Starting phenix.real_space_refine on Sun Jul 5 13:37:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rz6_24752/07_2026/7rz6_24752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rz6_24752/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7rz6_24752/07_2026/7rz6_24752.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rz6_24752/07_2026/7rz6_24752.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rz6_24752/07_2026/7rz6_24752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rz6_24752/07_2026/7rz6_24752.map" model { file = "/net/cci-nas-00/data/ceres_data/7rz6_24752/07_2026/7rz6_24752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rz6_24752/07_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-6108/lib/python3.11/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: 28 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: 28 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: 6.09, per 1000 atoms: 0.22 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: 2.28 Conformation dependent library (CDL) restraints added in 1.2 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: 1.12 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: 6.30 Time building geometry restraints manager: 3.09 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: 15820 15.11 - 30.22: 764 30.22 - 45.33: 272 45.33 - 60.45: 32 60.45 - 75.56: 12 Dihedral angle restraints: 16900 sinusoidal: 6728 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 16897 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: 0.06 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: 3.040 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.850 Find NCS groups from input model: 0.270 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4841 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 : 10.679 74.759 10370 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/Z covalent geometry : bond 0.00482 / 0.24 (28504) covalent geometry : angle 0.92754 / 0.50 (38498) SS BOND : bond 0.00920 / 0.60 ( 10) SS BOND : angle 1.04045 / 0.72 ( 20) hydrogen bonds : bond 0.29374 / 19.49 ( 1213) hydrogen bonds : angle 9.25694 / 6.48 ( 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 : 1.015 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: 0.1914 time to fit residues: 253.3690 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 : 0.615 ------------------------------------------------------------------------------- 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... 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 ** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.114337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.086955 restraints weight = 97778.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.089354 restraints weight = 58201.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090982 restraints weight = 40617.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.092114 restraints weight = 31620.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.092843 restraints weight = 26486.082| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5284 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28514 Z= 0.140 Angle : 0.633 9.181 38518 Z= 0.331 Chirality : 0.042 0.214 4282 Planarity : 0.005 0.074 4848 Dihedral : 5.838 59.531 3844 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.99 % 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: -2.09 (0.13), residues: 3502 helix: -0.73 (0.11), residues: 1682 sheet: -1.27 (0.24), residues: 438 loop : -2.14 (0.15), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 369 TYR 0.025 0.001 TYR A 177 PHE 0.028 0.002 PHE B 109 TRP 0.036 0.002 TRP B 526 HIS 0.005 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (28504) covalent geometry : angle 0.63232 / 0.33 (38498) SS BOND : bond 0.00455 / 0.26 ( 10) SS BOND : angle 0.97104 / 0.70 ( 20) hydrogen bonds : bond 0.04857 / 3.23 ( 1213) hydrogen bonds : angle 4.80528 / 3.34 ( 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 601 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 598 time to evaluate : 1.030 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: A 73 ILE cc_start: 0.5234 (mt) cc_final: 0.4973 (mt) REVERT: A 113 MET cc_start: 0.3912 (tpp) cc_final: 0.3353 (tpp) REVERT: A 574 PHE cc_start: 0.7103 (t80) cc_final: 0.6794 (m-80) REVERT: A 605 TRP cc_start: 0.7012 (t-100) cc_final: 0.5900 (t-100) REVERT: A 608 PHE cc_start: 0.7735 (t80) cc_final: 0.7302 (t80) REVERT: A 702 TYR cc_start: 0.5974 (t80) cc_final: 0.5324 (t80) REVERT: A 721 MET cc_start: 0.3609 (ppp) cc_final: 0.2861 (ppp) REVERT: A 907 MET cc_start: 0.6217 (mtm) cc_final: 0.5735 (tpt) REVERT: A 988 MET cc_start: 0.4795 (ttm) cc_final: 0.4039 (ttm) REVERT: A 1005 TRP cc_start: 0.3343 (m100) cc_final: 0.2377 (m-10) REVERT: A 1023 MET cc_start: 0.5414 (mtp) cc_final: 0.5103 (mtp) REVERT: B 25 GLU cc_start: 0.7569 (mp0) cc_final: 0.7106 (mp0) REVERT: B 179 SER cc_start: 0.7748 (m) cc_final: 0.7502 (t) REVERT: B 198 ARG cc_start: 0.4204 (mtp180) cc_final: 0.3923 (ttp80) REVERT: B 208 VAL cc_start: 0.6815 (t) cc_final: 0.6449 (t) REVERT: B 329 ILE cc_start: 0.5449 (mt) cc_final: 0.5045 (mt) REVERT: B 412 HIS cc_start: 0.1901 (p-80) cc_final: 0.1159 (t70) REVERT: B 525 ILE cc_start: 0.7044 (mt) cc_final: 0.6320 (mt) REVERT: B 629 MET cc_start: 0.1950 (tpt) cc_final: 0.0617 (tmm) REVERT: B 661 ARG cc_start: 0.8049 (pmt-80) cc_final: 0.6778 (ptm160) REVERT: B 708 MET cc_start: 0.7514 (ttm) cc_final: 0.7208 (tpt) REVERT: B 720 THR cc_start: 0.7218 (p) cc_final: 0.6871 (p) REVERT: B 732 TYR cc_start: 0.7049 (m-10) cc_final: 0.6339 (m-10) REVERT: B 797 TYR cc_start: 0.6868 (m-80) cc_final: 0.6033 (t80) REVERT: B 805 LEU cc_start: 0.8109 (tt) cc_final: 0.7825 (pp) REVERT: C 125 ILE cc_start: 0.5590 (mm) cc_final: 0.4526 (mm) REVERT: C 141 ARG cc_start: 0.4200 (mtm180) cc_final: 0.3669 (mmt180) REVERT: C 299 LEU cc_start: 0.6921 (tp) cc_final: 0.6239 (tp) REVERT: C 328 GLU cc_start: 0.7990 (tt0) cc_final: 0.7158 (tm-30) REVERT: C 460 TRP cc_start: 0.6547 (m-10) cc_final: 0.6001 (m-10) REVERT: C 629 MET cc_start: 0.8070 (ptt) cc_final: 0.7568 (ppp) REVERT: C 722 LYS cc_start: 0.8561 (ttpt) cc_final: 0.7797 (tttt) REVERT: C 723 VAL cc_start: 0.6333 (m) cc_final: 0.5435 (m) REVERT: C 907 MET cc_start: 0.3352 (mtm) cc_final: 0.3084 (mmt) REVERT: C 924 MET cc_start: 0.7859 (mpp) cc_final: 0.7246 (mmp) REVERT: C 960 PHE cc_start: 0.7796 (t80) cc_final: 0.7509 (t80) REVERT: C 1028 PHE cc_start: 0.5650 (t80) cc_final: 0.5091 (t80) REVERT: C 1029 MET cc_start: 0.6974 (tmm) cc_final: 0.6173 (ttm) REVERT: D 113 MET cc_start: 0.7678 (mmp) cc_final: 0.7446 (mmt) REVERT: D 266 GLU cc_start: 0.7367 (tp30) cc_final: 0.7147 (tp30) REVERT: D 380 MET cc_start: 0.7509 (pmm) cc_final: 0.7274 (pmm) REVERT: D 408 MET cc_start: 0.7058 (tpp) cc_final: 0.6603 (tpp) REVERT: D 438 PHE cc_start: 0.6694 (m-80) cc_final: 0.6361 (m-10) REVERT: D 463 MET cc_start: 0.6428 (ttm) cc_final: 0.6175 (ttt) REVERT: D 684 ARG cc_start: 0.6682 (pmt170) cc_final: 0.5772 (tpm170) outliers start: 3 outliers final: 1 residues processed: 599 average time/residue: 0.1807 time to fit residues: 174.0077 Evaluate side-chains 414 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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: 5.9990 chunk 277 optimal weight: 0.4980 chunk 238 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 140 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 292 optimal weight: 0.3980 chunk 131 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 GLN A 586 GLN A 619 ASN A 791 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 35 GLN B 290 GLN C 619 ASN C 950 HIS D 24 GLN D 65 GLN D 224 ASN D 236 GLN D 355 ASN D 359 ASN D 411 ASN D 575 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 = 0.3995 r_free = 0.3995 target = 0.113901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.086872 restraints weight = 100228.