Starting phenix.real_space_refine on Tue May 5 01:45:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jrd_61751/05_2026/9jrd_61751_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jrd_61751/05_2026/9jrd_61751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jrd_61751/05_2026/9jrd_61751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jrd_61751/05_2026/9jrd_61751.map" model { file = "/net/cci-nas-00/data/ceres_data/9jrd_61751/05_2026/9jrd_61751_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jrd_61751/05_2026/9jrd_61751_neut.cif" } resolution = 3.9 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15823 2.51 5 N 4266 2.21 5 O 4654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24871 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6371 Classifications: {'peptide': 811} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 783} Chain breaks: 2 Chain: "B" Number of atoms: 6050 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 769, 6039 Classifications: {'peptide': 769} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 741} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 769, 6039 Classifications: {'peptide': 769} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 741} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 6150 Chain: "C" Number of atoms: 6380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6380 Classifications: {'peptide': 813} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 785} Chain breaks: 2 Chain: "D" Number of atoms: 6070 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 771, 6059 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 743} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 771, 6059 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 743} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 6170 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG B 226 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG B 226 " occ=0.48 residue: pdb=" N AARG D 226 " occ=0.52 ... (20 atoms not shown) pdb=" NH2BARG D 226 " occ=0.48 Time building chain proxies: 8.25, per 1000 atoms: 0.33 Number of scatterers: 24871 At special positions: 0 Unit cell: (193.5, 90.3, 201.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4654 8.00 N 4266 7.00 C 15823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 128 " distance=2.04 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 306 " distance=2.04 Simple disulfide: pdb=" SG CYS A 756 " - pdb=" SG CYS A 811 " distance=2.03 Simple disulfide: pdb=" SG CYS B 80 " - pdb=" SG CYS B 351 " distance=2.04 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 128 " distance=2.05 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 811 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 351 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 128 " distance=2.04 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS C 306 " distance=2.04 Simple disulfide: pdb=" SG CYS C 756 " - pdb=" SG CYS C 811 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 351 " distance=2.04 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 128 " distance=2.05 Simple disulfide: pdb=" SG CYS D 756 " - pdb=" SG CYS D 811 " distance=2.03 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: 1.81 Conformation dependent library (CDL) restraints added in 1.5 seconds 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5952 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 34 sheets defined 48.7% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 34 through 52 Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.504A pdb=" N THR A 84 " --> pdb=" O CYS A 80 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 110 removed outlier: 3.519A pdb=" N ALA A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.549A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.551A pdb=" N ASP A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 317 through 340 Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.975A pdb=" N ALA A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.763A pdb=" N SER A 528 " --> pdb=" O PRO A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.631A pdb=" N LEU A 557 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 587 removed outlier: 3.698A pdb=" N ALA A 570 " --> pdb=" O TRP A 566 " (cutoff:3.500A) Proline residue: A 574 - end of helix removed outlier: 3.748A pdb=" N PHE A 581 " --> pdb=" O GLY A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'A' and resid 626 through 659 removed outlier: 4.188A pdb=" N MET A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 635 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 648 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 649 " --> pdb=" O CYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 674 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.612A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 690 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 694 " --> pdb=" O TYR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 713 removed outlier: 3.966A pdb=" N ARG A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.913A pdb=" N ALA A 718 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.593A pdb=" N ARG A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 753 removed outlier: 3.649A pdb=" N THR A 752 " --> pdb=" O TYR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 792 removed outlier: 3.813A pdb=" N GLN A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 788 " --> pdb=" O PHE A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 805 removed outlier: 3.568A pdb=" N LEU A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN A 802 " --> pdb=" O ASP A 798 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP A 804 " --> pdb=" O LEU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 818 removed outlier: 3.987A pdb=" N HIS A 816 " --> pdb=" O ASP A 812 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 818 " --> pdb=" O THR A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 853 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.675A pdb=" N LEU B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 148 through 160 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 200 through 212 removed outlier: 3.995A pdb=" N PHE B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 208 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 317 through 340 Processing helix chain 'B' and resid 361 through 371 Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.735A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 removed outlier: 3.702A pdb=" N GLY B 506 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.412A pdb=" N SER B 528 " --> pdb=" O PRO B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 559 removed outlier: 3.573A pdb=" N SER B 556 " --> pdb=" O SER B 553 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU B 557 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 559 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 588 removed outlier: 3.550A pdb=" N TRP B 566 " --> pdb=" O ASP B 562 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Proline residue: B 574 - end of helix Processing helix chain 'B' and resid 628 through 658 removed outlier: 3.968A pdb=" N ILE B 632 " --> pdb=" O VAL B 628 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 649 " --> pdb=" O CYS B 645 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 654 " --> pdb=" O ALA B 650 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 658 " --> pdb=" O ALA B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 674 Processing helix chain 'B' and resid 685 through 697 removed outlier: 4.047A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 690 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 691 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 697 " --> pdb=" O ALA B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 713 removed outlier: 3.548A pdb=" N THR B 711 " --> pdb=" O GLU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 Processing helix chain 'B' and resid 724 through 735 removed outlier: 3.549A pdb=" N LYS B 734 " --> pdb=" O ARG B 730 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 735 " --> pdb=" O LYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 753 Processing helix chain 'B' and resid 780 through 794 removed outlier: 3.802A pdb=" N ARG B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 802 removed outlier: 3.735A pdb=" N VAL B 799 " --> pdb=" O GLY B 795 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN B 802 " --> pdb=" O ASP B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 818 removed outlier: 3.825A pdb=" N HIS B 816 " --> pdb=" O ASP B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 857 removed outlier: 5.671A pdb=" N GLY B 833 " --> pdb=" O HIS B 829 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL B 834 " --> pdb=" O SER B 830 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE B 835 " --> pdb=" O PHE B 831 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 837 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 838 " --> pdb=" O VAL B 