Starting phenix.real_space_refine on Sun Sep 13 09:49:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pw4_20498/09_2026/6pw4_20498.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pw4_20498/09_2026/6pw4_20498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pw4_20498/09_2026/6pw4_20498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pw4_20498/09_2026/6pw4_20498.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pw4_20498/09_2026/6pw4_20498.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pw4_20498/09_2026/6pw4_20498.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pw4_20498/09_2026/6pw4_20498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pw4_20498/09_2026/6pw4_20498.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 22 5.49 5 S 170 5.16 5 C 14462 2.51 5 N 3634 2.21 5 O 4060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 179 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22348 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5553 Classifications: {'peptide': 696} Link IDs: {'PTRANS': 24, 'TRANS': 671} Chain breaks: 4 Chain: "B" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5372 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 23, 'TRANS': 651} Chain breaks: 4 Chain: "C" Number of atoms: 5553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5553 Classifications: {'peptide': 696} Link IDs: {'PTRANS': 24, 'TRANS': 671} Chain breaks: 4 Chain: "D" Number of atoms: 5372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5372 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 23, 'TRANS': 651} Chain breaks: 4 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'CPL': 1, 'PCW': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 126 Unusual residues: {'PIK': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'CPL': 1, 'PCW': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'CPL:plan-3': 1, 'CPL:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 126 Unusual residues: {'PIK': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.12, per 1000 atoms: 0.18 Number of scatterers: 22348 At special positions: 0 Unit cell: (136.74, 147.34, 114.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 170 16.00 P 22 15.00 O 4060 8.00 N 3634 7.00 C 14462 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.0 seconds 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5228 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 0 sheets defined 65.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.585A pdb=" N GLU A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 removed outlier: 3.624A pdb=" N TYR A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.876A pdb=" N ALA A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 105 removed outlier: 4.476A pdb=" N LEU A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.757A pdb=" N LEU A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.770A pdb=" N ALA A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 removed outlier: 4.174A pdb=" N TYR A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.655A pdb=" N GLU A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 220 removed outlier: 4.086A pdb=" N THR A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TRP A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 333 through 348 removed outlier: 3.565A pdb=" N LEU A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 removed outlier: 3.536A pdb=" N ILE A 355 " --> pdb=" O CYS A 351 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 384 removed outlier: 3.933A pdb=" N ALA A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 396 removed outlier: 3.620A pdb=" N ALA A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 423 through 433 removed outlier: 4.260A pdb=" N LYS A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 444 through 463 removed outlier: 4.433A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 474 removed outlier: 3.655A pdb=" N VAL A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 Processing helix chain 'A' and resid 493 through 496 removed outlier: 3.590A pdb=" N HIS A 496 " --> pdb=" O PHE A 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 497 through 522 removed outlier: 3.984A pdb=" N LEU A 504 " --> pdb=" O TYR A 500 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.699A pdb=" N CYS A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 576 removed outlier: 3.841A pdb=" N VAL A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 575 " --> pdb=" O MET A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 588 removed outlier: 4.237A pdb=" N LEU A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 617 removed outlier: 3.738A pdb=" N ASN A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET A 612 " --> pdb=" O ALA A 608 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.994A pdb=" N ILE A 631 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET A 633 " --> pdb=" O PRO A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 662 removed outlier: 3.713A pdb=" N LEU A 648 " --> pdb=" O ARG A 644 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 655 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 666 removed outlier: 4.490A pdb=" N GLU A 666 " --> pdb=" O LEU A 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 663 through 666' Processing helix chain 'A' and resid 718 through 752 removed outlier: 4.089A pdb=" N PHE A 723 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE A 727 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 728 " --> pdb=" O TYR A 724 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 746 " --> pdb=" O MET A 742 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 764 Processing helix chain 'A' and resid 767 through 772 removed outlier: 3.621A pdb=" N ARG A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 767 through 772' Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.565A pdb=" N ALA A 788 " --> pdb=" O LEU A 784 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 789 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 791 " --> pdb=" O ALA A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 814 removed outlier: 3.742A pdb=" N VAL A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 removed outlier: 4.341A pdb=" N VAL A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 835 " --> pdb=" O VAL A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 856 removed outlier: 4.273A pdb=" N VAL A 847 " --> pdb=" O ASN A 843 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 856 " --> pdb=" O GLU A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 869 removed outlier: 4.577A pdb=" N HIS A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU A 864 " --> pdb=" O ASN A 860 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 867 " --> pdb=" O HIS A 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.581A pdb=" N LYS B 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 64 through 75 removed outlier: 3.680A pdb=" N LYS B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 removed outlier: 3.694A pdb=" N TYR B 95 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 96 " --> pdb=" O ALA B 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 96' Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.923A pdb=" N LEU B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.670A pdb=" N HIS B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 135 Processing helix chain 'B' and resid 139 through 152 removed outlier: 4.287A pdb=" N TYR B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.694A pdb=" N ALA B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 193 removed outlier: 3.631A pdb=" N GLU B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 220 removed outlier: 3.583A pdb=" N TRP B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.765A pdb=" N ILE B 241 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 removed outlier: 3.725A pdb=" N ALA B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.644A pdb=" N GLY B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 337 through 346 removed outlier: 3.537A pdb=" N VAL B 342 " --> pdb=" O GLN B 338 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.823A pdb=" N ILE B 355 " --> pdb=" O CYS B 351 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 360 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 362 " --> pdb=" O CYS B 358 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 384 removed outlier: 3.717A pdb=" N ALA B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.710A pdb=" N LEU