Starting phenix.real_space_refine on Fri Mar 6 04:47:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rz6_24752/03_2026/7rz6_24752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rz6_24752/03_2026/7rz6_24752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rz6_24752/03_2026/7rz6_24752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rz6_24752/03_2026/7rz6_24752.map" model { file = "/net/cci-nas-00/data/ceres_data/7rz6_24752/03_2026/7rz6_24752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rz6_24752/03_2026/7rz6_24752.cif" } resolution = 4.4 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= -0.000 sd= 0.002 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 2 5.49 5 S 142 5.16 5 C 17972 2.51 5 N 4596 2.21 5 O 5210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27922 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7740 Classifications: {'peptide': 983} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 956} Chain breaks: 4 Chain: "B" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6178 Classifications: {'peptide': 784} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 760} Chain breaks: 2 Chain: "C" Number of atoms: 7740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7740 Classifications: {'peptide': 983} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 956} Chain breaks: 4 Chain: "D" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6178 Classifications: {'peptide': 784} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 760} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'PCW': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'PCW': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 6.35, per 1000 atoms: 0.23 Number of scatterers: 27922 At special positions: 0 Unit cell: (125.892, 164.628, 190.452, 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 142 16.00 P 2 15.00 O 5210 8.00 N 4596 7.00 C 17972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.4 seconds 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6500 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 32 sheets defined 50.0% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 54 through 69 removed outlier: 3.557A pdb=" N GLY A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.580A pdb=" N GLY A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.531A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.525A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.571A pdb=" N THR A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.756A pdb=" N GLY A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.558A pdb=" N GLN A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 237' Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.617A pdb=" N THR A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.633A pdb=" N ALA A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.101A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.516A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.825A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.943A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 630 removed outlier: 3.555A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.502A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.798A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.643A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 715 " --> pdb=" O TYR A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.809A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 770 removed outlier: 3.597A pdb=" N LYS A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS A 770 " --> pdb=" O TRP A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 819 removed outlier: 4.019A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 858 removed outlier: 4.046A pdb=" N ALA A 836 " --> pdb=" O CYS A 832 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 839 " --> pdb=" O LYS A 835 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 854 " --> pdb=" O GLY A 850 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 926 removed outlier: 3.777A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 951 removed outlier: 3.825A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 991 removed outlier: 4.076A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A 972 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1035 removed outlier: 3.509A pdb=" N ALA A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1016 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A1017 " --> pdb=" O SER A1013 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A1034 " --> pdb=" O LYS A1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 removed outlier: 3.903A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 69 removed outlier: 3.536A pdb=" N VAL B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.735A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.531A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.639A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.546A pdb=" N VAL B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 252 through 264 removed outlier: 4.062A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 300 removed outlier: 3.768A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 291 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 4.011A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 413 removed outlier: 4.611A pdb=" N GLU B 413 " --> pdb=" O LYS B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.545A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 522 through 546 removed outlier: 3.579A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.848A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.830A pdb=" N ILE B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 653 through 659 removed outlier: 3.739A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.558A pdb=" N LYS B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 755 Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.513A pdb=" N LEU B 762 " --> pdb=" O VAL B 758 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 4.096A pdb=" N GLY B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 775 through 780' Processing helix chain 'B' and resid 792 through 818 removed outlier: 4.107A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 54 through 69 removed outlier: 3.557A pdb=" N GLY C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.579A pdb=" N GLY C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.532A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 187 removed outlier: 3.524A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 removed outlier: 3.572A pdb=" N THR C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.756A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.558A pdb=" N GLN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 237' Processing helix chain 'C' and resid 252 through 264 Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.616A pdb=" N THR C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.632A pdb=" N ALA C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.101A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR C 421 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.517A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.825A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.943A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 removed outlier: 3.555A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 654 through 659 removed outlier: 3.503A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.798A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 715 removed outlier: 3.642A pdb=" N ILE C 712 " --> pdb=" O MET C 708 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 715 " --> pdb=" O TYR C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.808A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 770 removed outlier: 3.599A pdb=" N LYS C 765 " --> pdb=" O LYS C 761 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS C 770 " --> pdb=" O TRP C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 819 removed outlier: 4.017A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 805 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 806 " --> pdb=" O GLY C 802 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 858 removed outlier: 4.047A pdb=" N ALA C 836 " --> pdb=" O CYS C 832 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 843 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 854 " --> pdb=" O GLY C 850 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 858 " --> pdb=" O ILE C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 926 removed outlier: 3.776A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 951 removed outlier: 3.825A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE C 937 " --> pdb=" O LEU C 933 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 939 " --> pdb=" O SER C 935 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 990 removed outlier: 4.077A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 970 " --> pdb=" O PHE C 966 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 972 " --> pdb=" O LEU C 968 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 989 " --> pdb=" O ASN C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1035 removed outlier: 3.508A pdb=" N ALA C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C1016 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C1017 " --> pdb=" O SER C1013 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU C1018 " --> pdb=" O PHE C1014 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C1022 " --> pdb=" O GLU C1018 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C1034 " --> pdb=" O LYS C1030 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.903A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 69 removed outlier: 3.537A pdb=" N VAL D 58 " --> pdb=" O ASN D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 81 through 92 Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.735A pdb=" N ILE D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 156 removed outlier: 3.532A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.639A pdb=" N THR D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.546A pdb=" N VAL D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 252 through 264 removed outlier: 4.061A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 300 removed outlier: 3.769A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 291 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.010A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 335 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 413 removed outlier: 4.611A pdb=" N GLU D 413 " --> pdb=" O LYS D 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 410 through 413' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.545A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 522 through 546 removed outlier: 3.578A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.847A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.829A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 612 " --> pdb=" O PHE D 608 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 642 Processing helix chain 'D' and resid 653 through 659 removed outlier: 3.740A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.558A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 755 Processing helix chain 'D' and resid 757 through 767 removed outlier: 3.512A pdb=" N LEU D 762 " --> pdb=" O VAL D 758 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 removed outlier: 4.096A pdb=" N GLY D 779 " --> pdb=" O ALA D 775 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 775 through 780' Processing helix chain 'D' and resid 792 through 818 removed outlier: 4.106A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET D 807 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 821 No H-bonds generated for 'chain 'D' and resid 819 through 821' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 50 removed outlier: 6.126A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N HIS A 46 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASP A 48 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU A 50 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE A 18 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N ALA A 72 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.400A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 222 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 339 removed outlier: 3.799A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374 removed outlier: 3.575A pdb=" N VAL A 381 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 399 removed outlier: 5.945A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA7, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.324A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 721 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 900 through 902 removed outlier: 3.616A pdb=" N CYS A 890 " --> pdb=" O HIS A 883 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS A 883 " --> pdb=" O CYS A 890 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL A 878 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE A 868 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER A 884 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 862 " --> pdb=" O SER A 884 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A1002 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 867 " --> pdb=" O TYR A 998 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.741A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.021A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.210A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.210A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 358 " --> pdb=" O TRP B 374 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 346 through 347 removed outlier: 3.688A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB7, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.640A pdb=" N TYR B 702 " --> pdb=" O MET B 503 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.126A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.402A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C 222 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 338 through 339 removed outlier: 3.798A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 346 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 373 through 374 removed outlier: 3.574A pdb=" N VAL C 381 " --> pdb=" O TYR C 373 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 395 through 399 removed outlier: 5.946A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AC5, first strand: chain 'C' and resid 646 through 649 removed outlier: 6.324A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET C 721 " --> pdb=" O ILE C 504 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 900 through 902 removed outlier: 3.616A pdb=" N CYS C 890 " --> pdb=" O HIS C 883 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS C 883 " --> pdb=" O CYS C 890 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL C 878 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE C 868 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER C 884 " --> pdb=" O LEU C 862 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 862 " --> pdb=" O SER C 884 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C1002 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 867 " --> pdb=" O TYR C 998 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.740A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.021A pdb=" N GLY D 15 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.210A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.210A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 358 " --> pdb=" O TRP D 374 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 346 through 347 removed outlier: 3.688A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD4, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD5, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.640A pdb=" N TYR D 702 " --> pdb=" O MET D 503 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3663 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: 5.97 Time building geometry restraints manager: 3.11 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: 4570 1.31 - 1.44: 7741 1.44 - 1.57: 15955 1.57 - 1.70: 6 1.70 - 1.83: 232 Bond restraints: 28504 Sorted by residual: bond pdb=" C31 PCW C1101 " pdb=" O2 PCW C1101 " ideal model delta sigma weight residual 1.333 1.431 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C31 PCW A1101 " pdb=" O2 PCW A1101 " ideal model delta sigma weight residual 1.333 1.430 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C31 PCW C1101 " pdb=" C32 PCW C1101 " ideal model delta sigma weight residual 1.502 1.558 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" C31 PCW A1101 " pdb=" C32 PCW A1101 " ideal model delta sigma weight residual 1.502 1.557 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" CA THR C 457 " pdb=" C THR C 457 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.34e-02 5.57e+03 6.93e+00 ... (remaining 28499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 38214 3.89 - 7.78: 250 7.78 - 11.68: 26 11.68 - 15.57: 6 15.57 - 19.46: 2 Bond angle restraints: 38498 Sorted by residual: angle pdb=" CA LEU C 43 " pdb=" CB LEU C 43 " pdb=" CG LEU C 43 " ideal model delta sigma weight residual 116.30 135.76 -19.46 3.50e+00 8.16e-02 3.09e+01 angle pdb=" CA LEU A 43 " pdb=" CB LEU A 43 " pdb=" CG LEU A 43 " ideal model delta sigma weight residual 116.30 135.74 -19.44 3.50e+00 8.16e-02 3.08e+01 angle pdb=" N ILE A 304 " pdb=" CA ILE A 304 " pdb=" C ILE A 304 " ideal model delta sigma weight residual 111.91 107.15 4.76 8.90e-01 1.26e+00 2.86e+01 angle pdb=" N ILE C 304 " pdb=" CA ILE C 304 " pdb=" C ILE C 304 " ideal model delta sigma weight residual 111.91 107.16 4.75 8.90e-01 1.26e+00 2.84e+01 angle pdb=" C THR A 457 " pdb=" N LYS A 458 " pdb=" CA LYS A 458 " ideal model delta sigma weight residual 122.07 129.00 -6.93 1.43e+00 4.89e-01 2.35e+01 ... (remaining 38493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 15827 15.11 - 30.22: 765 30.22 - 45.33: 280 45.33 - 60.45: 32 60.45 - 75.56: 12 Dihedral angle restraints: 16916 sinusoidal: 6744 harmonic: 10172 Sorted by residual: dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 168.56 -75.56 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 168.55 -75.55 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CA LYS A 716 " pdb=" C LYS A 716 " pdb=" N PRO A 717 " pdb=" CA PRO A 717 " ideal model delta harmonic sigma weight residual 180.00 139.50 40.50 0 5.00e+00 4.00e-02 6.56e+01 ... (remaining 16913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3394 0.057 - 0.115: 737 0.115 - 0.172: 134 0.172 - 0.229: 13 0.229 - 0.286: 4 Chirality restraints: 4282 Sorted by residual: chirality pdb=" CG LEU A 882 " pdb=" CB LEU A 882 " pdb=" CD1 LEU A 882 " pdb=" CD2 LEU A 882 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CG LEU C 882 " pdb=" CB LEU C 882 " pdb=" CD1 LEU C 882 " pdb=" CD2 LEU C 882 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CG LEU A 989 " pdb=" CB LEU A 989 " pdb=" CD1 LEU A 989 " pdb=" CD2 LEU A 989 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4279 not shown) Planarity restraints: 4848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO C 717 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 716 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO A 717 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " 0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B 99 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " 0.044 5.00e-02 4.00e+02 ... (remaining 4845 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3626 2.75 - 3.29: 27113 3.29 - 3.83: 45481 3.83 - 4.36: 53206 4.36 - 4.90: 88667 Nonbonded interactions: 218093 Sorted by model distance: nonbonded pdb=" OG SER C 87 " pdb=" OD1 ASN D 54 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR D 77 " pdb=" O PHE D 101 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR B 77 " pdb=" O PHE B 101 " model vdw 2.220 3.040 nonbonded pdb=" OG SER C 662 " pdb=" OD1 ASP C 668 " model vdw 2.281 3.040 nonbonded pdb=" OG SER A 662 " pdb=" OD1 ASP A 668 " model vdw 2.282 3.040 ... (remaining 218088 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: 4.