Starting phenix.real_space_refine on Mon Jun 23 22:04:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wte_32780/06_2025/7wte_32780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wte_32780/06_2025/7wte_32780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wte_32780/06_2025/7wte_32780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wte_32780/06_2025/7wte_32780.map" model { file = "/net/cci-nas-00/data/ceres_data/7wte_32780/06_2025/7wte_32780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wte_32780/06_2025/7wte_32780.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 152 5.16 5 C 17172 2.51 5 N 4735 2.21 5 O 5089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27160 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "B" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "C" Number of atoms: 8869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8869 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 65, 'TRANS': 1080} Chain: "D" Number of atoms: 8877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8877 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 65, 'TRANS': 1081} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'ACO': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'ACO': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.03, per 1000 atoms: 0.70 Number of scatterers: 27160 At special positions: 0 Unit cell: (161.7, 160.6, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 12 15.00 O 5089 8.00 N 4735 7.00 C 17172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 786 " distance=2.03 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.02 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.02 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.02 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.94 Conformation dependent library (CDL) restraints added in 8.1 seconds 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6430 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 24 sheets defined 47.8% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 540 through 549 removed outlier: 4.032A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 583 through 598 removed outlier: 3.852A pdb=" N LEU A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 608 through 613 removed outlier: 4.277A pdb=" N PHE A 612 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 613' Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.975A pdb=" N GLU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.674A pdb=" N VAL A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.605A pdb=" N MET A 686 " --> pdb=" O TYR A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 Processing helix chain 'A' and resid 748 through 761 Processing helix chain 'A' and resid 778 through 788 Processing helix chain 'A' and resid 809 through 817 removed outlier: 3.552A pdb=" N LEU A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 843 removed outlier: 3.936A pdb=" N VAL A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 854 removed outlier: 4.205A pdb=" N THR A 853 " --> pdb=" O ASP A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 867 through 882 Processing helix chain 'A' and resid 883 through 886 Processing helix chain 'A' and resid 887 through 901 removed outlier: 3.955A pdb=" N VAL A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 924 Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 941 through 949 Processing helix chain 'A' and resid 960 through 969 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.968A pdb=" N SER A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.733A pdb=" N LEU A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1013 through 1028 Processing helix chain 'A' and resid 1034 through 1040 Processing helix chain 'B' and resid 496 through 510 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 571 through 578 removed outlier: 4.200A pdb=" N GLN B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 590 through 598 removed outlier: 3.701A pdb=" N HIS B 596 " --> pdb=" O PRO B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 612 removed outlier: 3.787A pdb=" N THR B 611 " --> pdb=" O GLY B 608 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 612 " --> pdb=" O GLY B 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 608 through 612' Processing helix chain 'B' and resid 613 through 618 Processing helix chain 'B' and resid 622 through 631 removed outlier: 3.533A pdb=" N GLU B 629 " --> pdb=" O ARG B 625 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 630 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 removed outlier: 3.554A pdb=" N VAL B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 697 removed outlier: 3.571A pdb=" N MET B 686 " --> pdb=" O TYR B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 734 removed outlier: 3.823A pdb=" N TYR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 removed outlier: 3.526A pdb=" N ARG B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 790 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 809 through 817 removed outlier: 3.862A pdb=" N LEU B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 843 removed outlier: 4.049A pdb=" N VAL B 831 " --> pdb=" O PRO B 827 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 867 through 881 removed outlier: 3.845A pdb=" N ASN B 873 " --> pdb=" O GLY B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 902 removed outlier: 3.781A pdb=" N GLU B 889 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 925 Processing helix chain 'B' and resid 927 through 934 Processing helix chain 'B' and resid 941 through 950 Processing helix chain 'B' and resid 960 through 969 removed outlier: 3.797A pdb=" N ARG B 964 " --> pdb=" O PRO B 960 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 969 " --> pdb=" O SER B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 987 through 998 removed outlier: 3.524A pdb=" N GLU B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1013 Processing helix chain 'B' and resid 1013 through 1028 Processing helix chain 'B' and resid 1034 through 1040 Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.663A pdb=" N ILE C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 109 removed outlier: 3.548A pdb=" N ASN C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.675A pdb=" N ALA C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 149 Processing helix chain 'C' and resid 151 through 162 removed outlier: 3.847A pdb=" N ALA C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA C 162 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.547A pdb=" N TYR C 187 " --> pdb=" O PHE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 227 removed outlier: 3.759A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 303 