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089366 restraints weight = 59065.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091068 restraints weight = 40948.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.092244 restraints weight = 31603.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.092944 restraints weight = 26323.690| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5412 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 28514 Z= 0.114 Angle : 0.577 8.852 38518 Z= 0.297 Chirality : 0.041 0.382 4282 Planarity : 0.004 0.076 4848 Dihedral : 5.256 59.650 3844 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.07 % Allowed : 3.15 % Favored : 96.79 % 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: -1.14 (0.14), residues: 3502 helix: 0.30 (0.12), residues: 1678 sheet: -1.18 (0.24), residues: 444 loop : -1.89 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 198 TYR 0.021 0.001 TYR C 980 PHE 0.025 0.001 PHE C 62 TRP 0.021 0.002 TRP C 766 HIS 0.004 0.001 HIS D 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (28504) covalent geometry : angle 0.57670 / 0.30 (38498) SS BOND : bond 0.00392 / 0.22 ( 10) SS BOND : angle 0.96646 / 0.65 ( 20) hydrogen bonds : bond 0.03819 / 2.52 ( 1213) hydrogen bonds : angle 4.25610 / 2.94 ( 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 550 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 548 time to evaluate : 1.125 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: A 73 ILE cc_start: 0.5428 (mt) cc_final: 0.5193 (mt) REVERT: A 113 MET cc_start: 0.4639 (tpp) cc_final: 0.3831 (tpp) REVERT: A 144 SER cc_start: 0.7314 (t) cc_final: 0.7025 (p) REVERT: A 292 MET cc_start: 0.5050 (ttm) cc_final: 0.4813 (mmp) REVERT: A 328 GLU cc_start: 0.7243 (mp0) cc_final: 0.5567 (tt0) REVERT: A 608 PHE cc_start: 0.7561 (t80) cc_final: 0.7282 (t80) REVERT: A 702 TYR cc_start: 0.6485 (t80) cc_final: 0.6132 (t80) REVERT: A 707 THR cc_start: 0.6105 (m) cc_final: 0.5895 (t) REVERT: A 708 MET cc_start: 0.7628 (ptp) cc_final: 0.7076 (pmm) REVERT: A 721 MET cc_start: 0.4031 (ppp) cc_final: 0.3370 (ppp) REVERT: A 907 MET cc_start: 0.5772 (mtm) cc_final: 0.5465 (tpt) REVERT: A 931 PHE cc_start: 0.6427 (m-80) cc_final: 0.6023 (m-80) REVERT: A 988 MET cc_start: 0.4680 (ttm) cc_final: 0.4289 (ttm) REVERT: A 1005 TRP cc_start: 0.3296 (m100) cc_final: 0.2386 (m-10) REVERT: A 1023 MET cc_start: 0.5640 (mtp) cc_final: 0.5284 (mtp) REVERT: A 1030 LYS cc_start: 0.4462 (ttpt) cc_final: 0.3911 (tmmt) REVERT: B 25 GLU cc_start: 0.6420 (mp0) cc_final: 0.5750 (tm-30) REVERT: B 179 SER cc_start: 0.7952 (m) cc_final: 0.7635 (t) REVERT: B 208 VAL cc_start: 0.6967 (t) cc_final: 0.6750 (t) REVERT: B 242 VAL cc_start: 0.8118 (t) cc_final: 0.7905 (t) REVERT: B 328 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6930 (mp0) REVERT: B 358 ILE cc_start: 0.6116 (tp) cc_final: 0.5710 (tp) REVERT: B 412 HIS cc_start: 0.2103 (p-80) cc_final: 0.1071 (t70) REVERT: B 708 MET cc_start: 0.7394 (ttm) cc_final: 0.7139 (tpt) REVERT: B 732 TYR cc_start: 0.6960 (m-10) cc_final: 0.6249 (m-10) REVERT: B 797 TYR cc_start: 0.6651 (m-80) cc_final: 0.6069 (t80) REVERT: B 805 LEU cc_start: 0.8421 (tt) cc_final: 0.7991 (pp) REVERT: C 111 ILE cc_start: 0.4472 (mm) cc_final: 0.3807 (mm) REVERT: C 125 ILE cc_start: 0.5496 (mm) cc_final: 0.4433 (mm) REVERT: C 138 ASP cc_start: 0.5796 (t0) cc_final: 0.5427 (t70) REVERT: C 299 LEU cc_start: 0.7038 (tp) cc_final: 0.6475 (tp) REVERT: C 328 GLU cc_start: 0.8152 (tt0) cc_final: 0.7599 (tm-30) REVERT: C 407 MET cc_start: 0.6556 (mmm) cc_final: 0.6157 (mmm) REVERT: C 519 ASP cc_start: 0.7578 (m-30) cc_final: 0.7346 (m-30) REVERT: C 629 MET cc_start: 0.8100 (ptt) cc_final: 0.7386 (ppp) REVERT: C 637 GLU cc_start: 0.8803 (mp0) cc_final: 0.8560 (mp0) REVERT: C 722 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7872 (tttt) REVERT: C 807 MET cc_start: 0.7377 (ttp) cc_final: 0.7061 (tpp) REVERT: C 861 TRP cc_start: 0.7205 (m100) cc_final: 0.6847 (m100) REVERT: C 920 ASN cc_start: 0.8782 (t0) cc_final: 0.8403 (t0) REVERT: C 924 MET cc_start: 0.7591 (mpp) cc_final: 0.7262 (mpp) REVERT: C 960 PHE cc_start: 0.7663 (t80) cc_final: 0.7404 (t80) REVERT: C 1001 TYR cc_start: 0.8084 (p90) cc_final: 0.7570 (p90) REVERT: C 1023 MET cc_start: 0.7335 (mtm) cc_final: 0.7116 (mtt) REVERT: C 1029 MET cc_start: 0.7162 (tmm) cc_final: 0.6370 (ttm) REVERT: D 111 ILE cc_start: 0.8854 (mm) cc_final: 0.8647 (mm) REVERT: D 113 MET cc_start: 0.7413 (mmp) cc_final: 0.7022 (mmt) REVERT: D 175 GLU cc_start: 0.6556 (pp20) cc_final: 0.6143 (pm20) REVERT: D 278 ILE cc_start: 0.6990 (tt) cc_final: 0.6620 (mp) REVERT: D 380 MET cc_start: 0.7602 (pmm) cc_final: 0.7356 (pmm) REVERT: D 408 MET cc_start: 0.7080 (tpp) cc_final: 0.6619 (tpp) REVERT: D 463 MET cc_start: 0.6536 (ttm) cc_final: 0.6317 (ttt) REVERT: D 496 MET cc_start: 0.3911 (pmm) cc_final: 0.3502 (pmm) REVERT: D 684 ARG cc_start: 0.6702 (pmt170) cc_final: 0.5739 (tpm170) REVERT: C 1102 GLU cc_start: 0.6172 (tp30) cc_final: 0.5941 (tp30) outliers start: 2 outliers final: 0 residues processed: 549 average time/residue: 0.1758 time to fit residues: 157.1963 Evaluate side-chains 403 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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: 5.9990 chunk 207 optimal weight: 0.0470 chunk 335 optimal weight: 9.9990 chunk 123 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 313 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 342 optimal weight: 0.9980 chunk 103 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN A 791 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 60 ASN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN B 355 ASN C 619 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 224 ASN D 355 ASN D 714 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.113648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.086624 restraints weight = 102122.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089156 restraints weight = 60218.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.090869 restraints weight = 41700.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.092027 restraints weight = 32189.