B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.759A pdb=" N ILE B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 429 " --> pdb=" O GLN B 425 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 520 removed outlier: 3.873A pdb=" N LEU B 504 " --> pdb=" O TYR B 500 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 509 " --> pdb=" O THR B 505 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 534 removed outlier: 3.560A pdb=" N ALA B 531 " --> pdb=" O PRO B 528 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 532 " --> pdb=" O VAL B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 557 removed outlier: 4.455A pdb=" N LEU B 548 " --> pdb=" O CYS B 544 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 567 through 586 removed outlier: 4.077A pdb=" N MET B 571 " --> pdb=" O GLY B 567 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 573 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 576 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR B 579 " --> pdb=" O MET B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 591 removed outlier: 3.719A pdb=" N VAL B 590 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 616 removed outlier: 3.840A pdb=" N VAL B 602 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 612 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 623 removed outlier: 3.601A pdb=" N VAL B 620 " --> pdb=" O MET B 617 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 622 " --> pdb=" O SER B 619 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 623 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 641 removed outlier: 4.045A pdb=" N LEU B 638 " --> pdb=" O MET B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 662 removed outlier: 3.528A pdb=" N LEU B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 655 " --> pdb=" O VAL B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 753 removed outlier: 3.503A pdb=" N LEU B 725 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 726 " --> pdb=" O ILE B 722 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 730 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B 745 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG B 749 " --> pdb=" O ASP B 745 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 767 removed outlier: 3.576A pdb=" N ARG B 761 " --> pdb=" O GLU B 757 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 838 removed outlier: 3.596A pdb=" N VAL B 832 " --> pdb=" O ARG B 828 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG B 835 " --> pdb=" O VAL B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 850 removed outlier: 3.971A pdb=" N VAL B 847 " --> pdb=" O ASN B 843 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 850 " --> pdb=" O ARG B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 861 Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.580A pdb=" N GLU C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 75 removed outlier: 3.637A pdb=" N TYR C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 96 removed outlier: 3.875A pdb=" N ALA C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS C 94 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 removed outlier: 4.466A pdb=" N LEU C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 121 removed outlier: 3.784A pdb=" N LEU C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR C 117 " --> pdb=" O THR C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.782A pdb=" N ALA C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 153 removed outlier: 4.172A pdb=" N TYR C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 179 through 195 removed outlier: 3.650A pdb=" N GLU C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 220 removed outlier: 4.130A pdb=" N THR C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU C 211 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 240 Processing helix chain 'C' and resid 333 through 348 removed outlier: 3.962A pdb=" N SER C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 removed outlier: 3.536A pdb=" N ILE C 355 " --> pdb=" O CYS C 351 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 360 " --> pdb=" O MET C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 384 removed outlier: 3.843A pdb=" N ALA C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 396 removed outlier: 3.621A pdb=" N ALA C 394 " --> pdb=" O GLN C 390 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 423 through 433 removed outlier: 4.260A pdb=" N LYS C 431 " --> pdb=" O ILE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 440 Processing helix chain 'C' and resid 444 through 463 removed outlier: 4.435A pdb=" N VAL C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 463 " --> pdb=" O ALA C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 474 removed outlier: 3.666A pdb=" N VAL C 470 " --> pdb=" O PRO C 466 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 471 " --> pdb=" O LEU C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 484 Processing helix chain 'C' and resid 493 through 496 removed outlier: 3.590A pdb=" N HIS C 496 " --> pdb=" O PHE C 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 493 through 496' Processing helix chain 'C' and resid 497 through 522 removed outlier: 3.983A pdb=" N LEU C 504 " --> pdb=" O TYR C 500 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 553 removed outlier: 3.701A pdb=" N CYS C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 576 removed outlier: 3.841A pdb=" N VAL C 573 " --> pdb=" O ASN C 569 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 575 " --> pdb=" O MET C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 588 removed outlier: 4.237A pdb=" N LEU C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 617 removed outlier: 3.739A pdb=" N ASN C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP C 614 " --> pdb=" O ALA C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 622 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.943A pdb=" N ILE C 631 " --> pdb=" O ILE C 627 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 632 " --> pdb=" O GLY C 628 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET C 633 " --> pdb=" O PRO C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 662 removed outlier: 3.713A pdb=" N LEU C 648 " --> pdb=" O ARG C 644 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY C 655 " --> pdb=" O VAL C 651 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 752 removed outlier: 4.107A pdb=" N PHE C 723 " --> pdb=" O THR C 719 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE C 727 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 728 " --> pdb=" O TYR C 724 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 745 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 746 " --> pdb=" O MET C 742 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 748 " --> pdb=" O ALA C 744 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR C 752 " --> pdb=" O THR C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 764 Processing helix chain 'C' and resid 767 through 772 removed outlier: 3.641A pdb=" N ARG C 771 " --> pdb=" O ALA C 767 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 772 " --> pdb=" O SER C 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 767 through 772' Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.566A pdb=" N ALA C 788 " --> pdb=" O LEU C 784 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 789 " --> pdb=" O VAL C 785 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 791 " --> pdb=" O ALA C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 814 removed outlier: 3.751A pdb=" N VAL C 814 " --> pdb=" O LYS C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 835 removed outlier: 4.324A pdb=" N VAL C 832 " --> pdb=" O ARG C 828 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 835 " --> pdb=" O VAL C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 856 removed outlier: 3.520A pdb=" N ARG C 846 " --> pdb=" O LEU C 842 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL C 847 " --> pdb=" O ASN C 843 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 850 " --> pdb=" O ARG C 846 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 856 " --> pdb=" O GLU C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 869 removed outlier: 4.607A pdb=" N HIS C 863 " --> pdb=" O PRO C 859 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 864 " --> pdb=" O ASN C 860 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 867 " --> pdb=" O HIS C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 