Starting phenix.real_space_refine on Fri Mar 6 10:30:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yup_34109/03_2026/7yup_34109.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yup_34109/03_2026/7yup_34109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yup_34109/03_2026/7yup_34109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yup_34109/03_2026/7yup_34109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yup_34109/03_2026/7yup_34109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yup_34109/03_2026/7yup_34109.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.062 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 19190 2.51 5 N 5335 2.21 5 O 5745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30375 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Time building chain proxies: 7.48, per 1000 atoms: 0.25 Number of scatterers: 30375 At special positions: 0 Unit cell: (179.58, 162.36, 184.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 5745 8.00 N 5335 7.00 C 19190 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: 2.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7180 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 34 sheets defined 44.7% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 27 through 38 Processing helix chain 'A' and resid 117 through 137 Processing helix chain 'A' and resid 157 through 169 Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.624A pdb=" N LYS A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 237 removed outlier: 4.235A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 removed outlier: 3.661A pdb=" N GLY A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 243' Processing helix chain 'A' and resid 245 through 254 Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 276 through 280 removed outlier: 4.514A pdb=" N GLY A 279 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 403 through 412 removed outlier: 3.863A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 444 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 494 through 506 Processing helix chain 'A' and resid 506 through 514 Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.860A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 560 removed outlier: 3.860A pdb=" N GLU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 630 through 647 removed outlier: 3.658A pdb=" N LYS A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 691 removed outlier: 3.734A pdb=" N MET A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 728 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 741 through 745 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 761 through 769 removed outlier: 3.748A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 58 through 62 removed outlier: 4.061A pdb=" N ASP B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 62 " --> pdb=" O PRO B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 62' Processing helix chain 'B' and resid 117 through 137 removed outlier: 4.004A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 169 Processing helix chain 'B' and resid 172 through 180 removed outlier: 3.611A pdb=" N ILE B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 237 removed outlier: 4.020A pdb=" N LEU B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 removed outlier: 3.606A pdb=" N LEU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 283 through 296 removed outlier: 4.086A pdb=" N VAL B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 removed outlier: 3.545A pdb=" N GLN B 313 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 338 removed outlier: 3.621A pdb=" N ARG B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 403 through 412 removed outlier: 4.067A pdb=" N HIS B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 4.185A pdb=" N MET B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 447 through 450 Processing helix chain 'B' and resid 494 through 506 Processing helix chain 'B' and resid 506 through 514 removed outlier: 3.515A pdb=" N SER B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 630 through 647 Processing helix chain 'B' and resid 648 through 651 Processing helix chain 'B' and resid 679 through 693 removed outlier: 3.836A pdb=" N MET B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.944A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 741 removed outlier: 3.925A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 4.224A pdb=" N LEU B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 747 through 752' Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.667A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 137 Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 150 through 155 removed outlier: 4.220A pdb=" N GLY C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 168 removed outlier: 3.602A pdb=" N ALA C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 removed outlier: 3.669A pdb=" N LYS C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 235 removed outlier: 4.231A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 244 through 254 removed outlier: 4.286A pdb=" N ALA C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 removed outlier: 4.846A pdb=" N LYS C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 307 through 318 removed outlier: 3.973A pdb=" N THR C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 360 through 372 removed outlier: 3.861A pdb=" N LEU C 364 " --> pdb=" O GLY C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 403 through 412 removed outlier: 4.023A pdb=" N HIS C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.654A pdb=" N ASP C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 450 removed outlier: 3.882A pdb=" N THR C 450 " --> pdb=" O GLN C 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 447 through 450' Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.854A pdb=" N ASP C 483 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 506 Processing helix chain 'C' and resid 506 through 514 Processing helix chain 'C' and resid 524 through 535 removed outlier: 4.308A pdb=" N THR C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 Processing helix chain 'C' and resid 586 through 590 removed outlier: 3.929A pdb=" N THR C 590 " --> pdb=" O LYS C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 647 Processing helix chain 'C' and resid 648 through 651 Processing helix chain 'C' and resid 679 through 693 removed outlier: 3.514A pdb=" N MET C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.941A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 728 " --> pdb=" O ALA C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 740 No H-bonds generated for 'chain 'C' and resid 738 through 740' Processing helix chain 'C' and resid 749 through 753 removed outlier: 3.794A pdb=" N GLY C 753 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 769 Processing helix chain 'D' and resid 30 through 39 removed outlier: 3.656A pdb=" N GLY D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 62 removed outlier: 3.525A pdb=" N ASP D 61 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 62 " --> pdb=" O PRO D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 62' Processing helix chain 'D' and resid 117 through 137 removed outlier: 4.114A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 removed outlier: 3.738A pdb=" N GLN D 148 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 145 through 149' Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.760A pdb=" N LYS D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 237 Processing helix chain 'D' and resid 239 through 256 removed outlier: 5.640A pdb=" N LEU D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 283 