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.092789 restraints weight = 26885.347| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5575 moved from start: 0.5588 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= 0.107 Angle : 0.553 8.859 38518 Z= 0.285 Chirality : 0.041 0.329 4282 Planarity : 0.004 0.079 4848 Dihedral : 4.927 51.737 3844 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % 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: -0.63 (0.14), residues: 3502 helix: 0.84 (0.13), residues: 1654 sheet: -0.88 (0.26), residues: 402 loop : -1.78 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 20 TYR 0.021 0.001 TYR C 980 PHE 0.031 0.001 PHE D 66 TRP 0.033 0.002 TRP C 460 HIS 0.003 0.000 HIS B 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (28504) covalent geometry : angle 0.55298 / 0.28 (38498) SS BOND : bond 0.00280 / 0.16 ( 10) SS BOND : angle 0.78011 / 0.54 ( 20) hydrogen bonds : bond 0.03345 / 2.20 ( 1213) hydrogen bonds : angle 4.05232 / 2.81 ( 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 531 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 529 time to evaluate : 1.076 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: A 113 MET cc_start: 0.5295 (tpp) cc_final: 0.4292 (tpp) REVERT: A 144 SER cc_start: 0.7844 (t) cc_final: 0.7616 (p) REVERT: A 245 PHE cc_start: 0.2662 (m-80) cc_final: 0.2196 (m-80) REVERT: A 292 MET cc_start: 0.5310 (ttm) cc_final: 0.4954 (mmp) REVERT: A 651 ASP cc_start: 0.6990 (p0) cc_final: 0.6788 (p0) REVERT: A 674 MET cc_start: 0.6562 (ttt) cc_final: 0.6124 (ttt) REVERT: A 707 THR cc_start: 0.6370 (m) cc_final: 0.6109 (t) REVERT: A 708 MET cc_start: 0.7695 (ptp) cc_final: 0.7021 (pmm) REVERT: A 721 MET cc_start: 0.3982 (ppp) cc_final: 0.3222 (ppp) REVERT: A 880 MET cc_start: 0.2358 (tmm) cc_final: 0.1767 (ptm) REVERT: A 907 MET cc_start: 0.5544 (mtm) cc_final: 0.5142 (tpt) REVERT: A 951 ILE cc_start: 0.4005 (mm) cc_final: 0.3589 (pt) REVERT: A 988 MET cc_start: 0.4385 (ttm) cc_final: 0.3943 (ttm) REVERT: A 1005 TRP cc_start: 0.3387 (m100) cc_final: 0.2433 (m-10) REVERT: A 1015 LEU cc_start: 0.8139 (mm) cc_final: 0.7820 (pt) REVERT: B 179 SER cc_start: 0.8126 (m) cc_final: 0.7791 (t) REVERT: B 208 VAL cc_start: 0.7461 (t) cc_final: 0.7132 (t) REVERT: B 242 VAL cc_start: 0.8033 (t) cc_final: 0.7731 (t) REVERT: B 328 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6980 (mp0) REVERT: B 358 ILE cc_start: 0.6306 (tp) cc_final: 0.6015 (tp) REVERT: B 661 ARG cc_start: 0.7648 (pmt-80) cc_final: 0.6554 (mpt180) REVERT: B 708 MET cc_start: 0.7526 (ttm) cc_final: 0.7226 (tpt) REVERT: B 732 TYR cc_start: 0.7174 (m-10) cc_final: 0.6503 (m-10) REVERT: B 797 TYR cc_start: 0.7039 (m-80) cc_final: 0.6411 (t80) REVERT: B 805 LEU cc_start: 0.8439 (tt) cc_final: 0.7951 (pp) REVERT: B 807 MET cc_start: 0.8462 (mmm) cc_final: 0.7915 (ttt) REVERT: C 125 ILE cc_start: 0.5757 (mm) cc_final: 0.4458 (mm) REVERT: C 138 ASP cc_start: 0.5884 (t0) cc_final: 0.5440 (t70) REVERT: C 261 ARG cc_start: 0.6875 (ttt180) cc_final: 0.6389 (ttt180) REVERT: C 299 LEU cc_start: 0.7088 (tp) cc_final: 0.6516 (tp) REVERT: C 328 GLU cc_start: 0.8239 (tt0) cc_final: 0.7710 (tm-30) REVERT: C 380 MET cc_start: 0.6016 (tpt) cc_final: 0.5660 (tpt) REVERT: C 407 MET cc_start: 0.7084 (mmm) cc_final: 0.5978 (mmm) REVERT: C 524 GLU cc_start: 0.4946 (pp20) cc_final: 0.3909 (pp20) REVERT: C 629 MET cc_start: 0.8306 (ptt) cc_final: 0.7568 (ppp) REVERT: C 722 LYS cc_start: 0.8289 (ttpt) cc_final: 0.7943 (tttt) REVERT: C 807 MET cc_start: 0.7495 (ttp) cc_final: 0.7215 (tpp) REVERT: C 861 TRP cc_start: 0.7051 (m100) cc_final: 0.6768 (m100) REVERT: C 960 PHE cc_start: 0.7819 (t80) cc_final: 0.7526 (t80) REVERT: C 1023 MET cc_start: 0.7491 (mtm) cc_final: 0.7131 (mtt) REVERT: C 1029 MET cc_start: 0.7108 (tmm) cc_final: 0.6445 (ttm) REVERT: D 117 LEU cc_start: 0.8150 (tp) cc_final: 0.7924 (tp) REVERT: D 175 GLU cc_start: 0.6938 (pp20) cc_final: 0.6623 (pm20) REVERT: D 278 ILE cc_start: 0.6957 (tt) cc_final: 0.6678 (mp) REVERT: D 380 MET cc_start: 0.7771 (pmm) cc_final: 0.7438 (pmm) REVERT: D 408 MET cc_start: 0.7019 (tpp) cc_final: 0.6535 (tpp) REVERT: D 496 MET cc_start: 0.3876 (pmm) cc_final: 0.3380 (pmm) REVERT: D 503 MET cc_start: 0.7939 (tpp) cc_final: 0.7337 (tpp) REVERT: D 609 THR cc_start: 0.6195 (p) cc_final: 0.5060 (p) outliers start: 2 outliers final: 0 residues processed: 529 average time/residue: 0.1737 time to fit residues: 150.7541 Evaluate side-chains 403 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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: 5.9990 chunk 249 optimal weight: 6.9990 chunk 234 optimal weight: 0.7980 chunk 278 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 619 ASN A 791 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 355 ASN ** C 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS C 219 HIS C 619 ASN D 10 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 169 ASN D 224 ASN D 355 ASN D 575 ASN D 714 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.112702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.086207 restraints weight = 102163.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.088635 restraints weight = 60686.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.090273 restraints weight = 42245.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.091382 restraints weight = 32795.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.092157 restraints weight = 27510.659| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.7141 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= 0.143 Angle : 0.619 9.936 38518 Z= 0.324 Chirality : 0.042 0.204 4282 Planarity : 0.005 0.073 4848 Dihedral : 5.048 57.970 3844 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.03 % Allowed : 2.88 % Favored : 97.08 % 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: -0.48 (0.14), residues: 3502 helix: 0.88 (0.12), residues: 1694 sheet: -0.77 (0.25), residues: 416 loop : -1.67 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 198 TYR 0.025 0.002 TYR B 220 PHE 0.036 0.002 PHE C1009 TRP 0.040 0.003 TRP D 158 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (28504) covalent geometry : angle 0.61897 / 0.32 (38498) SS BOND : bond 0.00280 / 0.17 ( 10) SS BOND : angle 0.81295 / 0.59 ( 20) hydrogen bonds : bond 0.03577 / 2.36 ( 1213) hydrogen bonds : angle 4.11990 / 2.84 ( 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 579 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 578 time to evaluate : 1.097 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 113 MET cc_start: 0.5572 (tpp) cc_final: 0.4868 (tpp) REVERT: A 194 LEU cc_start: 0.7587 (mt) cc_final: 0.7220 (tp) REVERT: A 408 MET cc_start: 0.5986 (mmm) cc_final: 0.4681 (tmm) REVERT: A 524 GLU cc_start: 0.7230 (mp0) cc_final: 0.6634 (pp20) REVERT: A 525 ILE cc_start: 0.7677 (mt) cc_final: 0.6645 (mt) REVERT: A 527 MET cc_start: 0.3527 (mmp) cc_final: 0.2641 (mmt) REVERT: A 528 CYS cc_start: 0.7599 (m) cc_final: 0.6413 (m) REVERT: A 531 PHE cc_start: 0.7374 (m-80) cc_final: 0.6849 (m-80) REVERT: A 590 ASP cc_start: 0.6268 (t0) cc_final: 0.5616 (t0) REVERT: A 674 MET cc_start: 0.6667 (ttt) cc_final: 0.6418 (ttm) REVERT: A 707 THR cc_start: 0.7065 (m) cc_final: 0.6787 (t) REVERT: A 721 MET cc_start: 0.5330 (ppp) cc_final: 0.4746 (ppp) REVERT: A 880 MET cc_start: 0.2088 (tmm) cc_final: 