45 through 49 removed outlier: 4.580A pdb=" N LYS D 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 Processing helix chain 'D' and resid 64 through 75 removed outlier: 3.683A pdb=" N LYS D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.693A pdb=" N TYR D 95 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY D 96 " --> pdb=" O ALA D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 96' Processing helix chain 'D' and resid 98 through 109 removed outlier: 3.925A pdb=" N LEU D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 121 removed outlier: 3.698A pdb=" N HIS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 135 Processing helix chain 'D' and resid 139 through 153 removed outlier: 4.293A pdb=" N TYR D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 178 removed outlier: 3.691A pdb=" N ALA D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA D 175 " --> pdb=" O MET D 171 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 removed outlier: 3.631A pdb=" N GLU D 184 " --> pdb=" O THR D 180 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL D 185 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 220 removed outlier: 3.563A pdb=" N THR D 207 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 211 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 241 removed outlier: 3.763A pdb=" N ILE D 241 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 removed outlier: 3.728A pdb=" N ALA D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.681A pdb=" N GLY D 259 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 Processing helix chain 'D' and resid 337 through 346 removed outlier: 3.541A pdb=" N VAL D 342 " --> pdb=" O GLN D 338 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER D 343 " --> pdb=" O GLY D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 364 removed outlier: 3.827A pdb=" N ILE D 355 " --> pdb=" O CYS D 351 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER D 360 " --> pdb=" O MET D 356 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 362 " --> pdb=" O CYS D 358 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D 364 " --> pdb=" O SER D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 384 removed outlier: 3.721A pdb=" N ALA D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN D 374 " --> pdb=" O ASP D 370 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.712A pdb=" N LEU D 419 " --> pdb=" O ASP D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 433 removed outlier: 3.782A pdb=" N ILE D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D 428 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR D 429 " --> pdb=" O GLN D 425 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS D 431 " --> pdb=" O ILE D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 520 removed outlier: 3.875A pdb=" N LEU D 504 " --> pdb=" O TYR D 500 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 509 " --> pdb=" O THR D 505 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 520 " --> pdb=" O LEU D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 534 removed outlier: 3.560A pdb=" N ALA D 531 " --> pdb=" O PRO D 528 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER D 532 " --> pdb=" O VAL D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 559 removed outlier: 4.485A pdb=" N LEU D 548 " --> pdb=" O CYS D 544 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D 558 " --> pdb=" O GLU D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 564 Processing helix chain 'D' and resid 567 through 586 removed outlier: 4.080A pdb=" N MET D 571 " --> pdb=" O GLY D 567 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 573 " --> pdb=" O ASN D 569 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR D 579 " --> pdb=" O MET D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 591 removed outlier: 3.711A pdb=" N VAL D 590 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 616 removed outlier: 3.843A pdb=" N VAL D 602 " --> pdb=" O ILE D 598 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 612 " --> pdb=" O ALA D 608 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 613 " --> pdb=" O ALA D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 623 removed outlier: 3.564A pdb=" N VAL D 620 " --> pdb=" O MET D 617 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU D 622 " --> pdb=" O SER D 619 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU D 623 " --> pdb=" O VAL D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 641 removed outlier: 4.046A pdb=" N LEU D 638 " --> pdb=" O MET D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 662 removed outlier: 3.510A pdb=" N LEU D 650 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 651 " --> pdb=" O LEU D 647 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY D 655 " --> pdb=" O VAL D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 753 removed outlier: 3.506A pdb=" N LEU D 725 " --> pdb=" O VAL D 721 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 730 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 738 " --> pdb=" O LEU D 734 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP D 745 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG D 749 " --> pdb=" O ASP D 745 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 752 " --> pdb=" O THR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 766 removed outlier: 3.576A pdb=" N ARG D 761 " --> pdb=" O GLU D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 850 removed outlier: 3.593A pdb=" N VAL D 832 " --> pdb=" O ARG D 828 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG D 835 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP D 839 " --> pdb=" O ARG D 835 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL D 847 " --> pdb=" O ASN D 843 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE D 850 " --> pdb=" O ARG D 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 861 890 hydrogen bonds defined for protein. 2586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3524 1.31 - 1.44: 6111 1.44 - 1.57: 12874 1.57 - 1.70: 33 1.70 - 1.83: 282 Bond restraints: 22824 Sorted by residual: bond pdb=" C31 PCW C1002 " pdb=" O2 PCW C1002 " ideal model delta sigma weight residual 1.333 1.444 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C31 PCW A1002 " pdb=" O2 PCW A1002 " ideal model delta sigma weight residual 1.333 1.444 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C11 PCW A1002 " pdb=" O3 PCW A1002 " ideal model delta sigma weight residual 1.326 1.431 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C11 PCW C1002 " pdb=" O3 PCW C1002 " ideal model delta sigma weight residual 1.326 1.431 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" CA1 PIK D1002 " pdb=" OA1 PIK D1002 " ideal model delta sigma weight residual 1.332 1.405 -0.073 2.00e-02 2.50e+03 1.32e+01 ... (remaining 22819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 29985 3.13 - 6.27: 780 6.27 - 9.40: 135 9.40 - 12.53: 28 12.53 - 15.67: 12 Bond angle restraints: 30940 Sorted by residual: angle pdb=" N VAL D 246 " pdb=" CA VAL D 246 " pdb=" C VAL D 246 " ideal model delta sigma weight residual 113.71 106.24 7.47 9.50e-01 1.11e+00 6.18e+01 angle pdb=" N VAL B 246 " pdb=" CA VAL B 246 " pdb=" C VAL B 246 " ideal model delta sigma weight residual 113.71 106.24 7.47 9.50e-01 1.11e+00 6.18e+01 angle pdb=" N ILE A 627 " pdb=" CA ILE A 627 " pdb=" C ILE A 627 " ideal model delta sigma weight residual 113.53 105.99 7.54 9.80e-01 1.04e+00 5.93e+01 angle pdb=" N GLN B 114 " pdb=" CA GLN B 114 " pdb=" C GLN B 114 " ideal model delta sigma weight residual 114.04 104.63 9.41 1.24e+00 6.50e-01 5.76e+01 angle pdb=" N GLN D 114 " pdb=" CA GLN D 114 " pdb=" C GLN D 114 " ideal model delta sigma weight residual 114.04 104.68 9.36 1.24e+00 6.50e-01 5.70e+01 ... (remaining 30935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 13146 35.70 - 71.40: 364 71.40 - 107.10: 26 107.10 - 142.81: 12 142.81 - 178.51: 2 Dihedral angle restraints: 13550 sinusoidal: 5484 harmonic: 8066 Sorted by residual: dihedral pdb=" CA SER B 232 " pdb=" C SER B 232 " pdb=" N PHE B 233 " pdb=" CA PHE B 233 " ideal model delta harmonic sigma weight residual 180.00 134.47 45.53 0 5.00e+00 4.00e-02 8.29e+01 dihedral pdb=" CA SER D 232 " pdb=" C SER D 232 " pdb=" N PHE D 233 " pdb=" CA PHE D 233 " ideal model delta harmonic sigma weight residual 180.00 134.49 45.51 0 5.00e+00 4.00e-02 8.28e+01 dihedral pdb=" CA CYS A 776 " pdb=" C CYS A 776 " pdb=" N PRO A 777 " pdb=" CA PRO A 777 " ideal model delta harmonic