Processing helix chain 'C' and resid 332 through 341 removed outlier: 4.516A pdb=" N THR C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 354 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 435 through 450 Processing helix chain 'C' and resid 458 through 468 removed outlier: 3.621A pdb=" N LEU C 462 " --> pdb=" O ASN C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 474 removed outlier: 3.517A pdb=" N GLY C 474 " --> pdb=" O GLN C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 481 removed outlier: 4.384A pdb=" N ILE C 481 " --> pdb=" O THR C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.663A pdb=" N LEU C 500 " --> pdb=" O ARG C 496 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 571 through 578 removed outlier: 4.208A pdb=" N GLN C 575 " --> pdb=" O ARG C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 589 removed outlier: 3.838A pdb=" N LYS C 589 " --> pdb=" O ASP C 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 586 through 589' Processing helix chain 'C' and resid 590 through 598 removed outlier: 3.700A pdb=" N HIS C 596 " --> pdb=" O PRO C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.739A pdb=" N THR C 611 " --> pdb=" O GLY C 608 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE C 612 " --> pdb=" O GLY C 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 622 through 634 removed outlier: 4.417A pdb=" N GLU C 629 " --> pdb=" O ARG C 625 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 630 " --> pdb=" O ARG C 626 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU C 632 " --> pdb=" O GLN C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 removed outlier: 3.658A pdb=" N GLY C 670 " --> pdb=" O ALA C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 697 removed outlier: 3.688A pdb=" N MET C 686 " --> pdb=" O TYR C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 734 removed outlier: 3.593A pdb=" N TYR C 723 " --> pdb=" O SER C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 removed outlier: 4.327A pdb=" N ARG C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 790 Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.504A pdb=" N SER C 802 " --> pdb=" O ASP C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 817 removed outlier: 3.802A pdb=" N LEU C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 843 removed outlier: 4.198A pdb=" N VAL C 831 " --> pdb=" O PRO C 827 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE C 832 " --> pdb=" O MET C 828 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 846 No H-bonds generated for 'chain 'C' and resid 844 through 846' Processing helix chain 'C' and resid 860 through 865 removed outlier: 4.024A pdb=" N ASN C 864 " --> pdb=" O ASP C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 881 removed outlier: 3.880A pdb=" N THR C 872 " --> pdb=" O GLY C 868 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASN C 873 " --> pdb=" O GLY C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 893 removed outlier: 3.658A pdb=" N VAL C 890 " --> pdb=" O LYS C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 902 Processing helix chain 'C' and resid 908 through 925 removed outlier: 4.282A pdb=" N LYS C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 934 Processing helix chain 'C' and resid 941 through 950 removed outlier: 3.713A pdb=" N GLY C 950 " --> pdb=" O GLU C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 968 removed outlier: 4.386A pdb=" N ARG C 964 " --> pdb=" O PRO C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 987 through 998 removed outlier: 3.931A pdb=" N GLU C 991 " --> pdb=" O LEU C 987 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1013 Processing helix chain 'C' and resid 1013 through 1027 removed outlier: 3.704A pdb=" N ALA C1025 " --> pdb=" O LYS C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1040 Processing helix chain 'D' and resid 46 through 59 removed outlier: 3.510A pdb=" N LEU D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 124 through 134 removed outlier: 3.841A pdb=" N ALA D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 150 Processing helix chain 'D' and resid 151 through 162 removed outlier: 3.954A pdb=" N ALA D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 removed outlier: 3.596A pdb=" N TYR D 187 " --> pdb=" O PHE D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 228 removed outlier: 3.798A pdb=" N GLU D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 303 Processing helix chain 'D' and resid 332 through 340 removed outlier: 3.994A pdb=" N THR D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 339 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 354 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 435 through 450 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 468 through 474 removed outlier: 3.538A pdb=" N LEU D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 481 removed outlier: 4.245A pdb=" N ILE D 481 " --> pdb=" O THR D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 488 removed outlier: 3.647A pdb=" N PHE D 488 " --> pdb=" O PRO D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 510 removed outlier: 3.629A pdb=" N LEU D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 548 removed outlier: 3.773A pdb=" N LEU D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 571 through 578 removed outlier: 3.507A pdb=" N GLN D 575 " --> pdb=" O ARG D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.744A pdb=" N LEU D 587 " --> pdb=" O ARG D 583 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 608 through 618 removed outlier: 3.522A pdb=" N PHE D 612 " --> pdb=" O GLY D 608 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP D 613 " --> pdb=" O GLY D 609 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET D 616 " --> pdb=" O PHE D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 655 through 670 removed outlier: 3.567A pdb=" N VAL D 659 " --> pdb=" O PRO D 655 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 697 Processing helix chain 'D' and resid 719 through 734 Processing helix chain 'D' and resid 748 through 761 Processing helix chain 'D' and resid 778 through 790 Processing helix chain 'D' and resid 798 through 802 Processing helix chain 'D' and resid 809 through 817 removed outlier: 3.723A pdb=" N LEU D 813 " --> pdb=" O SER D 809 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR D 817 " --> pdb=" O LEU D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 843 removed outlier: 3.885A pdb=" N VAL D 831 " --> pdb=" O PRO D 827 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 846 No H-bonds generated for 'chain 'D' and resid 844 through 846' Processing helix chain 'D' and resid 849 through 853 removed outlier: 3.756A pdb=" N ALA D 852 " --> pdb=" O