Starting phenix.real_space_refine on Thu Jun 26 04:13:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yup_34109/06_2025/7yup_34109.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yup_34109/06_2025/7yup_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yup_34109/06_2025/7yup_34109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yup_34109/06_2025/7yup_34109.map" model { file = "/net/cci-nas-00/data/ceres_data/7yup_34109/06_2025/7yup_34109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yup_34109/06_2025/7yup_34109.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.95s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.09, per 1000 atoms: 0.53 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: 6.22 Conformation dependent library (CDL) restraints added in 3.5 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: 3.85 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: 11.42 Time building geometry restraints manager: 7.56 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: 0.09 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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 62.070 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.470 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.060 0.006 TRP E 563 HIS 0.025 0.004 HIS D 319 PHE 0.036 0.004 PHE C 110 TYR 0.066 0.005 TYR B 320 ARG 0.019 0.002 ARG A 541 Details of bonding type rmsd hydrogen bonds : bond 0.18345 ( 1201) hydrogen bonds : angle 8.22827 ( 3462) covalent geometry : bond 0.01411 (30920) covalent geometry : angle 1.57028 (41900) *********************** 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 : 3.452 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: 0.6010 (tpt) REVERT: A 268 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8259 (ttpp) REVERT: A 276 MET cc_start: 0.8192 (mmp) cc_final: 0.7986 (mmm) REVERT: A 280 SER cc_start: 0.6346 (m) cc_final: 0.5758 (t) REVERT: A 386 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: A 660 LYS cc_start: 0.8264 (mttp) cc_final: 0.7929 (mtmm) 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: 0.7445 (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: 0.4224 (tpt) REVERT: C 427 MET cc_start: 0.7599 (ttm) cc_final: 0.7188 (ttp) REVERT: C 431 TRP cc_start: 0.6416 (t-100) cc_final: 0.6077 (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 237 LEU cc_start: 0.6254 (mm) cc_final: 0.6003 (tp) REVERT: E 331 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8247 (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: 0.8871 (tpp) REVERT: E 426 LYS cc_start: 0.5551 (mmtm) cc_final: 0.5278 (ttpt) REVERT: E 431 TRP cc_start: 0.5637 (t-100) cc_final: 0.5079 (t-100) REVERT: E 496 MET cc_start: 0.8735 (mmt) cc_final: 0.8438 (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: 15 residues processed: 439 average time/residue: 0.4840 time to fit residues: 321.8839 Evaluate side-chains 260 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 3.167 ------------------------------------------------------------------------------- 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 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 325 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 301 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 349 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.195781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.160533 restraints weight = 87391.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.154356 restraints weight = 66776.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.155373 restraints weight = 57953.139| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30920 Z= 0.163 Angle : 0.774 11.843 41900 Z= 0.399 Chirality : 0.047 0.250 4770 Planarity : 0.007 0.061 5460 Dihedral : 7.806 54.654 4281 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.63 % Favored : 92.35 % Rotamer: Outliers : 2.25 % Allowed : 8.63 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.82 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.12), residues: 3855 helix: -1.33 (0.12), residues: 1634 sheet: -2.51 (0.22), residues: 439 loop : -3.07 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 563 HIS 0.007 0.001 HIS C 319 PHE 0.019 0.001 PHE C 45 TYR 0.020 0.002 TYR B 534 ARG 0.013 0.001 ARG E 104 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 1201) hydrogen bonds : angle 5.70165 ( 3462) covalent geometry : bond 0.00352 (30920) covalent geometry : angle 0.77435 (41900) *********************** 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 407 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 334 time to evaluate : 3.098 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 199 ASP cc_start: 0.6121 (m-30) cc_final: 0.5903 (m-30) REVERT: A 230 MET cc_start: 0.6591 (ttt) cc_final: 0.6371 (tpt) REVERT: A 439 MET cc_start: 0.8982 (tpp) cc_final: 0.8744 (tpp) REVERT: A 660 LYS cc_start: 0.8145 (mttp) cc_final: 0.7872 (mtmm) REVERT: A 731 HIS cc_start: 0.7434 (m90) cc_final: 0.6863 (t-170) REVERT: B 374 ARG cc_start: 0.8405 (mtp85) cc_final: 0.8003 (ptm160) REVERT: B 401 MET cc_start: 0.7521 (mtm) cc_final: 0.7303 (ptp) REVERT: C 230 MET cc_start: 0.4726 (tmm) cc_final: 0.3859 (tpt) REVERT: C 427 MET cc_start: 0.7121 (ttm) cc_final: 0.6481 (ttp) REVERT: C 503 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6300 (mmm160) REVERT: D 38 MET cc_start: 0.0902 (mmm) cc_final: 0.0430 (mmm) REVERT: D 352 VAL cc_start: 0.8940 (t) cc_final: 0.8659 (p) REVERT: D 535 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7705 (p) REVERT: E 233 ILE cc_start: 0.5984 (OUTLIER) cc_final: 0.5526 (pt) REVERT: E 243 LEU cc_start: 0.7284 (mm) cc_final: 0.7013 (mp) REVERT: E 276 MET cc_start: 0.2692 (tpp) cc_final: 0.2262 (tpt) REVERT: E 331 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8176 (mm-30) REVERT: E 398 ILE cc_start: 0.5771 (OUTLIER) cc_final: 0.5534 (tt) REVERT: E 431 TRP cc_start: 0.4670 (t-100) cc_final: 0.4259 (t-100) REVERT: E 556 LYS cc_start: 0.7176 (ttpm) cc_final: 0.6716 (mptt) outliers start: 73 outliers final: 34 residues processed: 387 average time/residue: 0.4337 time to fit residues: 262.8244 Evaluate side-chains 285 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 247 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 385 ARG 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 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 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 299 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 365 optimal weight: 5.9990 chunk 210 optimal weight: 0.0010 chunk 143 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 323 optimal weight: 40.0000 chunk 294 optimal weight: 7.9990 chunk 287 optimal weight: 30.0000 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN 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 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS D 68 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.194210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.157229 restraints weight = 87862.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.150215 restraints weight = 69116.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.150518 restraints weight = 63966.491| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30920 Z= 0.169 Angle : 0.723 10.571 41900 Z= 0.369 Chirality : 0.046 0.216 4770 Planarity : 0.006 0.061 5460 Dihedral : 6.973 52.250 4268 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.66 % Favored : 91.28 % Rotamer: Outliers : 2.80 % Allowed : 10.85 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.13), residues: 3855 helix: -0.58 (0.12), residues: 1632 sheet: -2.28 (0.23), residues: 446 loop : -2.86 (0.13), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 563 HIS 0.007 0.001 HIS D 319 PHE 0.015 0.001 PHE C 466 TYR 0.019 0.002 TYR E 63 ARG 0.008 0.000 ARG E 567 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 1201) hydrogen bonds : angle 5.23213 ( 3462) covalent geometry : bond 0.00378 (30920) covalent geometry : angle 0.72277 (41900) *********************** 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 363 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 272 time to evaluate : 4.513 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: A 230 MET cc_start: 0.6795 (ttt) cc_final: 0.6444 (tpt) REVERT: A 485 MET cc_start: 0.5436 (mmm) cc_final: 0.4760 (mtt) REVERT: A 660 LYS cc_start: 0.8143 (mttp) cc_final: 0.7887 (mtmm) REVERT: A 731 HIS cc_start: 0.7447 (m90) cc_final: 0.6876 (t-170) REVERT: B 374 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8022 (ptm160) REVERT: B 386 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7583 (p0) REVERT: B 420 LEU cc_start: 0.9013 (tp) cc_final: 0.8810 (tp) REVERT: C 262 VAL cc_start: 0.7157 (OUTLIER) cc_final: 0.6832 (t) REVERT: C 267 LEU cc_start: 0.8538 (mt) cc_final: 0.8068 (pp) REVERT: C 534 TYR cc_start: 0.8180 (m-80) cc_final: 0.7971 (m-10) REVERT: D 38 MET cc_start: 0.0719 (mmm) cc_final: 0.0286 (mmm) REVERT: D 351 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7856 (tt) REVERT: E 223 GLU cc_start: 0.7666 (mt-10) cc_final: 0.6895 (tp30) REVERT: E 226 LEU cc_start: 0.7546 (mt) cc_final: 0.7213 (mt) REVERT: E 243 LEU cc_start: 0.7293 (mm) cc_final: 0.7004 (mp) REVERT: E 331 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8247 (mm-30) REVERT: E 398 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5363 (tt) REVERT: E 431 TRP cc_start: 0.4804 (t-100) cc_final: 0.4130 (t-100) REVERT: E 519 ARG cc_start: 0.7390 (tmt-80) cc_final: 0.6849 (tmt170) REVERT: E 556 LYS cc_start: 0.7158 (ttpm) cc_final: 0.6632 (mmtm) outliers start: 91 outliers final: 49 residues processed: 345 average time/residue: 0.5905 time to fit residues: 331.2497 Evaluate side-chains 297 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 405 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 667 VAL 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 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 580 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain C residue 262 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 574 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 708 LEU 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 439 MET Chi-restraints excluded: chain D residue 474 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 765 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 398 ILE 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 700 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 12 optimal weight: 50.0000 chunk 155 optimal weight: 20.0000 chunk 374 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 211 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 251 optimal weight: 20.0000 chunk 348 optimal weight: 20.0000 chunk 345 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 overall best weight: 5.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS 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 337 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS C 229 GLN D 664 HIS ** D 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.191447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.154028 restraints weight = 83009.