sigma weight residual 180.00 139.71 40.29 0 5.00e+00 4.00e-02 6.49e+01 ... (remaining 13547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2596 0.055 - 0.110: 764 0.110 - 0.166: 137 0.166 - 0.221: 29 0.221 - 0.276: 12 Chirality restraints: 3538 Sorted by residual: chirality pdb=" CB THR A 593 " pdb=" CA THR A 593 " pdb=" OG1 THR A 593 " pdb=" CG2 THR A 593 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB THR C 593 " pdb=" CA THR C 593 " pdb=" OG1 THR C 593 " pdb=" CG2 THR C 593 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL C 775 " pdb=" CA VAL C 775 " pdb=" CG1 VAL C 775 " pdb=" CG2 VAL C 775 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 3535 not shown) Planarity restraints: 3804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 776 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO A 777 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 777 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 777 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 776 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO C 777 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 777 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 777 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 776 " -0.053 5.00e-02 4.00e+02 7.89e-02 9.95e+00 pdb=" N PRO B 777 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 777 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 777 " -0.043 5.00e-02 4.00e+02 ... (remaining 3801 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7034 2.82 - 3.34: 19629 3.34 - 3.86: 35425 3.86 - 4.38: 42975 4.38 - 4.90: 71742 Nonbonded interactions: 176805 Sorted by model distance: nonbonded pdb=" O PHE A 727 " pdb=" OG1 THR A 731 " model vdw 2.302 3.040 nonbonded pdb=" O PHE C 727 " pdb=" OG1 THR C 731 " model vdw 2.303 3.040 nonbonded pdb=" O SER B 565 " pdb=" OG SER B 565 " model vdw 2.308 3.040 nonbonded pdb=" O SER D 565 " pdb=" OG SER D 565 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR B 39 " pdb=" O MET B 44 " model vdw 2.312 3.040 ... (remaining 176800 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.380 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.008 0.111 22832 Z= 0.360 Angle : 1.257 15.667 30940 Z= 0.643 Chirality : 0.056 0.276 3538 Planarity : 0.007 0.088 3804 Dihedral : 17.388 178.506 8322 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.66 % Favored : 89.27 % Rotamer: Outliers : 0.38 % Allowed : 10.28 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.92 (0.09), residues: 2702 helix: -4.68 (0.05), residues: 1758 sheet: None (None), residues: 0 loop : -3.99 (0.16), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 851 TYR 0.027 0.002 TYR D 22 PHE 0.022 0.002 PHE B 841 TRP 0.030 0.003 TRP D 543 HIS 0.007 0.002 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.36 (22824) covalent geometry : angle 1.25719 / 0.64 (30940) hydrogen bonds : bond 0.31275 / 20.61 ( 890) hydrogen bonds : angle 10.83114 / 7.38 ( 2586) Misc. bond : bond 0.00144 / 0.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 517 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 TRP cc_start: 0.7136 (m-90) cc_final: 0.6918 (m-90) REVERT: A 722 ILE cc_start: 0.7537 (mm) cc_final: 0.7121 (tt) REVERT: A 737 ASN cc_start: 0.8786 (t0) cc_final: 0.8335 (t0) REVERT: A 827 MET cc_start: 0.8266 (ttm) cc_final: 0.8025 (ttm) REVERT: A 865 MET cc_start: 0.7696 (ptm) cc_final: 0.7401 (ptm) REVERT: B 225 TYR cc_start: 0.7030 (p90) cc_final: 0.6644 (p90) REVERT: B 366 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7493 (ttp-170) REVERT: B 723 PHE cc_start: 0.7455 (m-80) cc_final: 0.7024 (m-80) REVERT: B 739 PHE cc_start: 0.7893 (t80) cc_final: 0.7383 (t80) REVERT: B 840 ASP cc_start: 0.7306 (m-30) cc_final: 0.7003 (m-30) REVERT: B 843 ASN cc_start: 0.8100 (t0) cc_final: 0.7798 (t0) REVERT: C 604 ASP cc_start: 0.7896 (t0) cc_final: 0.7686 (t0) REVERT: C 722 ILE cc_start: 0.7547 (mm) cc_final: 0.7117 (tt) REVERT: C 737 ASN cc_start: 0.8774 (t0) cc_final: 0.8274 (t0) REVERT: C 827 MET cc_start: 0.8261 (ttm) cc_final: 0.8007 (ttm) REVERT: C 865 MET cc_start: 0.7755 (ptm) cc_final: 0.7445 (ptm) REVERT: D 225 TYR cc_start: 0.7018 (p90) cc_final: 0.6644 (p90) REVERT: D 366 ARG cc_start: 0.7806 (ttm170) cc_final: 0.7471 (ttp-170) REVERT: D 551 GLU cc_start: 0.6633 (mp0) cc_final: 0.6107 (mp0) REVERT: D 554 GLU cc_start: 0.7174 (tt0) cc_final: 0.6708 (tt0) REVERT: D 723 PHE cc_start: 0.7411 (m-80) cc_final: 0.6973 (m-80) REVERT: D 739 PHE cc_start: 0.7844 (t80) cc_final: 0.7446 (t80) outliers start: 9 outliers final: 2 residues processed: 526 average time/residue: 0.1639 time to fit residues: 132.0390 Evaluate side-chains 408 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 406 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain D residue 592 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 425 GLN A 553 GLN A 665 GLN A 860 ASN B 27 HIS B 169 ASN B 179 HIS B 221 HIS B 359 GLN B 426 GLN B 506 GLN ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 GLN C 425 GLN C 553 GLN C 632 GLN C 665 GLN C 860 ASN D 27 HIS D 169 ASN D 179 HIS D 221 HIS D 359 GLN D 426 GLN D 506 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.183383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.150562 restraints weight = 26989.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.153512 restraints weight = 17085.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.155412 restraints weight = 13025.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.156406 restraints weight = 11114.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.157164 restraints weight = 10166.355| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22832 Z= 0.133 Angle : 0.692 14.724 30940 Z= 0.354 Chirality : 0.040 0.146 3538 Planarity : 0.006 0.078 3804 Dihedral : 13.053 174.017 3226 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 2.27 % Allowed : 15.67 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.18 (0.12), residues: 2702 helix: -3.21 (0.09), residues: 1788 sheet: None (None), residues: 0 loop : -3.56 (0.17), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 231 TYR 0.018 0.002 TYR C 747 PHE 0.014 0.001 PHE D 233 TRP 0.015 0.001 TRP A 83 HIS 0.005 0.001 HIS C 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (22824) covalent geometry : angle 0.69157 / 0.35 (30940) hydrogen bonds : bond 0.04488 / 2.94 ( 890) hydrogen bonds : angle 5.20235 / 3.52 ( 2586) Misc. bond : bond 0.00255 / 0.11 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 456 time to evaluate : 0.742 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 123 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.3925 (mmp-170) REVERT: A 349 MET cc_start: 0.7740 (mtt) cc_final: 0.7537 (mtt) REVERT: A 634 MET cc_start: 0.7620 (tpt) cc_final: 0.7367 (tpt) REVERT: A 737 ASN cc_start: 0.8739 (t0) cc_final: 0.8509 (t0) REVERT: A 827 MET cc_start: 0.8128 (ttm) cc_final: 0.7922 (ttm) REVERT: B 104 MET cc_start: 0.6941 (tmm) cc_final: 0.6738 (tmm) REVERT: B 366 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7456 (ttp80) REVERT: B 370 ASP cc_start: 0.7276 (t0) cc_final: 0.7033 (t0) REVERT: B 515 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7723 (mp) REVERT: B 554 GLU cc_start: 0.7018 (tt0) cc_final: 0.6745 (mt-10) REVERT: B 605 LEU cc_start: 0.8633 (mt) cc_final: 0.8398 (mm) REVERT: B 648 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7671 (tt) REVERT: B 723 PHE cc_start: 0.7089 (m-80) cc_final: 0.6817 (m-80) REVERT: B 840 ASP cc_start: 0.7391 (m-30) cc_final: 0.7092 (m-30) REVERT: C 123 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.4041 (mmp-170) REVERT: C 349 MET cc_start: 0.7749 (mtt) cc_final: 0.7539 (mtt) REVERT: C 737 ASN cc_start: 0.8749 (t0) cc_final: 0.8483 (t0) REVERT: C 827 MET cc_start: 0.8122 (ttm) cc_final: 0.7918 (ttm) REVERT: D 104 MET cc_start: 0.6935 (tmm) cc_final: 0.6702 (tmm) REVERT: D 143 MET cc_start: 0.7950 (tpp) cc_final: 0.7474 (tpp) REVERT: D 273 THR cc_start: 0.7818 (m) cc_final: 0.7580 (t) REVERT: D 366 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7449 (ttp80) REVERT: D 433 ASP cc_start: 0.8052 (t0) cc_final: 0.7793 (t0) REVERT: D 515 LEU cc_start: 0.7772 (tt) cc_final: 0.7491 (mt) REVERT: D 554 GLU cc_start: 0.6942 (tt0) cc_final: 0.6472 (tt0) REVERT: D 569 ASN cc_start: 0.7222 (m-40) cc_final: 0.5663 (m-40) REVERT: D 580 ILE cc_start: 0.8689 (tp) cc_final: 0.8489 (tp) REVERT: D 605 LEU cc_start: 0.8616 (mt) cc_final: 0.8362 (mm) REVERT: D 640 LYS cc_start: 0.7606 (mtpp) cc_final: 0.7289 (mttp) REVERT: D 723 PHE cc_start: 0.7031 (m-80) cc_final: 0.6770 (m-80) outliers start: 54 outliers final: 25 residues processed: 485 average time/residue: 0.1475 time to fit residues: 114.0467 Evaluate side-chains 433 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 404 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 612 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 30 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 238 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 246 optimal weight: 0.0570 chunk 225 optimal weight: 0.2980 chunk 221 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 122 optimal weight: 0.0170 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 HIS D 632 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.185819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.152838 restraints weight = 26987.