ASP D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 870 Processing helix chain 'D' and resid 871 through 882 removed outlier: 3.791A pdb=" N ALA D 878 " --> pdb=" O LEU D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 removed outlier: 3.731A pdb=" N TYR D 894 " --> pdb=" O VAL D 890 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL D 895 " --> pdb=" O LYS D 891 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 925 Processing helix chain 'D' and resid 927 through 934 Processing helix chain 'D' and resid 941 through 950 Processing helix chain 'D' and resid 960 through 969 Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 988 through 998 Processing helix chain 'D' and resid 1003 through 1013 removed outlier: 3.904A pdb=" N VAL D1007 " --> pdb=" O THR D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1027 Processing helix chain 'D' and resid 1034 through 1040 Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.738A pdb=" N LEU A 564 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL A 796 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N MET A 566 " --> pdb=" O VAL A 796 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 604 through 605 removed outlier: 6.520A pdb=" N MET A 604 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LEU A 642 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET A 641 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 674 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 700 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N CYS A 739 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA A 702 " --> pdb=" O CYS A 739 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LYS A 741 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 704 " --> pdb=" O LYS A 741 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 738 " --> pdb=" O HIS A 769 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N HIS A 771 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 740 " --> pdb=" O HIS A 771 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 4.034A pdb=" N LEU A1058 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA A1062 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A1064 " --> pdb=" O PHE A1077 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.933A pdb=" N LEU B 564 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL B 796 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N MET B 566 " --> pdb=" O VAL B 796 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 604 through 605 removed outlier: 5.823A pdb=" N MET B 604 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU B 642 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE B 639 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ARG B 675 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET B 641 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE B 677 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 643 " --> pdb=" O PHE B 677 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL B 700 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N CYS B 739 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 702 " --> pdb=" O CYS B 739 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS B 741 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N HIS B 771 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE B 740 " --> pdb=" O HIS B 771 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 6.867A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 85 removed outlier: 6.486A pdb=" N VAL C 40 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE C 66 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL C 42 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS C 39 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N HIS C 115 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET C 41 " --> pdb=" O HIS C 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 206 through 207 removed outlier: 3.771A pdb=" N GLU C 236 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 325 through 326 removed outlier: 6.323A pdb=" N GLU C 246 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU C 262 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN C 248 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER C 266 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL C 275 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN C 268 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS C 273 " --> pdb=" O GLN C 268 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL C 274 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG C 377 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N CYS C 372 " --> pdb=" O HIS C 432 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N HIS C 432 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 374 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE C 430 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS C 376 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS C 428 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL C 378 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 381 through 382 removed outlier: 3.702A pdb=" N GLN C 388 " --> pdb=" O ASP C 382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.138A pdb=" N GLY C 392 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 396 through 398 removed outlier: 4.078A pdb=" N ARG C 451 " --> pdb=" O ARG C 398 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 564 through 566 removed outlier: 6.416A pdb=" N LEU C 564 " --> pdb=" O VAL C 794 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 768 " --> pdb=" O VAL C 793 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ASP C 795 " --> pdb=" O LEU C 768 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE C 770 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU C 738 " --> pdb=" O HIS C 769 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N HIS C 771 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE C 740 " --> pdb=" O HIS C 771 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL C 700 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N CYS C 739 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 702 " --> pdb=" O CYS C 739 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LYS C 741 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE C 704 " --> pdb=" O LYS C 741 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 701 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE C 639 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ARG C 675 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET C 641 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE C 677 " --> pdb=" O MET C 641 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU C 643 " --> pdb=" O