt) cc_final: 0.4775 (mmm) REVERT: D 102 TYR cc_start: 0.5920 (m-80) cc_final: 0.5270 (m-80) REVERT: D 244 MET cc_start: 0.8497 (mtm) cc_final: 0.7930 (mmp) REVERT: D 522 MET cc_start: 0.8572 (mtt) cc_final: 0.7817 (mtt) REVERT: D 606 MET cc_start: 0.5974 (mtp) cc_final: 0.5462 (mtm) REVERT: C 49 THR cc_start: 0.8532 (p) cc_final: 0.8226 (p) REVERT: C 113 LEU cc_start: 0.7849 (mp) cc_final: 0.7649 (mt) REVERT: C 128 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7672 (ptm-80) REVERT: C 268 HIS cc_start: 0.7458 (OUTLIER) cc_final: 0.7087 (m90) REVERT: C 494 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7669 (tt0) REVERT: C 540 GLU cc_start: 0.6580 (mp0) cc_final: 0.6323 (mp0) REVERT: C 546 SER cc_start: 0.8269 (m) cc_final: 0.7959 (t) REVERT: C 597 ASP cc_start: 0.8282 (t0) cc_final: 0.8058 (t0) outliers start: 43 outliers final: 33 residues processed: 237 average time/residue: 0.3577 time to fit residues: 128.4010 Evaluate side-chains 244 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 2.263 ------------------------------------------------------------------------------- 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 606 MET Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 456 ILE 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 362 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 544 ASP Chi-restraints excluded: chain C residue 569 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 184 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 0.0870 chunk 83 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 HIS C 222 ASN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.200026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.179370 restraints weight = 22049.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.168307 restraints weight = 57775.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.159319 restraints weight = 43510.880| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20981 Z= 0.197 Angle : 0.518 9.609 28452 Z= 0.268 Chirality : 0.041 0.210 3064 Planarity : 0.003 0.045 3653 Dihedral : 4.790 58.262 2895 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.01 % Allowed : 21.69 % Favored : 76.31 % 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: -0.43 (0.17), residues: 2525 helix: 0.84 (0.15), residues: 1272 sheet: -1.94 (0.28), residues: 349 loop : -1.09 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.002 TRP A 182 HIS 0.015 0.001 HIS B 240 PHE 0.038 0.001 PHE C 617 TYR 0.047 0.001 TYR D 221 ARG 0.004 0.000 ARG B 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4094.89 seconds wall clock time: 76 minutes 6.61 seconds (4566.61 seconds total)