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.148971 restraints weight = 68691.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.146900 restraints weight = 74009.735| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 30920 Z= 0.278 Angle : 0.835 15.960 41900 Z= 0.421 Chirality : 0.049 0.207 4770 Planarity : 0.006 0.060 5460 Dihedral : 7.095 54.335 4267 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 3.91 % Allowed : 11.96 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.13), residues: 3855 helix: -0.55 (0.12), residues: 1644 sheet: -2.46 (0.22), residues: 427 loop : -2.88 (0.13), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 563 HIS 0.009 0.002 HIS E 726 PHE 0.022 0.002 PHE D 466 TYR 0.027 0.002 TYR C 651 ARG 0.007 0.001 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.04928 ( 1201) hydrogen bonds : angle 5.39825 ( 3462) covalent geometry : bond 0.00632 (30920) covalent geometry : angle 0.83502 (41900) *********************** 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 367 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 240 time to evaluate : 3.673 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 230 MET cc_start: 0.6795 (ttt) cc_final: 0.6421 (tpt) REVERT: A 485 MET cc_start: 0.5450 (mmm) cc_final: 0.5112 (mpp) REVERT: B 293 LEU cc_start: 0.8704 (mt) cc_final: 0.8376 (tt) REVERT: B 516 MET cc_start: 0.6895 (mmm) cc_final: 0.6691 (mmm) REVERT: B 664 HIS cc_start: 0.6939 (OUTLIER) cc_final: 0.6530 (t-90) REVERT: C 45 PHE cc_start: 0.6345 (t80) cc_final: 0.6101 (t80) REVERT: C 503 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6526 (mmm160) REVERT: C 534 TYR cc_start: 0.8695 (m-80) cc_final: 0.8231 (m-80) REVERT: C 612 ILE cc_start: 0.8957 (mt) cc_final: 0.8720 (pt) REVERT: E 89 ARG cc_start: 0.5722 (mtm180) cc_final: 0.5506 (tpt-90) REVERT: E 217 MET cc_start: 0.4146 (ttt) cc_final: 0.3884 (ttt) REVERT: E 223 GLU cc_start: 0.7645 (mt-10) cc_final: 0.6814 (tp30) REVERT: E 226 LEU cc_start: 0.7648 (mt) cc_final: 0.7399 (mt) REVERT: E 233 ILE cc_start: 0.6075 (OUTLIER) cc_final: 0.5696 (pt) REVERT: E 243 LEU cc_start: 0.7278 (mm) cc_final: 0.6967 (mp) REVERT: E 276 MET cc_start: 0.1073 (tpt) cc_final: 0.0780 (tpt) REVERT: E 331 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8324 (mm-30) REVERT: E 398 ILE cc_start: 0.5556 (OUTLIER) cc_final: 0.5335 (tt) REVERT: E 431 TRP cc_start: 0.4963 (t-100) cc_final: 0.4413 (t-100) REVERT: E 556 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6667 (mmtm) outliers start: 127 outliers final: 79 residues processed: 337 average time/residue: 0.4217 time to fit residues: 230.6272 Evaluate side-chains 302 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 218 time to evaluate : 3.321 ------------------------------------------------------------------------------- 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 405 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 431 TRP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 468 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 702 MET 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 335 VAL 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 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 664 HIS 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 359 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 503 ARG 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 708 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 439 MET 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 635 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 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 398 ILE Chi-restraints excluded: chain E residue 487 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 698 MET 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 346 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 247 optimal weight: 50.0000 chunk 347 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 338 optimal weight: 0.1980 chunk 238 optimal weight: 0.0060 chunk 119 optimal weight: 0.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- 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 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 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.195343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.160025 restraints weight = 90976.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.153695 restraints weight = 69408.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.154571 restraints weight = 58031.122| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30920 Z= 0.124 Angle : 0.656 15.720 41900 Z= 0.331 Chirality : 0.044 0.209 4770 Planarity : 0.005 0.056 5460 Dihedral : 6.317 59.315 4267 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.13 % Favored : 92.84 % Rotamer: Outliers : 2.77 % Allowed : 13.04 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.13), residues: 3855 helix: 0.07 (0.13), residues: 1647 sheet: -2.23 (0.22), residues: 464 loop : -2.57 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 431 HIS 0.030 0.001 HIS B 664 PHE 0.017 0.001 PHE C 466 TYR 0.015 0.001 TYR A 332 ARG 0.007 0.000 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 1201) hydrogen bonds : angle 4.77727 ( 3462) covalent geometry : bond 0.00268 (30920) covalent geometry : angle 0.65641 (41900) *********************** 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 370 