PHE C 677 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET C 604 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N LEU C 642 " --> pdb=" O MET C 604 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N ASN C 606 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 12.562A pdb=" N ARG C 644 " --> pdb=" O ASN C 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1048 through 1050 removed outlier: 3.531A pdb=" N PHE C1048 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C1060 " --> pdb=" O PHE C1048 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA C1062 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C1064 " --> pdb=" O PHE C1077 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1111 through 1112 removed outlier: 4.457A pdb=" N LEU C1175 " --> pdb=" O ILE C1112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1146 through 1150 removed outlier: 3.778A pdb=" N VAL C1149 " --> pdb=" O CYS C1138 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N CYS C1138 " --> pdb=" O VAL C1149 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C1122 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER C1141 " --> pdb=" O VAL C1120 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C1120 " --> pdb=" O SER C1141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 82 through 85 removed outlier: 6.340A pdb=" N VAL D 40 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE D 66 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL D 42 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 113 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 204 through 207 removed outlier: 3.509A pdb=" N ARG D 205 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 257 through 259 removed outlier: 3.842A pdb=" N GLU D 324 " --> pdb=" O GLU D 311 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 275 through 277 removed outlier: 3.657A pdb=" N VAL D 427 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 381 through 382 removed outlier: 3.802A pdb=" N GLN D 388 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 564 through 567 removed outlier: 8.587A pdb=" N GLU D 605 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP D 567 " --> pdb=" O GLU D 605 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TRP D 607 " --> pdb=" O ASP D 567 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 13.206A pdb=" N ARG D 644 " --> pdb=" O ASN D 606 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE D 639 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ARG D 675 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET D 641 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N PHE D 677 " --> pdb=" O MET D 641 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU D 643 " --> pdb=" O PHE D 677 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL D 700 " --> pdb=" O ILE D 737 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N CYS D 739 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA D 702 " --> pdb=" O CYS D 739 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS D 741 " --> pdb=" O ALA D 702 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE D 704 " --> pdb=" O LYS D 741 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU D 564 " --> pdb=" O VAL D 794 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL D 796 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N MET D 566 " --> pdb=" O VAL D 796 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1047 through 1051 removed outlier: 6.927A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL D1065 " --> pdb=" O GLN D1075 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN D1075 " --> pdb=" O VAL D1065 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1140 through 1141 removed outlier: 3.586A pdb=" N LEU D1140 " --> pdb=" O THR D1147 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR D1147 " --> pdb=" O LEU D1140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 1106 hydrogen bonds defined for protein. 3225 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: 15.61 Time building geometry restraints manager: 8.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6340 1.33 - 1.45: 5556 1.45 - 1.57: 15588 1.57 - 1.70: 20 1.70 - 1.82: 264 Bond restraints: 27768 Sorted by residual: bond pdb=" N ILE C 516 " pdb=" CA ILE C 516 " ideal model delta sigma weight residual 1.458 1.493 -0.036 7.70e-03 1.69e+04 2.15e+01 bond pdb=" N ILE D 516 " pdb=" CA ILE D 516 " ideal model delta sigma weight residual 1.460 1.493 -0.034 7.50e-03 1.78e+04 2.05e+01 bond pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.11e-02 8.12e+03 1.31e+01 bond pdb=" N VAL D 826 " pdb=" CA VAL D 826 " ideal model delta sigma weight residual 1.462 1.495 -0.034 1.01e-02 9.80e+03 1.10e+01 bond pdb=" N VAL C 164 " pdb=" CA VAL C 164 " ideal model delta sigma weight residual 1.461 1.501 -0.039 1.23e-02 6.61e+03 1.03e+01 ... (remaining 27763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 36966 2.50 - 4.99: 650 4.99 - 7.49: 53 7.49 - 9.98: 4 9.98 - 12.48: 4 Bond angle restraints: 37677 Sorted by residual: angle pdb=" C3B ACO C2001 " pdb=" O3B ACO C2001 " pdb=" P3B ACO C2001 " ideal model delta sigma weight residual 121.12 110.00 11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" C3B ACO D2001 " pdb=" O3B ACO D2001 " pdb=" P3B ACO D2001 " ideal model delta sigma weight residual 121.12 110.04 11.08 1.00e+00 1.00e+00 1.23e+02 angle pdb=" PB ATP C2000 " pdb=" O3B ATP C2000 " pdb=" PG ATP C2000 " ideal model delta sigma weight residual 139.87 132.70 7.17 1.00e+00 1.00e+00 5.14e+01 angle pdb=" N VAL C 649 " pdb=" CA VAL C 649 " pdb=" C VAL C 649 " ideal model delta sigma weight residual 113.71 108.47 5.24 9.50e-01 1.11e+00 3.04e+01 angle pdb=" C ARG C 202 " pdb=" CA ARG C 202 " pdb=" CB ARG C 202 " ideal model delta sigma weight residual 116.63 110.97 5.66 1.16e+00 7.43e-01 2.38e+01 ... (remaining 37672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15106 17.95 - 35.89: 1350 35.89 - 53.84: 275 53.84 - 71.78: 107 71.78 - 89.72: 29 Dihedral angle restraints: 16867 sinusoidal: 6846 harmonic: 10021 Sorted by residual: dihedral pdb=" CB CYS B 752 " pdb=" SG CYS B 752 " pdb=" SG CYS B 786 " pdb=" CB CYS B 786 " ideal model delta sinusoidal sigma weight residual 93.00 179.39 -86.39 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS A 752 " pdb=" SG CYS A 752 " pdb=" SG CYS A 786 " pdb=" CB CYS A 786 " ideal model delta sinusoidal sigma weight residual 93.00 169.54 -76.54 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS D 752 " pdb=" SG CYS D 752 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual 93.00 141.06 -48.06 1 1.00e+01 1.00e-02 3.18e+01 ... (remaining 16864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3655 0.074 - 0.148: 478 0.148 - 0.221: 