0.1693 (ptm) REVERT: A 924 MET cc_start: 0.8498 (mmp) cc_final: 0.8251 (mmm) REVERT: A 951 ILE cc_start: 0.4341 (mm) cc_final: 0.3729 (pt) REVERT: A 988 MET cc_start: 0.4936 (ttm) cc_final: 0.4565 (mtp) REVERT: A 1005 TRP cc_start: 0.3982 (m100) cc_final: 0.2807 (m-10) REVERT: B 179 SER cc_start: 0.8703 (m) cc_final: 0.8265 (t) REVERT: B 236 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7236 (pp30) REVERT: B 328 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7164 (mp0) REVERT: B 408 MET cc_start: 0.5878 (tmm) cc_final: 0.5415 (tmm) REVERT: B 503 MET cc_start: 0.3886 (ttt) cc_final: 0.3377 (tmm) REVERT: B 661 ARG cc_start: 0.7805 (pmt-80) cc_final: 0.6649 (mpt180) REVERT: B 674 MET cc_start: 0.6018 (tpp) cc_final: 0.5580 (tmm) REVERT: B 708 MET cc_start: 0.7931 (ttm) cc_final: 0.7367 (tpt) REVERT: B 720 THR cc_start: 0.6602 (p) cc_final: 0.6394 (p) REVERT: B 721 MET cc_start: 0.7465 (tpt) cc_final: 0.7180 (tpp) REVERT: B 732 TYR cc_start: 0.7392 (m-10) cc_final: 0.6337 (m-10) REVERT: B 797 TYR cc_start: 0.7574 (m-80) cc_final: 0.6984 (t80) REVERT: B 805 LEU cc_start: 0.8614 (tt) cc_final: 0.8165 (pp) REVERT: C 33 MET cc_start: 0.5105 (mtp) cc_final: 0.4633 (mtm) REVERT: C 109 PHE cc_start: 0.7433 (m-80) cc_final: 0.6943 (m-10) REVERT: C 111 ILE cc_start: 0.5122 (mm) cc_final: 0.4469 (mm) REVERT: C 125 ILE cc_start: 0.6577 (mm) cc_final: 0.5351 (mm) REVERT: C 138 ASP cc_start: 0.6392 (t0) cc_final: 0.6000 (t0) REVERT: C 150 LEU cc_start: 0.7499 (mt) cc_final: 0.7197 (mt) REVERT: C 260 GLU cc_start: 0.8216 (mp0) cc_final: 0.7910 (mp0) REVERT: C 307 SER cc_start: 0.6532 (t) cc_final: 0.6323 (p) REVERT: C 328 GLU cc_start: 0.8388 (tt0) cc_final: 0.7900 (tt0) REVERT: C 380 MET cc_start: 0.6671 (tpt) cc_final: 0.6235 (tpt) REVERT: C 407 MET cc_start: 0.7312 (mmm) cc_final: 0.6630 (mmm) REVERT: C 503 MET cc_start: 0.8209 (ppp) cc_final: 0.7933 (tmm) REVERT: C 606 TRP cc_start: 0.7368 (m-10) cc_final: 0.6673 (m-10) REVERT: C 617 THR cc_start: 0.8255 (m) cc_final: 0.8040 (m) REVERT: C 629 MET cc_start: 0.8391 (ptt) cc_final: 0.7681 (ppp) REVERT: C 861 TRP cc_start: 0.7408 (m100) cc_final: 0.7054 (m100) REVERT: C 921 VAL cc_start: 0.7162 (t) cc_final: 0.6863 (t) REVERT: C 924 MET cc_start: 0.7674 (mpp) cc_final: 0.7456 (mpp) REVERT: C 1028 PHE cc_start: 0.6517 (t80) cc_final: 0.6260 (t80) REVERT: C 1029 MET cc_start: 0.7278 (tmm) cc_final: 0.6784 (ttm) REVERT: D 54 ASN cc_start: 0.7567 (t0) cc_final: 0.6863 (t0) REVERT: D 117 LEU cc_start: 0.8779 (tp) cc_final: 0.8560 (tp) REVERT: D 118 LYS cc_start: 0.8568 (ptpp) cc_final: 0.8242 (pttm) REVERT: D 175 GLU cc_start: 0.7389 (pp20) cc_final: 0.6889 (pm20) REVERT: D 187 LYS cc_start: 0.8034 (tppt) cc_final: 0.7667 (tppt) REVERT: D 189 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7103 (mm-30) REVERT: D 237 PHE cc_start: 0.8328 (m-80) cc_final: 0.8126 (m-80) REVERT: D 278 ILE cc_start: 0.7224 (tt) cc_final: 0.6607 (mt) REVERT: D 380 MET cc_start: 0.8012 (pmm) cc_final: 0.7503 (pmm) REVERT: D 405 TYR cc_start: 0.7984 (m-10) cc_final: 0.7733 (m-80) REVERT: D 408 MET cc_start: 0.6827 (tpp) cc_final: 0.6295 (tpp) REVERT: D 438 PHE cc_start: 0.6594 (m-80) cc_final: 0.6314 (m-10) REVERT: D 500 ILE cc_start: 0.6996 (mt) cc_final: 0.6484 (mt) REVERT: D 503 MET cc_start: 0.7754 (tpp) cc_final: 0.7362 (tpp) REVERT: D 612 ILE cc_start: 0.8427 (mm) cc_final: 0.8131 (mm) REVERT: D 686 THR cc_start: 0.6978 (m) cc_final: 0.6412 (m) REVERT: D 721 MET cc_start: 0.8545 (ttp) cc_final: 0.8318 (ptm) outliers start: 1 outliers final: 0 residues processed: 579 average time/residue: 0.1736 time to fit residues: 163.9328 Evaluate side-chains 413 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 4.9990 chunk 291 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 321 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 ASN A 147 GLN A 170 ASN A 298 ASN A 335 GLN A 412 HIS A 569 ASN A 575 ASN A 619 ASN A 791 ASN B 10 ASN B 147 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN C 10 ASN ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 575 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 872 GLN C 985 ASN D 10 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.110077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082654 restraints weight = 102513.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.084970 restraints weight = 61767.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.086520 restraints weight = 43615.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.087521 restraints weight = 34268.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.088280 restraints weight = 29103.615| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 1.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 28514 Z= 0.251 Angle : 0.846 12.790 38518 Z= 0.442 Chirality : 0.050 0.356 4282 Planarity : 0.006 0.075 4848 Dihedral : 6.098 53.510 3844 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % 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: -1.29 (0.13), residues: 3502 helix: 0.03 (0.12), residues: 1702 sheet: -1.20 (0.28), residues: 306 loop : -1.77 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 178 TYR 0.032 0.003 TYR C 702 PHE 0.039 0.003 PHE D 66 TRP 0.051 0.003 TRP A 605 HIS 0.015 0.002 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 (28504) covalent geometry : angle 0.84590 / 0.44 (38498) SS BOND : bond 0.00471 / 0.27 ( 10) SS BOND : angle 0.95288 / 0.67 ( 20) hydrogen bonds : bond 0.04902 / 3.25 ( 1213) hydrogen bonds : angle 4.99815 / 3.48 ( 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 589 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 588 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7405 (t0) cc_final: 0.6716 (p0) REVERT: A 196 CYS cc_start: 0.5707 (m) cc_final: 0.3073 (m) REVERT: A 278 ILE cc_start: 0.5307 (tt) cc_final: 0.4479 (tt) REVERT: A 408 MET cc_start: 0.5587 (mmm) cc_final: 0.4745 (mmm) REVERT: A 479 LEU cc_start: 0.8717 (mm) cc_final: 0.8487 (mm) REVERT: A 524 GLU cc_start: 0.7521 (mp0) cc_final: 0.7027 (pp20) REVERT: A 527 MET cc_start: 0.5109 (mmp) cc_final: 0.4240 (mmt) REVERT: A 528 CYS cc_start: 0.8346 (m) cc_final: 0.7985 (m) REVERT: A 531 PHE cc_start: 0.7887 (m-10) cc_final: 0.7632 (m-80) REVERT: A 580 SER cc_start: 0.9200 (m) cc_final: 0.8812 (p) REVERT: A 619 ASN cc_start: 0.8479 (t160) cc_final: 0.8023 (t0) REVERT: A 939 MET cc_start: 0.4176 (ppp) cc_final: 0.3638 (ppp) REVERT: A 979 LEU cc_start: 0.8901 (mm) cc_final: 0.8668 (mm) REVERT: A 981 ILE cc_start: 0.7222 (pt) cc_final: 0.6206 (mp) REVERT: B 33 MET cc_start: 0.2791 (mmt) cc_final: 0.2488 (ptt) REVERT: B 225 LEU cc_start: 0.8505 (mt) cc_final: 0.8205 (mt) REVERT: B 255 VAL cc_start: 0.7838 (p) cc_final: 0.7633 (p) REVERT: B 316 LEU cc_start: 0.5782 (mt) cc_final: 0.5073 (pp) REVERT: B 329 ILE cc_start: 0.6392 (mt) cc_final: 0.6142 (mt) REVERT: B 531 PHE cc_start: 0.8834 (m-80) cc_final: 0.8526 (m-80) REVERT: B 571 PHE cc_start: 0.7092 (m-80) cc_final: 0.6403 (m-80) REVERT: B 609 THR cc_start: 0.9515 (p) cc_final: 0.9309 (t) REVERT: B 661 ARG cc_start: 0.7888 (pmt-80) cc_final: 0.6427 (mmt-90) REVERT: B 721 MET cc_start: 0.8386 (tpt) cc_final: 