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.680 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4999 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 : 0.005 0.098 28514 Z= 0.237 Angle : 0.928 19.460 38518 Z= 0.497 Chirality : 0.050 0.286 4282 Planarity : 0.007 0.103 4848 Dihedral : 10.731 74.759 10386 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.46 % Allowed : 4.97 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.11), residues: 3502 helix: -3.13 (0.08), residues: 1608 sheet: -1.87 (0.23), residues: 432 loop : -2.57 (0.13), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 178 TYR 0.019 0.002 TYR C 768 PHE 0.021 0.002 PHE D 101 TRP 0.021 0.003 TRP C 323 HIS 0.012 0.002 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00482 (28504) covalent geometry : angle 0.92754 (38498) SS BOND : bond 0.00920 ( 10) SS BOND : angle 1.04045 ( 20) hydrogen bonds : bond 0.29374 ( 1213) hydrogen bonds : angle 9.25694 ( 3663) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 858 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: -0.1197 (OUTLIER) cc_final: -0.1742 (mp) REVERT: A 60 ASN cc_start: 0.6301 (m-40) cc_final: 0.5542 (t0) REVERT: A 113 MET cc_start: 0.3719 (tpp) cc_final: 0.2800 (tpp) REVERT: A 292 MET cc_start: 0.5632 (mtt) cc_final: 0.5024 (mmp) REVERT: A 408 MET cc_start: 0.6947 (mmt) cc_final: 0.6665 (mmp) REVERT: A 574 PHE cc_start: 0.7041 (t80) cc_final: 0.6750 (m-80) REVERT: A 674 MET cc_start: 0.7845 (mtm) cc_final: 0.7514 (ttm) REVERT: A 702 TYR cc_start: 0.5965 (t80) cc_final: 0.5111 (t80) REVERT: A 707 THR cc_start: 0.6838 (m) cc_final: 0.6470 (t) REVERT: A 907 MET cc_start: 0.6706 (mtm) cc_final: 0.6236 (tpt) REVERT: A 924 MET cc_start: 0.8565 (mmp) cc_final: 0.8058 (mmm) REVERT: A 935 SER cc_start: 0.7605 (m) cc_final: 0.7305 (p) REVERT: B 26 TYR cc_start: 0.8012 (t80) cc_final: 0.7748 (t80) REVERT: B 27 SER cc_start: 0.7477 (m) cc_final: 0.6692 (p) REVERT: B 220 TYR cc_start: 0.6126 (m-80) cc_final: 0.5828 (m-80) REVERT: B 271 PRO cc_start: 0.6008 (Cg_endo) cc_final: 0.5789 (Cg_exo) REVERT: B 382 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6006 (pp) REVERT: B 518 LEU cc_start: 0.7506 (pp) cc_final: 0.6172 (pp) REVERT: B 708 MET cc_start: 0.7401 (ttm) cc_final: 0.7046 (tpt) REVERT: B 711 TYR cc_start: 0.8024 (t80) cc_final: 0.7424 (t80) REVERT: B 797 TYR cc_start: 0.7213 (m-80) cc_final: 0.6071 (t80) REVERT: B 805 LEU cc_start: 0.7966 (tt) cc_final: 0.7679 (pp) REVERT: C 12 ILE cc_start: 0.6940 (pp) cc_final: 0.6423 (pt) REVERT: C 93 HIS cc_start: 0.5582 (m90) cc_final: 0.5119 (m-70) REVERT: C 255 VAL cc_start: 0.8538 (t) cc_final: 0.7999 (t) REVERT: C 479 LEU cc_start: 0.8142 (tp) cc_final: 0.7835 (mt) REVERT: C 593 PRO cc_start: 0.6080 (Cg_exo) cc_final: 0.5675 (Cg_endo) REVERT: C 633 ILE cc_start: 0.5887 (pp) cc_final: 0.4935 (pt) REVERT: C 713 GLU cc_start: 0.8423 (tt0) cc_final: 0.8113 (tm-30) REVERT: C 891 PHE cc_start: 0.6498 (m-10) cc_final: 0.5255 (m-10) REVERT: C 907 MET cc_start: 0.3489 (mtm) cc_final: 0.3071 (mmp) REVERT: C 920 ASN cc_start: 0.8408 (t160) cc_final: 0.8015 (t0) REVERT: C 921 VAL cc_start: 0.6633 (t) cc_final: 0.6223 (t) REVERT: C 960 PHE cc_start: 0.7668 (t80) cc_final: 0.7354 (t80) REVERT: C 983 SER cc_start: 0.8017 (m) cc_final: 0.7690 (p) REVERT: C 1001 TYR cc_start: 0.8557 (p90) cc_final: 0.7746 (p90) REVERT: D 97 ILE cc_start: 0.8110 (mp) cc_final: 0.7734 (mp) REVERT: D 124 LEU cc_start: 0.7637 (tp) cc_final: 0.7381 (tp) REVERT: D 204 ILE cc_start: 0.5950 (mt) cc_final: 0.5375 (pt) REVERT: D 684 ARG cc_start: 0.6597 (pmt170) cc_final: 0.5592 (tpm170) REVERT: D 720 THR cc_start: 0.7409 (p) cc_final: 0.5886 (p) REVERT: D 721 MET cc_start: 0.8868 (ttt) cc_final: 0.7942 (ttp) outliers start: 14 outliers final: 4 residues processed: 870 average time/residue: 0.2045 time to fit residues: 269.6755 Evaluate side-chains 473 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 467 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.0060 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 642 GLN A 714 GLN A 791 ASN A 872 GLN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 ASN B 35 GLN B 60 ASN B 290 GLN B 355 ASN B 411 ASN B 461 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN C 619 ASN C 642 GLN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 950 HIS ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 355 ASN D 435 HIS D 575 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.112925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.085749 restraints weight = 98325.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.088245 restraints weight = 57815.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.089958 restraints weight = 39917.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091102 restraints weight = 30672.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.091909 restraints weight = 25546.012| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28514 Z= 0.156 Angle : 0.639 9.439 38518 Z= 0.335 Chirality : 0.042 0.205 4282 Planarity : 0.005 0.072 4848 Dihedral : 6.017 57.968 3860 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.13), residues: 3502 helix: -0.69 (0.11), residues: 1682 sheet: -1.27 (0.24), residues: 438 loop : -2.15 (0.15), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 369 TYR 0.025 0.001 TYR A 177 PHE 0.027 0.002 PHE B 109 TRP 0.037 0.002 TRP A 766 HIS 0.004 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00304 (28504) covalent geometry : angle 0.63834 (38498) SS BOND : bond 0.00398 ( 10) SS BOND : angle 1.01830 ( 20) hydrogen bonds : bond 0.04894 ( 1213) hydrogen bonds : angle 4.80865 ( 3663) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 600 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.5196 (mt) cc_final: 0.4943 (mt) REVERT: A 113 MET cc_start: 0.3919 (tpp) cc_final: 0.3349 (tpp) REVERT: A 574 PHE cc_start: 0.6988 (t80) cc_final: 0.6706 (m-80) REVERT: A 605 TRP cc_start: 0.6964 (t-100) cc_final: 0.5880 (t-100) REVERT: A 608 PHE cc_start: 0.7684 (t80) cc_final: 0.7274 (t80) REVERT: A 702 TYR cc_start: 0.5973 (t80) cc_final: 0.5325 (t80) REVERT: A 721 MET cc_start: 0.3667 (ppp) cc_final: 0.2944 (ppp) REVERT: A 907 MET cc_start: 0.6176 (mtm) cc_final: 0.5712 (tpt) REVERT: A 988 MET cc_start: 0.4882 (ttm) cc_final: 0.4130 (ttm) REVERT: A 1005 TRP cc_start: 0.3370 (m100) cc_final: 0.2380 (m-10) REVERT: A 1023 MET cc_start: 0.5528 (mtp) cc_final: 0.5233 (mtp) REVERT: B 25 GLU cc_start: 0.7610 (mp0) cc_final: 0.7121 (mp0) REVERT: B 179 SER cc_start: 0.7771 (m) cc_final: 0.7519 (t) REVERT: B 198 ARG cc_start: 0.4174 (mtp180) cc_final: 0.3971 (ttp80) REVERT: B 208 VAL cc_start: 0.6851 (t) cc_final: 0.6486 (t) REVERT: B 329 ILE cc_start: 0.5547 (mt) cc_final: 0.5126 (mt) REVERT: B 412 HIS cc_start: 0.1902 (p-80) cc_final: 0.1132 (t70) REVERT: B 525 ILE cc_start: 0.7027 (mt) cc_final: 0.6335 (mt) REVERT: B 629 MET cc_start: 0.1983 (tpt) cc_final: 0.0682 (tmm) REVERT: B 661 ARG cc_start: 0.8087 (pmt-80) cc_final: 0.6553 (ptm-80) REVERT: B 708 MET cc_start: 0.7542 (ttm) cc_final: 0.7235 (tpt) REVERT: B 720 THR cc_start: 0.7216 (p) cc_final: 0.6887 (p) REVERT: B 732 TYR cc_start: 0.7063 (m-10) cc_final: 0.6331 (m-10) REVERT: B 797 TYR cc_start: 0.6888 (m-80) cc_final: 0.6068 (t80) REVERT: B 805 LEU cc_start: 0.8111 (tt) cc_final: 0.7829 (pp) REVERT: C 125 ILE cc_start: 0.5584 (mm) cc_final: 0.4509 (mm) REVERT: C 141 ARG cc_start: 0.4209 (mtm180) cc_final: 0.3690 (mmt180) REVERT: C 299 LEU cc_start: 0.7079 (tp) cc_final: 0.6425 (tp) REVERT: C 328 GLU cc_start: 0.7952 (tt0) cc_final: 0.7123 (tm-30) REVERT: C 460 TRP cc_start: 0.6613 (m-10) cc_final: 0.6022 (m-10) REVERT: C 629 MET cc_start: 0.8059 (ptt) cc_final: 0.7542 (ppp) REVERT: C 722 LYS cc_start: 0.8567 (ttpt) cc_final: 0.7804 (tttt) REVERT: C 723 VAL cc_start: 0.6259 (m) cc_final: 0.5386 (m) REVERT: C 907 MET cc_start: 0.3289 (mtm) cc_final: 0.3040 (mmt) REVERT: C 924 MET cc_start: 0.7821 (mpp) cc_final: 0.7215 (mmp) REVERT: C 960 PHE cc_start: 0.7749 (t80) cc_final: 0.7468 (t80) REVERT: C 1001 TYR cc_start: 0.8316 (p90) cc_final: 0.8017 (p90) REVERT: C 1028 PHE cc_start: 0.5643 (t80) cc_final: 0.5086 (t80) REVERT: C 1029 MET cc_start: 0.7001 (tmm) cc_final: 0.6144 (ttm) REVERT: D 113 MET cc_start: 0.7728 (mmp) cc_final: 0.7445 (mmt) REVERT: D 266 GLU cc_start: 0.7366 (tp30) cc_final: 0.7151 (tp30) REVERT: D 408 MET cc_start: 0.6933 (tpp) cc_final: 0.6447 (tpp) REVERT: D 438 PHE cc_start: 0.6679 (m-80) cc_final: 0.6357 (m-10) REVERT: D 463 MET cc_start: 0.6409 (ttm) cc_final: 0.6177 (ttt) REVERT: D 684 ARG cc_start: 0.6727 (pmt170) cc_final: 0.5812 (tpm170) REVERT: D 789 LEU cc_start: 0.7504 (tp) cc_final: 0.7211 (tp) outliers start: 3 outliers final: 1 residues processed: 601 average time/residue: 0.1703 time to fit residues: 164.8107 Evaluate side-chains 419 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 418 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 347 optimal weight: 6.9990 chunk 292 optimal weight: 0.4980 chunk 131 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 619 ASN A 791 ASN B 35 GLN B 60 ASN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS C 412 HIS C 619 ASN C 714 GLN D 10 ASN D 65 GLN D 169 ASN D 236 GLN D 355 ASN D 359 ASN D 411 ASN D 587 GLN D 714 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.111916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085192 restraints weight = 101704.