29 0.221 - 0.295: 1 0.295 - 0.369: 3 Chirality restraints: 4166 Sorted by residual: chirality pdb=" CB VAL C 164 " pdb=" CA VAL C 164 " pdb=" CG1 VAL C 164 " pdb=" CG2 VAL C 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA VAL C 164 " pdb=" N VAL C 164 " pdb=" C VAL C 164 " pdb=" CB VAL C 164 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ASN C 495 " pdb=" N ASN C 495 " pdb=" C ASN C 495 " pdb=" CB ASN C 495 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 4163 not shown) Planarity restraints: 4955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO D2001 " -0.099 2.00e-02 2.50e+03 8.17e-02 8.35e+01 pdb=" C5P ACO D2001 " 0.027 2.00e-02 2.50e+03 pdb=" C6P ACO D2001 " -0.074 2.00e-02 2.50e+03 pdb=" N4P ACO D2001 " 0.130 2.00e-02 2.50e+03 pdb=" O5P ACO D2001 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO C2001 " 0.099 2.00e-02 2.50e+03 8.16e-02 8.33e+01 pdb=" C5P ACO C2001 " -0.027 2.00e-02 2.50e+03 pdb=" C6P ACO C2001 " 0.074 2.00e-02 2.50e+03 pdb=" N4P ACO C2001 " -0.130 2.00e-02 2.50e+03 pdb=" O5P ACO C2001 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 199 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C GLY C 199 " 0.073 2.00e-02 2.50e+03 pdb=" O GLY C 199 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY C 200 " -0.024 2.00e-02 2.50e+03 ... (remaining 4952 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 1 1.81 - 2.58: 254 2.58 - 3.36: 35280 3.36 - 4.13: 63382 4.13 - 4.90: 113087 Nonbonded interactions: 212004 Sorted by model distance: nonbonded pdb=" CD2 LEU B1063 " pdb=" OE2 GLU B1079 " model vdw 1.040 3.460 nonbonded pdb=" CG LEU B1063 " pdb=" OE2 GLU B1079 " model vdw 1.859 3.470 nonbonded pdb=" O GLY C 199 " pdb=" O3A ATP C2000 " model vdw 1.948 3.040 nonbonded pdb=" OD1 ASP D 112 " pdb=" NH1 ARG D 137 " model vdw 1.956 3.120 nonbonded pdb=" O GLY C 199 " pdb=" O1A ATP C2000 " model vdw 1.989 3.040 ... (remaining 211999 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 33 through 1178) selection = (chain 'D' and resid 33 through 1178) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 20.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 74.020 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.416 27773 Z= 0.365 Angle : 0.745 12.475 37685 Z= 0.451 Chirality : 0.048 0.369 4166 Planarity : 0.005 0.082 4955 Dihedral : 15.109 89.725 10425 Min Nonbonded Distance : 1.040 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.54 % Favored : 93.40 % Rotamer: Outliers : 1.95 % Allowed : 1.08 % Favored : 96.97 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3485 helix: 1.05 (0.14), residues: 1419 sheet: -0.29 (0.23), residues: 501 loop : -1.63 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 607 HIS 0.009 0.001 HIS B 875 PHE 0.014 0.001 PHE C 920 TYR 0.023 0.001 TYR D 304 ARG 0.009 0.001 ARG D1070 Details of bonding type rmsd hydrogen bonds : bond 0.19418 ( 1106) hydrogen bonds : angle 7.00864 ( 3225) SS BOND : bond 0.00605 ( 4) SS BOND : angle 3.85671 ( 8) covalent geometry : bond 0.00419 (27768) covalent geometry : angle 0.74288 (37677) Misc. bond : bond 0.41585 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 376 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 828 MET cc_start: 0.8905 (mmm) cc_final: 0.8350 (mmm) REVERT: A 1022 ASP cc_start: 0.8510 (m-30) cc_final: 0.8277 (m-30) REVERT: B 566 MET cc_start: 0.8619 (ppp) cc_final: 0.8268 (ppp) REVERT: B 686 MET cc_start: 0.8958 (mpp) cc_final: 0.7907 (mpp) REVERT: B 923 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.9131 (pp30) REVERT: C 399 SER cc_start: 0.7462 (p) cc_final: 0.7144 (t) REVERT: C 663 CYS cc_start: 0.8510 (m) cc_final: 0.8301 (m) REVERT: C 724 MET cc_start: 0.8937 (mmp) cc_final: 0.8237 (mmm) REVERT: C 1054 ARG cc_start: 0.8425 (tmm-80) cc_final: 0.8220 (ttp80) REVERT: C 1116 MET cc_start: 0.0337 (tpt) cc_final: -0.0361 (mmt) REVERT: D 58 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7023 (tm-30) REVERT: D 139 ILE cc_start: 0.6372 (mt) cc_final: 0.5487 (mm) REVERT: D 401 GLU cc_start: 0.6891 (pm20) cc_final: 0.6557 (pm20) REVERT: D 430 ILE cc_start: 0.7248 (mt) cc_final: 0.6849 (mt) REVERT: D 881 MET cc_start: 0.8538 (mpp) cc_final: 0.8278 (mpp) REVERT: D 900 MET cc_start: 0.8479 (ptp) cc_final: 0.8218 (mtt) REVERT: D 967 VAL cc_start: 0.9055 (t) cc_final: 0.8841 (m) REVERT: D 1098 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7981 (tmm) outliers start: 56 outliers final: 4 residues processed: 408 average time/residue: 0.4212 time to fit residues: 262.9709 Evaluate side-chains 244 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 238 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 923 GLN Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 1020 PHE Chi-restraints excluded: chain D residue 1098 MET Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 316 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN A 769 HIS ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 GLN B 585 HIS B 681 ASN ** B 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN B 923 GLN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN C 350 HIS ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 GLN C1040 GLN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN D 640 GLN D 653 ASN D1075 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.080190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.062240 restraints weight = 123684.301| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 6.07 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27773 Z= 0.226 Angle : 0.696 11.138 37685 Z= 0.359 Chirality : 0.046 0.308 4166 Planarity : 0.005 0.099 4955 Dihedral : 8.251 70.701 3971 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer: Outliers : 1.43 % Allowed : 9.58 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3485 helix: 0.84 (0.14), residues: 1474 sheet: -0.37 (0.22), residues: 530 loop : -1.67 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 624 HIS 0.016 0.002 HIS B 879 PHE 0.029 0.002 PHE C 387 TYR 0.024 0.002 TYR D 261 ARG 0.009 0.001 ARG D 270 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 1106) hydrogen bonds : angle 5.52641 ( 3225) SS BOND : bond 0.00578 ( 4) SS BOND : angle 2.16259 ( 8) covalent geometry : bond 0.00491 (27768) covalent geometry : angle 0.69585 (37677) Misc. bond : bond 0.00396 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 3.193 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: B 566 MET cc_start: 0.8696 (ppp) cc_final: 0.8331 (ppp) REVERT: B 686 MET cc_start: 0.8997 (mpp) cc_final: 0.8204 (mpp) REVERT: B 690 MET cc_start: 0.9220 (mpp) cc_final: 0.8859 (mpp) REVERT: C 183 PHE cc_start: 0.8199 (m-80) cc_final: 0.7938 (m-80) REVERT: C 377 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7972 (ptt90) REVERT: C 395 