834 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 843 " --> pdb=" O ALA B 839 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP B 854 " --> pdb=" O ALA B 850 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP B 855 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 856 " --> pdb=" O GLU B 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 52 Processing helix chain 'C' and resid 71 through 85 removed outlier: 3.503A pdb=" N THR C 84 " --> pdb=" O CYS C 80 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 110 removed outlier: 3.520A pdb=" N ALA C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 160 removed outlier: 3.548A pdb=" N VAL C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 177 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 200 through 212 Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.550A pdb=" N ASP C 222 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 317 through 340 Processing helix chain 'C' and resid 361 through 371 Processing helix chain 'C' and resid 465 through 479 Processing helix chain 'C' and resid 503 through 510 Processing helix chain 'C' and resid 523 through 530 removed outlier: 3.721A pdb=" N SER C 528 " --> pdb=" O PRO C 524 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 4.354A pdb=" N LEU C 557 " --> pdb=" O ILE C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 589 Proline residue: C 574 - end of helix removed outlier: 3.706A pdb=" N GLY C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 617 removed outlier: 3.950A pdb=" N ALA C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 616 " --> pdb=" O VAL C 612 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 617 " --> pdb=" O TYR C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 660 removed outlier: 3.521A pdb=" N ARG C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 639 " --> pdb=" O GLY C 635 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR C 649 " --> pdb=" O CYS C 645 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 674 Processing helix chain 'C' and resid 685 through 696 removed outlier: 4.046A pdb=" N THR C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 713 removed outlier: 3.580A pdb=" N ILE C 712 " --> pdb=" O LEU C 708 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 713 " --> pdb=" O TRP C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 722 removed outlier: 3.926A pdb=" N VAL C 722 " --> pdb=" O ASP C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 732 removed outlier: 4.443A pdb=" N ARG C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 753 removed outlier: 3.760A pdb=" N TYR C 748 " --> pdb=" O ALA C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 795 removed outlier: 3.890A pdb=" N GLN C 786 " --> pdb=" O ASP C 782 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG C 787 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 788 " --> pdb=" O PHE C 784 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 790 " --> pdb=" O GLN C 786 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP C 793 " --> pdb=" O LEU C 789 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 805 removed outlier: 3.566A pdb=" N LYS C 801 " --> pdb=" O LEU C 797 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN C 802 " --> pdb=" O ASP C 798 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 818 removed outlier: 3.657A pdb=" N SER C 818 " --> pdb=" O THR C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 852 removed outlier: 3.655A pdb=" N PHE C 831 " --> pdb=" O LYS C 827 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY C 833 " --> pdb=" O HIS C 829 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL C 834 " --> pdb=" O SER C 830 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE C 835 " --> pdb=" O PHE C 831 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 50 removed outlier: 3.675A pdb=" N LEU D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 148 through 160 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 200 through 212 removed outlier: 3.996A pdb=" N PHE D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 208 " --> pdb=" O VAL D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 263 through 274 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 317 through 340 Processing helix chain 'D' and resid 361 through 371 Processing helix chain 'D' and resid 465 through 478 removed outlier: 3.602A pdb=" N ALA D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 511 removed outlier: 3.836A pdb=" N LEU D 508 " --> pdb=" O MET D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 530 removed outlier: 3.711A pdb=" N SER D 528 " --> pdb=" O PRO D 524 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 529 " --> pdb=" O GLU D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 559 removed outlier: 3.931A pdb=" N ALA D 559 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 589 removed outlier: 3.817A pdb=" N ALA D 567 " --> pdb=" O PHE D 563 " (cutoff:3.500A) Proline residue: D 574 - end of helix Processing helix chain 'D' and resid 629 through 658 removed outlier: 3.765A pdb=" N SER D 636 " --> pdb=" O ILE D 632 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP D 637 " --> pdb=" O VAL D 633 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 649 " --> pdb=" O CYS D 645 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 654 " --> pdb=" O ALA D 650 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 656 " --> pdb=" O LEU D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 674 removed outlier: 3.589A pdb=" N LYS D 673 " --> pdb=" O GLN D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.786A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE D 691 " --> pdb=" O VAL D 687 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN D 697 " --> pdb=" O ALA D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 713 removed outlier: 3.687A pdb=" N GLU D 707 " --> pdb=" O SER D 703 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 711 " --> pdb=" O GLU D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 735 removed outlier: 3.599A pdb=" N GLY D 728 " --> pdb=" O ASN D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 752 Processing helix chain 'D' and resid 780 through 795 removed outlier: 3.611A pdb=" N ARG D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 790 " --> pdb=" O GLN D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 805 removed outlier: 3.956A pdb=" N LYS D 803 " --> pdb=" O VAL D 799 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 859 removed outlier: 3.552A pdb=" N PHE D 835 " --> pdb=" O PHE D 831 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 837 " --> pdb=" O GLY D 833 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 838 " --> pdb=" O VAL D 834 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 67 removed outlier: 6.121A pdb=" N ILE A 24 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N SER A 63 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE A 26 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS A 65 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA A 28 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE A 67 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 30 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N VAL A 91 " --> pdb=" O HIS A 25 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY A 27 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N SER A 93 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 29 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS A 113 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 196 removed outlier: 7.516A pdb=" N LYS A 164 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ILE A 228 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 166 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU A 230 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE A 168 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET A 278 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY A 398 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LYS A 411 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N THR A 400 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N MET A 409 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER A 402 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS A 407 " --> pdb=" O SER A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 376 Processing sheet with id=AA5, first strand: chain 'A' and resid 481 through 483 removed outlier: 3.505A pdb=" N GLU A 483 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 441 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 515 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 517 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N SER A 518 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA A 773 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE A 520 " --> pdb=" O GLY A 771 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 481 through 483 removed outlier: 3.505A pdb=" N GLU A 483 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 441 