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.087694 restraints weight = 59212.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089391 restraints weight = 40744.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.090569 restraints weight = 31339.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.091353 restraints weight = 26034.361| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 28514 Z= 0.173 Angle : 0.675 12.341 38518 Z= 0.350 Chirality : 0.044 0.343 4282 Planarity : 0.005 0.076 4848 Dihedral : 5.664 59.473 3860 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3502 helix: 0.27 (0.12), residues: 1670 sheet: -1.11 (0.25), residues: 432 loop : -1.84 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 694 TYR 0.026 0.002 TYR C 980 PHE 0.031 0.002 PHE A 965 TRP 0.026 0.002 TRP B 158 HIS 0.005 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00380 (28504) covalent geometry : angle 0.67398 (38498) SS BOND : bond 0.01516 ( 10) SS BOND : angle 1.36411 ( 20) hydrogen bonds : bond 0.04186 ( 1213) hydrogen bonds : angle 4.48331 ( 3663) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 607 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.6008 (mt) cc_final: 0.5617 (mt) REVERT: A 113 MET cc_start: 0.5629 (tpp) cc_final: 0.4815 (tpp) REVERT: A 144 SER cc_start: 0.7981 (t) cc_final: 0.7746 (p) REVERT: A 245 PHE cc_start: 0.4120 (m-80) cc_final: 0.3685 (m-80) REVERT: A 280 TYR cc_start: 0.7128 (p90) cc_final: 0.6300 (p90) REVERT: A 292 MET cc_start: 0.5314 (mtt) cc_final: 0.4516 (mmp) REVERT: A 408 MET cc_start: 0.5446 (mmp) cc_final: 0.5086 (tmm) REVERT: A 524 GLU cc_start: 0.7043 (mp0) cc_final: 0.6439 (pp20) REVERT: A 525 ILE cc_start: 0.7431 (mt) cc_final: 0.6585 (mt) REVERT: A 528 CYS cc_start: 0.7792 (m) cc_final: 0.7377 (m) REVERT: A 531 PHE cc_start: 0.7329 (m-80) cc_final: 0.7096 (m-80) REVERT: A 605 TRP cc_start: 0.8005 (t-100) cc_final: 0.6855 (t-100) REVERT: A 608 PHE cc_start: 0.8042 (t80) cc_final: 0.7702 (t80) REVERT: A 674 MET cc_start: 0.7104 (ttt) cc_final: 0.6503 (ttt) REVERT: A 702 TYR cc_start: 0.7484 (t80) cc_final: 0.6914 (t80) REVERT: A 707 THR cc_start: 0.6932 (m) cc_final: 0.6576 (t) REVERT: A 708 MET cc_start: 0.7267 (ptp) cc_final: 0.7016 (pmm) REVERT: A 721 MET cc_start: 0.5249 (ppp) cc_final: 0.4489 (ppp) REVERT: A 907 MET cc_start: 0.5305 (mtm) cc_final: 0.4584 (tpt) REVERT: A 931 PHE cc_start: 0.6587 (m-80) cc_final: 0.6209 (m-80) REVERT: A 951 ILE cc_start: 0.4266 (mm) cc_final: 0.3735 (pt) REVERT: A 988 MET cc_start: 0.5116 (ttm) cc_final: 0.4805 (ttm) REVERT: A 1005 TRP cc_start: 0.3633 (m100) cc_final: 0.2602 (m-10) REVERT: A 1015 LEU cc_start: 0.8540 (mm) cc_final: 0.7850 (pp) REVERT: A 1023 MET cc_start: 0.5659 (mtp) cc_final: 0.5369 (mtp) REVERT: B 179 SER cc_start: 0.8683 (m) cc_final: 0.8419 (t) REVERT: B 225 LEU cc_start: 0.7850 (mt) cc_final: 0.7543 (mt) REVERT: B 358 ILE cc_start: 0.6614 (tp) cc_final: 0.6354 (tp) REVERT: B 503 MET cc_start: 0.3919 (ttt) cc_final: 0.3571 (tmm) REVERT: B 661 ARG cc_start: 0.7967 (pmt-80) cc_final: 0.7393 (pmt-80) REVERT: B 708 MET cc_start: 0.7847 (ttm) cc_final: 0.7427 (tpt) REVERT: B 720 THR cc_start: 0.6744 (p) cc_final: 0.6530 (p) REVERT: B 721 MET cc_start: 0.7430 (tpt) cc_final: 0.7110 (tpp) REVERT: B 732 TYR cc_start: 0.7303 (m-10) cc_final: 0.6386 (m-10) REVERT: B 797 TYR cc_start: 0.7316 (m-80) cc_final: 0.6699 (t80) REVERT: C 48 ASP cc_start: 0.7508 (m-30) cc_final: 0.7266 (m-30) REVERT: C 109 PHE cc_start: 0.7193 (m-80) cc_final: 0.6668 (m-10) REVERT: C 125 ILE cc_start: 0.6437 (mm) cc_final: 0.5453 (mm) REVERT: C 138 ASP cc_start: 0.6681 (t0) cc_final: 0.6322 (t0) REVERT: C 150 LEU cc_start: 0.7156 (mt) cc_final: 0.6937 (mp) REVERT: C 284 LEU cc_start: 0.7169 (mt) cc_final: 0.6824 (mt) REVERT: C 299 LEU cc_start: 0.7196 (tp) cc_final: 0.6655 (tp) REVERT: C 328 GLU cc_start: 0.8510 (tt0) cc_final: 0.7967 (tm-30) REVERT: C 407 MET cc_start: 0.7292 (mmm) cc_final: 0.6901 (mmm) REVERT: C 503 MET cc_start: 0.8091 (tmm) cc_final: 0.7872 (tmm) REVERT: C 529 ILE cc_start: 0.8672 (mt) cc_final: 0.8451 (mt) REVERT: C 606 TRP cc_start: 0.7561 (m-10) cc_final: 0.7224 (m-10) REVERT: C 617 THR cc_start: 0.8363 (m) cc_final: 0.8142 (m) REVERT: C 629 MET cc_start: 0.8363 (ptt) cc_final: 0.7607 (ppp) REVERT: C 649 THR cc_start: 0.5542 (p) cc_final: 0.5125 (p) REVERT: C 656 LYS cc_start: 0.7380 (tptp) cc_final: 0.6051 (mmmm) REVERT: C 861 TRP cc_start: 0.7137 (m100) cc_final: 0.6829 (m100) REVERT: C 924 MET cc_start: 0.7979 (mpp) cc_final: 0.7525 (mmp) REVERT: C 1001 TYR cc_start: 0.8243 (p90) cc_final: 0.7984 (p90) REVERT: C 1029 MET cc_start: 0.7304 (tmm) cc_final: 0.6553 (ttm) REVERT: D 54 ASN cc_start: 0.7351 (t0) cc_final: 0.6323 (t0) REVERT: D 175 GLU cc_start: 0.7614 (pp20) cc_final: 0.6900 (pm20) REVERT: D 220 TYR cc_start: 0.9185 (m-80) cc_final: 0.8646 (m-80) REVERT: D 237 PHE cc_start: 0.8314 (m-80) cc_final: 0.8033 (m-80) REVERT: D 278 ILE cc_start: 0.7230 (tt) cc_final: 0.6529 (mp) REVERT: D 408 MET cc_start: 0.6938 (tpp) cc_final: 0.6467 (tpp) REVERT: D 438 PHE cc_start: 0.6864 (m-80) cc_final: 0.6646 (m-80) REVERT: D 503 MET cc_start: 0.7941 (tpp) cc_final: 0.7601 (tpp) REVERT: D 584 PHE cc_start: 0.7915 (t80) cc_final: 0.7701 (t80) REVERT: D 609 THR cc_start: 0.7696 (p) cc_final: 0.6878 (t) REVERT: D 612 ILE cc_start: 0.8176 (mm) cc_final: 0.7877 (mm) REVERT: D 686 THR cc_start: 0.6776 (m) cc_final: 0.6036 (m) REVERT: D 709 ASN cc_start: 0.8026 (t0) cc_final: 0.7587 (t0) REVERT: C 1102 GLU cc_start: 0.7116 (tp30) cc_final: 0.6801 (tp30) outliers start: 4 outliers final: 1 residues processed: 609 average time/residue: 0.1773 time to fit residues: 176.3446 Evaluate side-chains 427 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 426 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 334 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 335 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 313 optimal weight: 8.9990 chunk 134 optimal weight: 0.7980 chunk 342 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 285 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 170 ASN A 586 GLN A 619 ASN A 791 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 207 GLN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN C 10 ASN C 46 HIS C 107 HIS C 246 GLN C 575 ASN C 872 GLN D 10 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.110580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.083401 restraints weight = 103887.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.085848 restraints weight = 61353.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.087506 restraints weight = 42703.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.088646 restraints weight = 33092.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.089398 restraints weight = 27718.133| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.8167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28514 Z= 0.169 Angle : 0.649 11.794 38518 Z= 0.338 Chirality : 0.043 0.234 4282 Planarity : 0.005 0.075 4848 Dihedral : 5.496 45.678 3860 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.07 % Allowed : 3.41 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3502 helix: 0.62 (0.12), residues: 1688 sheet: -1.05 (0.25), residues: 400 loop : -1.75 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 660 TYR 0.025 0.002 TYR C 980 PHE 0.020 0.002 PHE B 181 TRP 0.053 0.002 TRP D 158 HIS 0.006 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00377 (28504) covalent geometry : angle 0.64889 (38498) SS BOND : bond 0.00356 ( 10) SS BOND : angle 0.98412 ( 20) hydrogen bonds : bond 0.03765 ( 1213) hydrogen bonds : angle 4.38290 ( 3663) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 603 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.4823 (mt) cc_final: 0.4581 (mt) REVERT: A 78 ASP cc_start: 0.5541 (t0) cc_final: 0.4998 (p0) REVERT: A 84 THR cc_start: 0.8107 (m) cc_final: 0.7842 (p) REVERT: A 85 ILE cc_start: 0.7762 (mm) cc_final: 0.7426 (mm) REVERT: A 121 LEU cc_start: 0.8065 (mt) cc_final: 0.7822 (mt) REVERT: A 278 ILE cc_start: 0.4638 (tt) cc_final: 0.4128 (tt) REVERT: A 292 MET cc_start: 0.5763 (mtt) cc_final: 0.5060 (mmp) REVERT: A 439 LYS cc_start: 0.8039 (mmpt) cc_final: 0.7740 (mmtm) REVERT: A 524 GLU cc_start: 0.7253 (mp0) cc_final: 0.6555 (pp20) REVERT: A 525 ILE cc_start: 0.7861 (mt) cc_final: 0.6990 (mt) REVERT: A 527 MET cc_start: 0.4805 (mmm) cc_final: 0.4237 (mmm) REVERT: A 528 CYS cc_start: 