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.155825 restraints weight = 17240.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.157730 restraints weight = 13180.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.158677 restraints weight = 11260.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.159519 restraints weight = 10324.030| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22832 Z= 0.108 Angle : 0.621 12.366 30940 Z= 0.314 Chirality : 0.039 0.146 3538 Planarity : 0.005 0.071 3804 Dihedral : 11.446 178.538 3226 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.32 % Allowed : 18.41 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.14), residues: 2702 helix: -2.07 (0.11), residues: 1786 sheet: None (None), residues: 0 loop : -3.22 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.021 0.001 TYR C 747 PHE 0.016 0.001 PHE B 233 TRP 0.018 0.001 TRP A 568 HIS 0.009 0.001 HIS D 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (22824) covalent geometry : angle 0.62057 / 0.31 (30940) hydrogen bonds : bond 0.03343 / 2.16 ( 890) hydrogen bonds : angle 4.35922 / 2.95 ( 2586) Misc. bond : bond 0.00175 / 0.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 435 time to evaluate : 0.829 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: A 123 ARG cc_start: 0.5360 (OUTLIER) cc_final: 0.3261 (mmp-170) REVERT: A 352 MET cc_start: 0.8776 (tpp) cc_final: 0.8485 (tpp) REVERT: A 653 LEU cc_start: 0.8157 (tp) cc_final: 0.7762 (tt) REVERT: B 136 TYR cc_start: 0.7810 (t80) cc_final: 0.7249 (t80) REVERT: B 143 MET cc_start: 0.7905 (tpp) cc_final: 0.7445 (tpp) REVERT: B 366 ARG cc_start: 0.7749 (ttm170) cc_final: 0.7318 (ttp80) REVERT: B 554 GLU cc_start: 0.6848 (tt0) cc_final: 0.6522 (mt-10) REVERT: B 723 PHE cc_start: 0.7028 (m-80) cc_final: 0.6756 (m-80) REVERT: B 840 ASP cc_start: 0.7411 (m-30) cc_final: 0.7064 (m-30) REVERT: B 866 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6005 (mt) REVERT: C 123 ARG cc_start: 0.5282 (OUTLIER) cc_final: 0.3217 (mmp-170) REVERT: C 352 MET cc_start: 0.8780 (tpp) cc_final: 0.8492 (tpp) REVERT: C 653 LEU cc_start: 0.8189 (tp) cc_final: 0.7820 (tt) REVERT: C 827 MET cc_start: 0.8093 (ttm) cc_final: 0.7863 (ttm) REVERT: D 136 TYR cc_start: 0.7874 (t80) cc_final: 0.7128 (t80) REVERT: D 273 THR cc_start: 0.7749 (m) cc_final: 0.7526 (t) REVERT: D 366 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7342 (ttp80) REVERT: D 515 LEU cc_start: 0.7758 (tt) cc_final: 0.7496 (mt) REVERT: D 554 GLU cc_start: 0.6884 (tt0) cc_final: 0.6420 (tt0) REVERT: D 562 GLU cc_start: 0.7168 (tp30) cc_final: 0.6709 (tp30) REVERT: D 569 ASN cc_start: 0.7360 (m-40) cc_final: 0.6076 (m-40) REVERT: D 580 ILE cc_start: 0.8643 (tp) cc_final: 0.8425 (tp) REVERT: D 640 LYS cc_start: 0.7489 (mtpp) cc_final: 0.7180 (mttp) REVERT: D 723 PHE cc_start: 0.6977 (m-80) cc_final: 0.6700 (m-80) REVERT: D 866 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.5987 (mt) outliers start: 55 outliers final: 27 residues processed: 462 average time/residue: 0.1494 time to fit residues: 109.9492 Evaluate side-chains 419 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 388 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 495 TRP Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 866 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 208 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 215 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 HIS A 177 GLN ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 GLN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.173296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.139925 restraints weight = 27575.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.142408 restraints weight = 18607.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.144032 restraints weight = 14797.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.144867 restraints weight = 12952.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.145558 restraints weight = 11995.555| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 22832 Z= 0.309 Angle : 0.783 13.421 30940 Z= 0.394 Chirality : 0.047 0.205 3538 Planarity : 0.006 0.070 3804 Dihedral : 11.590 163.974 3224 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 4.13 % Allowed : 19.63 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.15), residues: 2702 helix: -1.85 (0.11), residues: 1828 sheet: None (None), residues: 0 loop : -3.21 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 616 TYR 0.020 0.002 TYR D 22 PHE 0.023 0.002 PHE A 234 TRP 0.020 0.002 TRP A 568 HIS 0.010 0.002 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.31 (22824) covalent geometry : angle 0.78332 / 0.39 (30940) hydrogen bonds : bond 0.04149 / 2.68 ( 890) hydrogen bonds : angle 4.80194 / 3.25 ( 2586) Misc. bond : bond 0.00215 / 0.10 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 392 time to evaluate : 0.823 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 62 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7799 (mm) REVERT: A 123 ARG cc_start: 0.6149 (OUTLIER) cc_final: 0.3995 (mmp-170) REVERT: A 159 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8310 (tt) REVERT: B 269 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7651 (pp) REVERT: B 366 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7569 (ttp-170) REVERT: B 439 ASP cc_start: 0.8040 (t0) cc_final: 0.7757 (t0) REVERT: B 554 GLU cc_start: 0.6991 (tt0) cc_final: 0.6739 (mt-10) REVERT: B 580 ILE cc_start: 0.8682 (tp) cc_final: 0.8479 (tp) REVERT: B 723 PHE cc_start: 0.7142 (m-80) cc_final: 0.6907 (m-80) REVERT: B 840 ASP cc_start: 0.7433 (m-30) cc_final: 0.7058 (m-30) REVERT: B 845 ASN cc_start: 0.8111 (m-40) cc_final: 0.7841 (m110) REVERT: B 866 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6360 (mt) REVERT: C 61 GLU cc_start: 0.7309 (tt0) cc_final: 0.7018 (tt0) REVERT: C 123 ARG cc_start: 0.6135 (OUTLIER) cc_final: 0.4076 (mmp-170) REVERT: C 159 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8282 (tt) REVERT: D 143 MET cc_start: 0.8288 (tpp) cc_final: 0.7570 (tpp) REVERT: D 366 ARG cc_start: 0.7862 (ttm170) cc_final: 0.7567 (ttp-170) REVERT: D 554 GLU cc_start: 0.6848 (tt0) cc_final: 0.6416 (tt0) REVERT: D 569 ASN cc_start: 0.7252 (m-40) cc_final: 0.5710 (m-40) REVERT: D 580 ILE cc_start: 0.8712 (tp) cc_final: 0.8450 (tp) REVERT: D 723 PHE cc_start: 0.7121 (m-80) cc_final: 0.6871 (m-80) REVERT: D 866 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6330 (mt) outliers start: 98 outliers final: 68 residues processed: 451 average time/residue: 0.1406 time to fit residues: 103.5263 Evaluate side-chains 441 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 365 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 495 TRP Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 270 HIS Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 734 LEU Chi-restraints excluded: chain D residue 818 SER Chi-restraints excluded: chain D residue 866 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 184 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 231 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 131 optimal weight: 0.0060 chunk 228 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS A 553 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 HIS C 553 GLN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.179463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.146677 restraints weight = 27026.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.149339 restraints weight = 18279.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.151006 restraints weight = 14471.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.151813 restraints weight = 12652.