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 515 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 517 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N SER A 518 " --> pdb=" O ALA A 773 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA A 773 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE A 520 " --> pdb=" O GLY A 771 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS A 768 " --> pdb=" O TYR A 539 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 451 through 453 removed outlier: 4.631A pdb=" N ARG A 462 " --> pdb=" O ALA A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 494 through 495 removed outlier: 3.793A pdb=" N HIS A 494 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 502 " --> pdb=" O HIS A 494 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 679 through 680 removed outlier: 7.249A pdb=" N GLY A 680 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 10.048A pdb=" N ASP A 742 " --> pdb=" O GLY A 680 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 739 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 761 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 67 removed outlier: 6.362A pdb=" N ILE B 24 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER B 63 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE B 26 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LYS B 65 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA B 28 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE B 67 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 30 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N VAL B 91 " --> pdb=" O HIS B 25 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY B 27 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER B 93 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 29 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 90 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL B 116 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR B 92 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS B 113 " --> pdb=" O LEU B 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 191 through 197 removed outlier: 7.338A pdb=" N LYS B 164 " --> pdb=" O AARG B 226 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ILE B 228 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL B 166 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 230 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE B 168 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLY B 398 " --> pdb=" O LYS B 411 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS B 411 " --> pdb=" O GLY B 398 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 373 through 376 Processing sheet with id=AB4, first strand: chain 'B' and resid 481 through 483 removed outlier: 6.519A pdb=" N LEU B 439 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU B 515 " --> pdb=" O LYS B 440 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B 442 " --> pdb=" O LEU B 515 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AB6, first strand: chain 'B' and resid 495 through 496 removed outlier: 3.657A pdb=" N SER B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.519A pdb=" N TYR B 539 " --> pdb=" O LYS B 768 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS B 768 " --> pdb=" O TYR B 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 679 through 681 removed outlier: 3.715A pdb=" N GLY B 680 " --> pdb=" O ALA B 738 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 740 " --> pdb=" O GLY B 680 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRP B 741 " --> pdb=" O GLY B 542 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 67 removed outlier: 6.120A pdb=" N ILE C 24 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER C 63 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE C 26 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS C 65 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA C 28 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE C 67 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE C 30 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N VAL C 91 " --> pdb=" O HIS C 25 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY C 27 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N SER C 93 " --> pdb=" O GLY C 27 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 29 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS C 113 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 191 through 196 removed outlier: 7.516A pdb=" N LYS C 164 " --> pdb=" O ARG C 226 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ILE C 228 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 166 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU C 230 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE C 168 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET C 278 " --> pdb=" O THR C 399 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY C 398 " --> pdb=" O LYS C 411 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS C 411 " --> pdb=" O GLY C 398 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N THR C 400 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N MET C 409 " --> pdb=" O THR C 400 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N SER C 402 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LYS C 407 " --> pdb=" O SER C 402 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AC3, first strand: chain 'C' and resid 373 through 376 Processing sheet with id=AC4, first strand: chain 'C' and resid 481 through 486 removed outlier: 6.870A pdb=" N LEU C 439 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N TYR C 485 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL C 441 " --> pdb=" O TYR C 485 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 515 " --> pdb=" O LYS C 440 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 442 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE C 517 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 773 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER C 518 " --> pdb=" O GLY C 771 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLY C 771 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 520 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY C 769 " --> pdb=" O ILE C 520 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 481 through 486 removed outlier: 6.870A pdb=" N LEU C 439 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N TYR C 485 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL C 441 " --> pdb=" O TYR C 485 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 515 " --> pdb=" O LYS C 440 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 442 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE C 517 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 773 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N SER C 518 " --> pdb=" O GLY C 771 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLY C 771 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 520 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY C 769 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 768 " --> pdb=" O TYR C 539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AC7, first strand: chain 'C' and resid 494 through 496 removed outlier: 3.769A pdb=" N HIS C 494 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 678 through 680 removed outlier: 6.301A pdb=" N SER C 678 " --> pdb=" O ALA C 738 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU C 740 " --> pdb=" O SER C 678 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLY C 680 " --> pdb=" O LEU C 740 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N ASP C 742 " --> pdb=" O GLY C 680 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N TYR C 737 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS C 546 " --> pdb=" O TYR C 737 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP C 741 " --> pdb=" O GLY C 542 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 545 " --> pdb=" O THR C 759 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 759 " --> pdb=" O ILE C 545 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 60 through 67 removed outlier: 6.362A pdb=" N ILE D 24 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N SER D 63 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE D 26 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LYS D 65 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA D 28 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE D 67 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE D 30 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N VAL D 91 " --> pdb=" O HIS D 25 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY D 27 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER D 93 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE D 29 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU D 90 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL D 116 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR D 92 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS D 113 " --> pdb=" O