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7337 (mt-10) REVERT: C 399 SER cc_start: 0.8318 (p) cc_final: 0.8034 (m) REVERT: C 663 CYS cc_start: 0.8890 (m) cc_final: 0.8638 (m) REVERT: C 724 MET cc_start: 0.9052 (mmp) cc_final: 0.8259 (mmm) REVERT: C 828 MET cc_start: 0.8508 (ppp) cc_final: 0.8301 (ppp) REVERT: C 1067 ASP cc_start: 0.9285 (m-30) cc_final: 0.8848 (t70) REVERT: C 1086 SER cc_start: 0.7757 (p) cc_final: 0.7550 (p) REVERT: C 1116 MET cc_start: -0.0024 (tpt) cc_final: -0.0506 (tpp) REVERT: C 1143 MET cc_start: 0.5355 (ppp) cc_final: 0.4996 (ppp) REVERT: D 58 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7739 (tm-30) REVERT: D 139 ILE cc_start: 0.6423 (mt) cc_final: 0.5825 (mm) REVERT: D 471 PHE cc_start: 0.8242 (t80) cc_final: 0.7899 (t80) REVERT: D 820 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7806 (p) REVERT: D 1116 MET cc_start: 0.3899 (ttt) cc_final: 0.2672 (ptt) outliers start: 41 outliers final: 25 residues processed: 278 average time/residue: 0.4983 time to fit residues: 228.8532 Evaluate side-chains 243 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 6.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 187 TYR Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 208 HIS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 1020 PHE Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 249 optimal weight: 0.7980 chunk 309 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 314 optimal weight: 0.9980 chunk 336 optimal weight: 0.6980 chunk 259 optimal weight: 7.9990 chunk 292 optimal weight: 1.9990 chunk 246 optimal weight: 6.9990 chunk 331 optimal weight: 0.9980 chunk 226 optimal weight: 8.9990 chunk 326 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 GLN B 769 HIS B 864 ASN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.081890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.063927 restraints weight = 120824.584| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 5.99 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27773 Z= 0.114 Angle : 0.612 10.367 37685 Z= 0.303 Chirality : 0.043 0.150 4166 Planarity : 0.004 0.051 4955 Dihedral : 7.855 81.755 3965 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 1.60 % Allowed : 11.91 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3485 helix: 1.14 (0.14), residues: 1470 sheet: -0.20 (0.23), residues: 529 loop : -1.66 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 838 HIS 0.008 0.001 HIS C 259 PHE 0.020 0.001 PHE A 876 TYR 0.018 0.001 TYR D 261 ARG 0.004 0.000 ARG C 377 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 1106) hydrogen bonds : angle 5.06005 ( 3225) SS BOND : bond 0.00400 ( 4) SS BOND : angle 1.61633 ( 8) covalent geometry : bond 0.00249 (27768) covalent geometry : angle 0.61122 (37677) Misc. bond : bond 0.00203 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7331 (pp) REVERT: B 566 MET cc_start: 0.8598 (ppp) cc_final: 0.8173 (ppp) REVERT: B 641 MET cc_start: 0.8868 (ppp) cc_final: 0.8457 (ppp) REVERT: B 686 MET cc_start: 0.9021 (mpp) cc_final: 0.8484 (mpp) REVERT: B 804 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7609 (tpp) REVERT: B 854 MET cc_start: 0.7431 (ppp) cc_final: 0.7143 (ppp) REVERT: C 149 MET cc_start: 0.8150 (mmp) cc_final: 0.7746 (mmt) REVERT: C 183 PHE cc_start: 0.8236 (m-80) cc_final: 0.7829 (m-80) REVERT: C 377 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7886 (ptt90) REVERT: C 395 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7436 (mt-10) REVERT: C 625 ARG cc_start: 0.9127 (mmm160) cc_final: 0.8830 (mmp80) REVERT: C 663 CYS cc_start: 0.8966 (m) cc_final: 0.8701 (m) REVERT: C 724 MET cc_start: 0.9130 (mmp) cc_final: 0.8325 (mmm) REVERT: C 828 MET cc_start: 0.8309 (ppp) cc_final: 0.8003 (ppp) REVERT: C 1058 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7945 (pp) REVERT: C 1079 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: C 1086 SER cc_start: 0.7602 (p) cc_final: 0.7381 (p) REVERT: C 1096 LYS cc_start: 0.9338 (ptpp) cc_final: 0.9119 (ptpp) REVERT: C 1143 MET cc_start: 0.5220 (ppp) cc_final: 0.4788 (ppp) REVERT: D 139 ILE cc_start: 0.6337 (mt) cc_final: 0.5398 (mm) REVERT: D 471 PHE cc_start: 0.8279 (t80) cc_final: 0.7892 (t80) REVERT: D 820 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7618 (p) REVERT: D 1116 MET cc_start: 0.4421 (ttt) cc_final: 0.3051 (ptt) outliers start: 46 outliers final: 26 residues processed: 285 average time/residue: 0.3776 time to fit residues: 174.6536 Evaluate side-chains 250 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 187 TYR Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1059 HIS Chi-restraints excluded: chain C residue 1079 GLU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 1020 PHE Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 339 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 320 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 310 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 chunk 305 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1073 GLN ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.081472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.063536 restraints weight = 123054.245| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 6.18 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27773 Z= 0.118 Angle : 0.596 10.054 37685 Z= 0.296 Chirality : 0.042 0.257 4166 Planarity : 0.004 0.051 4955 Dihedral : 7.605 89.052 3965 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.74 % Allowed : 13.44 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3485 helix: 1.17 (0.14), residues: 1481 sheet: -0.17 (0.23), residues: 530 loop : -1.63 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 838 HIS 0.006 0.001 HIS C 259 PHE 0.017 0.001 PHE A 876 TYR 0.018 0.001 TYR D 261 ARG 0.008 0.000 ARG B1070 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 1106) hydrogen bonds : angle 4.89566 ( 3225) SS BOND : bond 0.00416 ( 4) SS BOND : angle 1.67068 ( 8) covalent geometry : bond 0.00265 (27768) covalent geometry : angle 0.59550 (37677) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 3.338 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 822 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7174 (pp) REVERT: A 848 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8077 (p90) REVERT: B 566 MET cc_start: 0.8536 (ppp) cc_final: 0.8060 (ppp) REVERT: B 641 MET cc_start: 0.8837 (ppp) cc_final: 0.8351 (ppp) REVERT: B 686 MET cc_start: 0.9028 (mpp) cc_final: 0.8473 (mpp) REVERT: B 724 MET cc_start: 0.9046 (mpp) cc_final: 0.8775 (mpp) REVERT: B 804 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7591 (tpp) REVERT: C 149 MET cc_start: 0.8215 (mmp) cc_final: 0.7829 (mmt) REVERT: C 395 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7538 (mt-10) REVERT: C 663 CYS cc_start: 0.9020 (m) cc_final: 0.8755 (m) REVERT: C 686 MET cc_start: 0.9066 (mmt) cc_final: 0.8622 (mmt) REVERT: C 724 MET cc_start: 0.9127 (mmp) cc_final: 0.8302 (mmm) REVERT: C 828 MET cc_start: 0.8243 (ppp) cc_final: 0.7928 (ppp) REVERT: C 1058 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8118 (pp) REVERT: C 1067 ASP cc_start: 0.9307 (m-30) cc_final: 0.8850 (t70) REVERT: C 1079 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: C 1086 SER cc_start: 0.7651 (p) cc_final: 0.7416 (p) REVERT: C 1096 LYS cc_start: 0.9328 (ptpp) cc_final: 0.9083 (ptpp) REVERT: C 1143 MET cc_start: 0.5293 (ppp) cc_final: 0.4848 (ppp) REVERT: D 44 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7347 (m-40) REVERT: D 471 PHE cc_start: 0.8266 (t80) cc_final: 0.7865 (t80) REVERT: D 820 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7658 (p) REVERT: D 1145 MET cc_start: 0.5810 (ppp) cc_final: 0.4520 (mmp) outliers start: 50 outliers final: 28 residues processed: 267 average time/residue: 0.3752 time to fit residues: 163.0748 Evaluate side-chains 249 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 804 MET Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 691 GLU Chi-restraints excluded: chain C residue 896 GLU Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1059 HIS Chi-restraints excluded: chain C residue 1079 GLU Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 896 GLU Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1020 PHE Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 15 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 chunk 338 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 HIS ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 HIS ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN D 346 HIS ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 HIS ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1101 HIS ** 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 = 0.3815 r_free = 0.3815 target = 0.076579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.058643 restraints weight = 127566.134| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 6.11 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 27773 Z= 0.295 Angle : 0.755 9.372 37685 Z= 0.388 Chirality : 0.046 0.294 4166 Planarity : 0.005 0.083 4955 Dihedral : 7.555 78.218 3965 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.92 % Favored : 92.05 % Rotamer: Outliers : 2.96 % Allowed : 13.97 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3485 helix: 0.67 (0.13), residues: 1486 sheet: -0.62 (0.22), residues: 532 loop : -1.69 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 607 HIS 0.009 0.002 HIS B 574 PHE 0.019 0.002 PHE C1038 TYR 0.020 0.002 TYR D 503 ARG 0.006 0.001 ARG C1036 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 1106) hydrogen bonds : angle 5.31008 ( 3225) SS BOND : bond 0.00588 ( 4) SS BOND : angle 2.01616 ( 8) covalent geometry : bond 0.00646 (27768) covalent geometry : angle 0.75469 (37677) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 204 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 TYR cc_start: 0.8181 (m-10) cc_final: 0.7956 (m-10) REVERT: A 822 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7387 (pp) REVERT: A 848 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8222 (p90) REVERT: A 1070 ARG cc_start: 0.8638 (mmm160) cc_final: 0.8414 (mmm160) REVERT: B 612 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 641 MET cc_start: 0.8848 (ppp) cc_final: 0.8357 (ppp) REVERT: B 671 MET cc_start: 0.8672 (tpp) cc_final: 0.8272 (tpp) REVERT: B 686 MET cc_start: 0.9017 (mpp) cc_final: 0.8457 (mpp) REVERT: B 828 MET cc_start: 0.8018 (ptm) cc_final: 0.7759 (ptm) REVERT: C 47 GLU cc_start: 0.7533 (pm20) cc_final: 0.7310 (pm20) REVERT: C 377 ARG cc_start: 0.7356 (ptt90) cc_final: 0.7118 (ptt90) REVERT: C 395 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7500 (mt-10) REVERT: C 663 CYS cc_start: 0.8944 (m) cc_final: 0.8660 (m) REVERT: C 724 MET cc_start: 0.9177 (mmp) cc_final: 0.8285 (mmm) REVERT: C 828 MET cc_start: 0.8399 (ppp) cc_final: 0.8157 (ppp) REVERT: C 1054 ARG cc_start: 0.8555 (tpt170) cc_final: 0.8243 (tpt-90) REVERT: C 1058 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8323 (pp) REVERT: C 1096 LYS cc_start: 0.9358 (ptpp) cc_final: 0.9119 (ptpp) REVERT: C 1143 MET cc_start: 0.5807 (ppp) cc_final: 0.5274 (ppp) REVERT: D 58 GLU cc_start: 0.8522 (tp30) cc_final: 0.8179 (tm-30) REVERT: D 75 MET cc_start: 0.8179 (tpt) cc_final: 0.7925 (tpt) REVERT: D 423 ASP cc_start: 0.7790 (t0) cc_final: 0.7548 (t0) REVERT: D 430 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7062 (mm) REVERT: D 471 PHE cc_start: 0.8469 (t80) cc_final: 0.8086 (t80) REVERT: D 604 MET cc_start: 0.8448 (tpp) cc_final: 0.8216 (tpp) REVERT: D 848 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7427 (p90) REVERT: D 1116 MET cc_start: 0.3439 (mtp) cc_final: 0.2234 (ptt) REVERT: D 1145 MET cc_start: 0.5943 (ppp) cc_final: 0.5117 (mmp) outliers start: 85 outliers final: 45 residues processed: 272 average time/residue: 0.3706 time to fit residues: 164.4654 Evaluate side-chains 247 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 739 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1026 THR Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 169 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 chunk 21 optimal weight: 0.0020 chunk 263 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** A 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 864 ASN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 HIS C1075 GLN D 44 ASN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 956 HIS D1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.078535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.060501 restraints weight = 123886.299| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 6.04 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27773 Z= 0.139 Angle : 0.633 10.396 37685 Z= 0.317 Chirality : 0.043 0.268 4166 Planarity : 0.004 0.064 4955 Dihedral : 7.063 62.684 3962 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.85 % Allowed : 15.36 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3485 helix: 0.91 (0.14), residues: 1491 sheet: -0.41 (0.23), residues: 526 loop : -1.62 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 838 HIS 0.006 0.001 HIS B 574 PHE 0.014 0.001 PHE D 920 TYR 0.018 0.001 TYR D 261 ARG 0.004 0.000 ARG C 243 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 1106) hydrogen bonds : angle 4.97658 ( 3225) SS BOND : bond 0.00407 ( 4) SS BOND : angle 1.88466 ( 8) covalent geometry : bond 0.00314 (27768) covalent geometry : angle 0.63228 (37677) Misc. bond : bond 0.00108 