through 295 Processing helix chain 'D' and resid 307 through 315 removed outlier: 3.566A pdb=" N THR D 311 " --> pdb=" O ASP D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.803A pdb=" N ARG D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 Processing helix chain 'D' and resid 403 through 412 removed outlier: 4.160A pdb=" N HIS D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 444 removed outlier: 4.057A pdb=" N ALA D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'D' and resid 478 through 483 removed outlier: 4.406A pdb=" N ASP D 483 " --> pdb=" O ARG D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 514 removed outlier: 5.700A pdb=" N TRP D 507 " --> pdb=" O ARG D 503 " (cutoff:3.500A) Proline residue: D 508 - end of helix Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.952A pdb=" N ILE D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 560 Processing helix chain 'D' and resid 573 through 577 Processing helix chain 'D' and resid 630 through 646 removed outlier: 4.353A pdb=" N LYS D 634 " --> pdb=" O GLY D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.702A pdb=" N ASN D 659 " --> pdb=" O ASP D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 728 removed outlier: 3.835A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 740 Processing helix chain 'D' and resid 742 through 746 removed outlier: 3.783A pdb=" N GLU D 745 " --> pdb=" O GLN D 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 117 through 138 Processing helix chain 'E' and resid 157 through 166 Processing helix chain 'E' and resid 172 through 181 Processing helix chain 'E' and resid 185 through 236 removed outlier: 4.076A pdb=" N LEU E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU E 228 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 256 removed outlier: 4.347A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 272 Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.877A pdb=" N THR E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 316 removed outlier: 3.519A pdb=" N ASP E 316 " --> pdb=" O ARG E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.531A pdb=" N ARG E 328 " --> pdb=" O ASP E 324 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 329 " --> pdb=" O VAL E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 removed outlier: 6.497A pdb=" N GLY E 341 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E 342 " --> pdb=" O THR E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 435 through 444 removed outlier: 4.010A pdb=" N ASP E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 483 removed outlier: 3.659A pdb=" N ASP E 483 " --> pdb=" O PRO E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 514 removed outlier: 5.454A pdb=" N TRP E 507 " --> pdb=" O ARG E 503 " (cutoff:3.500A) Proline residue: E 508 - end of helix removed outlier: 4.564A pdb=" N SER E 514 " --> pdb=" O GLN E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 534 Processing helix chain 'E' and resid 540 through 560 Processing helix chain 'E' and resid 573 through 578 removed outlier: 3.522A pdb=" N TYR E 577 " --> pdb=" O ASP E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 647 Processing helix chain 'E' and resid 656 through 659 Processing helix chain 'E' and resid 679 through 691 Processing helix chain 'E' and resid 717 through 726 Processing helix chain 'E' and resid 738 through 743 removed outlier: 3.550A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN E 742 " --> pdb=" O ASN E 739 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 752 removed outlier: 4.148A pdb=" N LEU E 751 " --> pdb=" O PRO E 747 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 93 removed outlier: 3.553A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 69 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL A 47 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE A 8 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 5 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA A 105 " --> pdb=" O LEU A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.887A pdb=" N VAL A 86 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN A 73 " --> pdb=" O MET A 85 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU A 87 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL A 71 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 removed outlier: 6.245A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 384 through 386 removed outlier: 6.558A pdb=" N VAL A 384 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP A 430 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP A 386 " --> pdb=" O ASP A 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 596 through 601 removed outlier: 3.585A pdb=" N ALA A 615 " --> pdb=" O HIS A 664 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.191A pdb=" N ALA A 701 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.778A pdb=" N ALA B 105 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG B 106 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 95 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLN B 93 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.847A pdb=" N THR B 21 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 86 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN B 73 " --> pdb=" O MET B 85 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU B 87 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL B 71 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG B 89 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ALA B 69 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG B 91 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 67 " --> pdb=" O ARG B 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AB1, first strand: chain 'B' and resid 608 through 613 removed outlier: 4.271A pdb=" N ALA B 601 " --> pdb=" O THR B 608 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 597 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ILE B 700 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLN B 598 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET B 702 " --> pdb=" O GLN B 598 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 701 " --> pdb=" O LYS B 732 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU B 755 " --> pdb=" O ILE B 733 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 623 through 626 removed outlier: 6.627A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 705 through 706 removed outlier: 3.787A pdb=" N GLU B 705 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.745A pdb=" N LEU C 5 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 8 through 10 removed outlier: 4.116A pdb=" N ILE C 44 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA C 69 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU C 46 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL C 67 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ALA C 88 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB7, first strand: chain 'C' and resid 352 through 354 removed outlier: 6.879A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 377 through 378 removed outlier: 7.553A pdb=" N HIS C 377 " --> pdb=" O LEU C 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AC1, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.801A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 598 through 601 Processing sheet with id=AC3, first strand: chain 'C' and resid 614 through 615 Processing sheet with id=AC4, first strand: chain 'C' and resid 700 through 702 removed outlier: 7.190A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.655A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 82 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARG D 91 