LEU D 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 191 through 197 removed outlier: 7.339A pdb=" N LYS D 164 " --> pdb=" O AARG D 226 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE D 228 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 166 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU D 230 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE D 168 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY D 398 " --> pdb=" O LYS D 411 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS D 411 " --> pdb=" O GLY D 398 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 373 through 376 Processing sheet with id=AD3, first strand: chain 'D' and resid 483 through 486 removed outlier: 3.606A pdb=" N TYR D 485 " --> pdb=" O VAL D 441 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR D 443 " --> pdb=" O TYR D 485 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 515 " --> pdb=" O LYS D 440 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 442 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 451 through 453 removed outlier: 4.193A pdb=" N ARG D 462 " --> pdb=" O ALA D 453 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AD6, first strand: chain 'D' and resid 538 through 539 removed outlier: 4.043A pdb=" N LYS D 768 " --> pdb=" O TYR D 539 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 679 through 681 removed outlier: 7.497A pdb=" N GLY D 680 " --> pdb=" O LEU D 740 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N ASP D 742 " --> pdb=" O GLY D 680 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP D 741 " --> pdb=" O GLY D 542 " (cutoff:3.500A) 1118 hydrogen bonds defined for protein. 3245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8110 1.34 - 1.46: 5864 1.46 - 1.59: 11199 1.59 - 1.71: 0 1.71 - 1.83: 206 Bond restraints: 25379 Sorted by residual: bond pdb=" CA THR B 140 " pdb=" CB THR B 140 " ideal model delta sigma weight residual 1.528 1.552 -0.024 1.35e-02 5.49e+03 3.23e+00 bond pdb=" CA THR D 140 " pdb=" CB THR D 140 " ideal model delta sigma weight residual 1.528 1.552 -0.024 1.35e-02 5.49e+03 3.16e+00 bond pdb=" CA ILE A 175 " pdb=" CB ILE A 175 " ideal model delta sigma weight residual 1.542 1.563 -0.021 1.28e-02 6.10e+03 2.65e+00 bond pdb=" CA ILE C 175 " pdb=" CB ILE C 175 " ideal model delta sigma weight residual 1.542 1.563 -0.021 1.28e-02 6.10e+03 2.63e+00 bond pdb=" CA ALA D 75 " pdb=" CB ALA D 75 " ideal model delta sigma weight residual 1.528 1.504 0.025 1.56e-02 4.11e+03 2.56e+00 ... (remaining 25374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 33279 1.94 - 3.89: 967 3.89 - 5.83: 121 5.83 - 7.77: 14 7.77 - 9.72: 3 Bond angle restraints: 34384 Sorted by residual: angle pdb=" N ARG B 353 " pdb=" CA ARG B 353 " pdb=" C ARG B 353 " ideal model delta sigma weight residual 111.82 121.54 -9.72 1.16e+00 7.43e-01 7.02e+01 angle pdb=" N ARG D 353 " pdb=" CA ARG D 353 " pdb=" C ARG D 353 " ideal model delta sigma weight residual 111.82 121.49 -9.67 1.16e+00 7.43e-01 6.94e+01 angle pdb=" N ILE B 352 " pdb=" CA ILE B 352 " pdb=" C ILE B 352 " ideal model delta sigma weight residual 110.72 116.10 -5.38 1.01e+00 9.80e-01 2.84e+01 angle pdb=" N ILE D 352 " pdb=" CA ILE D 352 " pdb=" C ILE D 352 " ideal model delta sigma weight residual 110.72 116.10 -5.38 1.01e+00 9.80e-01 2.83e+01 angle pdb=" N VAL B 204 " pdb=" CA VAL B 204 " pdb=" C VAL B 204 " ideal model delta sigma weight residual 110.30 115.04 -4.74 9.70e-01 1.06e+00 2.39e+01 ... (remaining 34379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 14170 17.73 - 35.47: 871 35.47 - 53.20: 161 53.20 - 70.93: 25 70.93 - 88.66: 9 Dihedral angle restraints: 15236 sinusoidal: 6038 harmonic: 9198 Sorted by residual: dihedral pdb=" CB CYS D 756 " pdb=" SG CYS D 756 " pdb=" SG CYS D 811 " pdb=" CB CYS D 811 " ideal model delta sinusoidal sigma weight residual 93.00 178.75 -85.75 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS A 756 " pdb=" SG CYS A 756 " pdb=" SG CYS A 811 " pdb=" CB CYS A 811 " ideal model delta sinusoidal sigma weight residual -86.00 -170.82 84.82 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS C 756 " pdb=" SG CYS C 756 " pdb=" SG CYS C 811 " pdb=" CB CYS C 811 " ideal model delta sinusoidal sigma weight residual 93.00 171.49 -78.49 1 1.00e+01 1.00e-02 7.69e+01 ... (remaining 15233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3233 0.050 - 0.099: 519 0.099 - 0.149: 145 0.149 - 0.199: 6 0.199 - 0.249: 6 Chirality restraints: 3909 Sorted by residual: chirality pdb=" CA ILE C 24 " pdb=" N ILE C 24 " pdb=" C ILE C 24 " pdb=" CB ILE C 24 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE A 24 " pdb=" N ILE A 24 " pdb=" C ILE A 24 " pdb=" CB ILE A 24 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ARG B 353 " pdb=" N ARG B 353 " pdb=" C ARG B 353 " pdb=" CB ARG B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 3906 not shown) Planarity restraints: 4376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 190 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C LEU D 190 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU D 190 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP D 191 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 190 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.64e+00 pdb=" C LEU B 190 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU B 190 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP B 191 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 778 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 779 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 779 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 779 " -0.026 5.00e-02 4.00e+02 ... (remaining 4373 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 306 2.67 - 3.23: 23995 3.23 - 3.78: 36535 3.78 - 4.34: 51232 4.34 - 4.90: 81375 Nonbonded interactions: 193443 Sorted by model distance: nonbonded pdb=" O ALA A 706 " pdb=" OG1 THR A 711 " model vdw 2.110 3.040 nonbonded pdb=" OH TYR A 463 " pdb=" NE2 GLN A 486 " model vdw 2.188 3.120 nonbonded pdb=" OH TYR B 463 " pdb=" OE1 GLN B 486 " model vdw 2.202 3.040 nonbonded pdb=" NH1 ARG C 683 " pdb=" O ASN C 720 " model vdw 2.227 3.120 nonbonded pdb=" O ASN C 350 " pdb=" OG1 THR C 356 " model vdw 2.250 3.040 ... (remaining 193438 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 51 or resid 57 through 225 or resid 227 through \ 288 or (resid 299 and (name N or name CA or name C or name O or name CB )) or r \ esid 300 through 309 or (resid 310 and (name N or name CA or name C or name O or \ name CB )) or resid 311 through 399 or resid 406 through 424 or resid 433 throu \ gh 587 or resid 615 or resid 629 through 852)) selection = (chain 'B' and (resid 22 through 225 or resid 227 through 588 or resid 629 throu \ gh 852)) selection = (chain 'C' and (resid 22 through 51 or resid 57 through 225 or resid 227 through \ 288 or (resid 299 and (name N or name CA or name C or name O or name CB )) or r \ esid 300 through 309 or (resid 310 and (name N or name CA or name C or name O or \ name CB )) or resid 311 through 399 or resid 406 through 424 or resid 433 throu \ gh 587 or resid 615 or resid 629 through 852)) selection = (chain 'D' and (resid 22 through 225 or resid 227 through 588 or resid 629 throu \ gh 852)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.48 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: 10.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 26.290 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4133 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 : 0.004 0.053 25393 Z= 0.253 Angle : 0.815 26.629 34412 Z= 0.517 Chirality : 0.042 0.249 3909 Planarity : 0.003 0.049 4376 Dihedral : 11.953 88.665 9242 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.17 % Favored : 97.70 % Rotamer: Outliers : 0.95 % Allowed : 1.17 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: -0.76 (0.14), residues: 3134 helix: -0.14 (0.13), residues: 1369 sheet: -0.73 (0.23), residues: 382 loop : -0.66 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 512 TYR 0.031 0.002 TYR B 485 PHE 0.022 0.001 PHE C 640 TRP 0.026 0.001 TRP A 804 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00401 (25379) covalent geometry : angle 0.78131 (34384) SS BOND : bond 0.00852 ( 14) SS BOND : angle 8.16542 ( 28) hydrogen bonds : bond 0.26968 ( 1114) hydrogen bonds : angle 6.97437 ( 3245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 416 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASP cc_start: -0.1525 (OUTLIER) cc_final: -0.1880 (m-30) REVERT: A 346 MET cc_start: 0.3186 (tpt) cc_final: 0.1613 (pmm) REVERT: A 435 GLN cc_start: 0.6397 (tp40) cc_final: 0.6195 (pm20) REVERT: B 409 MET cc_start: 0.2514 (tpp) cc_final: 0.1085 (ptp) REVERT: B 501 TRP cc_start: 0.3432 (m100) cc_final: 0.1047 (m100) REVERT: B 581 PHE cc_start: 0.3916 (t80) cc_final: 0.3552 (m-10) REVERT: B 630 MET cc_start: 0.4427 (ptt) cc_final: 0.3909 (tmm) REVERT: B 659 SER cc_start: 0.7952 (t) cc_final: 0.7531 (p) REVERT: B 681 THR cc_start: 0.7412 (t) cc_final: 0.6964 (p) REVERT: C 290 ASP cc_start: -0.1821 (OUTLIER) cc_final: -0.2168 (m-30) REVERT: C 346 MET cc_start: 0.3310 (tpt) cc_final: 0.1796 (pmm) REVERT: C 566 TRP cc_start: 0.7921 (m100) cc_final: 0.4853 (t60) REVERT: C 568 CYS cc_start: 0.7225 (m) cc_final: 0.6879 (m) REVERT: C 631 ARG cc_start: 0.6909 (mtm180) cc_final: 0.6081 (tpt-90) REVERT: C 661 MET cc_start: 0.2481 (mmm) cc_final: 0.2060 (mmp) REVERT: C 671 LEU cc_start: 0.3453 (mt) cc_final: 0.2826 (tp) REVERT: C 824 LYS cc_start: 0.5777 (mtmm) cc_final: 0.5459 (mptt) REVERT: D 409 MET cc_start: 0.2552 (tpp) cc_final: 0.1090 (ptp) REVERT: D 492 TYR cc_start: 0.7036 (m-80) cc_final: 0.6237 (p90) REVERT: D 660 ARG cc_start: 0.2870 (mtt90) cc_final: 0.1852 (ptp-170) REVERT: D 670 ASP cc_start: 0.6899 (m-30) cc_final: 0.6512 (t0) REVERT: D 681 THR cc_start: 0.7705 (t) cc_final: 0.7305 (p) REVERT: D 755 ASP cc_start: 0.4263 (p0) cc_final: 0.3292 (p0) REVERT: D 790 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6451 (mm-30) outliers start: 26 outliers final: 2 residues processed: 437 average time/residue: 0.1799 time to fit residues: 118.8856 Evaluate side-chains 243 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 239 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain D residue 353 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 241 ASN A 283 GLN A 373 HIS A 618 GLN A 669 GLN C 200 ASN C 241 ASN C 283 GLN C 373 HIS ** C 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 858 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.276927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.255233 restraints weight = 65934.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.254647 restraints weight = 61258.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.252209 restraints weight = 40150.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.251865 restraints weight = 40336.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.250754 restraints weight = 33123.031| |-----------------------------------------------------------------------------| r_work (final): 0.4935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4935 r_free = 0.4935 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4935 r_free = 0.4935 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4739 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25393 Z= 0.145 Angle : 0.603 8.450 34412 Z= 0.322 Chirality : 0.042 0.170 3909 Planarity : 0.004 0.053 4376 Dihedral : 4.354 23.269 3419 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.95 % Allowed : 7.08 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: 0.09 (0.15), residues: 3134 helix: 0.91 (0.13), residues: 1418 sheet: -0.57 (0.24), residues: 409 loop : -0.56 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 660 TYR 0.024 0.001 TYR D 688 PHE 0.025 0.002 PHE A 691 TRP 0.041 0.001 TRP B 854 HIS 0.009 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00296 (25379) covalent geometry : angle 0.60281 (34384) SS BOND : bond 0.00295 ( 14) SS BOND : angle 0.95495 ( 28) hydrogen bonds : bond 0.05974 ( 1114) hydrogen bonds : angle 4.75854 ( 3245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 0.857 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 346 MET cc_start: 0.3007 (tpt) cc_final: 0.1404 (pmm) REVERT: A 579 LEU cc_start: 0.6589 (tp) cc_final: 0.6333 (tp) REVERT: A 677 MET cc_start: 0.4873 (mmt) cc_final: 0.4578 (mmt) REVERT: B 109 MET cc_start: 0.0375 (mtp) cc_final: -0.1156 (mmt) REVERT: B 247 ASN cc_start: 0.5007 (t0) cc_final: 0.4246 (p0) REVERT: B 409 MET cc_start: 0.3042 (tpp) cc_final: 0.1570 (ptp) REVERT: B 501 TRP cc_start: 0.3897 (m100) cc_final: 0.1628 (m100) REVERT: B 659 SER cc_start: 0.7158 (t) cc_final: 0.6913 (p) REVERT: B 681 THR cc_start: 0.7016 (t) cc_final: 0.6542 (p) REVERT: B 704 THR cc_start: 0.6881 (p) cc_final: 0.6676 (t) REVERT: C 346 MET cc_start: 0.3088 (tpt) cc_final: 0.1541 (pmm) REVERT: C 566 TRP cc_start: 0.7633 (m100) cc_final: 0.4966 (t60) REVERT: C 634 MET cc_start: 0.6438 (tmm) cc_final: 0.5737 (mmp) REVERT: C 661 MET cc_start: 0.3781 (mmm) cc_final: 0.3409 (mmp) REVERT: D 247 ASN cc_start: 0.5178 (t0) cc_final: 0.4535 (p0) REVERT: D 409 MET cc_start: 0.3085 (tpp) cc_final: 0.1363 (ptm) REVERT: D 660 ARG cc_start: 0.2729 (mtt90) cc_final: 0.1637 (mtt-85) REVERT: D 661 MET cc_start: 0.6784 (tpp) cc_final: 0.6525 (tpp) REVERT: D 681 THR cc_start: 0.7383 (t) cc_final: 0.7090 (p) outliers start: 26 outliers final: 16 residues processed: 276 average time/residue: 0.1783 time to fit residues: 75.0018 Evaluate side-chains 214 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 351 CYS Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 467 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 216 optimal weight: 1.9990 chunk 90 optimal weight: 50.0000 chunk 255 optimal weight: 6.9990 chunk 268 optimal weight: 7.9990 chunk 118 optimal weight: 30.0000 chunk 12 optimal weight: 40.0000 chunk 286 optimal weight: 0.3980 chunk 298 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS A 455 ASN A 486 GLN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 HIS D 110 HIS ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.269248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.247351 restraints weight = 69887.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.247409 restraints weight = 64709.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.244284 restraints weight = 47375.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.243892 restraints weight = 49936.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.243548 restraints weight = 34933.576| |-----------------------------------------------------------------------------| r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4893 r_free = 0.4893 target_work(ls_wunit_k1) = 0.242 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4893 r_free = 0.4893 target_work(ls_wunit_k1) = 0.242 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4942 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 25393 Z= 0.214 Angle : 0.678 15.330 34412 Z= 0.359 Chirality : 0.045 0.220 3909 Planarity : 0.005 0.083 4376 Dihedral : 4.515 24.722 3407 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.65 % Allowed : 9.50 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: -0.05 (0.15), residues: 3134 helix: 0.79 (0.13), residues: 1419 sheet: -0.41 (0.24), residues: 427 loop : -0.73 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 535 TYR 0.026 0.002 TYR D 539 PHE 0.033 0.002 PHE A 691 TRP 0.026 0.002 TRP B 854 HIS 0.006 0.001 HIS D 816 Details of bonding type rmsd covalent geometry : bond 0.00498 (25379) covalent geometry : angle 0.67777 (34384) SS BOND : bond 0.00156 ( 14) SS BOND : angle 0.65908 ( 28) hydrogen bonds : bond 0.06244 ( 1114) hydrogen bonds : angle 4.89482 ( 3245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 MET cc_start: 0.2418 (mpp) cc_final: 0.2142 (mpp) REVERT: A 346 MET cc_start: 0.3038 (tpt) cc_final: 0.1294 (pmm) REVERT: A 579 LEU cc_start: 0.6732 (tp) cc_final: 0.6094 (tt) REVERT: A 630 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7306 (mmp) REVERT: A 677 MET cc_start: 0.5099 (mmt) cc_final: 0.4609 (mmt) REVERT: B 109 MET cc_start: 0.0884 (mtp) cc_final: -0.0748 (mmt) REVERT: B 247 ASN cc_start: 0.5187 (t0) cc_final: 0.4420 (p0) REVERT: B 409 MET cc_start: 0.3108 (tpp) cc_final: 0.1637 (ptp) REVERT: B 501 TRP cc_start: 0.4280 (m100) cc_final: 0.1614 (m100) REVERT: B 638 TRP cc_start: 0.5819 (m-10) cc_final: 0.5616 (m-90) REVERT: B 659 SER cc_start: 0.7115 (t) cc_final: 0.6898 (p) REVERT: C 212 MET cc_start: 0.2301 (mpp) cc_final: 0.2030 (mpp) REVERT: C 346 MET cc_start: 0.3153 (tpt) cc_final: 0.1376 (pmm) REVERT: C 619 GLN cc_start: 0.5802 (tm-30) cc_final: 0.5541 (tp40) REVERT: C 634 MET cc_start: 0.6307 (tmm) cc_final: 0.5752 (mmp) REVERT: C 661 MET cc_start: 0.4039 (mmm) cc_final: 0.3365 (mmm) REVERT: D 247 ASN cc_start: 0.5502 (t0) cc_final: 0.5284 (t0) REVERT: D 329 MET cc_start: 0.0250 (tpt) cc_final: -0.0100 (tmm) REVERT: D 409 MET cc_start: 0.3058 (tpp) cc_final: 0.1782 (ptp) REVERT: D 634 MET cc_start: 0.7756 (mmm) cc_final: 0.6405 (mmt) outliers start: 45 outliers final: 35 residues processed: 236 average time/residue: 0.1598 time to fit residues: 60.3932 Evaluate side-chains 217 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 486 GLN Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 351 CYS Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 713 SER Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 790 GLU Chi-restraints excluded: chain D residue 796 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 228 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 241 optimal weight: 6.9990 chunk 302 optimal weight: 0.8980 chunk 205 optimal weight: 0.1980 chunk 254 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 24 optimal weight: 40.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 HIS ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN ** C 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 786 GLN D 110 HIS D 254 HIS ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.263900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.244279 restraints weight = 59236.