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 280 time to evaluate : 3.392 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: A 85 MET cc_start: 0.5335 (mmm) cc_final: 0.4172 (ppp) REVERT: A 217 MET cc_start: 0.7580 (tmm) cc_final: 0.6089 (ptp) REVERT: A 230 MET cc_start: 0.6761 (ttt) cc_final: 0.6475 (tpt) REVERT: A 439 MET cc_start: 0.8927 (tpp) cc_final: 0.8636 (tpp) REVERT: A 485 MET cc_start: 0.5496 (mmm) cc_final: 0.4511 (mtt) REVERT: A 535 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7252 (t) REVERT: B 293 LEU cc_start: 0.8621 (mt) cc_final: 0.8414 (tt) REVERT: B 374 ARG cc_start: 0.8347 (mtp85) cc_final: 0.8107 (ptm160) REVERT: B 409 MET cc_start: 0.7391 (tpp) cc_final: 0.7041 (tpt) REVERT: C 45 PHE cc_start: 0.6359 (t80) cc_final: 0.6060 (t80) REVERT: C 361 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7459 (mmtp) REVERT: C 496 MET cc_start: 0.7629 (mpp) cc_final: 0.7428 (mpp) REVERT: C 534 TYR cc_start: 0.8199 (m-80) cc_final: 0.7891 (m-10) REVERT: D 38 MET cc_start: 0.0762 (mmm) cc_final: 0.0277 (mmm) REVERT: E 104 ARG cc_start: 0.4127 (OUTLIER) cc_final: 0.3670 (mmm160) REVERT: E 223 GLU cc_start: 0.7641 (mt-10) cc_final: 0.6754 (tp30) REVERT: E 243 LEU cc_start: 0.7348 (mm) cc_final: 0.7053 (mp) REVERT: E 331 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8262 (mm-30) REVERT: E 431 TRP cc_start: 0.4634 (t-100) cc_final: 0.4086 (t-100) REVERT: E 545 ARG cc_start: 0.4582 (mtm110) cc_final: 0.3186 (mmt90) REVERT: E 556 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6796 (tppt) REVERT: E 721 LYS cc_start: 0.7280 (mtpp) cc_final: 0.6814 (mmtt) outliers start: 90 outliers final: 51 residues processed: 349 average time/residue: 0.4391 time to fit residues: 246.5046 Evaluate side-chains 298 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 5.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 603 THR 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 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 521 GLU 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 681 ILE 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 424 ILE Chi-restraints excluded: chain C residue 482 LEU 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 535 THR 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 104 ARG Chi-restraints excluded: chain E residue 224 TYR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 335 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 681 ILE Chi-restraints excluded: chain E residue 703 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 251 optimal weight: 20.0000 chunk 330 optimal weight: 30.0000 chunk 93 optimal weight: 50.0000 chunk 291 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 253 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 357 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 370 optimal weight: 5.9990 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 68 GLN ** A 139 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS C 234 GLN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 GLN ** 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 = 0.4666 r_free = 0.4666 target = 0.192113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.152975 restraints weight = 82560.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.145716 restraints weight = 65960.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.144840 restraints weight = 79059.607| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 30920 Z= 0.227 Angle : 0.756 16.488 41900 Z= 0.379 Chirality : 0.047 0.201 4770 Planarity : 0.006 0.063 5460 Dihedral : 6.416 48.916 4264 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.57 % Allowed : 13.53 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.13), residues: 3855 helix: -0.04 (0.13), residues: 1651 sheet: -2.22 (0.22), residues: 433 loop : -2.64 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 431 HIS 0.010 0.001 HIS A 319 PHE 0.016 0.002 PHE D 466 TYR 0.021 0.002 TYR C 651 ARG 0.014 0.001 ARG C 503 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 1201) hydrogen bonds : angle 4.98275 ( 3462) covalent geometry : bond 0.00524 (30920) covalent geometry : angle 0.75642 (41900) *********************** 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 353 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 237 time to evaluate : 6.493 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: A 85 MET cc_start: 0.5396 (mmm) cc_final: 0.4492 (ppp) REVERT: A 230 MET cc_start: 0.6822 (ttt) cc_final: 0.6504 (tpt) REVERT: A 289 TYR cc_start: 0.6772 (t80) cc_final: 0.6538 (t80) REVERT: A 439 MET cc_start: 0.9017 (tpp) cc_final: 0.8776 (tpp) REVERT: A 715 ILE cc_start: 0.2740 (OUTLIER) cc_final: 0.2200 (tt) REVERT: B 293 LEU cc_start: 0.8579 (mt) cc_final: 0.8344 (tt) REVERT: B 374 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7700 (ptm160) REVERT: B 534 TYR cc_start: 0.8288 (m-10) cc_final: 0.7946 (m-10) REVERT: C 45 PHE cc_start: 0.5907 (t80) cc_final: 0.5676 (t80) REVERT: C 361 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7687 (mmtp) REVERT: C 534 TYR cc_start: 0.8393 (m-80) cc_final: 0.7988 (m-80) REVERT: D 38 MET cc_start: 0.0561 (mmm) cc_final: 0.0143 (mmm) REVERT: D 272 ARG cc_start: 0.8872 (ptm-80) cc_final: 0.8391 (tmm-80) REVERT: D 598 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7263 (mt0) REVERT: E 89 ARG cc_start: 0.5890 (mtm180) cc_final: 0.5592 (tpt-90) REVERT: E 104 ARG cc_start: 0.3850 (OUTLIER) cc_final: 0.3644 (mmm160) REVERT: E 223 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6761 (tp30) REVERT: E 331 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8339 (mm-30) REVERT: E 431 TRP cc_start: 0.5274 (t-100) cc_final: 0.4712 (t-100) REVERT: E 496 MET cc_start: 0.9056 (ttp) cc_final: 0.8572 (tmm) REVERT: E 556 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6631 (tppt) REVERT: E 558 TRP cc_start: 0.3728 (OUTLIER) cc_final: 0.2279 (p-90) REVERT: E 721 LYS cc_start: 0.7221 (mtpp) cc_final: 0.6674 (mmtt) outliers start: 116 outliers final: 86 residues processed: 327 average time/residue: 0.4333 time to fit residues: 235.6065 Evaluate side-chains 310 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 218 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 314 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 443 LEU 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 698 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 290 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 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 521 GLU 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 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 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 574 ILE 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 160 MET Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 350 ILE 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 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 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 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 516 MET Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 558 TRP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 152 optimal weight: 0.0670 chunk 327 optimal weight: 50.0000 chunk 25 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 41 optimal weight: 0.0040 chunk 366 optimal weight: 4.9990 chunk 94 optimal weight: 50.0000 chunk 242 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 overall best weight: 1.6134 ------------------------------------------------------------------------------- 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 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** B 664 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.194066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.156384 restraints weight = 86452.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.149603 restraints weight = 64689.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.150240 restraints weight = 54988.326| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30920 Z= 0.133 Angle : 0.652 15.479 41900 Z= 0.329 Chirality : 0.044 0.200 4770 Planarity : 0.005 0.056 5460 Dihedral : 5.991 49.288 4264 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.99 % Allowed : 14.45 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.13), residues: 3855 helix: 0.30 (0.13), residues: 1649 sheet: -1.97 (0.23), residues: 444 loop : -2.48 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 602 HIS 0.006 0.001 HIS A 319 PHE 0.013 0.001 PHE C 466 TYR 0.013 0.001 TYR A 455 ARG 0.013 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 1201) hydrogen bonds : angle 4.64000 ( 3462) covalent geometry : bond 0.00297 (30920) covalent geometry : angle 0.65164 (41900) *********************** 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 342 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 245 time to evaluate : 3.523 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: A 85 MET cc_start: 0.5425 (mmm) cc_final: 0.4333 (ppp) REVERT: A 217 MET cc_start: 0.7497 (tmm) cc_final: 0.6011 (ptp) REVERT: A 230 MET cc_start: 0.6752 (ttt) cc_final: 0.6423 (tpt) REVERT: A 439 MET cc_start: 0.8998 (tpp) cc_final: 0.8780 (tpp) REVERT: A 485 MET cc_start: 0.5293 (mmm) cc_final: 0.4571 (mtt) REVERT: A 715 ILE cc_start: 0.2351 (OUTLIER) cc_final: 0.1764 (tt) REVERT: B 230 MET cc_start: 0.5064 (tmm) cc_final: 0.4826 (tmm) REVERT: B 268 LYS cc_start: 0.7755 (mmtm) cc_final: 0.6711 (tttp) REVERT: B 374 ARG cc_start: 0.8426 (mtp85) cc_final: 0.7930 (ptm160) REVERT: C 45 PHE cc_start: 0.6144 (t80) cc_final: 0.5807 (t80) REVERT: C 361 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7417 (mmtp) REVERT: C 534 TYR cc_start: 0.8425 (m-80) cc_final: 0.7868 (m-80) REVERT: D 38 MET cc_start: 0.0734 (mmm) cc_final: 0.0274 (mmm) REVERT: D 272 ARG cc_start: 0.8926 (ptm-80) cc_final: 0.8460 (tmm-80) REVERT: E 89 ARG cc_start: 0.5701 (mtm180) cc_final: 0.5441 (tpt-90) REVERT: E 223 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6677 (tp30) REVERT: E 331 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8268 (mm-30) REVERT: E 431 TRP cc_start: 0.4958 (t-100) cc_final: 0.4394 (t-100) REVERT: E 496 MET cc_start: 0.9064 (ttp) cc_final: 0.8569 (tmm) REVERT: E 556 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6649 (tppt) REVERT: E 558 TRP cc_start: 0.3854 (OUTLIER) cc_final: 0.2364 (p-90) REVERT: E 602 TRP cc_start: 0.5830 (t-100) cc_final: 0.5114 (t-100) REVERT: E 721 LYS cc_start: 0.7223 (mtpp) cc_final: 0.6670 (mmtt) REVERT: E 742 GLN cc_start: 0.7750 (mp10) cc_final: 0.7426 (mp10) outliers start: 97 outliers final: 68 residues processed: 321 average time/residue: 0.4029 time to fit residues: 211.4173 Evaluate side-chains 307 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 235 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 354 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 603 THR 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 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 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 617 VAL Chi-restraints excluded: chain B residue 641 LEU 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 765 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 84 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 648 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 535 THR 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 224 TYR 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 516 MET Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 558 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 271 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 197 optimal weight: 0.5980 chunk 262 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 50.0000 chunk 264 optimal weight: 3.9990 chunk 344 optimal weight: 20.0000 chunk 95 optimal weight: 50.