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N PHE D 110 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN D 93 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU D 108 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG D 106 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N TYR D 97 " --> pdb=" O ARG D 104 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ARG D 104 " --> pdb=" O TYR D 97 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU D 103 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 107 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 3 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE D 45 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D 8 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL D 47 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA D 90 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LYS D 72 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL D 86 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ALA D 74 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL D 84 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 376 through 380 removed outlier: 3.771A pdb=" N HIS D 377 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE D 419 " --> pdb=" O ILE D 468 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N THR D 470 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU D 421 " --> pdb=" O THR D 470 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AC8, first strand: chain 'D' and resid 596 through 597 removed outlier: 6.352A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 602 through 603 removed outlier: 3.822A pdb=" N THR D 603 " --> pdb=" O GLY D 606 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AD2, first strand: chain 'E' and resid 20 through 25 removed outlier: 3.596A pdb=" N VAL E 23 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL E 25 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU E 82 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET E 85 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 20 through 25 removed outlier: 3.596A pdb=" N VAL E 23 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL E 25 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU E 82 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N MET E 85 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ARG E 91 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE E 110 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN E 93 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR E 95 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ARG E 106 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TYR E 97 " --> pdb=" O ARG E 104 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG E 104 " --> pdb=" O TYR E 97 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 469 through 470 removed outlier: 6.871A pdb=" N VAL E 352 " --> pdb=" O ILE E 488 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 376 through 379 removed outlier: 6.946A pdb=" N HIS E 377 " --> pdb=" O LEU E 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 596 through 601 removed outlier: 3.924A pdb=" N ALA E 601 " --> pdb=" O THR E 608 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR E 608 " --> pdb=" O ALA E 601 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 700 through 702 removed outlier: 6.885A pdb=" N ALA E 701 " --> pdb=" O VAL E 734 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE E 733 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL E 759 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU E 735 " --> pdb=" O VAL E 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 1206 hydrogen bonds defined for protein. 3462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.50 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6660 1.32 - 1.45: 6653 1.45 - 1.57: 17395 1.57 - 1.70: 2 1.70 - 1.82: 210 Bond restraints: 30920 Sorted by residual: bond pdb=" CA THR B 469 " pdb=" CB THR B 469 " ideal model delta sigma weight residual 1.530 1.427 0.103 1.68e-02 3.54e+03 3.76e+01 bond pdb=" C ILE A 574 " pdb=" N PRO A 575 " ideal model delta sigma weight residual 1.336 1.407 -0.071 1.25e-02 6.40e+03 3.26e+01 bond pdb=" C ILE E 574 " pdb=" N PRO E 575 " ideal model delta sigma weight residual 1.337 1.399 -0.063 1.11e-02 8.12e+03 3.21e+01 bond pdb=" C VAL A 712 " pdb=" N MET A 713 " ideal model delta sigma weight residual 1.331 1.255 0.076 1.48e-02 4.57e+03 2.64e+01 bond pdb=" C PHE C 467 " pdb=" N ILE C 468 " ideal model delta sigma weight residual 1.332 1.308 0.024 5.60e-03 3.19e+04 1.84e+01 ... (remaining 30915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 40362 3.65 - 7.29: 1333 7.29 - 10.94: 167 10.94 - 14.58: 30 14.58 - 18.23: 8 Bond angle restraints: 41900 Sorted by residual: angle pdb=" C VAL A 712 " pdb=" N MET A 713 " pdb=" CA MET A 713 " ideal model delta sigma weight residual 121.03 139.16 -18.13 1.60e+00 3.91e-01 1.28e+02 angle pdb=" N ASP A 318 " pdb=" CA ASP A 318 " pdb=" C ASP A 318 " ideal model delta sigma weight residual 114.62 104.57 10.05 1.14e+00 7.69e-01 7.77e+01 angle pdb=" N GLY C 607 " pdb=" CA GLY C 607 " pdb=" C GLY C 607 " ideal model delta sigma weight residual 112.25 122.41 -10.16 1.34e+00 5.57e-01 5.75e+01 angle pdb=" N PHE A 657 " pdb=" CA PHE A 657 " pdb=" C PHE A 657 " ideal model delta sigma weight residual 113.30 103.84 9.46 1.34e+00 5.57e-01 4.99e+01 angle pdb=" C ARG B 503 " pdb=" N GLN B 504 " pdb=" CA GLN B 504 " ideal model delta sigma weight residual 122.11 110.54 11.57 1.64e+00 3.72e-01 4.97e+01 ... (remaining 41895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 17635 16.57 - 33.14: 1234 33.14 - 49.70: 184 49.70 - 66.27: 21 66.27 - 82.84: 31 Dihedral angle restraints: 19105 sinusoidal: 7950 harmonic: 11155 Sorted by residual: dihedral pdb=" CA ASP C 51 " pdb=" C ASP C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta harmonic sigma weight residual -180.00 -114.62 -65.38 0 5.00e+00 4.00e-02 1.71e+02 dihedral pdb=" CA ASP E 51 " pdb=" C ASP E 51 " pdb=" N PRO E 52 " pdb=" CA PRO E 52 " ideal model delta harmonic sigma weight residual 180.00 -120.89 -59.11 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA ASP A 51 " pdb=" C ASP A 51 " pdb=" N PRO A 52 " pdb=" CA PRO A 52 " ideal model delta harmonic sigma weight residual -180.00 -121.66 -58.34 0 5.00e+00 4.00e-02 1.36e+02 ... (remaining 19102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3752 0.088 - 0.176: 893 0.176 - 0.263: 111 0.263 - 0.351: 12 0.351 - 0.439: 2 Chirality restraints: 4770 Sorted by residual: chirality pdb=" CB VAL D 344 " pdb=" CA VAL D 344 " pdb=" CG1 VAL D 344 " pdb=" CG2 VAL D 344 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CB ILE B 379 " pdb=" CA ILE B 379 " pdb=" CG1 ILE B 379 " pdb=" CG2 ILE B 379 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CG LEU D 405 " pdb=" CB LEU D 405 " pdb=" CD1 LEU D 405 " pdb=" CD2 LEU D 405 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 4767 not shown) Planarity restraints: 5460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 320 " 0.014 2.00e-02 2.50e+03 2.96e-02 1.75e+01 pdb=" CG TYR B 320 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR B 320 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR B 320 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 320 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 320 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 320 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 320 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 335 " 0.019 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C VAL D 335 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL D 335 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG D 336 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP B 507 " 0.062 5.00e-02 4.00e+02 9.16e-02 1.34e+01 pdb=" N PRO B 508 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 508 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 508 " 0.051 5.00e-02 4.00e+02 ... (remaining 5457 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4711 2.75 - 3.29: 28898 3.29 - 3.83: 49539 3.83 - 4.36: 58573 4.36 - 4.90: 96737 Nonbonded interactions: 238458 Sorted by model distance: nonbonded pdb=" OG1 THR D 603 " pdb=" O GLY D 606 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR B 672 " pdb=" O GLY B 676 " model vdw 2.221 3.040 nonbonded pdb=" O TYR D 63 " pdb=" OH TYR D 97 " model vdw 2.229 3.040 nonbonded pdb=" O ALA B 688 " pdb=" OG SER B 692 " model vdw 2.238 3.040 nonbonded pdb=" O SER A 363 " pdb=" OG SER A 367 " model vdw 2.240 3.040 ... (remaining 238453 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.320 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 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 : 0.014 0.134 30920 Z= 0.624 Angle : 1.570 18.227 41900 Z= 0.870 Chirality : 0.075 0.439 4770 Planarity : 0.010 0.092 5460 Dihedral : 11.982 82.838 11925 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.65 % Favored : 88.17 % Rotamer: Outliers : 0.96 % Allowed : 4.50 % Favored : 94.55 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 3.64 % Twisted General : 0.80 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.88 (0.10), residues: 3855 helix: -2.98 (0.09), residues: 1597 sheet: -3.13 (0.22), residues: 377 loop : -3.51 (0.11), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 541 TYR 0.066 0.005 TYR B 320 PHE 0.036 0.004 PHE C 110 TRP 0.060 0.006 TRP E 563 HIS 0.025 0.004 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.01411 (30920) covalent geometry : angle 1.57028 (41900) hydrogen bonds : bond 0.18345 ( 1201) hydrogen bonds : angle 8.22827 ( 3462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 411 time to evaluate : 1.095 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.6335 (ttt) cc_final: 0.6012 (tpt) REVERT: A 268 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8260 (ttpp) REVERT: A 276 MET cc_start: 0.8192 (mmp) cc_final: 0.7982 (mmm) REVERT: A 280 SER cc_start: 0.6346 (m) cc_final: 0.5765 (t) REVERT: A 386 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: A 660 LYS cc_start: 0.8264 (mttp) cc_final: 0.8008 (tptt) REVERT: A 731 HIS cc_start: 0.7517 (m90) cc_final: 0.6729 (t-170) REVERT: B 291 ASP cc_start: 0.7786 (m-30) cc_final: 0.7444 (m-30) REVERT: B 612 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8691 (mp) REVERT: C 230 MET cc_start: 0.4714 (tmm) cc_final: 0.4061 (tpt) REVERT: C 427 MET cc_start: 0.7599 (ttm) cc_final: 0.7190 (ttp) REVERT: C 431 TRP cc_start: 0.6415 (t-100) cc_final: 0.6078 (t-100) REVERT: C 633 MET cc_start: 0.8387 (mmp) cc_final: 0.8179 (mmt) REVERT: D 425 ASP cc_start: 0.7480 (p0) cc_final: 0.6962 (p0) REVERT: E 208 ARG cc_start: 0.4733 (mtm-85) cc_final: 0.3961 (ttt180) REVERT: E 237 LEU cc_start: 0.6254 (mm) cc_final: 0.6003 (tp) REVERT: E 331 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8252 (mm-30) REVERT: E 368 ILE cc_start: 0.9475 (mt) cc_final: 0.9219 (mt) REVERT: E 372 MET cc_start: 0.9450 (mtp) cc_final: 0.8873 (tpp) REVERT: E 426 LYS cc_start: 0.5551 (mmtm) cc_final: 0.5277 (ttpt) REVERT: E 431 TRP cc_start: 0.5637 (t-100) cc_final: 0.5080 (t-100) REVERT: E 496 MET cc_start: 0.8735 (mmt) cc_final: 0.8437 (ttp) REVERT: E 519 ARG cc_start: 0.6263 (mtm180) cc_final: 0.5937 (mtp180) REVERT: E 556 LYS cc_start: 0.7021 (ttpm) cc_final: 0.6768 (tppt) REVERT: E 731 HIS cc_start: 0.7820 (m-70) cc_final: 0.7606 (m90) outliers start: 31 outliers final: 16 residues processed: 439 average time/residue: 0.2359 time to fit residues: 156.4401 Evaluate side-chains 261 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 508 PRO Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 275 ARG Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 535 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 50.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 138 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN A 278 GLN A 393 HIS A 407 HIS A 449 ASN A 454 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN B 319 HIS B 340 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN B 664 HIS C 83 GLN C 177 GLN C 309 ASN C 337 GLN C 346 ASN D 220 ASN D 407 HIS D 454 HIS D 495 ASN D 598 GLN D 726 HIS E 168 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN E 447 GLN E 598 GLN E 727 GLN E 731 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.195239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.160151 restraints weight = 85869.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.152890 restraints weight = 67875.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.154168 restraints weight = 56939.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.154176 restraints weight = 40577.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.154583 restraints weight = 39076.044| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30920 Z= 0.173 Angle : 0.783 11.844 41900 Z= 0.403 Chirality : 0.047 0.252 4770 Planarity : 0.007 0.061 5460 Dihedral : 7.872 55.856 4285 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.02 % Favored : 91.96 % Rotamer: Outliers : 2.37 % Allowed : 8.91 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.82 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.12), residues: 3855 helix: -1.35 (0.12), residues: 1639 sheet: -2.57 (0.22), residues: 448 loop : -3.08 (0.13), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 552 TYR 0.020 0.002 TYR B 493 PHE 0.021 0.002 PHE C 45 TRP 0.028 0.002 TRP E 563 HIS 0.006 0.001 HIS C 319 Details of bonding type rmsd covalent geometry : bond 0.00379 (30920) covalent geometry : angle 0.78331 (41900) hydrogen bonds : bond 0.05039 ( 1201) hydrogen bonds : angle 5.72341 ( 3462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 327 time to evaluate : 1.207 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5949 (mmm) cc_final: 0.4794 (ptm) REVERT: A 230 MET cc_start: 0.6570 (ttt) cc_final: 0.6364 (tpt) REVERT: A 439 MET cc_start: 0.8917 (tpp) cc_final: 0.8687 (tpp) REVERT: A 731 HIS cc_start: 0.7334 (m90) cc_final: 0.6921 (t-170) REVERT: B 374 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7923 (ptm160) REVERT: C 230 MET cc_start: 0.4573 (tmm) cc_final: 0.3493 (tpp) REVERT: C 503 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6329 (mmm160) REVERT: D 38 MET cc_start: 0.0945 (mmm) cc_final: 0.0450 (mmm) REVERT: D 272 ARG cc_start: 0.9055 (ptm160) cc_final: 0.8767 (ptp-170) REVERT: D 352 VAL cc_start: 0.8911 (t) cc_final: 0.8594 (p) REVERT: D 535 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7731 (p) REVERT: E 223 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7352 (mm-30) REVERT: E 233 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5562 (pt) REVERT: E 243 LEU cc_start: 0.7335 (mm) cc_final: 0.7049 (mp) REVERT: E 276 MET cc_start: 0.2760 (tpp) cc_final: 0.2338 (tpt) REVERT: E 331 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8164 (mm-30) REVERT: E 398 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5557 (tt) REVERT: E 431 TRP cc_start: 0.4491 (t-100) cc_final: 0.4122 (t-100) REVERT: E 556 LYS cc_start: 0.7190 (ttpm) cc_final: 0.6715 (mptt) outliers start: 77 outliers final: 37 residues processed: 385 average time/residue: 0.2060 time to fit residues: 125.7232 Evaluate side-chains 286 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 503 ARG Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 681 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 16 optimal weight: 40.0000 chunk 75 optimal weight: 7.9990 chunk 165 optimal weight: 30.0000 chunk 207 optimal weight: 3.9990 chunk 270 optimal weight: 20.0000 chunk 172 optimal weight: 40.0000 chunk 377 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 307 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 HIS ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** D 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 HIS ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.191606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.153264 restraints weight = 83355.