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.243080 restraints weight = 63348.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.240121 restraints weight = 57701.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.239112 restraints weight = 47201.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.236847 restraints weight = 48622.084| |-----------------------------------------------------------------------------| r_work (final): 0.4824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4824 r_free = 0.4824 target_work(ls_wunit_k1) = 0.234 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4824 r_free = 0.4824 target_work(ls_wunit_k1) = 0.234 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5146 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 25393 Z= 0.302 Angle : 0.804 13.486 34412 Z= 0.431 Chirality : 0.050 0.293 3909 Planarity : 0.006 0.086 4376 Dihedral : 5.271 28.394 3407 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.15 % Rotamer: Outliers : 3.01 % Allowed : 11.15 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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 (0.15), residues: 3134 helix: 0.26 (0.13), residues: 1420 sheet: -0.45 (0.25), residues: 401 loop : -1.12 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 535 TYR 0.041 0.003 TYR A 485 PHE 0.037 0.003 PHE A 668 TRP 0.061 0.003 TRP D 638 HIS 0.013 0.002 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00710 (25379) covalent geometry : angle 0.80385 (34384) SS BOND : bond 0.00170 ( 14) SS BOND : angle 0.68806 ( 28) hydrogen bonds : bond 0.06872 ( 1114) hydrogen bonds : angle 5.41178 ( 3245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 196 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4852 (mmm) cc_final: 0.3884 (mmt) REVERT: A 212 MET cc_start: 0.2905 (mpp) cc_final: 0.2629 (mpp) REVERT: A 346 MET cc_start: 0.3329 (tpt) cc_final: 0.1328 (pmm) REVERT: B 109 MET cc_start: 0.1171 (mtp) cc_final: -0.0695 (mmt) REVERT: B 247 ASN cc_start: 0.5330 (t0) cc_final: 0.5127 (t0) REVERT: B 329 MET cc_start: 0.1238 (ptm) cc_final: 0.0973 (ptt) REVERT: B 409 MET cc_start: 0.2982 (tpp) cc_final: 0.1700 (ptp) REVERT: C 212 MET cc_start: 0.2799 (mpp) cc_final: 0.2515 (mpp) REVERT: C 346 MET cc_start: 0.3528 (tpt) cc_final: 0.1453 (pmm) REVERT: C 433 ARG cc_start: 0.5792 (OUTLIER) cc_final: 0.4290 (ptp90) REVERT: C 515 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8350 (pp) REVERT: C 566 TRP cc_start: 0.8088 (m100) cc_final: 0.7711 (m100) REVERT: C 634 MET cc_start: 0.6769 (tmm) cc_final: 0.6151 (mmp) REVERT: D 247 ASN cc_start: 0.5419 (t0) cc_final: 0.5147 (t0) REVERT: D 278 MET cc_start: 0.2790 (ttt) cc_final: 0.2569 (ptm) REVERT: D 409 MET cc_start: 0.2971 (tpp) cc_final: 0.1583 (ptp) REVERT: D 529 VAL cc_start: 0.8007 (m) cc_final: 0.7791 (t) REVERT: D 685 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.7905 (m) outliers start: 82 outliers final: 57 residues processed: 263 average time/residue: 0.1611 time to fit residues: 68.0833 Evaluate side-chains 227 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 486 GLN Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain B residue 514 ASP Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 747 GLU Chi-restraints excluded: chain D residue 790 GLU Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 799 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 222 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 259 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 8 optimal weight: 30.0000 chunk 297 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 HIS ** C 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.270440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.250678 restraints weight = 73013.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.249865 restraints weight = 65727.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.246060 restraints weight = 49666.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.246343 restraints weight = 49419.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.246377 restraints weight = 33039.718| |-----------------------------------------------------------------------------| r_work (final): 0.4896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4895 r_free = 0.4895 target_work(ls_wunit_k1) = 0.243 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4895 r_free = 0.4895 target_work(ls_wunit_k1) = 0.243 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25393 Z= 0.132 Angle : 0.575 13.049 34412 Z= 0.303 Chirality : 0.041 0.164 3909 Planarity : 0.004 0.051 4376 Dihedral : 4.431 20.992 3407 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.50 % Allowed : 13.39 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: -0.16 (0.15), residues: 3134 helix: 0.78 (0.14), residues: 1434 sheet: -0.28 (0.25), residues: 425 loop : -0.99 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 353 TYR 0.018 0.002 TYR C 648 PHE 0.028 0.001 PHE A 691 TRP 0.073 0.002 TRP D 638 HIS 0.007 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00285 (25379) covalent geometry : angle 0.57324 (34384) SS BOND : bond 0.00443 ( 14) SS BOND : angle 1.60192 ( 28) hydrogen bonds : bond 0.05021 ( 1114) hydrogen bonds : angle 4.64225 ( 3245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4883 (mmm) cc_final: 0.3995 (mmt) REVERT: A 212 MET cc_start: 0.2900 (mpp) cc_final: 0.2627 (mpp) REVERT: A 579 LEU cc_start: 0.7048 (tp) cc_final: 0.6228 (tt) REVERT: A 630 MET cc_start: 0.7376 (mmp) cc_final: 0.7060 (mmp) REVERT: B 109 MET cc_start: 0.0962 (mtp) cc_final: -0.0786 (mmt) REVERT: B 247 ASN cc_start: 0.5304 (t0) cc_final: 0.5081 (t0) REVERT: B 409 MET cc_start: 0.2897 (tpp) cc_final: 0.1762 (ptp) REVERT: C 212 MET cc_start: 0.2918 (mpp) cc_final: 0.2673 (mpp) REVERT: C 346 MET cc_start: 0.3490 (tpt) cc_final: 0.1418 (pmm) REVERT: C 433 ARG cc_start: 0.5357 (OUTLIER) cc_final: 0.4237 (ptp90) REVERT: C 566 TRP cc_start: 0.8079 (m100) cc_final: 0.7689 (m100) REVERT: C 610 TRP cc_start: 0.6830 (t-100) cc_final: 0.6021 (t60) REVERT: C 634 MET cc_start: 0.6276 (tmm) cc_final: 0.5903 (mmp) REVERT: C 661 MET cc_start: 0.3928 (OUTLIER) cc_final: 0.3282 (tpp) REVERT: D 247 ASN cc_start: 0.5276 (t0) cc_final: 0.5067 (t0) REVERT: D 409 MET cc_start: 0.2995 (tpp) cc_final: 0.1675 (ptp) outliers start: 41 outliers final: 29 residues processed: 216 average time/residue: 0.1475 time to fit residues: 52.0445 Evaluate side-chains 203 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 826 LEU Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 799 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 62 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 160 optimal weight: 50.0000 chunk 158 optimal weight: 7.9990 chunk 285 optimal weight: 0.6980 chunk 283 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5087 r_free = 0.5087 target = 0.264664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.244523 restraints weight = 71706.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.243434 restraints weight = 67936.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.239610 restraints weight = 55941.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.238572 restraints weight = 62432.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.237505 restraints weight = 46024.145| |-----------------------------------------------------------------------------| r_work (final): 0.4826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4826 r_free = 0.4826 target_work(ls_wunit_k1) = 0.234 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4826 r_free = 0.4826 target_work(ls_wunit_k1) = 0.234 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5195 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 25393 Z= 0.296 Angle : 0.785 13.740 34412 Z= 0.415 Chirality : 0.049 0.268 3909 Planarity : 0.005 0.076 4376 Dihedral : 5.143 28.742 3407 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 3.15 % Allowed : 13.17 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: -0.70 (0.15), residues: 3134 helix: 0.33 (0.14), residues: 1433 sheet: -0.48 (0.26), residues: 408 loop : -1.29 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 535 TYR 0.040 0.003 TYR D 539 PHE 0.041 0.003 PHE A 691 TRP 0.068 0.003 TRP B 638 HIS 0.008 0.001 HIS D 829 Details of bonding type rmsd covalent geometry : bond 0.00699 (25379) covalent geometry : angle 0.78298 (34384) SS BOND : bond 0.00148 ( 14) SS BOND : angle 2.09749 ( 28) hydrogen bonds : bond 0.06675 ( 1114) hydrogen bonds : angle 5.27432 ( 3245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 171 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4838 (mmm) cc_final: 0.4094 (mmt) REVERT: B 109 MET cc_start: 0.1118 (mtp) cc_final: -0.0644 (mmt) REVERT: B 247 ASN cc_start: 0.5493 (t0) cc_final: 0.5289 (t0) REVERT: B 329 MET cc_start: 0.1920 (ptm) cc_final: 0.1590 (ptm) REVERT: B 409 MET cc_start: 0.2910 (tpp) cc_final: 0.1947 (ptp) REVERT: C 153 MET cc_start: 0.3747 (mmp) cc_final: 0.3365 (tpp) REVERT: C 212 MET cc_start: 0.2827 (mpp) cc_final: 