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 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 393 HIS B 472 ASN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.192637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.156922 restraints weight = 85413.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.149619 restraints weight = 65817.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.150283 restraints weight = 53298.144| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30920 Z= 0.169 Angle : 0.687 16.370 41900 Z= 0.343 Chirality : 0.045 0.216 4770 Planarity : 0.005 0.056 5460 Dihedral : 5.962 48.013 4264 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 3.39 % Allowed : 14.08 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3855 helix: 0.32 (0.13), residues: 1649 sheet: -2.04 (0.23), residues: 433 loop : -2.48 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 602 HIS 0.010 0.001 HIS A 319 PHE 0.035 0.002 PHE A 466 TYR 0.015 0.002 TYR B 493 ARG 0.010 0.000 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 1201) hydrogen bonds : angle 4.67003 ( 3462) covalent geometry : bond 0.00387 (30920) covalent geometry : angle 0.68684 (41900) *********************** 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 348 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 238 time to evaluate : 3.163 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: A 85 MET cc_start: 0.5388 (mmm) cc_final: 0.4170 (ppp) REVERT: A 212 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7289 (ptp-170) REVERT: A 217 MET cc_start: 0.7605 (tmm) cc_final: 0.6074 (ptp) REVERT: A 230 MET cc_start: 0.6673 (ttt) cc_final: 0.6413 (tpt) REVERT: A 535 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7349 (t) REVERT: A 715 ILE cc_start: 0.2611 (OUTLIER) cc_final: 0.1995 (tt) REVERT: B 252 LYS cc_start: 0.5661 (tptt) cc_final: 0.5328 (ptmm) REVERT: B 374 ARG cc_start: 0.8320 (mtp85) cc_final: 0.8104 (ptm160) REVERT: B 395 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6840 (tmm-80) REVERT: B 425 ASP cc_start: 0.8199 (p0) cc_final: 0.7955 (p0) REVERT: C 45 PHE cc_start: 0.6546 (t80) cc_final: 0.6143 (t80) REVERT: C 361 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7461 (mmtp) REVERT: C 534 TYR cc_start: 0.8393 (m-80) cc_final: 0.7885 (m-80) REVERT: C 683 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7982 (mtp) REVERT: D 38 MET cc_start: 0.0939 (mmm) cc_final: 0.0423 (mmm) REVERT: D 272 ARG cc_start: 0.8799 (ptm-80) cc_final: 0.8429 (tmm-80) REVERT: D 598 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7003 (mt0) REVERT: E 89 ARG cc_start: 0.5396 (mtm180) cc_final: 0.5176 (tpt-90) REVERT: E 104 ARG cc_start: 0.4659 (OUTLIER) cc_final: 0.4042 (mmm160) REVERT: E 223 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6773 (tp30) REVERT: E 431 TRP cc_start: 0.4535 (t-100) cc_final: 0.4060 (t-100) REVERT: E 496 MET cc_start: 0.9007 (ttp) cc_final: 0.8520 (tmm) REVERT: E 556 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6693 (tppt) REVERT: E 558 TRP cc_start: 0.4172 (OUTLIER) cc_final: 0.2346 (p-90) REVERT: E 602 TRP cc_start: 0.6100 (t-100) cc_final: 0.5503 (t-100) REVERT: E 721 LYS cc_start: 0.7254 (mtpp) cc_final: 0.6719 (mmtt) REVERT: E 742 GLN cc_start: 0.7756 (mp10) cc_final: 0.7444 (mp10) outliers start: 110 outliers final: 79 residues processed: 322 average time/residue: 0.4095 time to fit residues: 213.3633 Evaluate side-chains 316 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 228 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 443 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 535 THR 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 698 MET 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 395 ARG 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 485 MET Chi-restraints excluded: chain B residue 521 GLU 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 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 B residue 765 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 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 574 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 350 ILE 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 598 GLN 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 44 ILE Chi-restraints excluded: chain E residue 104 ARG Chi-restraints excluded: chain E residue 224 TYR 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 558 TRP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 283 optimal weight: 2.9990 chunk 79 optimal weight: 50.0000 chunk 161 optimal weight: 10.0000 chunk 295 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 293 optimal weight: 0.0870 chunk 235 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 297 optimal weight: 0.9990 chunk 19 optimal weight: 40.0000 overall best weight: 2.2166 ------------------------------------------------------------------------------- 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 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 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.193566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.153912 restraints weight = 85951.