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.152430 restraints weight = 11722.228| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22832 Z= 0.132 Angle : 0.643 12.744 30940 Z= 0.323 Chirality : 0.041 0.157 3538 Planarity : 0.005 0.062 3804 Dihedral : 10.844 158.965 3224 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.70 % Allowed : 21.61 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.15), residues: 2702 helix: -1.33 (0.12), residues: 1810 sheet: None (None), residues: 0 loop : -2.97 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 32 TYR 0.018 0.001 TYR C 747 PHE 0.015 0.001 PHE B 233 TRP 0.024 0.001 TRP A 568 HIS 0.008 0.001 HIS B 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (22824) covalent geometry : angle 0.64268 / 0.32 (30940) hydrogen bonds : bond 0.03190 / 2.05 ( 890) hydrogen bonds : angle 4.20639 / 2.84 ( 2586) Misc. bond : bond 0.00159 / 0.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 404 time to evaluate : 0.920 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 62 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7922 (mm) REVERT: A 123 ARG cc_start: 0.5620 (OUTLIER) cc_final: 0.3386 (mmp-170) REVERT: A 159 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8196 (tt) REVERT: A 653 LEU cc_start: 0.8181 (tp) cc_final: 0.7950 (tt) REVERT: B 431 LYS cc_start: 0.8699 (tptt) cc_final: 0.8086 (tttp) REVERT: B 521 PHE cc_start: 0.6760 (m-80) cc_final: 0.6189 (m-80) REVERT: B 554 GLU cc_start: 0.6798 (tt0) cc_final: 0.6474 (mt-10) REVERT: B 572 ASP cc_start: 0.7179 (m-30) cc_final: 0.6939 (m-30) REVERT: B 580 ILE cc_start: 0.8691 (tp) cc_final: 0.8464 (tp) REVERT: B 612 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.5294 (mmm) REVERT: B 723 PHE cc_start: 0.7103 (m-80) cc_final: 0.6869 (m-80) REVERT: B 840 ASP cc_start: 0.7366 (m-30) cc_final: 0.6996 (m-30) REVERT: B 845 ASN cc_start: 0.7886 (m-40) cc_final: 0.7634 (m-40) REVERT: B 866 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6242 (mt) REVERT: C 61 GLU cc_start: 0.7103 (tt0) cc_final: 0.6872 (tt0) REVERT: C 123 ARG cc_start: 0.5592 (OUTLIER) cc_final: 0.3380 (mmp-170) REVERT: C 159 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8229 (tt) REVERT: C 653 LEU cc_start: 0.8174 (tp) cc_final: 0.7737 (tt) REVERT: D 433 ASP cc_start: 0.8290 (t0) cc_final: 0.8002 (t0) REVERT: D 515 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7641 (mp) REVERT: D 521 PHE cc_start: 0.6451 (m-80) cc_final: 0.5952 (m-80) REVERT: D 554 GLU cc_start: 0.6746 (tt0) cc_final: 0.6164 (tt0) REVERT: D 569 ASN cc_start: 0.7195 (m-40) cc_final: 0.5866 (m-40) REVERT: D 580 ILE cc_start: 0.8712 (tp) cc_final: 0.8436 (tp) REVERT: D 723 PHE cc_start: 0.7072 (m-80) cc_final: 0.6833 (m-80) REVERT: D 866 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6181 (mt) outliers start: 64 outliers final: 36 residues processed: 448 average time/residue: 0.1437 time to fit residues: 103.9907 Evaluate side-chains 415 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 370 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 495 TRP Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 818 SER Chi-restraints excluded: chain D residue 866 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 211 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 246 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.182700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.150820 restraints weight = 27137.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.152883 restraints weight = 18262.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.153552 restraints weight = 13879.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.153599 restraints weight = 13575.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.153798 restraints weight = 13372.156| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22832 Z= 0.115 Angle : 0.626 12.116 30940 Z= 0.314 Chirality : 0.040 0.150 3538 Planarity : 0.004 0.063 3804 Dihedral : 10.385 160.860 3224 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 3.12 % Allowed : 21.06 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.16), residues: 2702 helix: -0.95 (0.12), residues: 1820 sheet: None (None), residues: 0 loop : -2.90 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.020 0.001 TYR C 747 PHE 0.022 0.001 PHE D 233 TRP 0.028 0.001 TRP A 568 HIS 0.007 0.001 HIS B 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (22824) covalent geometry : angle 0.62609 / 0.31 (30940) hydrogen bonds : bond 0.02912 / 1.86 ( 890) hydrogen bonds : angle 3.97692 / 2.68 ( 2586) Misc. bond : bond 0.00154 / 0.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 415 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7892 (mm) REVERT: A 123 ARG cc_start: 0.4976 (OUTLIER) cc_final: 0.2977 (mmp-170) REVERT: A 159 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8143 (tt) REVERT: A 516 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7894 (tt) REVERT: A 563 TYR cc_start: 0.8038 (t80) cc_final: 0.7390 (t80) REVERT: A 636 GLN cc_start: 0.8272 (tp40) cc_final: 0.7860 (tm-30) REVERT: A 653 LEU cc_start: 0.8111 (tp) cc_final: 0.7709 (tt) REVERT: B 143 MET cc_start: 0.7618 (tpp) cc_final: 0.7379 (tpp) REVERT: B 554 GLU cc_start: 0.6772 (tt0) cc_final: 0.6472 (mt-10) REVERT: B 580 ILE cc_start: 0.8639 (tp) cc_final: 0.8407 (tp) REVERT: B 612 MET cc_start: 0.6412 (OUTLIER) cc_final: 0.5321 (mmm) REVERT: B 723 PHE cc_start: 0.6928 (m-80) cc_final: 0.6694 (m-80) REVERT: B 840 ASP cc_start: 0.7321 (m-30) cc_final: 0.6984 (m-30) REVERT: B 845 ASN cc_start: 0.7795 (m-40) cc_final: 0.7591 (m-40) REVERT: B 866 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6305 (mt) REVERT: C 61 GLU cc_start: 0.7173 (tt0) cc_final: 0.6922 (tt0) REVERT: C 123 ARG cc_start: 0.4899 (OUTLIER) cc_final: 0.2933 (mmp-170) REVERT: C 159 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8129 (tt) REVERT: C 352 MET cc_start: 0.8792 (tpp) cc_final: 0.8458 (tpp) REVERT: C 516 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7893 (tt) REVERT: C 653 LEU cc_start: 0.8118 (tp) cc_final: 0.7724 (tt) REVERT: C 827 MET cc_start: 0.8158 (ttm) cc_final: 0.7770 (ttm) REVERT: D 115 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6379 (pp20) REVERT: D 515 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7718 (mp) REVERT: D 554 GLU cc_start: 0.6740 (tt0) cc_final: 0.6002 (tt0) REVERT: D 569 ASN cc_start: 0.7042 (m-40) cc_final: 0.5413 (t0) REVERT: D 612 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5309 (mmm) REVERT: D 622 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6949 (mt-10) REVERT: D 723 PHE cc_start: 0.7028 (m-80) cc_final: 0.6769 (m-80) REVERT: D 866 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6186 (mt) outliers start: 74 outliers final: 43 residues processed: 461 average time/residue: 0.1422 time to fit residues: 106.0176 Evaluate side-chains 438 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 382 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 495 TRP Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 818 SER Chi-restraints excluded: chain D residue 866 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 143 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 255 optimal weight: 0.9990 chunk 129 optimal weight: 0.4980 chunk 80 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 260 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS A 553 GLN A 632 GLN B 425 GLN B 496 HIS B 603 ASN B 632 GLN ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 HIS C 553 GLN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.182867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.150039 restraints weight = 26993.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.152682 restraints weight = 18339.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.154362 restraints weight = 14578.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.155321 restraints weight = 12742.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.155816 restraints weight = 11768.666| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22832 Z= 0.123 Angle : 0.635 12.065 30940 Z= 0.318 Chirality : 0.041 0.169 3538 Planarity : 0.004 0.061 3804 Dihedral : 10.240 161.977 3224 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.24 % Allowed : 21.61 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.16), residues: 2702 helix: -0.73 (0.12), residues: 1820 sheet: None (None), residues: 0 loop : -2.80 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 616 TYR 0.015 0.001 TYR C 518 PHE 0.022 0.001 PHE D 233 TRP 0.030 0.001 TRP A 568 HIS 0.012 0.001 HIS B 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (22824) covalent geometry : angle 0.63473 / 0.32 (30940) hydrogen bonds : bond 0.02946 / 1.88 ( 890) hydrogen bonds : angle 3.98075 / 2.68 ( 2586) Misc. bond : bond 0.00152 / 0.