0.2612 (mpp) REVERT: C 515 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8311 (pp) REVERT: C 634 MET cc_start: 0.6605 (tmm) cc_final: 0.6131 (mmp) REVERT: D 153 MET cc_start: 0.4294 (tpt) cc_final: 0.4053 (tpt) REVERT: D 247 ASN cc_start: 0.5727 (t0) cc_final: 0.5457 (t0) REVERT: D 409 MET cc_start: 0.2994 (tpp) cc_final: 0.1922 (ptp) REVERT: D 707 GLU cc_start: 0.6285 (tm-30) cc_final: 0.5932 (tm-30) outliers start: 86 outliers final: 67 residues processed: 243 average time/residue: 0.1611 time to fit residues: 63.5122 Evaluate side-chains 232 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 164 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 764 SER Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain C residue 837 ILE Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 586 ILE Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 747 GLU Chi-restraints excluded: chain D residue 754 ASP Chi-restraints excluded: chain D residue 790 GLU Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 799 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 246 optimal weight: 40.0000 chunk 278 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 0.0070 chunk 177 optimal weight: 8.9990 chunk 298 optimal weight: 0.7980 chunk 312 optimal weight: 2.9990 chunk 202 optimal weight: 0.5980 chunk 14 optimal weight: 7.9990 chunk 192 optimal weight: 30.0000 chunk 197 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.269247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.248021 restraints weight = 65702.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.245427 restraints weight = 60726.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.242975 restraints weight = 43013.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.242030 restraints weight = 45402.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.240781 restraints weight = 39022.490| |-----------------------------------------------------------------------------| r_work (final): 0.4856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4857 r_free = 0.4857 target_work(ls_wunit_k1) = 0.238 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4857 r_free = 0.4857 target_work(ls_wunit_k1) = 0.238 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5057 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25393 Z= 0.121 Angle : 0.582 12.516 34412 Z= 0.300 Chirality : 0.041 0.177 3909 Planarity : 0.004 0.052 4376 Dihedral : 4.414 20.621 3407 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.50 % Allowed : 15.48 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: -0.24 (0.15), residues: 3134 helix: 0.77 (0.14), residues: 1443 sheet: -0.34 (0.26), residues: 430 loop : -1.12 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 710 TYR 0.018 0.001 TYR C 648 PHE 0.027 0.001 PHE A 581 TRP 0.073 0.002 TRP B 638 HIS 0.006 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00260 (25379) covalent geometry : angle 0.58059 (34384) SS BOND : bond 0.00164 ( 14) SS BOND : angle 1.58802 ( 28) hydrogen bonds : bond 0.04808 ( 1114) hydrogen bonds : angle 4.54409 ( 3245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4837 (mmm) cc_final: 0.4003 (mmt) REVERT: A 212 MET cc_start: 0.2487 (mpp) cc_final: 0.2100 (mpp) REVERT: A 278 MET cc_start: 0.1418 (mtm) cc_final: 0.0479 (mtm) REVERT: A 579 LEU cc_start: 0.7055 (tp) cc_final: 0.6207 (tt) REVERT: B 109 MET cc_start: 0.0844 (mtp) cc_final: -0.0902 (mmt) REVERT: B 153 MET cc_start: 0.4313 (tpt) cc_final: 0.3124 (tpp) REVERT: B 212 MET cc_start: 0.0406 (mmp) cc_final: -0.1042 (mtm) REVERT: B 409 MET cc_start: 0.2796 (tpp) cc_final: 0.1900 (ptp) REVERT: B 504 MET cc_start: 0.5246 (tpt) cc_final: 0.4692 (tpt) REVERT: B 634 MET cc_start: 0.6933 (mmp) cc_final: 0.6373 (mmt) REVERT: C 153 MET cc_start: 0.3607 (mmp) cc_final: 0.3207 (tpp) REVERT: C 212 MET cc_start: 0.2777 (mpp) cc_final: 0.2555 (mpp) REVERT: C 278 MET cc_start: 0.1342 (mtm) cc_final: 0.0454 (mtm) REVERT: C 618 GLN cc_start: 0.6537 (mm110) cc_final: 0.4853 (tm-30) REVERT: C 634 MET cc_start: 0.6105 (tmm) cc_final: 0.5762 (mmp) REVERT: C 666 ARG cc_start: 0.5519 (OUTLIER) cc_final: 0.5033 (tpt90) REVERT: D 247 ASN cc_start: 0.5790 (t0) cc_final: 0.5543 (t0) REVERT: D 409 MET cc_start: 0.2824 (tpp) cc_final: 0.1851 (ptp) outliers start: 41 outliers final: 30 residues processed: 200 average time/residue: 0.1595 time to fit residues: 52.6869 Evaluate side-chains 197 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 315 MET Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 666 ARG Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 638 TRP Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 796 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 38 optimal weight: 7.9990 chunk 107 optimal weight: 40.0000 chunk 149 optimal weight: 0.8980 chunk 35 optimal weight: 40.0000 chunk 314 optimal weight: 6.9990 chunk 73 optimal weight: 0.0770 chunk 187 optimal weight: 6.9990 chunk 277 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 31 optimal weight: 50.0000 chunk 200 optimal weight: 0.5980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.268139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.246656 restraints weight = 79868.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.245192 restraints weight = 65156.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.241192 restraints weight = 49317.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.241400 restraints weight = 48065.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.241510 restraints weight = 32391.167| |-----------------------------------------------------------------------------| r_work (final): 0.4863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4863 r_free = 0.4863 target_work(ls_wunit_k1) = 0.239 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4863 r_free = 0.4863 target_work(ls_wunit_k1) = 0.239 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5039 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25393 Z= 0.137 Angle : 0.590 12.332 34412 Z= 0.304 Chirality : 0.041 0.187 3909 Planarity : 0.004 0.051 4376 Dihedral : 4.323 20.140 3407 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.76 % Allowed : 15.85 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: -0.17 (0.15), residues: 3134 helix: 0.86 (0.14), residues: 1437 sheet: -0.20 (0.26), residues: 412 loop : -1.15 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 710 TYR 0.018 0.002 TYR D 539 PHE 0.035 0.001 PHE A 691 TRP 0.063 0.002 TRP B 638 HIS 0.006 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00310 (25379) covalent geometry : angle 0.58947 (34384) SS BOND : bond 0.00159 ( 14) SS BOND : angle 1.26667 ( 28) hydrogen bonds : bond 0.04792 ( 1114) hydrogen bonds : angle 4.46970 ( 3245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4802 (mmm) cc_final: 0.3942 (mmt) REVERT: A 278 MET cc_start: 0.1371 (mtm) cc_final: 0.0493 (mtm) REVERT: A 381 MET cc_start: 0.0319 (mtp) cc_final: -0.1893 (ttt) REVERT: A 579 LEU cc_start: 0.6959 (tp) cc_final: 0.6170 (tt) REVERT: B 109 MET cc_start: 0.0913 (mtp) cc_final: -0.0860 (mmt) REVERT: B 153 MET cc_start: 0.4367 (tpt) cc_final: 0.3243 (tpp) REVERT: B 212 MET cc_start: 0.0159 (mmp) cc_final: -0.1087 (mtm) REVERT: B 329 MET cc_start: 0.1928 (ptm) cc_final: 0.1611 (ptm) REVERT: B 409 MET cc_start: 0.2833 (tpp) cc_final: 0.1942 (ptp) REVERT: B 634 MET cc_start: 0.6866 (mmp) cc_final: 0.6399 (mmt) REVERT: C 153 MET cc_start: 0.3684 (mmp) cc_final: 0.3067 (tpp) REVERT: C 212 MET cc_start: 0.2842 (mpp) cc_final: 0.2621 (mpp) REVERT: C 278 MET cc_start: 0.1416 (mtm) cc_final: 0.0627 (mtm) REVERT: C 381 MET cc_start: 0.0642 (mtp) cc_final: -0.1865 (ttt) REVERT: C 618 GLN cc_start: 0.6545 (mm110) cc_final: 0.4901 (tm-30) REVERT: C 634 MET cc_start: 0.6136 (tmm) cc_final: 0.5837 (mmp) REVERT: D 153 MET cc_start: 0.4435 (tpt) cc_final: 0.3223 (tpp) REVERT: D 212 MET cc_start: 0.0511 (mmp) cc_final: -0.0555 (mtm) REVERT: D 247 ASN cc_start: 0.5688 (t0) cc_final: 0.5436 (t0) REVERT: D 409 MET cc_start: 0.2843 (tpp) cc_final: 0.1887 (ptp) outliers start: 48 outliers final: 38 residues processed: 210 average time/residue: 0.1589 time to fit residues: 54.8198 Evaluate side-chains 205 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 754 ASP Chi-restraints excluded: chain D residue 796 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 162 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 293 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 264 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 166 optimal weight: 30.0000 chunk 207 optimal weight: 0.9980 chunk 310 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.269091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.246816 restraints weight = 63831.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.245162 restraints weight = 64092.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.241366 restraints weight = 49648.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.241040 restraints weight = 47219.