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.147426 restraints weight = 64428.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.147227 restraints weight = 62469.338| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30920 Z= 0.146 Angle : 0.670 16.085 41900 Z= 0.334 Chirality : 0.045 0.429 4770 Planarity : 0.005 0.055 5460 Dihedral : 5.816 47.385 4264 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.20 % Allowed : 14.67 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 3855 helix: 0.43 (0.13), residues: 1649 sheet: -2.01 (0.23), residues: 446 loop : -2.37 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 602 HIS 0.009 0.001 HIS A 319 PHE 0.036 0.001 PHE A 466 TYR 0.022 0.001 TYR B 534 ARG 0.011 0.000 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 1201) hydrogen bonds : angle 4.57762 ( 3462) covalent geometry : bond 0.00333 (30920) covalent geometry : angle 0.67010 (41900) *********************** 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 350 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 246 time to evaluate : 3.442 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: A 85 MET cc_start: 0.5254 (mmm) cc_final: 0.4294 (ppp) REVERT: A 212 ARG cc_start: 0.7726 (ttm110) cc_final: 0.7362 (ptp-170) REVERT: A 217 MET cc_start: 0.7491 (tmm) cc_final: 0.6144 (ptm) REVERT: A 230 MET cc_start: 0.6706 (ttt) cc_final: 0.6402 (tpt) REVERT: A 485 MET cc_start: 0.5152 (mmm) cc_final: 0.4439 (mtt) REVERT: A 715 ILE cc_start: 0.2202 (OUTLIER) cc_final: 0.1606 (tt) REVERT: B 252 LYS cc_start: 0.5804 (tptt) cc_final: 0.5454 (ptmm) REVERT: B 374 ARG cc_start: 0.8367 (mtp85) cc_final: 0.8126 (ptm160) REVERT: B 425 ASP cc_start: 0.8205 (p0) cc_final: 0.7899 (p0) REVERT: C 45 PHE cc_start: 0.5905 (t80) cc_final: 0.5627 (t80) REVERT: C 361 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7313 (mmtp) REVERT: C 534 TYR cc_start: 0.8326 (m-80) cc_final: 0.7857 (m-80) REVERT: C 683 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8102 (mtp) REVERT: D 38 MET cc_start: 0.0653 (mmm) cc_final: 0.0260 (mmm) REVERT: D 272 ARG cc_start: 0.8962 (ptm-80) cc_final: 0.8512 (tmm-80) REVERT: D 276 MET cc_start: 0.5469 (ttp) cc_final: 0.4836 (ttp) REVERT: E 89 ARG cc_start: 0.5664 (mtm180) cc_final: 0.5419 (tpt-90) REVERT: E 104 ARG cc_start: 0.4020 (OUTLIER) cc_final: 0.3739 (mmm160) REVERT: E 223 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6795 (tp30) REVERT: E 431 TRP cc_start: 0.5258 (t-100) cc_final: 0.4681 (t-100) REVERT: E 496 MET cc_start: 0.9069 (ttp) cc_final: 0.8565 (tmm) REVERT: E 556 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6634 (tppt) REVERT: E 558 TRP cc_start: 0.3802 (OUTLIER) cc_final: 0.2411 (p-90) REVERT: E 602 TRP cc_start: 0.5753 (t-100) cc_final: 0.5046 (t-100) REVERT: E 721 LYS cc_start: 0.7109 (mtpp) cc_final: 0.6590 (mmtt) REVERT: E 742 GLN cc_start: 0.7829 (mp10) cc_final: 0.7465 (mp10) outliers start: 104 outliers final: 83 residues processed: 324 average time/residue: 0.4204 time to fit residues: 222.2127 Evaluate side-chains 322 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 233 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE 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 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 443 LEU 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 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 412 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 485 MET 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 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 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 482 LEU Chi-restraints excluded: chain C residue 494 THR 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 683 MET Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain D residue 84 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 350 ILE Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 590 THR 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 224 TYR 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 516 MET Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 558 TRP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 244 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 142 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 chunk 247 optimal weight: 50.0000 chunk 273 optimal weight: 0.0470 chunk 248 optimal weight: 40.0000 chunk 310 optimal weight: 50.0000 chunk 272 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 overall best weight: 3.8084 ------------------------------------------------------------------------------- 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 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 HIS ** 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 666 HIS D 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.191681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.153227 restraints weight = 85093.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.145577 restraints weight = 64328.