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.144834 restraints weight = 67041.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.146092 restraints weight = 67972.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.144946 restraints weight = 54558.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.145551 restraints weight = 47310.123| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 30920 Z= 0.275 Angle : 0.863 12.969 41900 Z= 0.437 Chirality : 0.050 0.222 4770 Planarity : 0.007 0.063 5460 Dihedral : 7.560 56.004 4269 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.89 % Favored : 89.05 % Rotamer: Outliers : 3.70 % Allowed : 11.03 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.82 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.12), residues: 3855 helix: -0.89 (0.12), residues: 1639 sheet: -2.61 (0.22), residues: 428 loop : -3.07 (0.13), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 567 TYR 0.028 0.002 TYR C 651 PHE 0.021 0.002 PHE D 466 TRP 0.028 0.002 TRP E 563 HIS 0.009 0.002 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00626 (30920) covalent geometry : angle 0.86263 (41900) hydrogen bonds : bond 0.05223 ( 1201) hydrogen bonds : angle 5.60296 ( 3462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 238 time to evaluate : 1.174 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.8521 (tmm160) cc_final: 0.8279 (ttp80) REVERT: A 230 MET cc_start: 0.6756 (ttt) cc_final: 0.6405 (tpt) REVERT: A 683 MET cc_start: 0.7397 (ttm) cc_final: 0.7184 (ttm) REVERT: B 374 ARG cc_start: 0.8411 (mtp85) cc_final: 0.8016 (ptm160) REVERT: B 420 LEU cc_start: 0.9026 (tp) cc_final: 0.8817 (tp) REVERT: B 516 MET cc_start: 0.7282 (mmm) cc_final: 0.6947 (mmm) REVERT: B 702 MET cc_start: 0.7627 (ptp) cc_final: 0.7362 (mpp) REVERT: C 262 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6772 (t) REVERT: C 385 ARG cc_start: 0.6263 (mtp85) cc_final: 0.5881 (mtp85) REVERT: C 534 TYR cc_start: 0.8455 (m-80) cc_final: 0.7896 (m-80) REVERT: D 38 MET cc_start: 0.0532 (mmm) cc_final: 0.0119 (mmm) REVERT: D 351 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8119 (tt) REVERT: D 352 VAL cc_start: 0.9106 (t) cc_final: 0.8880 (p) REVERT: E 208 ARG cc_start: 0.4769 (mtm-85) cc_final: 0.4529 (ptp90) REVERT: E 223 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6936 (tp30) REVERT: E 233 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5717 (pt) REVERT: E 243 LEU cc_start: 0.7236 (mm) cc_final: 0.6941 (mp) REVERT: E 331 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8288 (mm-30) REVERT: E 431 TRP cc_start: 0.5294 (t-100) cc_final: 0.4548 (t-100) REVERT: E 556 LYS cc_start: 0.7202 (ttpm) cc_final: 0.6757 (mmtm) outliers start: 120 outliers final: 73 residues processed: 330 average time/residue: 0.1870 time to fit residues: 101.1779 Evaluate side-chains 294 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 218 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 757 LYS Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 698 MET Chi-restraints excluded: chain E residue 700 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 349 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 0 optimal weight: 70.0000 chunk 256 optimal weight: 10.0000 chunk 368 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS B 337 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 664 HIS E 411 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.194202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.155453 restraints weight = 86312.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.148378 restraints weight = 63058.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.148047 restraints weight = 65719.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.148128 restraints weight = 51153.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.148523 restraints weight = 41272.255| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30920 Z= 0.145 Angle : 0.683 11.358 41900 Z= 0.347 Chirality : 0.045 0.228 4770 Planarity : 0.005 0.058 5460 Dihedral : 6.753 56.767 4268 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.68 % Favored : 92.30 % Rotamer: Outliers : 2.87 % Allowed : 12.54 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.13), residues: 3855 helix: -0.29 (0.13), residues: 1646 sheet: -2.38 (0.22), residues: 435 loop : -2.79 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 567 TYR 0.020 0.002 TYR B 534 PHE 0.017 0.001 PHE C 466 TRP 0.022 0.002 TRP A 431 HIS 0.005 0.001 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00325 (30920) covalent geometry : angle 0.68295 (41900) hydrogen bonds : bond 0.04185 ( 1201) hydrogen bonds : angle 5.03692 ( 3462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 280 time to evaluate : 1.231 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5402 (mmm) cc_final: 0.4454 (ppp) REVERT: A 230 MET cc_start: 0.6794 (ttt) cc_final: 0.6434 (tpt) REVERT: A 277 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7419 (tp40) REVERT: B 230 MET cc_start: 0.5065 (tmm) cc_final: 0.4753 (tmm) REVERT: B 374 ARG cc_start: 0.8361 (mtp85) cc_final: 0.7993 (ptm160) REVERT: B 409 MET cc_start: 0.7688 (tpp) cc_final: 0.7204 (tpt) REVERT: B 420 LEU cc_start: 0.9007 (tp) cc_final: 0.8803 (tp) REVERT: C 45 PHE cc_start: 0.6073 (t80) cc_final: 0.5856 (t80) REVERT: C 534 TYR cc_start: 0.8322 (m-80) cc_final: 0.7907 (m-10) REVERT: C 698 MET cc_start: 0.6252 (mtm) cc_final: 0.6019 (mtm) REVERT: E 223 GLU cc_start: 0.7634 (mt-10) cc_final: 0.6834 (tp30) REVERT: E 243 LEU cc_start: 0.7339 (mm) cc_final: 0.7066 (mp) REVERT: E 331 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8264 (mm-30) REVERT: E 431 TRP cc_start: 0.4928 (t-100) cc_final: 0.4336 (t-100) REVERT: E 545 ARG cc_start: 0.4598 (mtm110) cc_final: 0.3150 (mmt-90) REVERT: E 556 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6841 (tppt) outliers start: 93 outliers final: 60 residues processed: 352 average time/residue: 0.1913 time to fit residues: 107.9055 Evaluate side-chains 297 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 235 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 703 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 48 optimal weight: 0.9990 chunk 326 optimal weight: 50.0000 chunk 324 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 269 optimal weight: 2.9990 chunk 375 optimal weight: 2.9990 chunk 295 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 343 optimal weight: 20.0000 chunk 323 optimal weight: 30.0000 chunk 122 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 593 GLN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 HIS E 211 GLN ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.191595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.151415 restraints weight = 85353.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.142690 restraints weight = 67376.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.143251 restraints weight = 69199.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.143488 restraints weight = 53306.