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.240243 restraints weight = 37530.538| |-----------------------------------------------------------------------------| r_work (final): 0.4846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4847 r_free = 0.4847 target_work(ls_wunit_k1) = 0.237 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4847 r_free = 0.4847 target_work(ls_wunit_k1) = 0.237 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5079 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25393 Z= 0.127 Angle : 0.577 12.265 34412 Z= 0.296 Chirality : 0.041 0.187 3909 Planarity : 0.004 0.052 4376 Dihedral : 4.215 19.239 3407 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.76 % Allowed : 15.85 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: -0.09 (0.15), residues: 3134 helix: 0.94 (0.14), residues: 1441 sheet: -0.29 (0.25), residues: 434 loop : -1.11 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 666 TYR 0.017 0.001 TYR C 648 PHE 0.034 0.001 PHE A 691 TRP 0.064 0.002 TRP B 638 HIS 0.015 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00287 (25379) covalent geometry : angle 0.57607 (34384) SS BOND : bond 0.00101 ( 14) SS BOND : angle 1.12132 ( 28) hydrogen bonds : bond 0.04556 ( 1114) hydrogen bonds : angle 4.36448 ( 3245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4746 (mmm) cc_final: 0.3996 (mmt) REVERT: A 278 MET cc_start: 0.1170 (mtm) cc_final: 0.0375 (mtm) REVERT: A 381 MET cc_start: 0.0643 (mtp) cc_final: -0.1700 (ttt) REVERT: A 579 LEU cc_start: 0.6859 (tp) cc_final: 0.6083 (tt) REVERT: B 109 MET cc_start: 0.1116 (mtp) cc_final: -0.0875 (mmt) REVERT: B 153 MET cc_start: 0.4435 (tpt) cc_final: 0.3376 (tpp) REVERT: B 212 MET cc_start: -0.0102 (mmp) cc_final: -0.1085 (mtm) REVERT: B 409 MET cc_start: 0.2770 (tpp) cc_final: 0.1904 (ptp) REVERT: C 153 MET cc_start: 0.3379 (mmp) cc_final: 0.2821 (tpp) REVERT: C 212 MET cc_start: 0.2728 (mpp) cc_final: 0.2514 (mpp) REVERT: C 381 MET cc_start: 0.0413 (mtp) cc_final: -0.1898 (ttt) REVERT: C 455 ASN cc_start: 0.1214 (OUTLIER) cc_final: 0.0787 (p0) REVERT: C 618 GLN cc_start: 0.6409 (mm110) cc_final: 0.4807 (tm-30) REVERT: C 634 MET cc_start: 0.6201 (tmm) cc_final: 0.5938 (mmp) REVERT: C 666 ARG cc_start: 0.5470 (OUTLIER) cc_final: 0.4906 (tpt90) REVERT: D 153 MET cc_start: 0.4489 (tpt) cc_final: 0.3309 (tpp) REVERT: D 212 MET cc_start: 0.0248 (mmp) cc_final: -0.0694 (mtm) REVERT: D 247 ASN cc_start: 0.5759 (t0) cc_final: 0.5509 (t0) REVERT: D 329 MET cc_start: 0.1726 (ptm) cc_final: 0.1472 (ptm) REVERT: D 409 MET cc_start: 0.2782 (tpp) cc_final: 0.1835 (ptp) outliers start: 48 outliers final: 38 residues processed: 209 average time/residue: 0.1626 time to fit residues: 55.4377 Evaluate side-chains 209 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 455 ASN Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 666 ARG Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 799 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 212 optimal weight: 0.9980 chunk 296 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 17 optimal weight: 30.0000 chunk 260 optimal weight: 20.0000 chunk 189 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 303 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 775 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.266990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.247198 restraints weight = 66390.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.245090 restraints weight = 63198.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.242216 restraints weight = 52351.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.241013 restraints weight = 43854.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.239034 restraints weight = 47468.693| |-----------------------------------------------------------------------------| r_work (final): 0.4841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4840 r_free = 0.4840 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4840 r_free = 0.4840 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5161 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25393 Z= 0.218 Angle : 0.691 12.370 34412 Z= 0.359 Chirality : 0.045 0.218 3909 Planarity : 0.005 0.065 4376 Dihedral : 4.652 24.663 3407 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.69 % Allowed : 15.92 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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 (0.15), residues: 3134 helix: 0.69 (0.14), residues: 1437 sheet: -0.37 (0.26), residues: 430 loop : -1.19 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 710 TYR 0.031 0.002 TYR D 539 PHE 0.045 0.002 PHE A 691 TRP 0.055 0.002 TRP B 638 HIS 0.007 0.001 HIS D 829 Details of bonding type rmsd covalent geometry : bond 0.00513 (25379) covalent geometry : angle 0.69033 (34384) SS BOND : bond 0.00126 ( 14) SS BOND : angle 0.97324 ( 28) hydrogen bonds : bond 0.05638 ( 1114) hydrogen bonds : angle 4.76117 ( 3245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4775 (mmm) cc_final: 0.4015 (mmt) REVERT: A 278 MET cc_start: 0.1373 (mtm) cc_final: 0.0584 (mtm) REVERT: A 381 MET cc_start: 0.0620 (mtp) cc_final: -0.1714 (ttt) REVERT: A 579 LEU cc_start: 0.7048 (tp) cc_final: 0.6219 (tt) REVERT: B 109 MET cc_start: 0.1209 (mtp) cc_final: -0.0814 (mmt) REVERT: B 153 MET cc_start: 0.4477 (tpt) cc_final: 0.3420 (tpp) REVERT: B 212 MET cc_start: 0.0146 (mmp) cc_final: -0.0801 (mtm) REVERT: B 409 MET cc_start: 0.2839 (tpp) cc_final: 0.1972 (ptp) REVERT: B 504 MET cc_start: 0.5450 (tpt) cc_final: 0.5189 (mmt) REVERT: C 153 MET cc_start: 0.3677 (mmp) cc_final: 0.3112 (tpp) REVERT: C 212 MET cc_start: 0.2935 (mpp) cc_final: 0.2733 (mpp) REVERT: C 278 MET cc_start: 0.1478 (mtm) cc_final: 0.0732 (mtm) REVERT: C 381 MET cc_start: 0.0737 (mtp) cc_final: -0.1867 (ttt) REVERT: C 618 GLN cc_start: 0.6627 (mm110) cc_final: 0.4824 (tm-30) REVERT: C 634 MET cc_start: 0.6302 (tmm) cc_final: 0.6012 (mmp) REVERT: C 666 ARG cc_start: 0.5702 (OUTLIER) cc_final: 0.5195 (tpt90) REVERT: D 153 MET cc_start: 0.4346 (tpt) cc_final: 0.3213 (tpp) REVERT: D 212 MET cc_start: 0.0164 (mmp) cc_final: -0.0632 (mtm) REVERT: D 409 MET cc_start: 0.2848 (tpp) cc_final: 0.1883 (ptp) outliers start: 46 outliers final: 41 residues processed: 204 average time/residue: 0.1620 time to fit residues: 54.0603 Evaluate side-chains 202 residues out of total 2726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 844 LEU Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 554 ILE Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 666 ARG Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 838 LEU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 117 GLN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 665 ILE Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 799 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 99 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 282 optimal weight: 6.9990 chunk 23 optimal weight: 40.0000 chunk 65 optimal weight: 0.8980 chunk 236 optimal weight: 0.9990 chunk 300 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 232 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 HIS ** B 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN ** C 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS D 237 HIS ** D 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.271155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.250274 restraints weight = 80257.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.250034 restraints weight = 74676.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.247226 restraints weight = 49165.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.247585 restraints weight = 40942.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.247064 restraints weight = 32075.613| |-----------------------------------------------------------------------------| r_work (final): 0.4905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4904 r_free = 0.4904 target_work(ls_wunit_k1) = 0.244 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4904 r_free = 0.4904 target_work(ls_wunit_k1) = 0.244 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4959 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25393 Z= 0.120 Angle : 0.574 12.194 34412 Z= 0.294 Chirality : 0.041 0.258 3909 Planarity : 0.004 0.052 4376 Dihedral : 4.222 19.025 3407 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.50 % Allowed : 16.21 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % 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: -0.08 (0.15), residues: 3134 helix: 0.95 (0.14), residues: 1446 sheet: -0.23 (0.26), residues: 422 loop : -1.13 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 710 TYR 0.023 0.001 TYR C 737 PHE 0.040 0.001 PHE A 581 TRP 0.065 0.002 TRP D 638 HIS 0.011 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00262 (25379) covalent geometry : angle 0.57355 (34384) SS BOND : bond 0.00131 ( 14) SS BOND : angle 0.96040 ( 28) hydrogen bonds : bond 0.04477 ( 1114) hydrogen bonds : angle 4.34820 ( 3245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3797.08 seconds wall clock time: 66 minutes 52.76 seconds (4012.76 seconds total)