0.7617 (tpp) REVERT: B 789 LEU cc_start: 0.9384 (tp) cc_final: 0.8711 (tt) REVERT: B 797 TYR cc_start: 0.8518 (m-80) cc_final: 0.7982 (t80) REVERT: B 803 LEU cc_start: 0.9366 (mt) cc_final: 0.9142 (mt) REVERT: C 33 MET cc_start: 0.5672 (mtp) cc_final: 0.5424 (ptt) REVERT: C 109 PHE cc_start: 0.7666 (m-80) cc_final: 0.7294 (m-10) REVERT: C 249 ASP cc_start: 0.8097 (t0) cc_final: 0.7861 (t70) REVERT: C 407 MET cc_start: 0.8149 (mmm) cc_final: 0.7726 (mmm) REVERT: C 474 ILE cc_start: 0.9280 (pt) cc_final: 0.9077 (mm) REVERT: C 480 THR cc_start: 0.9068 (p) cc_final: 0.8798 (p) REVERT: C 612 ILE cc_start: 0.9561 (pt) cc_final: 0.9317 (tp) REVERT: C 629 MET cc_start: 0.8404 (ptt) cc_final: 0.7714 (tmm) REVERT: C 722 LYS cc_start: 0.8805 (tttt) cc_final: 0.8593 (tttm) REVERT: C 861 TRP cc_start: 0.7485 (m100) cc_final: 0.7222 (m100) REVERT: C 891 PHE cc_start: 0.5849 (m-10) cc_final: 0.5475 (m-80) REVERT: C 921 VAL cc_start: 0.7258 (t) cc_final: 0.7039 (t) REVERT: C 1029 MET cc_start: 0.8180 (tmm) cc_final: 0.7820 (ttm) REVERT: D 50 LEU cc_start: 0.8304 (pt) cc_final: 0.7517 (pt) REVERT: D 118 LYS cc_start: 0.8732 (ptpp) cc_final: 0.8438 (pttm) REVERT: D 140 ASP cc_start: 0.7230 (m-30) cc_final: 0.6967 (t0) REVERT: D 156 LYS cc_start: 0.8716 (mmmt) cc_final: 0.8377 (tppp) REVERT: D 185 GLU cc_start: 0.7945 (tp30) cc_final: 0.7582 (tp30) REVERT: D 207 GLN cc_start: 0.8755 (pp30) cc_final: 0.8441 (mm-40) REVERT: D 380 MET cc_start: 0.8156 (pmm) cc_final: 0.7595 (pmm) REVERT: D 405 TYR cc_start: 0.8204 (m-10) cc_final: 0.8001 (m-80) REVERT: D 408 MET cc_start: 0.6896 (tpp) cc_final: 0.6558 (tpp) REVERT: D 438 PHE cc_start: 0.7106 (m-80) cc_final: 0.6783 (m-10) REVERT: D 503 MET cc_start: 0.7879 (tpp) cc_final: 0.7481 (tpp) REVERT: D 584 PHE cc_start: 0.9378 (t80) cc_final: 0.8957 (t80) REVERT: D 619 ASN cc_start: 0.9486 (t0) cc_final: 0.8714 (t0) REVERT: D 708 MET cc_start: 0.8331 (tmm) cc_final: 0.6856 (ppp) REVERT: D 726 ASN cc_start: 0.6111 (m-40) cc_final: 0.5795 (m110) REVERT: D 792 VAL cc_start: 0.9362 (m) cc_final: 0.9136 (m) REVERT: D 796 PHE cc_start: 0.7684 (m-10) cc_final: 0.7428 (m-80) outliers start: 1 outliers final: 0 residues processed: 589 average time/residue: 0.1652 time to fit residues: 160.2785 Evaluate side-chains 403 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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: 0.0570 chunk 34 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 305 optimal weight: 5.9990 chunk 144 optimal weight: 0.4980 chunk 203 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 ASN A 619 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 60 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN D 24 GLN D 65 GLN D 169 ASN D 355 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.111065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083723 restraints weight = 102767.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.086070 restraints weight = 61350.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.087632 restraints weight = 43049.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.088680 restraints weight = 33791.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.089358 restraints weight = 28638.241| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 1.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28514 Z= 0.121 Angle : 0.626 9.300 38518 Z= 0.324 Chirality : 0.043 0.312 4282 Planarity : 0.004 0.082 4848 Dihedral : 5.270 56.039 3844 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.62 (0.14), residues: 3502 helix: 0.75 (0.12), residues: 1678 sheet: -1.13 (0.27), residues: 322 loop : -1.58 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 68 TYR 0.021 0.001 TYR C 980 PHE 0.029 0.002 PHE B 237 TRP 0.045 0.002 TRP A 323 HIS 0.005 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (28504) covalent geometry : angle 0.62631 / 0.32 (38498) SS BOND : bond 0.00261 / 0.15 ( 10) SS BOND : angle 0.70977 / 0.54 ( 20) hydrogen bonds : bond 0.03520 / 2.32 ( 1213) hydrogen bonds : angle 4.32259 / 2.98 ( 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 577 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7319 (t0) cc_final: 0.6572 (p0) REVERT: A 113 MET cc_start: 0.6561 (ttt) cc_final: 0.6110 (ttt) REVERT: A 123 SER cc_start: 0.8747 (m) cc_final: 0.8469 (p) REVERT: A 207 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7434 (tp40) REVERT: A 278 ILE cc_start: 0.5220 (tt) cc_final: 0.4719 (tt) REVERT: A 408 MET cc_start: 0.5245 (mmm) cc_final: 0.4617 (mmm) REVERT: A 479 LEU cc_start: 0.8515 (mm) cc_final: 0.8252 (mm) REVERT: A 524 GLU cc_start: 0.7481 (mp0) cc_final: 0.7211 (pp20) REVERT: A 527 MET cc_start: 0.5453 (mmp) cc_final: 0.5228 (mmt) REVERT: A 540 LEU cc_start: 0.9028 (mm) cc_final: 0.8778 (mm) REVERT: A 619 ASN cc_start: 0.8473 (t160) cc_final: 0.8105 (t0) REVERT: A 670 MET cc_start: 0.8440 (mtm) cc_final: 0.7977 (mtm) REVERT: A 674 MET cc_start: 0.7396 (ttt) cc_final: 0.6645 (ttt) REVERT: A 730 LYS cc_start: 0.7962 (mptt) cc_final: 0.7702 (mmtt) REVERT: A 880 MET cc_start: 0.1973 (tmm) cc_final: 0.1651 (ptm) REVERT: A 924 MET cc_start: 0.8663 (mmp) cc_final: 0.8458 (mmm) REVERT: A 939 MET cc_start: 0.4066 (ppp) cc_final: 0.3719 (ppp) REVERT: A 979 LEU cc_start: 0.8960 (mm) cc_final: 0.8690 (mm) REVERT: A 981 ILE cc_start: 0.7518 (pt) cc_final: 0.6972 (mm) REVERT: A 1015 LEU cc_start: 0.8267 (mm) cc_final: 0.7946 (mm) REVERT: A 1029 MET cc_start: 0.7037 (tpt) cc_final: 0.6075 (ptt) REVERT: B 316 LEU cc_start: 0.5765 (mt) cc_final: 0.5065 (pp) REVERT: B 383 THR cc_start: 0.8173 (p) cc_final: 0.7784 (t) REVERT: B 496 MET cc_start: 0.7915 (pmm) cc_final: 0.7696 (pmm) REVERT: B 528 CYS cc_start: 0.8607 (t) cc_final: 0.8187 (t) REVERT: B 531 PHE cc_start: 0.8779 (m-80) cc_final: 0.8370 (m-80) REVERT: B 571 PHE cc_start: 0.7161 (m-80) cc_final: 0.6540 (m-80) REVERT: B 661 ARG cc_start: 0.7813 (pmt-80) cc_final: 0.6571 (mmt-90) REVERT: B 705 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8279 (tp30) REVERT: B 789 LEU cc_start: 0.8942 (tp) cc_final: 0.8369 (tt) REVERT: B 797 TYR cc_start: 0.8557 (m-80) cc_final: 0.7991 (t80) REVERT: B 813 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7564 (tm-30) REVERT: C 25 GLU cc_start: 0.9232 (mp0) cc_final: 0.8492 (mp0) REVERT: C 33 MET cc_start: 0.5752 (mtp) cc_final: 0.5536 (ptt) REVERT: C 74 PHE cc_start: 0.8600 (t80) cc_final: 0.8370 (t80) REVERT: C 147 GLN cc_start: 0.8344 (mp10) cc_final: 0.8072 (mp10) REVERT: C 249 ASP cc_start: 0.7986 (t0) cc_final: 0.7709 (t70) REVERT: C 260 GLU cc_start: 0.8272 (mp0) cc_final: 0.7952 (pp20) REVERT: C 328 GLU cc_start: 0.8087 (pt0) cc_final: 0.7830 (tt0) REVERT: C 474 ILE cc_start: 0.9225 (pt) cc_final: 0.9005 (mm) REVERT: C 524 GLU cc_start: 0.6652 (pp20) cc_final: 0.6025 (pp20) REVERT: C 610 LEU cc_start: 0.9578 (tp) cc_final: 0.9198 (mt) REVERT: C 624 LEU cc_start: 0.8379 (mm) cc_final: 0.8174 (mp) REVERT: C 629 MET cc_start: 0.8403 (ptt) cc_final: 0.7661 (tmm) REVERT: C 649 THR cc_start: 0.7502 (p) cc_final: 0.7302 (p) REVERT: C 891 PHE cc_start: 0.5640 (m-10) cc_final: 0.5237 (m-80) REVERT: C 921 VAL cc_start: 0.7329 (t) cc_final: 0.6804 (t) REVERT: C 924 MET cc_start: 0.7724 (mpp) cc_final: 0.6215 (mpp) REVERT: C 1029 MET cc_start: 0.8045 (tmm) cc_final: 0.7765 (ttm) REVERT: D 50 LEU cc_start: 0.8017 (pt) cc_final: 0.7295 (pt) REVERT: D 140 ASP cc_start: 0.7171 (m-30) cc_final: 0.6835 (t0) REVERT: D 229 ASP cc_start: 0.7957 (m-30) cc_final: 0.7472 (m-30) REVERT: D 339 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7358 (mm-30) REVERT: D 380 MET cc_start: 0.7773 (pmm) cc_final: 0.7298 (pmm) REVERT: D 405 TYR cc_start: 0.8121 (m-10) cc_final: 0.7735 (m-80) REVERT: D 408 MET cc_start: 0.6944 (tpp) cc_final: 0.6647 (tpp) REVERT: D 438 PHE cc_start: 0.7007 (m-80) cc_final: 0.6747 (m-10) REVERT: D 496 MET cc_start: 0.4746 (pmm) cc_final: 0.4285 (pmm) REVERT: D 503 MET cc_start: 0.7772 (tpp) cc_final: 0.7156 (tpp) REVERT: D 584 PHE cc_start: 0.8725 (t80) cc_final: 0.8171 (t80) REVERT: D 619 ASN cc_start: 0.8800 (t0) cc_final: 0.8551 (t0) REVERT: D 705 GLU cc_start: 0.8046 (tt0) cc_final: 0.7691 (tt0) REVERT: D 708 MET cc_start: 0.7587 (tmm) cc_final: 0.7013 (ppp) REVERT: D 709 ASN cc_start: 0.7660 (t0) cc_final: 0.7363 (t0) outliers start: 0 outliers final: 0 residues processed: 577 average time/residue: 0.1643 time to fit residues: 156.8337 Evaluate side-chains 401 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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: 11.9990 chunk 83 optimal weight: 0.0020 chunk 96 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 348 optimal weight: 20.0000 chunk 228 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 320 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 112 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** C 46 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 985 ASN D 10 ASN D 46 HIS D 65 GLN D 147 GLN D 335 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.110942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.083548 restraints weight = 102992.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.085939 restraints weight = 61492.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.087518 restraints weight = 43092.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.088567 restraints weight = 33729.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.089314 restraints weight = 28524.309| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 1.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28514 Z= 0.116 Angle : 0.617 10.134 38518 Z= 0.316 Chirality : 0.043 0.281 4282 Planarity : 0.004 0.081 4848 Dihedral : 4.973 53.891 3844 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.81 % 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: -0.35 (0.14), residues: 3502 helix: 1.03 (0.13), residues: 1676 sheet: -0.92 (0.28), residues: 326 loop : -1.55 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 261 TYR 0.020 0.001 TYR D 702 PHE 0.025 0.001 PHE C 109 TRP 0.027 0.002 TRP C 374 HIS 0.006 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (28504) covalent geometry : angle 0.61613 / 0.32 (38498) SS BOND : bond 0.00610 / 0.26 ( 10) SS BOND : angle 1.90052 / 1.23 ( 20) hydrogen bonds : bond 0.03456 / 2.23 ( 1213) hydrogen bonds : angle 4.22465 / 2.90 ( 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 537 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 536 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7904 (t0) cc_final: 0.6830 (p0) REVERT: A 123 SER cc_start: 0.8790 (m) cc_final: 0.8479 (p) REVERT: A 278 ILE cc_start: 0.5398 (tt) cc_final: 0.4806 (tt) REVERT: A 408 MET cc_start: 0.4940 (mmm) cc_final: 0.4407 (mmm) REVERT: A 479 LEU cc_start: 0.8494 (mm) cc_final: 0.8202 (mm) REVERT: A 496 MET cc_start: 0.5918 (ppp) cc_final: 0.5052 (ppp) REVERT: A 524 GLU cc_start: 0.7554 (mp0) cc_final: 0.7235 (pp20) REVERT: A 619 ASN cc_start: 0.8621 (t160) cc_final: 0.8155 (t0) REVERT: A 670 MET cc_start: 0.8376 (mtm) cc_final: 0.8022 (mtm) REVERT: A 674 MET cc_start: 0.7263 (ttt) cc_final: 0.6763 (mmm) REVERT: A 880 MET cc_start: 0.1753 (tmm) cc_final: 0.1498 (ptm) REVERT: A 939 MET cc_start: 0.4072 (ppp) cc_final: 0.3739 (ppp) REVERT: A 979 LEU cc_start: 0.8985 (mm) cc_final: 0.8734 (mm) REVERT: A 981 ILE cc_start: 0.7678 (pt) cc_final: 0.7193 (mm) REVERT: A 1015 LEU cc_start: 0.8234 (mm) cc_final: 0.7844 (mm) REVERT: B 89 CYS cc_start: 0.7843 (m) cc_final: 0.7460 (p) REVERT: B 316 LEU cc_start: 0.5942 (mt) cc_final: 0.5285 (pp) REVERT: B 361 MET cc_start: 0.7425 (mtm) cc_final: 0.6856 (mpp) REVERT: B 383 THR cc_start: 0.8290 (p) cc_final: 0.7876 (t) REVERT: B 528 CYS cc_start: 0.8721 (t) cc_final: 0.7900 (t) REVERT: B 531 PHE cc_start: 0.8773 (m-80) cc_final: 0.8452 (m-80) REVERT: B 661 ARG cc_start: 0.7881 (pmt-80) cc_final: 0.6720 (mmt-90) REVERT: B 732 TYR cc_start: 0.7178 (m-10) cc_final: 0.6855 (m-10) REVERT: B 789 LEU cc_start: 0.8909 (tp) cc_final: 0.8298 (tt) REVERT: B 797 TYR cc_start: 0.8587 (m-80) cc_final: 0.7998 (t80) REVERT: B 807 MET cc_start: 0.8868 (ttt) cc_final: 0.8523 (tmm) REVERT: B 813 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7610 (tm-30) REVERT: C 33 MET cc_start: 0.5954 (mtp) cc_final: 0.5685 (ptt) REVERT: C 93 HIS cc_start: 0.7383 (m-70) cc_final: 0.7173 (m-70) REVERT: C 147 GLN cc_start: 0.8253 (mp10) cc_final: 0.7482 (mp10) REVERT: C 151 ASP cc_start: 0.8647 (m-30) cc_final: 0.8409 (m-30) REVERT: C 260 GLU cc_start: 0.8320 (mp0) cc_final: 0.7970 (pp20) REVERT: C 406 VAL cc_start: 0.7796 (t) cc_final: 0.7393 (t) REVERT: C 474 ILE cc_start: 0.9275 (pt) cc_final: 0.9027 (mm) REVERT: C 490 ASP cc_start: 0.6622 (p0) cc_final: 0.6234 (p0) REVERT: C 511 LYS cc_start: 0.8069 (mmpt) cc_final: 0.7568 (tptt) REVERT: C 525 ILE cc_start: 0.8551 (mt) cc_final: 0.8249 (mm) REVERT: C 571 PHE cc_start: 0.7226 (m-80) cc_final: 0.6806 (m-80) REVERT: C 629 MET cc_start: 0.8356 (ptt) cc_final: 0.7707 (tmm) REVERT: C 891 PHE cc_start: 0.5679 (m-10) cc_final: 0.5306 (m-80) REVERT: C 960 PHE cc_start: 0.7526 (t80) cc_final: 0.7269 (t80) REVERT: C 1023 MET cc_start: 0.8534 (mtm) cc_final: 0.8320 (mtt) REVERT: C 1029 MET cc_start: 0.8083 (tmm) cc_final: 0.7852 (ttm) REVERT: D 50 LEU cc_start: 0.8040 (pt) cc_final: 0.7490 (pt) REVERT: D 199 ASP cc_start: 0.7944 (p0) cc_final: 0.7573 (p0) REVERT: D 229 ASP cc_start: 0.8057 (m-30) cc_final: 0.7571 (m-30) REVERT: D 278 ILE cc_start: 0.7494 (tt) cc_final: 0.6962 (mt) REVERT: D 293 THR cc_start: 0.8571 (m) cc_final: 0.8303 (p) REVERT: D 380 MET cc_start: 0.7737 (pmm) cc_final: 0.7187 (pmm) REVERT: D 405 TYR cc_start: 0.8043 (m-10) cc_final: 0.7783 (m-80) REVERT: D 408 MET cc_start: 0.6746 (tpp) cc_final: 0.6424 (tpp) REVERT: D 438 PHE cc_start: 0.7008 (m-80) cc_final: 0.6727 (m-10) REVERT: D 503 MET cc_start: 0.8037 (tpp) cc_final: 0.7393 (tpp) REVERT: D 515 PHE cc_start: 0.6312 (m-10) cc_final: 0.6070 (m-10) REVERT: D 584 PHE cc_start: 0.8673 (t80) cc_final: 0.8132 (t80) REVERT: D 585 MET cc_start: 0.8543 (tpp) cc_final: 0.8009 (mmm) REVERT: D 619 ASN cc_start: 0.9285 (t0) cc_final: 0.8443 (t0) REVERT: D 705 GLU cc_start: 0.8056 (tt0) cc_final: 0.7803 (tt0) REVERT: D 708 MET cc_start: 0.7795 (tmm) cc_final: 0.7242 (ppp) REVERT: D 709 ASN cc_start: 0.7647 (t0) cc_final: 0.7374 (t0) outliers start: 1 outliers final: 0 residues processed: 537 average time/residue: 0.1643 time to fit residues: 148.0015 Evaluate side-chains 415 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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: 9.9990 chunk 208 optimal weight: 3.9990 chunk 38 optimal weight: 0.0030 chunk 333 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 266 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 80 optimal weight: 40.0000 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS B 10 ASN B 60 ASN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 46 HIS D 93 HIS D 355 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.107693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.079779 restraints weight = 102318.