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.143862 restraints weight = 44069.095| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 30920 Z= 0.244 Angle : 0.784 16.150 41900 Z= 0.393 Chirality : 0.048 0.212 4770 Planarity : 0.006 0.060 5460 Dihedral : 6.775 58.234 4266 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.61 % Favored : 89.34 % Rotamer: Outliers : 4.22 % Allowed : 12.39 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.13), residues: 3855 helix: -0.28 (0.13), residues: 1651 sheet: -2.42 (0.22), residues: 447 loop : -2.81 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 503 TYR 0.022 0.002 TYR C 651 PHE 0.016 0.002 PHE D 466 TRP 0.021 0.002 TRP E 563 HIS 0.014 0.002 HIS D 664 Details of bonding type rmsd covalent geometry : bond 0.00561 (30920) covalent geometry : angle 0.78351 (41900) hydrogen bonds : bond 0.04595 ( 1201) hydrogen bonds : angle 5.20921 ( 3462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 242 time to evaluate : 1.139 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5389 (mmm) cc_final: 0.4575 (ppp) REVERT: A 230 MET cc_start: 0.6794 (ttt) cc_final: 0.6452 (tpt) REVERT: A 289 TYR cc_start: 0.6770 (t80) cc_final: 0.6508 (t80) REVERT: A 439 MET cc_start: 0.9175 (tpp) cc_final: 0.8885 (tpp) REVERT: A 715 ILE cc_start: 0.2499 (OUTLIER) cc_final: 0.2036 (tt) REVERT: B 230 MET cc_start: 0.4714 (tmm) cc_final: 0.4430 (tmm) REVERT: B 252 LYS cc_start: 0.5707 (tptp) cc_final: 0.4926 (ptmm) REVERT: B 293 LEU cc_start: 0.8732 (mt) cc_final: 0.8438 (tt) REVERT: B 374 ARG cc_start: 0.8409 (mtp85) cc_final: 0.8015 (ptm160) REVERT: B 420 LEU cc_start: 0.9029 (tp) cc_final: 0.8811 (tp) REVERT: C 361 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7670 (mmtp) REVERT: C 534 TYR cc_start: 0.8509 (m-80) cc_final: 0.7978 (m-80) REVERT: C 713 MET cc_start: 0.8227 (mmm) cc_final: 0.8017 (mmm) REVERT: D 351 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8070 (tt) REVERT: D 409 MET cc_start: 0.8349 (tpp) cc_final: 0.7657 (tpp) REVERT: D 544 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6627 (pm20) REVERT: D 598 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7043 (mt0) REVERT: D 633 MET cc_start: 0.7627 (mmt) cc_final: 0.7256 (mmt) REVERT: E 223 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6881 (tp30) REVERT: E 233 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5662 (pt) REVERT: E 243 LEU cc_start: 0.7175 (mm) cc_final: 0.6882 (mp) REVERT: E 331 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8343 (mm-30) REVERT: E 431 TRP cc_start: 0.5361 (t-100) cc_final: 0.4828 (t-100) REVERT: E 556 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6749 (tppt) REVERT: E 721 LYS cc_start: 0.7222 (mtpp) cc_final: 0.6722 (mmtt) outliers start: 137 outliers final: 97 residues processed: 344 average time/residue: 0.1727 time to fit residues: 98.7176 Evaluate side-chains 328 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 224 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 635 GLU Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 516 MET Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 698 MET Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 253 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 96 optimal weight: 50.0000 chunk 277 optimal weight: 0.8980 chunk 10 optimal weight: 40.0000 chunk 70 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 280 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 278 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.193346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.154725 restraints weight = 86486.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.146655 restraints weight = 74052.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.147253 restraints weight = 77477.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.146472 restraints weight = 64077.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.146898 restraints weight = 47954.313| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30920 Z= 0.161 Angle : 0.695 16.250 41900 Z= 0.347 Chirality : 0.045 0.234 4770 Planarity : 0.005 0.057 5460 Dihedral : 6.368 57.356 4266 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 3.67 % Allowed : 13.87 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.13), residues: 3855 helix: 0.05 (0.13), residues: 1647 sheet: -2.15 (0.23), residues: 432 loop : -2.66 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 227 TYR 0.015 0.001 TYR A 320 PHE 0.014 0.001 PHE C 466 TRP 0.018 0.001 TRP E 563 HIS 0.009 0.001 HIS D 664 Details of bonding type rmsd covalent geometry : bond 0.00367 (30920) covalent geometry : angle 0.69450 (41900) hydrogen bonds : bond 0.04054 ( 1201) hydrogen bonds : angle 4.89146 ( 3462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 258 time to evaluate : 0.909 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5293 (mmm) cc_final: 0.4317 (ppp) REVERT: A 217 MET cc_start: 0.7524 (tmm) cc_final: 0.6073 (ptp) REVERT: A 228 GLU cc_start: 0.8415 (pt0) cc_final: 0.7958 (tt0) REVERT: A 230 MET cc_start: 0.6842 (ttt) cc_final: 0.6478 (tpt) REVERT: A 439 MET cc_start: 0.9031 (tpp) cc_final: 0.8778 (tpp) REVERT: B 230 MET cc_start: 0.4925 (tmm) cc_final: 0.4655 (tmm) REVERT: B 252 LYS cc_start: 0.5526 (tptp) cc_final: 0.4954 (ptmm) REVERT: B 293 LEU cc_start: 0.8698 (mt) cc_final: 0.8464 (tt) REVERT: B 374 ARG cc_start: 0.8366 (mtp85) cc_final: 0.8006 (ptm160) REVERT: B 395 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6981 (tmm-80) REVERT: B 420 LEU cc_start: 0.9020 (tp) cc_final: 0.8809 (tp) REVERT: C 361 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7499 (mmtp) REVERT: C 534 TYR cc_start: 0.8401 (m-80) cc_final: 0.7955 (m-80) REVERT: D 38 MET cc_start: 0.0589 (mmm) cc_final: 0.0165 (mmm) REVERT: D 544 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6641 (pm20) REVERT: D 598 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6832 (mt0) REVERT: E 104 ARG cc_start: 0.3872 (OUTLIER) cc_final: 0.3608 (mmm160) REVERT: E 208 ARG cc_start: 0.4493 (mtt180) cc_final: 0.3495 (ttp-170) REVERT: E 223 GLU cc_start: 0.7639 (mt-10) cc_final: 0.6790 (tp30) REVERT: E 233 ILE cc_start: 0.5948 (OUTLIER) cc_final: 0.5596 (pt) REVERT: E 243 LEU cc_start: 0.7274 (mm) cc_final: 0.6964 (mp) REVERT: E 331 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8313 (mm-30) REVERT: E 431 TRP cc_start: 0.5109 (t-100) cc_final: 0.4589 (t-100) REVERT: E 496 MET cc_start: 0.9068 (ttp) cc_final: 0.8598 (tmm) REVERT: E 545 ARG cc_start: 0.4663 (mtm110) cc_final: 0.3294 (mmt90) REVERT: E 556 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6731 (tppt) REVERT: E 721 LYS cc_start: 0.7321 (mtpp) cc_final: 0.6823 (mmtt) outliers start: 119 outliers final: 81 residues processed: 354 average time/residue: 0.1875 time to fit residues: 108.7714 Evaluate side-chains 327 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 239 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 516 MET Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 703 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 61 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 210 optimal weight: 0.0370 chunk 340 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 312 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 270 optimal weight: 20.0000 chunk 231 optimal weight: 50.0000 overall best weight: 3.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 HIS E 313 GLN ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.192217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.153540 restraints weight = 84719.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.146897 restraints weight = 65789.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.145599 restraints weight = 68606.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.146086 restraints weight = 55672.