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 408 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7936 (mm) REVERT: A 123 ARG cc_start: 0.5006 (OUTLIER) cc_final: 0.3105 (mmp-170) REVERT: A 159 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8052 (tt) REVERT: A 516 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7884 (tt) REVERT: A 563 TYR cc_start: 0.8169 (t80) cc_final: 0.7540 (t80) REVERT: A 636 GLN cc_start: 0.8232 (tp40) cc_final: 0.7807 (tm-30) REVERT: A 653 LEU cc_start: 0.8130 (tp) cc_final: 0.7719 (tt) REVERT: B 104 MET cc_start: 0.6397 (tmm) cc_final: 0.6097 (tmm) REVERT: B 136 TYR cc_start: 0.7870 (t80) cc_final: 0.7153 (t80) REVERT: B 143 MET cc_start: 0.7865 (tpp) cc_final: 0.7205 (tpp) REVERT: B 431 LYS cc_start: 0.8556 (tptt) cc_final: 0.7828 (tttp) REVERT: B 554 GLU cc_start: 0.6711 (tt0) cc_final: 0.6359 (mt-10) REVERT: B 580 ILE cc_start: 0.8777 (tp) cc_final: 0.8561 (tp) REVERT: B 723 PHE cc_start: 0.6936 (m-80) cc_final: 0.6714 (m-80) REVERT: B 840 ASP cc_start: 0.7287 (m-30) cc_final: 0.6970 (m-30) REVERT: B 866 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6200 (mt) REVERT: C 123 ARG cc_start: 0.4926 (OUTLIER) cc_final: 0.3021 (mmp-170) REVERT: C 159 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8098 (tt) REVERT: C 636 GLN cc_start: 0.8200 (tp40) cc_final: 0.7879 (tm-30) REVERT: C 653 LEU cc_start: 0.8157 (tp) cc_final: 0.7742 (tt) REVERT: D 115 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6358 (pp20) REVERT: D 136 TYR cc_start: 0.7661 (t80) cc_final: 0.7108 (t80) REVERT: D 554 GLU cc_start: 0.6647 (tt0) cc_final: 0.5947 (tt0) REVERT: D 569 ASN cc_start: 0.7033 (m-40) cc_final: 0.5357 (t0) REVERT: D 612 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.4991 (mmm) REVERT: D 622 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6923 (mt-10) REVERT: D 723 PHE cc_start: 0.6932 (m-80) cc_final: 0.6711 (m-80) REVERT: D 866 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6126 (mt) outliers start: 77 outliers final: 45 residues processed: 453 average time/residue: 0.1427 time to fit residues: 104.4042 Evaluate side-chains 434 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 379 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 495 TRP Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 734 LEU Chi-restraints excluded: chain D residue 818 SER Chi-restraints excluded: chain D residue 866 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 76 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 196 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 83 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.185733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.153128 restraints weight = 26871.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.155751 restraints weight = 18207.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.157417 restraints weight = 14468.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.157980 restraints weight = 12641.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.158948 restraints weight = 11895.307| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22832 Z= 0.114 Angle : 0.629 12.018 30940 Z= 0.316 Chirality : 0.040 0.160 3538 Planarity : 0.005 0.073 3804 Dihedral : 9.933 163.367 3224 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.78 % Allowed : 22.37 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.16), residues: 2702 helix: -0.51 (0.12), residues: 1814 sheet: None (None), residues: 0 loop : -2.63 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 616 TYR 0.017 0.001 TYR C 555 PHE 0.023 0.001 PHE D 233 TRP 0.031 0.001 TRP A 568 HIS 0.005 0.001 HIS D 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (22824) covalent geometry : angle 0.62925 / 0.32 (30940) hydrogen bonds : bond 0.02862 / 1.83 ( 890) hydrogen bonds : angle 3.87176 / 2.60 ( 2586) Misc. bond : bond 0.00143 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 414 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7935 (mm) REVERT: A 123 ARG cc_start: 0.4906 (OUTLIER) cc_final: 0.2865 (mmp-170) REVERT: A 159 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8004 (tt) REVERT: A 563 TYR cc_start: 0.8122 (t80) cc_final: 0.7532 (t80) REVERT: A 636 GLN cc_start: 0.8147 (tp40) cc_final: 0.7720 (tm-30) REVERT: A 653 LEU cc_start: 0.8136 (tp) cc_final: 0.7737 (tt) REVERT: B 67 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7826 (mtpt) REVERT: B 136 TYR cc_start: 0.7794 (t80) cc_final: 0.7166 (t80) REVERT: B 431 LYS cc_start: 0.8419 (tptt) cc_final: 0.7730 (tttp) REVERT: B 521 PHE cc_start: 0.6498 (m-80) cc_final: 0.6062 (m-80) REVERT: B 554 GLU cc_start: 0.6785 (tt0) cc_final: 0.6463 (mt-10) REVERT: B 723 PHE cc_start: 0.6944 (m-80) cc_final: 0.6702 (m-80) REVERT: B 840 ASP cc_start: 0.7328 (m-30) cc_final: 0.6987 (m-30) REVERT: B 866 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6158 (mt) REVERT: C 123 ARG cc_start: 0.4844 (OUTLIER) cc_final: 0.2822 (mmp-170) REVERT: C 159 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8031 (tt) REVERT: C 563 TYR cc_start: 0.8033 (t80) cc_final: 0.7581 (t80) REVERT: C 636 GLN cc_start: 0.8044 (tp40) cc_final: 0.7740 (tm-30) REVERT: C 653 LEU cc_start: 0.8158 (tp) cc_final: 0.7782 (tt) REVERT: D 136 TYR cc_start: 0.7511 (t80) cc_final: 0.7067 (t80) REVERT: D 245 PRO cc_start: 0.6708 (Cg_exo) cc_final: 0.6406 (Cg_endo) REVERT: D 521 PHE cc_start: 0.6511 (m-80) cc_final: 0.6094 (m-80) REVERT: D 554 GLU cc_start: 0.6643 (tt0) cc_final: 0.5951 (tt0) REVERT: D 569 ASN cc_start: 0.6970 (m-40) cc_final: 0.5361 (t0) REVERT: D 723 PHE cc_start: 0.6887 (m-80) cc_final: 0.6658 (m-80) REVERT: D 866 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6128 (mt) outliers start: 66 outliers final: 50 residues processed: 453 average time/residue: 0.1392 time to fit residues: 101.9663 Evaluate side-chains 440 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 383 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 722 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 495 TRP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 734 LEU Chi-restraints excluded: chain D residue 818 SER Chi-restraints excluded: chain D residue 866 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 271 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 131 optimal weight: 0.0870 chunk 162 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS A 632 GLN ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.186266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.153736 restraints weight = 26919.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.156371 restraints weight = 18186.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.157758 restraints weight = 14364.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.159064 restraints weight = 12563.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.159572 restraints weight = 11563.978| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22832 Z= 0.115 Angle : 0.636 12.093 30940 Z= 0.316 Chirality : 0.041 0.358 3538 Planarity : 0.004 0.069 3804 Dihedral : 9.741 164.418 3224 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 2.57 % Allowed : 23.42 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.16), residues: 2702 helix: -0.35 (0.13), residues: 1832 sheet: None (None), residues: 0 loop : -2.61 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.016 0.001 TYR C 518 PHE 0.022 0.001 PHE B 233 TRP 0.031 0.001 TRP A 568 HIS 0.005 0.001 HIS D 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (22824) covalent geometry : angle 0.63615 / 0.32 (30940) hydrogen bonds : bond 0.02788 / 1.78 ( 890) hydrogen bonds : angle 3.84694 / 2.59 ( 2586) Misc. bond : bond 0.00132 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 393 time to evaluate : 0.820 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: A 62 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7939 (mm) REVERT: A 123 ARG cc_start: 0.4782 (OUTLIER) cc_final: 0.2872 (mmp-170) REVERT: A 157 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6427 (mm-30) REVERT: A 159 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.7907 (tt) REVERT: A 563 TYR cc_start: 0.8091 (t80) cc_final: 0.7328 (t80) REVERT: A 636 GLN cc_start: 0.8007 (tp40) cc_final: 0.7779 (tm-30) REVERT: A 