0.7974 (m) cc_final: 0.7121 (m) REVERT: A 531 PHE cc_start: 0.7746 (m-10) cc_final: 0.7524 (m-80) REVERT: A 585 MET cc_start: 0.8572 (tpp) cc_final: 0.8282 (tpp) REVERT: A 674 MET cc_start: 0.7086 (ttt) cc_final: 0.6412 (ttt) REVERT: A 702 TYR cc_start: 0.7752 (t80) cc_final: 0.7413 (t80) REVERT: A 707 THR cc_start: 0.7281 (m) cc_final: 0.7058 (t) REVERT: A 721 MET cc_start: 0.6427 (ppp) cc_final: 0.5944 (ppp) REVERT: A 924 MET cc_start: 0.8532 (mmp) cc_final: 0.8325 (mmm) REVERT: A 951 ILE cc_start: 0.4376 (mm) cc_final: 0.3959 (pt) REVERT: A 979 LEU cc_start: 0.8577 (mm) cc_final: 0.8078 (mp) REVERT: A 981 ILE cc_start: 0.7807 (mt) cc_final: 0.7465 (pt) REVERT: A 1005 TRP cc_start: 0.4036 (m100) cc_final: 0.2826 (m-10) REVERT: A 1023 MET cc_start: 0.5779 (mtp) cc_final: 0.5536 (mtp) REVERT: B 167 ASN cc_start: 0.7954 (p0) cc_final: 0.7747 (p0) REVERT: B 179 SER cc_start: 0.9114 (m) cc_final: 0.8652 (t) REVERT: B 197 GLU cc_start: 0.6398 (tm-30) cc_final: 0.6146 (tm-30) REVERT: B 198 ARG cc_start: 0.7142 (mtp180) cc_final: 0.6872 (ttp80) REVERT: B 316 LEU cc_start: 0.5147 (mt) cc_final: 0.4304 (pp) REVERT: B 408 MET cc_start: 0.5736 (tmm) cc_final: 0.5336 (tmm) REVERT: B 527 MET cc_start: 0.8349 (mmm) cc_final: 0.7520 (mtt) REVERT: B 528 CYS cc_start: 0.8419 (t) cc_final: 0.7912 (t) REVERT: B 531 PHE cc_start: 0.8709 (m-80) cc_final: 0.8382 (m-80) REVERT: B 536 VAL cc_start: 0.9198 (t) cc_final: 0.8846 (t) REVERT: B 629 MET cc_start: 0.2768 (tpt) cc_final: 0.2506 (tpp) REVERT: B 661 ARG cc_start: 0.7831 (pmt-80) cc_final: 0.6649 (mpt180) REVERT: B 708 MET cc_start: 0.8020 (ttm) cc_final: 0.7405 (tpt) REVERT: B 721 MET cc_start: 0.7993 (tpt) cc_final: 0.7735 (tpp) REVERT: B 732 TYR cc_start: 0.7582 (m-10) cc_final: 0.6312 (m-10) REVERT: B 797 TYR cc_start: 0.7974 (m-80) cc_final: 0.7313 (t80) REVERT: C 109 PHE cc_start: 0.7696 (m-80) cc_final: 0.7036 (m-10) REVERT: C 125 ILE cc_start: 0.7410 (mm) cc_final: 0.6719 (mm) REVERT: C 138 ASP cc_start: 0.7339 (t0) cc_final: 0.6963 (t0) REVERT: C 328 GLU cc_start: 0.8535 (tt0) cc_final: 0.8309 (tt0) REVERT: C 379 LYS cc_start: 0.8946 (tptm) cc_final: 0.8695 (tptp) REVERT: C 407 MET cc_start: 0.7447 (mmm) cc_final: 0.6699 (mmm) REVERT: C 474 ILE cc_start: 0.8464 (pt) cc_final: 0.8148 (mp) REVERT: C 524 GLU cc_start: 0.6210 (pp20) cc_final: 0.5628 (pp20) REVERT: C 629 MET cc_start: 0.8470 (ptt) cc_final: 0.7700 (ppp) REVERT: C 640 SER cc_start: 0.9133 (t) cc_final: 0.8782 (t) REVERT: C 649 THR cc_start: 0.6758 (p) cc_final: 0.6517 (p) REVERT: C 861 TRP cc_start: 0.7403 (m100) cc_final: 0.7058 (m100) REVERT: C 1029 MET cc_start: 0.7266 (tmm) cc_final: 0.6657 (ttm) REVERT: D 51 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7394 (tm-30) REVERT: D 54 ASN cc_start: 0.7394 (t0) cc_final: 0.6326 (t0) REVERT: D 113 MET cc_start: 0.7809 (mmp) cc_final: 0.7272 (mmt) REVERT: D 220 TYR cc_start: 0.9208 (m-80) cc_final: 0.8401 (m-80) REVERT: D 278 ILE cc_start: 0.7278 (tt) cc_final: 0.6915 (mt) REVERT: D 361 MET cc_start: 0.8201 (mpp) cc_final: 0.7759 (mpp) REVERT: D 380 MET cc_start: 0.8220 (pmm) cc_final: 0.7938 (pmm) REVERT: D 405 TYR cc_start: 0.8114 (m-10) cc_final: 0.7853 (m-80) REVERT: D 408 MET cc_start: 0.6841 (tpp) cc_final: 0.6479 (tpp) REVERT: D 438 PHE cc_start: 0.6980 (m-80) cc_final: 0.6741 (m-10) REVERT: D 496 MET cc_start: 0.4188 (pmm) cc_final: 0.3920 (pmm) REVERT: D 503 MET cc_start: 0.8226 (tpp) cc_final: 0.8020 (tpt) REVERT: D 619 ASN cc_start: 0.8675 (t0) cc_final: 0.8020 (t0) REVERT: D 686 THR cc_start: 0.6802 (m) cc_final: 0.5633 (p) REVERT: D 726 ASN cc_start: 0.5856 (m-40) cc_final: 0.4636 (p0) outliers start: 2 outliers final: 0 residues processed: 605 average time/residue: 0.1668 time to fit residues: 164.9445 Evaluate side-chains 433 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 135 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 234 optimal weight: 0.9990 chunk 278 optimal weight: 0.8980 chunk 333 optimal weight: 0.0060 chunk 165 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 791 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.111474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.084655 restraints weight = 102261.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087115 restraints weight = 60340.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.088737 restraints weight = 41851.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.089834 restraints weight = 32514.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.090604 restraints weight = 27296.418| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.8735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 28514 Z= 0.113 Angle : 0.576 9.167 38518 Z= 0.297 Chirality : 0.041 0.227 4282 Planarity : 0.004 0.077 4848 Dihedral : 5.137 44.646 3860 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.14), residues: 3502 helix: 0.98 (0.13), residues: 1702 sheet: -0.96 (0.25), residues: 410 loop : -1.63 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 30 TYR 0.023 0.001 TYR A 177 PHE 0.025 0.001 PHE C1009 TRP 0.042 0.002 TRP C 460 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00250 (28504) covalent geometry : angle 0.57632 (38498) SS BOND : bond 0.00252 ( 10) SS BOND : angle 0.72342 ( 20) hydrogen bonds : bond 0.03287 ( 1213) hydrogen bonds : angle 4.08826 ( 3663) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 561 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.5775 (t0) cc_final: 0.5165 (p0) REVERT: A 85 ILE cc_start: 0.7940 (mm) cc_final: 0.7539 (mm) REVERT: A 292 MET cc_start: 0.6121 (mtt) cc_final: 0.5590 (mmp) REVERT: A 439 LYS cc_start: 0.7956 (mmpt) cc_final: 0.7611 (mmtm) REVERT: A 479 LEU cc_start: 0.8099 (mm) cc_final: 0.7829 (mm) REVERT: A 503 MET cc_start: 0.4359 (ttp) cc_final: 0.4027 (ttp) REVERT: A 524 GLU cc_start: 0.7213 (mp0) cc_final: 0.6553 (pp20) REVERT: A 525 ILE cc_start: 0.7843 (mt) cc_final: 0.6897 (mt) REVERT: A 527 MET cc_start: 0.4903 (mmm) cc_final: 0.3736 (mmm) REVERT: A 528 CYS cc_start: 0.7810 (m) cc_final: 0.6835 (m) REVERT: A 531 PHE cc_start: 0.7702 (m-10) cc_final: 0.7194 (m-80) REVERT: A 573 ILE cc_start: 0.7631 (tp) cc_final: 0.7319 (tp) REVERT: A 585 MET cc_start: 0.8554 (tpp) cc_final: 0.7970 (tpp) REVERT: A 670 MET cc_start: 0.8075 (mtt) cc_final: 0.7780 (mtt) REVERT: A 674 MET cc_start: 0.7101 (ttt) cc_final: 0.6335 (ttt) REVERT: A 702 TYR cc_start: 0.7712 (t80) cc_final: 0.7432 (t80) REVERT: A 707 THR cc_start: 0.7530 (m) cc_final: 0.7287 (t) REVERT: A 721 MET cc_start: 0.6582 (ppp) cc_final: 0.6318 (ppp) REVERT: A 951 ILE cc_start: 0.4407 (mm) cc_final: 0.3944 (pt) REVERT: A 979 LEU cc_start: 0.8684 (mm) cc_final: 0.8399 (mm) REVERT: A 981 ILE cc_start: 0.7687 (mt) cc_final: 0.7460 (mm) REVERT: A 1005 TRP cc_start: 0.4111 (m100) cc_final: 0.2883 (m-10) REVERT: A 1023 MET cc_start: 0.5830 (mtp) cc_final: 0.5575 (mtp) REVERT: B 167 ASN cc_start: 0.8066 (p0) cc_final: 0.7817 (p0) REVERT: B 179 SER cc_start: 0.8933 (m) cc_final: 0.8545 (t) REVERT: B 289 VAL cc_start: 0.7464 (m) cc_final: 0.7233 (t) REVERT: B 316 LEU cc_start: 0.5068 (mt) cc_final: 0.4266 (pp) REVERT: B 536 VAL cc_start: 0.9202 (t) cc_final: 0.9001 (t) REVERT: B 574 PHE cc_start: 0.6708 (m-80) cc_final: 0.6477 (m-10) REVERT: B 629 MET cc_start: 0.2840 (tpt) cc_final: 0.2633 (tpp) REVERT: B 661 ARG cc_start: 0.7767 (pmt-80) cc_final: 0.6597 (mpt180) REVERT: B 708 MET cc_start: 0.8038 (ttm) cc_final: 0.7386 (tpt) REVERT: B 721 MET cc_start: 0.7960 (tpt) cc_final: 0.7677 (tpp) REVERT: B 732 TYR cc_start: 0.7551 (m-10) cc_final: 0.6193 (m-10) REVERT: B 797 TYR cc_start: 0.8072 (m-80) cc_final: 0.7456 (t80) REVERT: C 109 PHE cc_start: 0.7710 (m-80) cc_final: 0.7025 (m-10) REVERT: C 138 ASP cc_start: 0.7311 (t0) cc_final: 0.7032 (t0) REVERT: C 190 ARG cc_start: 0.6431 (mmt-90) cc_final: 0.5947 (mmp80) REVERT: C 249 ASP cc_start: 0.6783 (t0) cc_final: 0.6551 (t0) REVERT: C 328 GLU cc_start: 0.8552 (tt0) cc_final: 0.8134 (tt0) REVERT: C 379 LYS cc_start: 0.8988 (tptm) cc_final: 0.8720 (tptp) REVERT: C 407 MET cc_start: 0.7681 (mmm) cc_final: 0.7094 (mmm) REVERT: C 503 MET cc_start: 0.8053 (ppp) cc_final: 0.7620 (ppp) REVERT: C 524 GLU cc_start: 0.6520 (pp20) cc_final: 0.5751 (pp20) REVERT: C 525 ILE cc_start: 0.8271 (mp) cc_final: 0.7919 (mp) REVERT: C 629 MET cc_start: 0.8406 (ptt) cc_final: 0.7448 (tmm) REVERT: C 783 LYS cc_start: 0.7342 (pptt) cc_final: 0.6857 (mmmt) REVERT: C 921 VAL cc_start: 0.7707 (t) cc_final: 0.7397 (t) REVERT: C 986 ASP cc_start: 0.8122 (t70) cc_final: 0.7253 (m-30) REVERT: C 1028 PHE cc_start: 0.6542 (t80) cc_final: 0.6203 (t80) REVERT: C 1029 MET cc_start: 0.7525 (tmm) cc_final: 0.7112 (ttm) REVERT: D 51 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7148 (tm-30) REVERT: D 54 ASN cc_start: 0.7284 (t0) cc_final: 0.6129 (t0) REVERT: D 81 SER cc_start: 0.9008 (p) cc_final: 0.8801 (m) REVERT: D 124 LEU cc_start: 0.9257 (tp) cc_final: 0.9001 (tp) REVERT: D 361 MET cc_start: 0.7857 (mpp) cc_final: 0.7517 (mpp) REVERT: D 405 TYR cc_start: 0.8032 (m-10) cc_final: 0.7734 (m-80) REVERT: D 408 MET cc_start: 0.6842 (tpp) cc_final: 0.6516 (tpp) REVERT: D 500 ILE cc_start: 0.7239 (mt) cc_final: 0.6767 (mp) REVERT: D 503 MET cc_start: 0.8426 (tpp) cc_final: 0.8226 (tpt) REVERT: D 619 ASN cc_start: 0.8800 (t0) cc_final: 0.8159 (t0) REVERT: D 660 ARG cc_start: 0.6901 (mpt-90) cc_final: 0.6358 (mtt90) outliers start: 0 outliers final: 0 residues processed: 561 average time/residue: 0.1715 time to fit residues: 158.7207 Evaluate side-chains 433 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 149 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 291 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 246 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 321 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 412 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN B 10 ASN B 60 ASN B 112 GLN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN C 985 ASN D 10 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN D 207 GLN D 355 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.110034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.082730 restraints weight = 101374.