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.146387 restraints weight = 46329.217| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30920 Z= 0.178 Angle : 0.707 15.624 41900 Z= 0.352 Chirality : 0.046 0.190 4770 Planarity : 0.005 0.057 5460 Dihedral : 6.251 55.204 4266 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 4.04 % Allowed : 13.84 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.13), residues: 3855 helix: 0.10 (0.13), residues: 1653 sheet: -2.25 (0.22), residues: 446 loop : -2.59 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 272 TYR 0.016 0.002 TYR B 493 PHE 0.012 0.001 PHE C 466 TRP 0.017 0.001 TRP E 563 HIS 0.009 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00409 (30920) covalent geometry : angle 0.70671 (41900) hydrogen bonds : bond 0.04062 ( 1201) hydrogen bonds : angle 4.85951 ( 3462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 245 time to evaluate : 1.111 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.5372 (mmm) cc_final: 0.4405 (ppp) REVERT: A 217 MET cc_start: 0.7548 (tmm) cc_final: 0.6109 (ptp) REVERT: A 230 MET cc_start: 0.6859 (ttt) cc_final: 0.6525 (tpt) REVERT: A 439 MET cc_start: 0.8999 (tpp) cc_final: 0.8758 (tpp) REVERT: A 715 ILE cc_start: 0.2712 (OUTLIER) cc_final: 0.2142 (tt) REVERT: B 230 MET cc_start: 0.4907 (tmm) cc_final: 0.4667 (tmm) REVERT: B 293 LEU cc_start: 0.8618 (mt) cc_final: 0.8397 (tt) REVERT: B 374 ARG cc_start: 0.8331 (mtp85) cc_final: 0.7967 (ptm160) REVERT: B 769 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5378 (tp) REVERT: C 361 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7482 (mmtp) REVERT: C 534 TYR cc_start: 0.8369 (m-80) cc_final: 0.7938 (m-80) REVERT: D 38 MET cc_start: 0.0630 (mmm) cc_final: 0.0206 (mmm) REVERT: D 544 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6644 (pm20) REVERT: D 598 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7165 (mt0) REVERT: D 625 LEU cc_start: 0.7050 (mp) cc_final: 0.6808 (mp) REVERT: E 104 ARG cc_start: 0.3919 (OUTLIER) cc_final: 0.3671 (mmm160) REVERT: E 223 GLU cc_start: 0.7556 (mt-10) cc_final: 0.6738 (tp30) REVERT: E 233 ILE cc_start: 0.5937 (OUTLIER) cc_final: 0.5583 (pt) REVERT: E 331 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8294 (mm-30) REVERT: E 431 TRP cc_start: 0.5115 (t-100) cc_final: 0.4585 (t-100) REVERT: E 496 MET cc_start: 0.9073 (ttp) cc_final: 0.8568 (tmm) REVERT: E 545 ARG cc_start: 0.4689 (mtm110) cc_final: 0.3366 (mmt90) REVERT: E 556 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6720 (tppt) REVERT: E 721 LYS cc_start: 0.7254 (mtpp) cc_final: 0.6679 (mmtt) REVERT: E 742 GLN cc_start: 0.7780 (mp10) cc_final: 0.7438 (mp10) outliers start: 131 outliers final: 93 residues processed: 348 average time/residue: 0.1854 time to fit residues: 105.4900 Evaluate side-chains 333 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 232 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain D residue 281 PRO Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 631 GLU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 516 MET Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 221 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 353 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 238 optimal weight: 40.0000 chunk 341 optimal weight: 8.9990 chunk 367 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 168 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 HIS ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.190643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.151410 restraints weight = 84286.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.144603 restraints weight = 61055.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.144753 restraints weight = 59606.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.145137 restraints weight = 45269.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.145369 restraints weight = 40063.133| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 30920 Z= 0.227 Angle : 0.771 16.819 41900 Z= 0.384 Chirality : 0.047 0.213 4770 Planarity : 0.006 0.057 5460 Dihedral : 6.373 55.207 4265 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 4.28 % Allowed : 13.99 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.13), residues: 3855 helix: 0.03 (0.13), residues: 1652 sheet: -2.09 (0.24), residues: 394 loop : -2.65 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 227 TYR 0.020 0.002 TYR C 651 PHE 0.015 0.002 PHE D 466 TRP 0.021 0.002 TRP E 563 HIS 0.011 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00522 (30920) covalent geometry : angle 0.77097 (41900) hydrogen bonds : bond 0.04357 ( 1201) hydrogen bonds : angle 4.98014 ( 3462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 233 time to evaluate : 1.204 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.7507 (tmm) cc_final: 0.6034 (ptp) REVERT: A 230 MET cc_start: 0.6845 (ttt) cc_final: 0.6481 (tpt) REVERT: A 289 TYR cc_start: 0.6875 (t80) cc_final: 0.6657 (t80) REVERT: A 439 MET cc_start: 0.9058 (tpp) cc_final: 0.8844 (tpp) REVERT: A 715 ILE cc_start: 0.2716 (OUTLIER) cc_final: 0.2190 (tt) REVERT: B 230 MET cc_start: 0.4965 (tmm) cc_final: 0.4734 (tmm) REVERT: B 374 ARG cc_start: 0.8402 (mtp85) cc_final: 0.7970 (ptm160) REVERT: B 425 ASP cc_start: 0.8263 (p0) cc_final: 0.8004 (p0) REVERT: B 720 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5581 (mp0) REVERT: C 272 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7519 (tmm160) REVERT: C 361 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7552 (mmtp) REVERT: C 534 TYR cc_start: 0.8514 (m-80) cc_final: 0.8010 (m-80) REVERT: D 38 MET cc_start: 0.0645 (mmm) cc_final: 0.0183 (mmm) REVERT: D 544 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6674 (pm20) REVERT: D 598 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7198 (mt0) REVERT: E 223 GLU cc_start: 0.7636 (mt-10) cc_final: 0.6833 (tp30) REVERT: E 237 LEU cc_start: 0.7236 (mt) cc_final: 0.5743 (tp) REVERT: E 331 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8319 (mm-30) REVERT: E 431 TRP cc_start: 0.5055 (t-100) cc_final: 0.4600 (t-100) REVERT: E 496 MET cc_start: 0.9097 (ttp) cc_final: 0.8586 (tmm) REVERT: E 545 ARG cc_start: 0.4776 (mtm110) cc_final: 0.3466 (mmt90) REVERT: E 556 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6729 (tppt) REVERT: E 721 LYS cc_start: 0.7218 (mtpp) cc_final: 0.6686 (mmtt) outliers start: 139 outliers final: 103 residues processed: 344 average time/residue: 0.1771 time to fit residues: 100.4408 Evaluate side-chains 331 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 221 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 720 GLU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain D residue 268 LYS Chi-restraints excluded: chain D residue 281 PRO Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 263 optimal weight: 0.9980 chunk 1 optimal weight: 30.0000 chunk 33 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 0.0980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.191852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.152629 restraints weight = 85528.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.145256 restraints weight = 64304.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.145556 restraints weight = 60890.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.145690 restraints weight = 45768.