653 LEU cc_start: 0.8178 (tp) cc_final: 0.7808 (tt) REVERT: B 67 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7847 (mtpt) REVERT: B 136 TYR cc_start: 0.7662 (t80) cc_final: 0.7080 (t80) REVERT: B 521 PHE cc_start: 0.6559 (m-80) cc_final: 0.6028 (m-80) REVERT: B 554 GLU cc_start: 0.6782 (tt0) cc_final: 0.6480 (mt-10) REVERT: B 623 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7775 (mp) REVERT: B 723 PHE cc_start: 0.6948 (m-80) cc_final: 0.6702 (m-80) REVERT: B 840 ASP cc_start: 0.7319 (m-30) cc_final: 0.6985 (m-30) REVERT: B 866 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6161 (mt) REVERT: C 123 ARG cc_start: 0.4660 (OUTLIER) cc_final: 0.2757 (mmp-170) REVERT: C 157 GLU cc_start: 0.6885 (mm-30) cc_final: 0.6578 (mm-30) REVERT: C 159 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.7908 (tt) REVERT: C 563 TYR cc_start: 0.8194 (t80) cc_final: 0.7542 (t80) REVERT: C 636 GLN cc_start: 0.8020 (tp40) cc_final: 0.7743 (tm-30) REVERT: C 653 LEU cc_start: 0.8143 (tp) cc_final: 0.7775 (tt) REVERT: D 104 MET cc_start: 0.6197 (tmm) cc_final: 0.5907 (tmm) REVERT: D 136 TYR cc_start: 0.7449 (t80) cc_final: 0.7013 (t80) REVERT: D 245 PRO cc_start: 0.6722 (Cg_exo) cc_final: 0.6391 (Cg_endo) REVERT: D 521 PHE cc_start: 0.6603 (m-80) cc_final: 0.6058 (m-80) REVERT: D 562 GLU cc_start: 0.7087 (tp30) cc_final: 0.6672 (tp30) REVERT: D 723 PHE cc_start: 0.6920 (m-80) cc_final: 0.6678 (m-80) REVERT: D 742 MET cc_start: 0.8110 (ttm) cc_final: 0.7901 (ttm) REVERT: D 866 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6092 (mt) outliers start: 61 outliers final: 46 residues processed: 432 average time/residue: 0.1464 time to fit residues: 101.8964 Evaluate side-chains 421 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 367 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 818 SER Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 495 TRP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 627 ILE Chi-restraints excluded: chain D residue 740 ILE Chi-restraints excluded: chain D residue 818 SER Chi-restraints excluded: chain D residue 866 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 3 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 228 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 229 optimal weight: 0.0370 chunk 44 optimal weight: 0.0000 chunk 76 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 0.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN C 152 GLN ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.196033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.162042 restraints weight = 27633.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.165274 restraints weight = 17448.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.167314 restraints weight = 13322.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.168202 restraints weight = 11405.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.169160 restraints weight = 10505.876| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22832 Z= 0.113 Angle : 0.642 13.593 30940 Z= 0.317 Chirality : 0.041 0.324 3538 Planarity : 0.005 0.079 3804 Dihedral : 9.556 167.041 3224 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 2.36 % Allowed : 23.80 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.17), residues: 2702 helix: -0.18 (0.13), residues: 1852 sheet: None (None), residues: 0 loop : -2.48 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.017 0.001 TYR A 518 PHE 0.024 0.001 PHE D 233 TRP 0.031 0.001 TRP A 568 HIS 0.006 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (22824) covalent geometry : angle 0.64204 / 0.32 (30940) hydrogen bonds : bond 0.02691 / 1.72 ( 890) hydrogen bonds : angle 3.77083 / 2.52 ( 2586) Misc. bond : bond 0.00133 / 0.05 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5404 Ramachandran restraints generated. 2702 Oldfield, 0 Emsley, 2702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 406 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7926 (mm) REVERT: A 123 ARG cc_start: 0.4398 (OUTLIER) cc_final: 0.2746 (mmp-170) REVERT: A 157 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6322 (mm-30) REVERT: A 159 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.7842 (tt) REVERT: A 563 TYR cc_start: 0.7983 (t80) cc_final: 0.7273 (t80) REVERT: A 612 MET cc_start: 0.7481 (mmm) cc_final: 0.7258 (mmm) REVERT: A 617 MET cc_start: 0.8321 (tmm) cc_final: 0.8039 (ppp) REVERT: A 636 GLN cc_start: 0.7967 (tp40) cc_final: 0.7715 (tm-30) REVERT: A 653 LEU cc_start: 0.8132 (tp) cc_final: 0.7761 (tt) REVERT: B 67 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7817 (mtpt) REVERT: B 136 TYR cc_start: 0.7562 (t80) cc_final: 0.7045 (t80) REVERT: B 245 PRO cc_start: 0.6733 (Cg_exo) cc_final: 0.6436 (Cg_endo) REVERT: B 521 PHE cc_start: 0.6521 (m-80) cc_final: 0.5972 (m-80) REVERT: B 554 GLU cc_start: 0.6662 (tt0) cc_final: 0.6339 (mt-10) REVERT: B 623 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7865 (mp) REVERT: B 726 ILE cc_start: 0.7473 (tt) cc_final: 0.7022 (pt) REVERT: B 840 ASP cc_start: 0.7273 (m-30) cc_final: 0.6947 (m-30) REVERT: B 866 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6221 (mt) REVERT: C 123 ARG cc_start: 0.4251 (OUTLIER) cc_final: 0.2635 (mmp-170) REVERT: C 157 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6462 (mm-30) REVERT: C 159 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.7840 (tt) REVERT: C 563 TYR cc_start: 0.8081 (t80) cc_final: 0.7434 (t80) REVERT: C 653 LEU cc_start: 0.8072 (tp) cc_final: 0.7700 (tt) REVERT: D 136 TYR cc_start: 0.7424 (t80) cc_final: 0.7040 (t80) REVERT: D 245 PRO cc_start: 0.6788 (Cg_exo) cc_final: 0.6504 (Cg_endo) REVERT: D 431 LYS cc_start: 0.8534 (tptt) cc_final: 0.7918 (tttp) REVERT: D 521 PHE cc_start: 0.6567 (m-80) cc_final: 0.6021 (m-80) REVERT: D 554 GLU cc_start: 0.6695 (tt0) cc_final: 0.6097 (tt0) REVERT: D 562 GLU cc_start: 0.7082 (tp30) cc_final: 0.6725 (tp30) REVERT: D 726 ILE cc_start: 0.7460 (tt) cc_final: 0.6996 (pt) REVERT: D 866 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6068 (mt) outliers start: 56 outliers final: 41 residues processed: 442 average time/residue: 0.1472 time to fit residues: 103.9118 Evaluate side-chains 419 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 370 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 85 TYR Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 627 ILE Chi-restraints excluded: chain A residue 632 GLN Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 612 MET Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain C residue 85 TYR Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain C residue 123 ARG Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 495 TRP Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 551 GLU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 866 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 242 optimal weight: 0.0470 chunk 221 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN ** C 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** 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 = 0.4064 r_free = 0.4064 target = 0.189568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.154721 restraints weight = 27560.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.157718 restraints weight = 17831.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 87)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.159624 restraints weight = 13903.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.160658 restraints weight = 12041.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.161227 restraints weight = 11133.535| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22832 Z= 0.175 Angle : 0.704 12.684 30940 Z= 0.348 Chirality : 0.044 0.312 3538 Planarity : 0.005 0.073 3804 Dihedral : 9.718 164.342 3224 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 2.57 % Allowed : 24.14 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.16), residues: 2702 helix: -0.30 (0.12), residues: 1830 sheet: None (None), residues: 0 loop : -2.56 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 616 TYR 0.044 0.002 TYR A 225 PHE 0.030 0.002 PHE D 739 TRP 0.041 0.002 TRP A 614 HIS 0.010 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (22824) covalent geometry : angle 0.70360 / 0.35 (30940) hydrogen bonds : bond 0.03233 / 2.07 ( 890) hydrogen bonds : angle 3.99287 / 2.68 ( 2586) Misc. bond : bond 0.00138 / 0.06 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3881.02 seconds wall clock time: 68 minutes 12.91 seconds (4092.91 seconds total)