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082767 restraints weight = 64499.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.083600 restraints weight = 41881.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.084147 restraints weight = 32217.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.084394 restraints weight = 31077.733| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 1.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 28514 Z= 0.179 Angle : 0.691 9.329 38518 Z= 0.361 Chirality : 0.045 0.289 4282 Planarity : 0.005 0.083 4848 Dihedral : 5.287 58.801 3844 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: -0.66 (0.14), residues: 3502 helix: 0.67 (0.12), residues: 1710 sheet: -0.71 (0.28), residues: 314 loop : -1.69 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 261 TYR 0.039 0.002 TYR A 26 PHE 0.026 0.002 PHE B 237 TRP 0.033 0.002 TRP B 605 HIS 0.008 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (28504) covalent geometry : angle 0.69068 / 0.36 (38498) SS BOND : bond 0.00456 / 0.20 ( 10) SS BOND : angle 1.41321 / 0.93 ( 20) hydrogen bonds : bond 0.03811 / 2.51 ( 1213) hydrogen bonds : angle 4.48716 / 3.08 ( 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 531 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8789 (mp0) cc_final: 0.8309 (mp0) REVERT: A 78 ASP cc_start: 0.8626 (t0) cc_final: 0.7340 (p0) REVERT: A 123 SER cc_start: 0.8990 (m) cc_final: 0.8436 (p) REVERT: A 138 ASP cc_start: 0.6347 (t0) cc_final: 0.5493 (t0) REVERT: A 140 ASP cc_start: 0.7754 (m-30) cc_final: 0.7184 (m-30) REVERT: A 151 ASP cc_start: 0.8649 (t0) cc_final: 0.8387 (t0) REVERT: A 441 LYS cc_start: 0.8131 (tmtt) cc_final: 0.7931 (tptp) REVERT: A 496 MET cc_start: 0.6069 (ppp) cc_final: 0.5213 (ppp) REVERT: A 503 MET cc_start: 0.7246 (ttp) cc_final: 0.6733 (ttm) REVERT: A 544 SER cc_start: 0.8158 (m) cc_final: 0.7913 (p) REVERT: A 580 SER cc_start: 0.9254 (m) cc_final: 0.8919 (p) REVERT: A 605 TRP cc_start: 0.9039 (t-100) cc_final: 0.8817 (t-100) REVERT: A 619 ASN cc_start: 0.9036 (t0) cc_final: 0.8647 (t0) REVERT: A 670 MET cc_start: 0.8746 (mtm) cc_final: 0.8157 (mtm) REVERT: A 674 MET cc_start: 0.7593 (ttt) cc_final: 0.6829 (ttt) REVERT: A 688 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8915 (tt0) REVERT: A 924 MET cc_start: 0.8666 (mmp) cc_final: 0.8400 (mmm) REVERT: A 939 MET cc_start: 0.4365 (ppp) cc_final: 0.4010 (ppp) REVERT: A 980 TYR cc_start: 0.7556 (t80) cc_final: 0.7092 (t80) REVERT: B 89 CYS cc_start: 0.8139 (m) cc_final: 0.7746 (p) REVERT: B 113 MET cc_start: 0.7864 (pmm) cc_final: 0.7502 (pmm) REVERT: B 316 LEU cc_start: 0.6278 (mt) cc_final: 0.5653 (pp) REVERT: B 383 THR cc_start: 0.8471 (p) cc_final: 0.8203 (p) REVERT: B 496 MET cc_start: 0.8211 (pmm) cc_final: 0.7916 (pmm) REVERT: B 528 CYS cc_start: 0.8751 (t) cc_final: 0.7881 (t) REVERT: B 531 PHE cc_start: 0.8820 (m-80) cc_final: 0.8459 (m-80) REVERT: B 578 TRP cc_start: 0.8987 (t-100) cc_final: 0.8421 (t-100) REVERT: B 608 PHE cc_start: 0.8996 (t80) cc_final: 0.8626 (t80) REVERT: B 661 ARG cc_start: 0.7846 (pmt-80) cc_final: 0.6749 (mmt-90) REVERT: B 807 MET cc_start: 0.8980 (ttt) cc_final: 0.8734 (tmm) REVERT: B 813 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7848 (tm-30) REVERT: C 95 SER cc_start: 0.8169 (m) cc_final: 0.7586 (t) REVERT: C 147 GLN cc_start: 0.8588 (mp10) cc_final: 0.7989 (mp10) REVERT: C 503 MET cc_start: 0.8065 (ppp) cc_final: 0.7549 (ppp) REVERT: C 511 LYS cc_start: 0.8179 (mmpt) cc_final: 0.7570 (tptt) REVERT: C 571 PHE cc_start: 0.7454 (m-80) cc_final: 0.6993 (m-80) REVERT: C 649 THR cc_start: 0.7614 (p) cc_final: 0.7380 (p) REVERT: C 722 LYS cc_start: 0.8980 (tttm) cc_final: 0.8667 (tptt) REVERT: C 763 LYS cc_start: 0.8638 (tttp) cc_final: 0.8343 (tptp) REVERT: C 796 PHE cc_start: 0.8649 (m-80) cc_final: 0.8041 (m-10) REVERT: C 891 PHE cc_start: 0.5852 (m-10) cc_final: 0.5522 (m-80) REVERT: C 924 MET cc_start: 0.8245 (mtm) cc_final: 0.7605 (mmp) REVERT: D 118 LYS cc_start: 0.9286 (ptpt) cc_final: 0.9082 (ptpp) REVERT: D 199 ASP cc_start: 0.8157 (p0) cc_final: 0.7797 (p0) REVERT: D 229 ASP cc_start: 0.8480 (m-30) cc_final: 0.8018 (m-30) REVERT: D 260 GLU cc_start: 0.8887 (mp0) cc_final: 0.8677 (pm20) REVERT: D 293 THR cc_start: 0.8734 (m) cc_final: 0.8433 (p) REVERT: D 380 MET cc_start: 0.7907 (pmm) cc_final: 0.7278 (pmm) REVERT: D 438 PHE cc_start: 0.7255 (m-80) cc_final: 0.6981 (m-10) REVERT: D 503 MET cc_start: 0.8381 (tpp) cc_final: 0.8019 (tpp) REVERT: D 541 PHE cc_start: 0.8124 (t80) cc_final: 0.7800 (t80) REVERT: D 576 SER cc_start: 0.8387 (m) cc_final: 0.8020 (t) REVERT: D 584 PHE cc_start: 0.8961 (t80) cc_final: 0.8566 (t80) REVERT: D 585 MET cc_start: 0.8571 (tpp) cc_final: 0.8114 (mmt) REVERT: D 608 PHE cc_start: 0.8983 (t80) cc_final: 0.8730 (t80) REVERT: D 619 ASN cc_start: 0.9437 (t0) cc_final: 0.8611 (t0) REVERT: D 620 LEU cc_start: 0.9524 (tp) cc_final: 0.9208 (tp) REVERT: D 624 LEU cc_start: 0.9525 (mt) cc_final: 0.9317 (mp) REVERT: D 684 ARG cc_start: 0.6950 (mpp-170) cc_final: 0.6705 (mpp-170) REVERT: D 708 MET cc_start: 0.8092 (tmm) cc_final: 0.7390 (ppp) outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.1516 time to fit residues: 134.8180 Evaluate side-chains 395 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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: 3.9990 chunk 149 optimal weight: 0.9990 chunk 304 optimal weight: 10.0000 chunk 268 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 168 optimal weight: 0.0980 chunk 317 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS A 435 HIS ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN C 985 ASN D 46 HIS D 65 GLN D 147 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.109782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.081186 restraints weight = 100993.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.083531 restraints weight = 60238.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.085084 restraints weight = 42553.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.086155 restraints weight = 33534.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.086830 restraints weight = 28547.177| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 1.