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.146264 restraints weight = 64051.276| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30920 Z= 0.202 Angle : 0.736 16.017 41900 Z= 0.365 Chirality : 0.047 0.345 4770 Planarity : 0.005 0.056 5460 Dihedral : 6.003 50.837 4264 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 3.14 % Allowed : 14.95 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.13), residues: 3855 helix: 0.25 (0.13), residues: 1659 sheet: -2.06 (0.23), residues: 423 loop : -2.47 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 602 HIS 0.009 0.001 HIS B 319 PHE 0.036 0.002 PHE A 466 TYR 0.027 0.002 TYR A 289 ARG 0.011 0.000 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 1201) hydrogen bonds : angle 4.76831 ( 3462) covalent geometry : bond 0.00466 (30920) covalent geometry : angle 0.73554 (41900) ********************** 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 335 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 233 time to evaluate : 3.171 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: A 85 MET cc_start: 0.5321 (mmm) cc_final: 0.4376 (ppp) REVERT: A 217 MET cc_start: 0.7508 (tmm) cc_final: 0.6183 (ptm) REVERT: A 230 MET cc_start: 0.6697 (ttt) cc_final: 0.6387 (tpt) REVERT: A 715 ILE cc_start: 0.2429 (OUTLIER) cc_final: 0.1835 (tt) REVERT: B 258 MET cc_start: 0.7983 (tpp) cc_final: 0.7659 (tpp) REVERT: C 45 PHE cc_start: 0.6061 (t80) cc_final: 0.5745 (t80) REVERT: C 361 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7491 (mmtp) REVERT: C 534 TYR cc_start: 0.8452 (m-80) cc_final: 0.7949 (m-80) REVERT: C 683 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8153 (mtp) REVERT: D 38 MET cc_start: 0.0623 (mmm) cc_final: 0.0186 (mmm) REVERT: D 272 ARG cc_start: 0.9014 (ptm-80) cc_final: 0.8531 (tmm-80) REVERT: D 276 MET cc_start: 0.5573 (ttp) cc_final: 0.4806 (ttp) REVERT: D 516 MET cc_start: 0.7388 (mtt) cc_final: 0.7181 (mtp) REVERT: D 598 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.6992 (mt0) REVERT: E 89 ARG cc_start: 0.5579 (mtm180) cc_final: 0.5346 (tpt-90) REVERT: E 223 GLU cc_start: 0.7576 (mt-10) cc_final: 0.6784 (tp30) REVERT: E 276 MET cc_start: 0.1057 (tpt) cc_final: 0.0849 (tpt) REVERT: E 431 TRP cc_start: 0.5198 (t-100) cc_final: 0.4699 (t-100) REVERT: E 496 MET cc_start: 0.9083 (ttp) cc_final: 0.8545 (tmm) REVERT: E 556 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6683 (tppt) REVERT: E 558 TRP cc_start: 0.3964 (OUTLIER) cc_final: 0.2455 (p-90) REVERT: E 721 LYS cc_start: 0.7216 (mtpp) cc_final: 0.6646 (mmtt) REVERT: E 742 GLN cc_start: 0.7798 (mp10) cc_final: 0.7442 (mp10) outliers start: 102 outliers final: 87 residues processed: 308 average time/residue: 0.4297 time to fit residues: 216.3115 Evaluate side-chains 315 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 222 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE 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 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 443 LEU 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 544 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 698 MET 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 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 574 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 594 VAL 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 765 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 482 LEU Chi-restraints excluded: chain C residue 494 THR 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 683 MET Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain D residue 84 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 350 ILE 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 590 THR Chi-restraints excluded: chain D residue 598 GLN 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 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 224 TYR 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 516 MET Chi-restraints excluded: chain E residue 556 LYS Chi-restraints excluded: chain E residue 558 TRP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 74 optimal weight: 20.0000 chunk 369 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 375 optimal weight: 20.0000 chunk 300 optimal weight: 0.9990 chunk 341 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 349 optimal weight: 20.0000 chunk 295 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 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 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.193067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.145871 restraints weight = 84336.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.144265 restraints weight = 60304.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.144090 restraints weight = 50051.316| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30920 Z= 0.150 Angle : 0.683 15.880 41900 Z= 0.339 Chirality : 0.045 0.336 4770 Planarity : 0.005 0.056 5460 Dihedral : 5.792 49.403 4264 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.84 % Allowed : 15.53 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3855 helix: 0.42 (0.13), residues: 1655 sheet: -1.99 (0.23), residues: 448 loop : -2.34 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 171 HIS 0.007 0.001 HIS A 319 PHE 0.034 0.001 PHE A 466 TYR 0.018 0.001 TYR B 534 ARG 0.011 0.000 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 1201) hydrogen bonds : angle 4.61377 ( 3462) covalent geometry : bond 0.00343 (30920) covalent geometry : angle 0.68322 (41900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13015.27 seconds wall clock time: 232 minutes 54.09 seconds (13974.09 seconds total)