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.085081 restraints weight = 60231.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.086649 restraints weight = 42279.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.087615 restraints weight = 33151.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.088358 restraints weight = 28267.028| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 1.0238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 28514 Z= 0.158 Angle : 0.641 12.092 38518 Z= 0.333 Chirality : 0.043 0.235 4282 Planarity : 0.004 0.076 4848 Dihedral : 5.263 47.398 3860 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.07 % Allowed : 2.78 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3502 helix: 0.83 (0.12), residues: 1708 sheet: -1.08 (0.26), residues: 356 loop : -1.61 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 30 TYR 0.035 0.002 TYR A 177 PHE 0.033 0.002 PHE B 76 TRP 0.047 0.003 TRP B 606 HIS 0.006 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00359 (28504) covalent geometry : angle 0.64091 (38498) SS BOND : bond 0.00264 ( 10) SS BOND : angle 0.71867 ( 20) hydrogen bonds : bond 0.03631 ( 1213) hydrogen bonds : angle 4.23890 ( 3663) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 580 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.4987 (m-80) cc_final: 0.3970 (m-80) REVERT: A 78 ASP cc_start: 0.6865 (t0) cc_final: 0.6199 (p0) REVERT: A 123 SER cc_start: 0.9198 (m) cc_final: 0.8941 (p) REVERT: A 204 ILE cc_start: 0.8346 (mt) cc_final: 0.7754 (mt) REVERT: A 220 TYR cc_start: 0.7857 (m-10) cc_final: 0.7588 (m-80) REVERT: A 264 THR cc_start: 0.8647 (p) cc_final: 0.8411 (t) REVERT: A 278 ILE cc_start: 0.4808 (tt) cc_final: 0.4295 (tt) REVERT: A 292 MET cc_start: 0.6631 (mtt) cc_final: 0.6206 (mmm) REVERT: A 439 LYS cc_start: 0.8270 (mmpt) cc_final: 0.7968 (mmtm) REVERT: A 524 GLU cc_start: 0.7314 (mp0) cc_final: 0.7005 (pp20) REVERT: A 525 ILE cc_start: 0.8185 (mt) cc_final: 0.7052 (mt) REVERT: A 527 MET cc_start: 0.5471 (mmm) cc_final: 0.5121 (mmm) REVERT: A 574 PHE cc_start: 0.7626 (t80) cc_final: 0.7256 (m-80) REVERT: A 580 SER cc_start: 0.9094 (m) cc_final: 0.8670 (p) REVERT: A 585 MET cc_start: 0.8763 (tpp) cc_final: 0.8527 (tpp) REVERT: A 670 MET cc_start: 0.8361 (mtt) cc_final: 0.7937 (mtt) REVERT: A 688 GLU cc_start: 0.9097 (tt0) cc_final: 0.8536 (tt0) REVERT: A 708 MET cc_start: 0.8080 (ptp) cc_final: 0.7781 (pmm) REVERT: A 730 LYS cc_start: 0.8018 (mptt) cc_final: 0.7808 (mmtt) REVERT: A 924 MET cc_start: 0.8664 (mmp) cc_final: 0.8451 (mmm) REVERT: A 979 LEU cc_start: 0.8979 (mm) cc_final: 0.8753 (mm) REVERT: A 980 TYR cc_start: 0.6842 (t80) cc_final: 0.6043 (t80) REVERT: A 981 ILE cc_start: 0.8122 (mt) cc_final: 0.7892 (pt) REVERT: A 1005 TRP cc_start: 0.4356 (m100) cc_final: 0.2975 (m-10) REVERT: A 1023 MET cc_start: 0.6343 (mtp) cc_final: 0.6131 (mtp) REVERT: B 78 ASP cc_start: 0.7827 (t0) cc_final: 0.7383 (p0) REVERT: B 167 ASN cc_start: 0.8492 (p0) cc_final: 0.8046 (p0) REVERT: B 316 LEU cc_start: 0.5530 (mt) cc_final: 0.4628 (pp) REVERT: B 531 PHE cc_start: 0.8772 (m-80) cc_final: 0.8438 (m-80) REVERT: B 536 VAL cc_start: 0.9371 (t) cc_final: 0.9036 (p) REVERT: B 571 PHE cc_start: 0.6999 (m-80) cc_final: 0.6364 (m-80) REVERT: B 584 PHE cc_start: 0.9329 (t80) cc_final: 0.8934 (t80) REVERT: B 585 MET cc_start: 0.8836 (mtp) cc_final: 0.8183 (mtp) REVERT: B 629 MET cc_start: 0.2809 (tpt) cc_final: 0.2491 (tpp) REVERT: B 661 ARG cc_start: 0.7803 (pmt-80) cc_final: 0.6623 (mmt-90) REVERT: B 705 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7958 (tt0) REVERT: B 708 MET cc_start: 0.8380 (ttm) cc_final: 0.8052 (ttp) REVERT: B 721 MET cc_start: 0.8123 (tpt) cc_final: 0.7732 (mtt) REVERT: B 732 TYR cc_start: 0.7377 (m-10) cc_final: 0.6415 (m-10) REVERT: B 796 PHE cc_start: 0.9150 (m-80) cc_final: 0.8919 (m-10) REVERT: B 797 TYR cc_start: 0.8256 (m-80) cc_final: 0.7803 (t80) REVERT: C 25 GLU cc_start: 0.9276 (mp0) cc_final: 0.9059 (mp0) REVERT: C 109 PHE cc_start: 0.7837 (m-80) cc_final: 0.7188 (m-10) REVERT: C 138 ASP cc_start: 0.7652 (t0) cc_final: 0.7344 (t0) REVERT: C 249 ASP cc_start: 0.7610 (t0) cc_final: 0.7194 (t70) REVERT: C 407 MET cc_start: 0.7915 (mmm) cc_final: 0.7622 (mmm) REVERT: C 511 LYS cc_start: 0.7980 (mmpt) cc_final: 0.7478 (tptt) REVERT: C 524 GLU cc_start: 0.6738 (pp20) cc_final: 0.6151 (pp20) REVERT: C 629 MET cc_start: 0.8403 (ptt) cc_final: 0.7699 (tmm) REVERT: C 721 MET cc_start: 0.8175 (pmm) cc_final: 0.7896 (pmm) REVERT: C 861 TRP cc_start: 0.7242 (m100) cc_final: 0.6901 (m100) REVERT: C 924 MET cc_start: 0.7956 (mtm) cc_final: 0.7211 (mmp) REVERT: C 1029 MET cc_start: 0.7672 (tmm) cc_final: 0.7157 (ttm) REVERT: D 50 LEU cc_start: 0.7825 (pt) cc_final: 0.7316 (pt) REVERT: D 54 ASN cc_start: 0.8081 (t0) cc_final: 0.7687 (t0) REVERT: D 229 ASP cc_start: 0.7662 (m-30) cc_final: 0.7424 (m-30) REVERT: D 361 MET cc_start: 0.7948 (mpp) cc_final: 0.7529 (mpp) REVERT: D 408 MET cc_start: 0.6785 (tpp) cc_final: 0.6390 (tpp) REVERT: D 503 MET cc_start: 0.8453 (tpp) cc_final: 0.8182 (tpt) REVERT: D 515 PHE cc_start: 0.5864 (m-10) cc_final: 0.5632 (m-10) REVERT: D 619 ASN cc_start: 0.9271 (t0) cc_final: 0.8689 (t0) REVERT: D 620 LEU cc_start: 0.9148 (tt) cc_final: 0.8913 (tp) REVERT: D 726 ASN cc_start: 0.5775 (m-40) cc_final: 0.4522 (p0) outliers start: 2 outliers final: 0 residues processed: 582 average time/residue: 0.1619 time to fit residues: 156.9125 Evaluate side-chains 434 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 220 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 315 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 305 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 60 ASN A 107 HIS A 569 ASN A 575 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN C 147 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 147 GLN D 355 ASN D 435 HIS D 586 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.106873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.079238 restraints weight = 103519.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.081758 restraints weight = 69299.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082344 restraints weight = 43822.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082885 restraints weight = 39978.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.082936 restraints weight = 36939.487| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 1.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 28514 Z= 0.213 Angle : 0.736 12.075 38518 Z= 0.384 Chirality : 0.045 0.320 4282 Planarity : 0.005 0.080 4848 Dihedral : 5.750 68.314 3860 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.06 % 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: -0.90 (0.14), residues: 3502 helix: 0.46 (0.12), residues: 1714 sheet: -1.17 (0.28), residues: 308 loop : -1.71 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 660 TYR 0.033 0.002 TYR A 280 PHE 0.046 0.003 PHE C 659 TRP 0.031 0.003 TRP C 671 HIS 0.007 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00479 (28504) covalent geometry : angle 0.73601 (38498) SS BOND : bond 0.00342 ( 10) SS BOND : angle 0.71823 ( 20) hydrogen bonds : bond 0.04169 ( 1213) hydrogen bonds : angle 4.64876 ( 3663) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8441 (t0) cc_final: 0.7420 (p0) REVERT: A 123 SER cc_start: 0.9204 (m) cc_final: 0.8724 (t) REVERT: A 138 ASP cc_start: 0.6623 (t0) cc_final: 0.5657 (t0) REVERT: A 140 ASP cc_start: 0.7975 (m-30) cc_final: 0.7312 (m-30) REVERT: A 278 ILE cc_start: 0.6001 (tt) cc_final: 0.5399 (tt) REVERT: A 503 MET cc_start: 0.7014 (ttp) cc_final: 0.6454 (ttm) REVERT: A 524 GLU cc_start: 0.7578 (mp0) cc_final: 0.7298 (pp20) REVERT: A 525 ILE cc_start: 0.8723 (mt) cc_final: 0.8280 (mt) REVERT: A 580 SER cc_start: 0.9366 (m) cc_final: 0.8980 (p) REVERT: A 670 MET cc_start: 0.8838 (mtt) cc_final: 0.8290 (mtt) REVERT: A 674 MET cc_start: 0.7682 (ttt) cc_final: 0.7222 (mmm) REVERT: A 705 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8179 (mp0) REVERT: A 707 THR cc_start: 0.8678 (m) cc_final: 0.8274 (t) REVERT: A 732 TYR cc_start: 0.8337 (m-10) cc_final: 0.6452 (m-80) REVERT: A 863 TYR cc_start: 0.3604 (m-80) cc_final: 0.3399 (m-80) REVERT: A 924 MET cc_start: 0.8840 (mmp) cc_final: 0.8601 (mmm) REVERT: A 979 LEU cc_start: 0.9241 (mm) cc_final: 0.8981 (mm) REVERT: A 980 TYR cc_start: 0.7618 (t80) cc_final: 0.6952 (t80) REVERT: A 981 ILE cc_start: 0.8516 (mt) cc_final: 0.7668 (tp) REVERT: B 78 ASP cc_start: 0.8428 (t0) cc_final: 0.7972 (p0) REVERT: B 81 SER cc_start: 0.9074 (p) cc_final: 0.8874 (p) REVERT: B 89 CYS cc_start: 0.7987 (m) cc_final: 0.7534 (p) REVERT: B 260 GLU cc_start: 0.8775 (mp0) cc_final: 0.8543 (mp0) REVERT: B 316 LEU cc_start: 0.6182 (mt) cc_final: 0.5844 (pp) REVERT: B 329 ILE cc_start: 0.6493 (mt) cc_final: 0.6149 (mt) REVERT: B 346 LYS cc_start: 0.3653 (ttmt) cc_final: 0.3290 (tptt) REVERT: B 383 THR cc_start: 0.8434 (p) cc_final: 0.8084 (t) REVERT: B 531 PHE cc_start: 0.8949 (m-80) cc_final: 0.8449 (m-80) REVERT: B 533 TYR cc_start: 0.9022 (t80) cc_final: 0.8781 (t80) REVERT: B 661 ARG cc_start: 0.7978 (pmt-80) cc_final: 0.6799 (mmt-90) REVERT: B 705 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8341 (tt0) REVERT: B 708 MET cc_start: 0.8575 (ttm) cc_final: 0.8259 (ttp) REVERT: B 721 MET cc_start: 0.8325 (tpt) cc_final: 0.8085 (ttm) REVERT: B 789 LEU cc_start: 0.8722 (tp) cc_final: 0.7563 (tp) REVERT: B 797 TYR cc_start: 0.8666 (m-80) cc_final: 0.7998 (t80) REVERT: B 803 LEU cc_start: 0.9403 (mt) cc_final: 0.9202 (mt) REVERT: B 813 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7853 (tm-30) REVERT: C 25 GLU cc_start: 0.9433 (mp0) cc_final: 0.9146 (mp0) REVERT: C 112 GLN cc_start: 0.8082 (pm20) cc_final: 0.7864 (pm20) REVERT: C 126 GLU cc_start: 0.8912 (tt0) cc_final: 0.8677 (tt0) REVERT: C 138 ASP cc_start: 0.8203 (t0) cc_final: 0.7973 (t0) REVERT: C 232 LEU cc_start: 0.8874 (mt) cc_final: 0.8553 (mt) REVERT: C 374 TRP cc_start: 0.7502 (t60) cc_final: 0.7274 (t60) REVERT: C 406 VAL cc_start: 0.7711 (t) cc_final: 0.7348 (t) REVERT: C 407 MET cc_start: 0.8076 (mmm) cc_final: 0.7699 (mmm) REVERT: C 503 MET cc_start: 0.7952 (ppp) cc_final: 0.7614 (ppp) REVERT: C 511 LYS cc_start: 0.8186 (mmpt) cc_final: 0.7562 (tptt) REVERT: C 524 GLU cc_start: 0.7373 (pp20) cc_final: 0.6806 (pp20) REVERT: C 525 ILE cc_start: 0.8925 (mt) cc_final: 0.8703 (mt) REVERT: C 669 LYS cc_start: 0.8309 (pptt) cc_final: 0.7924 (tptt) REVERT: C 763 LYS cc_start: 0.8634 (tttp) cc_final: 0.8348 (tptp) REVERT: C 924 MET cc_start: 0.8383 (mtm) cc_final: 0.7621 (mmp) REVERT: C 985 ASN cc_start: 0.8459 (m-40) cc_final: 0.8182 (m-40) REVERT: C 986 ASP cc_start: 0.8311 (t70) cc_final: 0.7652 (m-30) REVERT: D 47 ILE cc_start: 0.7691 (mt) cc_final: 0.6972 (mm) REVERT: D 50 LEU cc_start: 0.8778 (pt) cc_final: 0.8369 (pt) REVERT: D 199 ASP cc_start: 0.8459 (p0) cc_final: 0.8139 (p0) REVERT: D 293 THR cc_start: 0.8751 (m) cc_final: 0.8453 (p) REVERT: D 408 MET cc_start: 0.6813 (tpp) cc_final: 0.6400 (tpp) REVERT: D 533 TYR cc_start: 0.9068 (t80) cc_final: 0.8813 (t80) REVERT: D 541 PHE cc_start: 0.8320 (t80) cc_final: 0.8021 (t80) REVERT: D 619 ASN cc_start: 0.9532 (t0) cc_final: 0.8654 (t0) outliers start: 0 outliers final: 0 residues processed: 559 average time/residue: 0.1759 time to fit residues: 161.7497 Evaluate side-chains 390 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 274 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 348 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 320 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 246 GLN A 791 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN D 10 ASN D 46 HIS D 274 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.104781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076566 restraints weight = 103835.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.079006 restraints weight = 71100.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.079666 restraints weight = 43474.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079999 restraints weight = 39610.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.080119 restraints weight = 36391.494| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 1.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 28514 Z= 0.226 Angle : 0.750 16.427 38518 Z= 0.392 Chirality : 0.046 0.286 4282 Planarity : 0.005 0.128 4848 Dihedral : 5.770 63.106 3860 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3502 helix: 0.33 (0.12), residues: 1700 sheet: -1.49 (0.25), residues: 380 loop : -1.72 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 660 TYR 0.027 0.002 TYR C 980 PHE 0.030 0.002 PHE C 62 TRP 0.036 0.002 TRP C 671 HIS 0.007 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00504 (28504) covalent geometry : angle 0.74837 (38498) SS BOND : bond 0.00602 ( 10) SS BOND : angle 2.11566 ( 20) hydrogen bonds : bond 0.04114 ( 1213) hydrogen bonds : angle 4.81800 ( 3663) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8849 (mp0) cc_final: 0.8449 (mp0) REVERT: A 123 SER cc_start: 0.9377 (m) cc_final: 0.8680 (t) REVERT: A 406 VAL cc_start: 0.8556 (t) cc_final: 0.8209 (t) REVERT: A 527 MET cc_start: 0.6241 (mmt) cc_final: 0.6022 (mmt) REVERT: A 580 SER cc_start: 0.9499 (m) cc_final: 0.9191 (p) REVERT: A 670 MET cc_start: 0.8943 (mtt) cc_final: 0.8656 (mtt) REVERT: A 674 MET cc_start: 0.7878 (ttt) cc_final: 0.7464 (mmm) REVERT: A 705 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8152 (mp0) REVERT: A 797 TYR cc_start: 0.7943 (m-10) cc_final: 0.7687 (m-80) REVERT: A 939 MET cc_start: 0.4237 (ppp) cc_final: 0.3848 (ppp) REVERT: A 979 LEU cc_start: 0.9379 (mm) cc_final: 0.9124 (mm) REVERT: A 980 TYR cc_start: 0.7840 (t80) cc_final: 0.7150 (t80) REVERT: A 1026 TYR cc_start: 0.6373 (m-10) cc_final: 0.5948 (m-80) REVERT: B 56 PHE cc_start: 0.7991 (t80) cc_final: 0.7251 (t80) REVERT: B 81 SER cc_start: 0.9028 (p) cc_final: 0.8685 (p) REVERT: B 89 CYS cc_start: 0.8312 (m) cc_final: 0.7957 (p) REVERT: B 305 GLU cc_start: 0.7773 (tt0) cc_final: 0.7551 (pp20) REVERT: B 329 ILE cc_start: 0.6715 (mt) cc_final: 0.6404 (mt) REVERT: B 346 LYS cc_start: 0.4289 (ttmt) cc_final: 0.3455 (tptt) REVERT: B 383 THR cc_start: 0.8718 (p) cc_final: 0.8511 (p) REVERT: B 528 CYS cc_start: 0.8888 (t) cc_final: 0.8646 (t) REVERT: B 531 PHE cc_start: 0.9033 (m-80) cc_final: 0.8688 (m-80) REVERT: B 578 TRP cc_start: 0.9151 (t-100) cc_final: 0.8585 (t-100) REVERT: B 661 ARG cc_start: 0.7956 (pmt-80) cc_final: 0.6835 (mmt-90) REVERT: B 705 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8320 (tt0) REVERT: B 708 MET cc_start: 0.8789 (ttm) cc_final: 0.8545 (ttp) REVERT: B 789 LEU cc_start: 0.8968 (tp) cc_final: 0.8695 (tt) REVERT: B 797 TYR cc_start: 0.8783 (m-80) cc_final: 0.8004 (t80) REVERT: B 813 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7959 (tm-30) REVERT: C 29 PHE cc_start: 0.8195 (t80) cc_final: 0.7962 (t80) REVERT: C 109 PHE cc_start: 0.8298 (m-80) cc_final: 0.7995 (m-10) REVERT: C 126 GLU cc_start: 0.8807 (tt0) cc_final: 0.8599 (tt0) REVERT: C 232 LEU cc_start: 0.9104 (mt) cc_final: 0.8776 (mt) REVERT: C 374 TRP cc_start: 0.7967 (t60) cc_final: 0.7628 (t60) REVERT: C 406 VAL cc_start: 0.7884 (t) cc_final: 0.7385 (t) REVERT: C 407 MET cc_start: 0.8189 (mmm) cc_final: 0.7929 (mmm) REVERT: C 408 MET cc_start: 0.8652 (tpp) cc_final: 0.8309 (mmm) REVERT: C 432 ILE cc_start: 0.8017 (tp) cc_final: 0.7721 (pt) REVERT: C 511 LYS cc_start: 0.8436 (mmpt) cc_final: 0.7973 (tptt) REVERT: C 571 PHE cc_start: 0.7608 (m-80) cc_final: 0.7160 (m-80) REVERT: C 620 LEU cc_start: 0.9311 (mm) cc_final: 0.9096 (mm) REVERT: C 629 MET cc_start: 0.8394 (tmm) cc_final: 0.7906 (tmm) REVERT: C 722 LYS cc_start: 0.8736 (tttp) cc_final: 0.8425 (tptt) REVERT: C 803 LEU cc_start: 0.9396 (tt) cc_final: 0.9110 (tt) REVERT: C 807 MET cc_start: 0.8434 (mtm) cc_final: 0.8144 (mtm) REVERT: C 924 MET cc_start: 0.8295 (mtm) cc_final: 0.7652 (mmp) REVERT: D 199 ASP cc_start: 0.8333 (p0) cc_final: 0.8043 (p0) REVERT: D 408 MET cc_start: 0.6803 (tpp) cc_final: 0.6576 (tpp) REVERT: D 503 MET cc_start: 0.8255 (tpt) cc_final: 0.7375 (tpt) REVERT: D 541 PHE cc_start: 0.8461 (t80) cc_final: 0.8146 (t80) REVERT: D 576 SER cc_start: 0.8430 (m) cc_final: 0.7971 (t) REVERT: D 619 ASN cc_start: 0.9397 (t0) cc_final: 0.8744 (t0) REVERT: D 721 MET cc_start: 0.8723 (ttm) cc_final: 0.8385 (ttm) outliers start: 0 outliers final: 0 residues processed: 511 average time/residue: 0.1614 time to fit residues: 138.4370 Evaluate side-chains 398 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 206 optimal weight: 20.0000 chunk 208 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 333 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 324 optimal weight: 0.0370 chunk 61 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 overall best weight: 2.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN A 883 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN D 10 ASN D 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.104007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.075883 restraints weight = 103138.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077522 restraints weight = 75986.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.078320 restraints weight = 48252.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.078797 restraints weight = 42835.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.078973 restraints weight = 38412.234| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 1.