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28514 Z= 0.118 Angle : 0.638 8.935 38518 Z= 0.326 Chirality : 0.043 0.270 4282 Planarity : 0.004 0.084 4848 Dihedral : 5.014 59.677 3844 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -0.38 (0.14), residues: 3502 helix: 0.94 (0.13), residues: 1698 sheet: -0.84 (0.28), residues: 332 loop : -1.54 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 178 TYR 0.023 0.001 TYR B 533 PHE 0.030 0.001 PHE A 347 TRP 0.023 0.002 TRP A 323 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (28504) covalent geometry : angle 0.63731 / 0.33 (38498) SS BOND : bond 0.00363 / 0.18 ( 10) SS BOND : angle 1.43356 / 0.92 ( 20) hydrogen bonds : bond 0.03347 / 2.18 ( 1213) hydrogen bonds : angle 4.30042 / 2.94 ( 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 531 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 0.940 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: 0.8639 (mp0) cc_final: 0.8412 (mp0) REVERT: A 78 ASP cc_start: 0.8664 (t0) cc_final: 0.7594 (p0) REVERT: A 123 SER cc_start: 0.9071 (m) cc_final: 0.8704 (p) REVERT: A 151 ASP cc_start: 0.8776 (t0) cc_final: 0.8456 (t0) REVERT: A 152 SER cc_start: 0.8637 (p) cc_final: 0.8374 (p) REVERT: A 278 ILE cc_start: 0.7417 (pt) cc_final: 0.6584 (mt) REVERT: A 441 LYS cc_start: 0.8172 (tmtt) cc_final: 0.7934 (tptp) REVERT: A 496 MET cc_start: 0.6243 (ppp) cc_final: 0.5484 (ppp) REVERT: A 524 GLU cc_start: 0.7780 (mp0) cc_final: 0.7008 (pp20) REVERT: A 525 ILE cc_start: 0.9405 (tt) cc_final: 0.9095 (tt) REVERT: A 527 MET cc_start: 0.5079 (mmt) cc_final: 0.4754 (mmt) REVERT: A 544 SER cc_start: 0.8124 (m) cc_final: 0.7844 (p) REVERT: A 571 PHE cc_start: 0.6172 (m-80) cc_final: 0.5868 (m-80) REVERT: A 580 SER cc_start: 0.9312 (m) cc_final: 0.8995 (p) REVERT: A 619 ASN cc_start: 0.8913 (t0) cc_final: 0.8563 (t0) REVERT: A 670 MET cc_start: 0.8775 (mtm) cc_final: 0.8244 (mtm) REVERT: A 674 MET cc_start: 0.7540 (ttt) cc_final: 0.6815 (ttt) REVERT: A 688 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8917 (tt0) REVERT: A 939 MET cc_start: 0.4439 (ppp) cc_final: 0.3758 (ppp) REVERT: A 980 TYR cc_start: 0.7692 (t80) cc_final: 0.7192 (t80) REVERT: A 981 ILE cc_start: 0.8126 (pt) cc_final: 0.7166 (pt) REVERT: A 1029 MET cc_start: 0.7276 (tpt) cc_final: 0.6363 (ptp) REVERT: B 33 MET cc_start: 0.7828 (ptt) cc_final: 0.7513 (ppp) REVERT: B 56 PHE cc_start: 0.7058 (t80) cc_final: 0.6307 (t80) REVERT: B 89 CYS cc_start: 0.8064 (m) cc_final: 0.7651 (p) REVERT: B 316 LEU cc_start: 0.6374 (mt) cc_final: 0.5819 (pp) REVERT: B 361 MET cc_start: 0.7341 (mtm) cc_final: 0.6627 (mpp) REVERT: B 383 THR cc_start: 0.8411 (p) cc_final: 0.8110 (t) REVERT: B 496 MET cc_start: 0.8028 (pmm) cc_final: 0.7781 (pmm) REVERT: B 528 CYS cc_start: 0.8528 (t) cc_final: 0.8117 (t) REVERT: B 531 PHE cc_start: 0.8775 (m-80) cc_final: 0.8426 (m-80) REVERT: B 533 TYR cc_start: 0.9083 (t80) cc_final: 0.8663 (t80) REVERT: B 661 ARG cc_start: 0.7834 (pmt-80) cc_final: 0.6711 (mmt-90) REVERT: B 789 LEU cc_start: 0.8982 (tt) cc_final: 0.8160 (tp) REVERT: C 93 HIS cc_start: 0.7685 (m-70) cc_final: 0.7073 (m90) REVERT: C 95 SER cc_start: 0.7999 (m) cc_final: 0.7459 (t) REVERT: C 116 ASP cc_start: 0.8180 (t70) cc_final: 0.7959 (t70) REVERT: C 260 GLU cc_start: 0.8550 (mp0) cc_final: 0.8269 (pp20) REVERT: C 301 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8200 (mmtp) REVERT: C 328 GLU cc_start: 0.8566 (tt0) cc_final: 0.8365 (tt0) REVERT: C 511 LYS cc_start: 0.8194 (mmpt) cc_final: 0.7617 (tptt) REVERT: C 528 CYS cc_start: 0.8670 (m) cc_final: 0.8461 (m) REVERT: C 571 PHE cc_start: 0.7445 (m-80) cc_final: 0.6975 (m-80) REVERT: C 596 LEU cc_start: 0.8312 (tt) cc_final: 0.8108 (tt) REVERT: C 629 MET cc_start: 0.8347 (tmm) cc_final: 0.7687 (tmm) REVERT: C 649 THR cc_start: 0.7431 (p) cc_final: 0.7204 (p) REVERT: C 722 LYS cc_start: 0.9031 (tttm) cc_final: 0.8691 (tptm) REVERT: C 796 PHE cc_start: 0.8592 (m-80) cc_final: 0.8069 (m-80) REVERT: C 891 PHE cc_start: 0.5966 (m-10) cc_final: 0.5604 (m-80) REVERT: C 924 MET cc_start: 0.8198 (mtm) cc_final: 0.7414 (mmp) REVERT: D 149 VAL cc_start: 0.9549 (p) cc_final: 0.9333 (t) REVERT: D 199 ASP cc_start: 0.8070 (p0) cc_final: 0.7705 (p0) REVERT: D 229 ASP cc_start: 0.8375 (m-30) cc_final: 0.7876 (m-30) REVERT: D 260 GLU cc_start: 0.8887 (mp0) cc_final: 0.8588 (mp0) REVERT: D 293 THR cc_start: 0.8657 (m) cc_final: 0.8385 (p) REVERT: D 380 MET cc_start: 0.7762 (pmm) cc_final: 0.7207 (pmm) REVERT: D 408 MET cc_start: 0.6450 (tpp) cc_final: 0.6044 (tpp) REVERT: D 438 PHE cc_start: 0.7198 (m-80) cc_final: 0.6927 (m-10) REVERT: D 496 MET cc_start: 0.4915 (pmm) cc_final: 0.3585 (pmm) REVERT: D 503 MET cc_start: 0.8533 (tpp) cc_final: 0.8139 (tpp) REVERT: D 541 PHE cc_start: 0.8092 (t80) cc_final: 0.7812 (t80) REVERT: D 576 SER cc_start: 0.8377 (m) cc_final: 0.8086 (t) REVERT: D 585 MET cc_start: 0.8576 (tpp) cc_final: 0.8133 (mmm) REVERT: D 619 ASN cc_start: 0.9344 (t0) cc_final: 0.8492 (t0) REVERT: D 620 LEU cc_start: 0.9377 (tp) cc_final: 0.9126 (tp) REVERT: D 624 LEU cc_start: 0.9516 (mt) cc_final: 0.9299 (mp) REVERT: D 638 ASP cc_start: 0.8658 (t0) cc_final: 0.8438 (p0) REVERT: D 684 ARG cc_start: 0.6966 (mpp-170) cc_final: 0.6617 (mpp-170) REVERT: D 708 MET cc_start: 0.8000 (tmm) cc_final: 0.7342 (ppp) outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.1510 time to fit residues: 134.6695 Evaluate side-chains 407 residues out of total 3018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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: 10.0000 chunk 332 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 313 optimal weight: 0.8980 chunk 351 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 272 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN D 10 ASN D 219 HIS D 355 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.107914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079157 restraints weight = 101881.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.081438 restraints weight = 60478.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.082951 restraints weight = 42722.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083978 restraints weight = 33800.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.084572 restraints weight = 28889.463| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 1.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28514 Z= 0.143 Angle : 0.660 9.941 38518 Z= 0.340 Chirality : 0.044 0.225 4282 Planarity : 0.004 0.083 4848 Dihedral : 5.076 59.651 3844 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % 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: -0.48 (0.14), residues: 3502 helix: 0.82 (0.13), residues: 1706 sheet: -0.75 (0.28), residues: 338 loop : -1.58 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 261 TYR 0.031 0.002 TYR A1026 PHE 0.030 0.002 PHE D 584 TRP 0.026 0.002 TRP D 158 HIS 0.005 0.001 HIS B 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (28504) covalent geometry : angle 0.65930 / 0.34 (38498) SS BOND : bond 0.00373 / 0.19 ( 10) SS BOND : angle 1.55084 / 0.96 ( 20) hydrogen bonds : bond 0.03487 / 2.28 ( 1213) hydrogen bonds : angle 4.38959 / 3.03 ( 3663) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5612.71 seconds wall clock time: 97 minutes 36.60 seconds (5856.60 seconds total)