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.145784 restraints weight = 40576.930| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30920 Z= 0.180 Angle : 0.715 16.341 41900 Z= 0.357 Chirality : 0.046 0.352 4770 Planarity : 0.005 0.057 5460 Dihedral : 6.179 52.206 4265 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 3.82 % Allowed : 14.61 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.13), residues: 3855 helix: 0.14 (0.13), residues: 1662 sheet: -2.04 (0.24), residues: 392 loop : -2.57 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 272 TYR 0.017 0.002 TYR B 493 PHE 0.013 0.001 PHE C 466 TRP 0.019 0.002 TRP E 563 HIS 0.009 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00415 (30920) covalent geometry : angle 0.71492 (41900) hydrogen bonds : bond 0.04077 ( 1201) hydrogen bonds : angle 4.83145 ( 3462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 232 time to evaluate : 1.183 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.7475 (tmm) cc_final: 0.6147 (ptp) REVERT: A 230 MET cc_start: 0.6870 (ttt) cc_final: 0.6537 (tpt) REVERT: A 715 ILE cc_start: 0.2445 (OUTLIER) cc_final: 0.1929 (tt) REVERT: B 230 MET cc_start: 0.4848 (tmm) cc_final: 0.4591 (tmm) REVERT: B 374 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7965 (ptm160) REVERT: B 425 ASP cc_start: 0.8270 (p0) cc_final: 0.7936 (p0) REVERT: C 361 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7575 (mmtp) REVERT: C 534 TYR cc_start: 0.8455 (m-80) cc_final: 0.7923 (m-80) REVERT: D 38 MET cc_start: 0.0529 (mmm) cc_final: 0.0110 (mmm) REVERT: D 544 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6686 (pm20) REVERT: D 598 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7029 (mt0) REVERT: E 331 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8315 (mm-30) REVERT: E 431 TRP cc_start: 0.5382 (t-100) cc_final: 0.4915 (t-100) REVERT: E 496 MET cc_start: 0.9087 (ttp) cc_final: 0.8554 (tmm) REVERT: E 545 ARG cc_start: 0.4701 (mtm110) cc_final: 0.3495 (mmt90) REVERT: E 556 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6679 (tppt) REVERT: E 721 LYS cc_start: 0.7122 (mtpp) cc_final: 0.6578 (mmtt) REVERT: E 742 GLN cc_start: 0.7782 (mp10) cc_final: 0.7369 (mp10) outliers start: 124 outliers final: 108 residues processed: 329 average time/residue: 0.1769 time to fit residues: 96.4442 Evaluate side-chains 339 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 226 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 720 GLU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 268 LYS Chi-restraints excluded: chain D residue 281 PRO Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 250 optimal weight: 40.0000 chunk 262 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 338 optimal weight: 20.0000 chunk 333 optimal weight: 9.9990 chunk 15 optimal weight: 40.0000 chunk 234 optimal weight: 50.0000 chunk 151 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.192599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.153116 restraints weight = 84062.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.146435 restraints weight = 63232.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.147028 restraints weight = 57314.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.146930 restraints weight = 44875.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.147133 restraints weight = 39732.907| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 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 0.047 30920 Z= 0.157 Angle : 0.693 16.096 41900 Z= 0.346 Chirality : 0.046 0.340 4770 Planarity : 0.005 0.064 5460 Dihedral : 5.991 50.223 4265 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.61 % Allowed : 14.82 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.13), residues: 3855 helix: 0.27 (0.13), residues: 1663 sheet: -1.91 (0.24), residues: 404 loop : -2.49 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 227 TYR 0.014 0.001 TYR B 493 PHE 0.040 0.001 PHE A 466 TRP 0.016 0.001 TRP E 563 HIS 0.010 0.001 HIS B 393 Details of bonding type rmsd covalent geometry : bond 0.00360 (30920) covalent geometry : angle 0.69302 (41900) hydrogen bonds : bond 0.03882 ( 1201) hydrogen bonds : angle 4.70980 ( 3462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 239 time to evaluate : 1.201 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.7544 (tmm) cc_final: 0.6137 (ptp) REVERT: A 230 MET cc_start: 0.6799 (ttt) cc_final: 0.6472 (tpt) REVERT: A 715 ILE cc_start: 0.2536 (OUTLIER) cc_final: 0.1925 (tt) REVERT: B 230 MET cc_start: 0.4939 (tmm) cc_final: 0.4702 (tmm) REVERT: B 374 ARG cc_start: 0.8359 (mtp85) cc_final: 0.8131 (ptm160) REVERT: B 439 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.7175 (tpp) REVERT: C 361 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7445 (mmtp) REVERT: C 534 TYR cc_start: 0.8434 (m-80) cc_final: 0.7894 (m-80) REVERT: D 38 MET cc_start: 0.0639 (mmm) cc_final: 0.0176 (mmm) REVERT: D 409 MET cc_start: 0.8393 (tpp) cc_final: 0.8163 (tpp) REVERT: D 544 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: D 598 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.6958 (mt0) REVERT: E 431 TRP cc_start: 0.5088 (t-100) cc_final: 0.4658 (t-100) REVERT: E 496 MET cc_start: 0.9084 (ttp) cc_final: 0.8552 (tmm) REVERT: E 556 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6706 (tppt) REVERT: E 602 TRP cc_start: 0.5953 (t-100) cc_final: 0.5330 (t-100) REVERT: E 721 LYS cc_start: 0.7156 (mtpp) cc_final: 0.6601 (mmtt) REVERT: E 742 GLN cc_start: 0.7825 (mp10) cc_final: 0.7453 (mp10) outliers start: 117 outliers final: 103 residues processed: 332 average time/residue: 0.1925 time to fit residues: 103.7469 Evaluate side-chains 337 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 228 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 603 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 698 MET Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 760 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 718 VAL Chi-restraints excluded: chain B residue 720 GLU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 598 GLN Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 765 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 528 LEU Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 605 VAL Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 703 THR Chi-restraints excluded: chain E residue 767 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 259 optimal weight: 10.0000 chunk 223 optimal weight: 0.0980 chunk 146 optimal weight: 0.8980 chunk 197 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 292 optimal weight: 8.9990 chunk 347 optimal weight: 20.0000 chunk 370 optimal weight: 20.0000 chunk 311 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.193915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.147064 restraints weight = 83358.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.144899 restraints weight = 59932.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.145904 restraints weight = 51684.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.146626 restraints weight = 35044.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.146609 restraints weight = 31687.845| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30920 Z= 0.152 Angle : 0.683 15.932 41900 Z= 0.341 Chirality : 0.045 0.335 4770 Planarity : 0.005 0.059 5460 Dihedral : 5.842 48.694 4265 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 3.48 % Allowed : 15.10 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.13), residues: 3855 helix: 0.33 (0.13), residues: 1663 sheet: -1.77 (0.25), residues: 389 loop : -2.43 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 272 TYR 0.014 0.001 TYR B 493 PHE 0.037 0.001 PHE A 466 TRP 0.015 0.001 TRP D 171 HIS 0.007 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00348 (30920) covalent geometry : angle 0.68278 (41900) hydrogen bonds : bond 0.03833 ( 1201) hydrogen bonds : angle 4.63558 ( 3462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6350.08 seconds wall clock time: 109 minutes 58.20 seconds (6598.20 seconds total)