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28514 Z= 0.200 Angle : 0.721 15.088 38518 Z= 0.376 Chirality : 0.045 0.256 4282 Planarity : 0.005 0.084 4848 Dihedral : 5.771 65.109 3860 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3502 helix: 0.46 (0.12), residues: 1692 sheet: -1.53 (0.28), residues: 286 loop : -1.74 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 353 TYR 0.049 0.002 TYR C1026 PHE 0.034 0.002 PHE A1014 TRP 0.044 0.003 TRP A 130 HIS 0.008 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00451 (28504) covalent geometry : angle 0.71960 (38498) SS BOND : bond 0.00364 ( 10) SS BOND : angle 1.99029 ( 20) hydrogen bonds : bond 0.03991 ( 1213) hydrogen bonds : angle 4.72524 ( 3663) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8853 (mp0) cc_final: 0.8493 (mp0) REVERT: A 78 ASP cc_start: 0.8727 (t0) cc_final: 0.7864 (p0) REVERT: A 126 GLU cc_start: 0.8846 (pt0) cc_final: 0.8540 (pt0) REVERT: A 359 ASN cc_start: 0.8197 (m110) cc_final: 0.7844 (m-40) REVERT: A 491 PHE cc_start: 0.7832 (m-80) cc_final: 0.7514 (m-80) REVERT: A 511 LYS cc_start: 0.8094 (mmpt) cc_final: 0.7891 (tppt) REVERT: A 580 SER cc_start: 0.9615 (m) cc_final: 0.9344 (p) REVERT: A 585 MET cc_start: 0.8681 (ttm) cc_final: 0.8392 (ttm) REVERT: A 670 MET cc_start: 0.9075 (mtt) cc_final: 0.8278 (mtt) REVERT: A 674 MET cc_start: 0.8027 (ttt) cc_final: 0.7332 (mtt) REVERT: A 705 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8298 (mp0) REVERT: A 863 TYR cc_start: 0.3750 (m-80) cc_final: 0.3550 (m-80) REVERT: A 924 MET cc_start: 0.8731 (mmp) cc_final: 0.8411 (mmm) REVERT: A 939 MET cc_start: 0.3938 (ppp) cc_final: 0.3609 (ppp) REVERT: A 980 TYR cc_start: 0.8086 (t80) cc_final: 0.7654 (t80) REVERT: A 1026 TYR cc_start: 0.6656 (m-10) cc_final: 0.6217 (m-80) REVERT: B 47 ILE cc_start: 0.7635 (tp) cc_final: 0.6911 (tp) REVERT: B 89 CYS cc_start: 0.8337 (m) cc_final: 0.7987 (p) REVERT: B 528 CYS cc_start: 0.8940 (t) cc_final: 0.8621 (t) REVERT: B 531 PHE cc_start: 0.8997 (m-80) cc_final: 0.8621 (m-80) REVERT: B 578 TRP cc_start: 0.9184 (t-100) cc_final: 0.8495 (t-100) REVERT: B 661 ARG cc_start: 0.7962 (pmt-80) cc_final: 0.6880 (mmt-90) REVERT: B 708 MET cc_start: 0.8840 (ttm) cc_final: 0.8502 (ttp) REVERT: B 813 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8025 (tm-30) REVERT: C 25 GLU cc_start: 0.9325 (mp0) cc_final: 0.8936 (mp0) REVERT: C 407 MET cc_start: 0.8291 (mmm) cc_final: 0.8013 (mmm) REVERT: C 408 MET cc_start: 0.8629 (tpp) cc_final: 0.8345 (mmm) REVERT: C 503 MET cc_start: 0.8347 (ttp) cc_final: 0.7751 (ttm) REVERT: C 511 LYS cc_start: 0.8514 (mmpt) cc_final: 0.7972 (tptt) REVERT: C 571 PHE cc_start: 0.7788 (m-80) cc_final: 0.7135 (m-80) REVERT: C 610 LEU cc_start: 0.9562 (tp) cc_final: 0.9277 (tp) REVERT: C 649 THR cc_start: 0.8086 (p) cc_final: 0.7843 (p) REVERT: C 722 LYS cc_start: 0.8535 (tttp) cc_final: 0.8172 (tptt) REVERT: C 803 LEU cc_start: 0.9287 (tt) cc_final: 0.9057 (tt) REVERT: C 807 MET cc_start: 0.8528 (mtm) cc_final: 0.8189 (mtm) REVERT: C 861 TRP cc_start: 0.7699 (m100) cc_final: 0.7407 (m100) REVERT: C 924 MET cc_start: 0.8163 (mtm) cc_final: 0.7722 (mmp) REVERT: D 199 ASP cc_start: 0.8397 (p0) cc_final: 0.8121 (p0) REVERT: D 408 MET cc_start: 0.6776 (tpp) cc_final: 0.6445 (tpp) REVERT: D 438 PHE cc_start: 0.7152 (m-80) cc_final: 0.6838 (m-80) REVERT: D 503 MET cc_start: 0.8110 (tpt) cc_final: 0.7261 (tpt) REVERT: D 533 TYR cc_start: 0.9037 (t80) cc_final: 0.8232 (t80) REVERT: D 576 SER cc_start: 0.8850 (m) cc_final: 0.8408 (t) REVERT: D 619 ASN cc_start: 0.9444 (t0) cc_final: 0.8745 (t0) REVERT: D 721 MET cc_start: 0.8728 (ttm) cc_final: 0.8464 (ttm) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.1575 time to fit residues: 134.3205 Evaluate side-chains 380 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 99 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 304 optimal weight: 8.9990 chunk 268 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 412 HIS A 435 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN D 10 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 355 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.104118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075597 restraints weight = 102274.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.078507 restraints weight = 65554.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079295 restraints weight = 41807.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079799 restraints weight = 34400.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080067 restraints weight = 31757.654| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 1.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28514 Z= 0.164 Angle : 0.699 10.870 38518 Z= 0.359 Chirality : 0.045 0.315 4282 Planarity : 0.004 0.087 4848 Dihedral : 5.604 65.268 3860 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3502 helix: 0.55 (0.13), residues: 1704 sheet: -1.33 (0.26), residues: 354 loop : -1.78 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 178 TYR 0.030 0.002 TYR C 616 PHE 0.037 0.002 PHE B 56 TRP 0.038 0.002 TRP A 130 HIS 0.006 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00374 (28504) covalent geometry : angle 0.69785 (38498) SS BOND : bond 0.00318 ( 10) SS BOND : angle 1.88644 ( 20) hydrogen bonds : bond 0.03724 ( 1213) hydrogen bonds : angle 4.56431 ( 3663) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 0.843 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 25 GLU cc_start: 0.8912 (mp0) cc_final: 0.8589 (mp0) REVERT: A 78 ASP cc_start: 0.8895 (t0) cc_final: 0.7875 (p0) REVERT: A 359 ASN cc_start: 0.8088 (m110) cc_final: 0.7662 (m110) REVERT: A 491 PHE cc_start: 0.7736 (m-80) cc_final: 0.7536 (m-80) REVERT: A 511 LYS cc_start: 0.8332 (mmpt) cc_final: 0.8093 (tppt) REVERT: A 527 MET cc_start: 0.5940 (mmt) cc_final: 0.5681 (mmt) REVERT: A 580 SER cc_start: 0.9609 (m) cc_final: 0.9341 (p) REVERT: A 670 MET cc_start: 0.9118 (mtt) cc_final: 0.8369 (mtt) REVERT: A 674 MET cc_start: 0.8158 (ttt) cc_final: 0.7432 (mtt) REVERT: A 726 ASN cc_start: 0.8544 (m-40) cc_final: 0.8093 (m-40) REVERT: A 924 MET cc_start: 0.8638 (mmp) cc_final: 0.8366 (mmm) REVERT: A 939 MET cc_start: 0.4215 (ppp) cc_final: 0.3980 (ppp) REVERT: A 980 TYR cc_start: 0.8141 (t80) cc_final: 0.7871 (t80) REVERT: A 1026 TYR cc_start: 0.6585 (m-10) cc_final: 0.6097 (m-80) REVERT: B 89 CYS cc_start: 0.8315 (m) cc_final: 0.7900 (p) REVERT: B 140 ASP cc_start: 0.7316 (m-30) cc_final: 0.6836 (t0) REVERT: B 185 GLU cc_start: 0.8336 (tp30) cc_final: 0.7881 (tp30) REVERT: B 330 GLU cc_start: 0.8093 (pt0) cc_final: 0.7836 (mm-30) REVERT: B 528 CYS cc_start: 0.8977 (t) cc_final: 0.8760 (t) REVERT: B 531 PHE cc_start: 0.8981 (m-80) cc_final: 0.8662 (m-80) REVERT: B 541 PHE cc_start: 0.9136 (t80) cc_final: 0.8936 (t80) REVERT: B 587 GLN cc_start: 0.8840 (mm-40) cc_final: 0.7861 (mm110) REVERT: B 661 ARG cc_start: 0.7955 (pmt-80) cc_final: 0.7063 (mmt-90) REVERT: B 705 GLU cc_start: 0.8981 (pt0) cc_final: 0.8531 (mm-30) REVERT: B 789 LEU cc_start: 0.8904 (tt) cc_final: 0.8581 (tt) REVERT: B 813 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8012 (tm-30) REVERT: C 25 GLU cc_start: 0.9206 (mp0) cc_final: 0.8913 (mp0) REVERT: C 137 TYR cc_start: 0.8477 (p90) cc_final: 0.8254 (p90) REVERT: C 362 GLU cc_start: 0.7868 (tt0) cc_final: 0.7408 (tm-30) REVERT: C 407 MET cc_start: 0.8338 (mmm) cc_final: 0.8136 (mmm) REVERT: C 428 LEU cc_start: 0.9368 (mm) cc_final: 0.9072 (mm) REVERT: C 503 MET cc_start: 0.8453 (ttp) cc_final: 0.7887 (ttm) REVERT: C 511 LYS cc_start: 0.8528 (mmpt) cc_final: 0.8001 (tptt) REVERT: C 545 ARG cc_start: 0.8047 (tpp-160) cc_final: 0.7195 (tpt170) REVERT: C 571 PHE cc_start: 0.7497 (m-80) cc_final: 0.6861 (m-80) REVERT: C 610 LEU cc_start: 0.9536 (tp) cc_final: 0.9318 (tp) REVERT: C 649 THR cc_start: 0.8190 (p) cc_final: 0.7958 (p) REVERT: C 674 MET cc_start: 0.8734 (mpp) cc_final: 0.8476 (mpp) REVERT: C 722 LYS cc_start: 0.8375 (tttp) cc_final: 0.8010 (tptt) REVERT: C 803 LEU cc_start: 0.9237 (tt) cc_final: 0.8971 (tt) REVERT: C 807 MET cc_start: 0.8456 (mtm) cc_final: 0.8133 (mtm) REVERT: C 861 TRP cc_start: 0.7527 (m100) cc_final: 0.7295 (m100) REVERT: C 924 MET cc_start: 0.8153 (mtm) cc_final: 0.7712 (mmp) REVERT: D 113 MET cc_start: 0.8596 (mpp) cc_final: 0.8341 (mpp) REVERT: D 199 ASP cc_start: 0.8486 (p0) cc_final: 0.8203 (p0) REVERT: D 438 PHE cc_start: 0.7379 (m-80) cc_final: 0.7085 (m-80) REVERT: D 576 SER cc_start: 0.9036 (m) cc_final: 0.8548 (t) REVERT: D 619 ASN cc_start: 0.9428 (t0) cc_final: 0.8721 (t0) REVERT: D 811 LEU cc_start: 0.9006 (mm) cc_final: 0.8741 (mt) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.1555 time to fit residues: 127.0471 Evaluate side-chains 375 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 276 optimal weight: 7.9990 chunk 332 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 246 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 313 optimal weight: 10.0000 chunk 351 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 272 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 791 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 219 HIS B 709 ASN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.105506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077035 restraints weight = 100668.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.080023 restraints weight = 64919.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.080700 restraints weight = 41243.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.081172 restraints weight = 33587.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081270 restraints weight = 32497.430| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 1.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28514 Z= 0.134 Angle : 0.678 9.974 38518 Z= 0.345 Chirality : 0.044 0.247 4282 Planarity : 0.004 0.089 4848 Dihedral : 5.473 64.499 3860 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 4.08 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3502 helix: 0.67 (0.13), residues: 1708 sheet: -1.26 (0.26), residues: 362 loop : -1.75 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 114 TYR 0.024 0.001 TYR C 980 PHE 0.031 0.002 PHE A1014 TRP 0.079 0.002 TRP A 130 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00303 (28504) covalent geometry : angle 0.67632 (38498) SS BOND : bond 0.00723 ( 10) SS BOND : angle 2.42596 ( 20) hydrogen bonds : bond 0.03558 ( 1213) hydrogen bonds : angle 4.43460 ( 3663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5381.75 seconds wall clock time: 93 minutes 45.41 seconds (5625.41 seconds total)