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 212 time to evaluate : 3.046 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 822 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7447 (pp) REVERT: A 848 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8242 (p90) REVERT: A 1070 ARG cc_start: 0.8629 (mmm160) cc_final: 0.8385 (mmm160) REVERT: B 566 MET cc_start: 0.8443 (ppp) cc_final: 0.8079 (ppp) REVERT: B 612 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: B 641 MET cc_start: 0.8850 (ppp) cc_final: 0.8382 (ppp) REVERT: B 686 MET cc_start: 0.9036 (mpp) cc_final: 0.8433 (mpp) REVERT: B 801 MET cc_start: 0.8410 (mpp) cc_final: 0.7989 (mpp) REVERT: B 828 MET cc_start: 0.7811 (ptm) cc_final: 0.7595 (ptm) REVERT: C 149 MET cc_start: 0.8440 (mmp) cc_final: 0.7702 (mmt) REVERT: C 204 MET cc_start: 0.6981 (mtp) cc_final: 0.6464 (mmp) REVERT: C 377 ARG cc_start: 0.7290 (ptt90) cc_final: 0.6901 (ptt90) REVERT: C 395 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7503 (mt-10) REVERT: C 401 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6963 (mm-30) REVERT: C 403 MET cc_start: 0.8133 (tpp) cc_final: 0.7876 (tpp) REVERT: C 625 ARG cc_start: 0.9205 (mmm-85) cc_final: 0.8604 (mmm160) REVERT: C 663 CYS cc_start: 0.8979 (m) cc_final: 0.8711 (m) REVERT: C 724 MET cc_start: 0.9146 (mmp) cc_final: 0.8298 (mmm) REVERT: C 828 MET cc_start: 0.8414 (ppp) cc_final: 0.8059 (ppp) REVERT: C 1058 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8161 (pp) REVERT: C 1067 ASP cc_start: 0.9334 (m-30) cc_final: 0.8806 (t0) REVERT: C 1096 LYS cc_start: 0.9320 (ptpp) cc_final: 0.9060 (ptpp) REVERT: C 1143 MET cc_start: 0.6042 (ppp) cc_final: 0.5510 (ppp) REVERT: D 75 MET cc_start: 0.8162 (tpt) cc_final: 0.7782 (tpt) REVERT: D 423 ASP cc_start: 0.7776 (t0) cc_final: 0.7513 (t0) REVERT: D 471 PHE cc_start: 0.8443 (t80) cc_final: 0.8154 (t80) REVERT: D 848 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.7370 (p90) REVERT: D 1095 MET cc_start: 0.7124 (tmm) cc_final: 0.6865 (tmm) REVERT: D 1116 MET cc_start: 0.3781 (mtp) cc_final: 0.2339 (ptt) REVERT: D 1145 MET cc_start: 0.5647 (ppp) cc_final: 0.4872 (mmp) outliers start: 53 outliers final: 40 residues processed: 253 average time/residue: 0.3786 time to fit residues: 154.9154 Evaluate side-chains 247 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 739 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 848 PHE Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1026 THR Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1059 HIS Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 287 optimal weight: 6.9990 chunk 228 optimal weight: 0.0170 chunk 76 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 290 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 271 optimal weight: 8.9990 chunk 323 optimal weight: 2.9990 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 GLN ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 879 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.078622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.060729 restraints weight = 123874.534| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 5.96 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27773 Z= 0.138 Angle : 0.630 11.731 37685 Z= 0.314 Chirality : 0.043 0.309 4166 Planarity : 0.004 0.060 4955 Dihedral : 6.915 56.012 3962 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.85 % Allowed : 15.95 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3485 helix: 0.96 (0.14), residues: 1495 sheet: -0.39 (0.23), residues: 530 loop : -1.62 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 838 HIS 0.009 0.001 HIS C1059 PHE 0.029 0.001 PHE C 183 TYR 0.017 0.001 TYR C 118 ARG 0.008 0.000 ARG C1070 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 1106) hydrogen bonds : angle 4.92810 ( 3225) SS BOND : bond 0.00417 ( 4) SS BOND : angle 1.83899 ( 8) covalent geometry : bond 0.00310 (27768) covalent geometry : angle 0.62940 (37677) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 211 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 822 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7201 (pp) REVERT: A 848 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8223 (p90) REVERT: A 1070 ARG cc_start: 0.8615 (mmm160) cc_final: 0.8393 (mmm160) REVERT: B 566 MET cc_start: 0.8437 (ppp) cc_final: 0.8027 (ppp) REVERT: B 612 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: B 641 MET cc_start: 0.8795 (ppp) cc_final: 0.8348 (ppp) REVERT: B 686 MET cc_start: 0.9038 (mpp) cc_final: 0.8428 (mpp) REVERT: B 801 MET cc_start: 0.8404 (mpp) cc_final: 0.7928 (mpp) REVERT: B 804 MET cc_start: 0.8657 (tpp) cc_final: 0.8395 (mmp) REVERT: B 823 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: C 149 MET cc_start: 0.8454 (mmp) cc_final: 0.8006 (mmt) REVERT: C 204 MET cc_start: 0.6871 (mtp) cc_final: 0.6393 (mmp) REVERT: C 377 ARG cc_start: 0.7290 (ptt90) cc_final: 0.6877 (ptt90) REVERT: C 395 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7486 (mt-10) REVERT: C 401 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7070 (mm-30) REVERT: C 403 MET cc_start: 0.8119 (tpp) cc_final: 0.7889 (tpp) REVERT: C 625 ARG cc_start: 0.9237 (mmm-85) cc_final: 0.8639 (mmm160) REVERT: C 663 CYS cc_start: 0.8991 (m) cc_final: 0.8747 (m) REVERT: C 686 MET cc_start: 0.9073 (mmt) cc_final: 0.8579 (mmt) REVERT: C 724 MET cc_start: 0.9213 (mmp) cc_final: 0.8293 (mmm) REVERT: C 828 MET cc_start: 0.8454 (ppp) cc_final: 0.8128 (ppp) REVERT: C 1058 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8170 (pp) REVERT: C 1067 ASP cc_start: 0.9376 (m-30) cc_final: 0.8847 (t0) REVERT: C 1096 LYS cc_start: 0.9359 (ptpp) cc_final: 0.9079 (ptpp) REVERT: C 1098 MET cc_start: 0.8404 (tpp) cc_final: 0.7871 (tpp) REVERT: C 1143 MET cc_start: 0.6112 (ppp) cc_final: 0.5580 (ppp) REVERT: C 1153 MET cc_start: 0.1104 (ppp) cc_final: 0.0845 (ppp) REVERT: D 75 MET cc_start: 0.8163 (tpt) cc_final: 0.7800 (tpt) REVERT: D 423 ASP cc_start: 0.7736 (t0) cc_final: 0.7482 (t0) REVERT: D 471 PHE cc_start: 0.8484 (t80) cc_final: 0.8193 (t80) REVERT: D 848 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.7456 (p90) REVERT: D 886 LYS cc_start: 0.8990 (mptt) cc_final: 0.8783 (ptmm) outliers start: 53 outliers final: 40 residues processed: 252 average time/residue: 0.3770 time to fit residues: 154.4062 Evaluate side-chains 250 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 739 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 848 PHE Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1026 THR Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1100 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 91 optimal weight: 5.9990 chunk 330 optimal weight: 2.9990 chunk 310 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 252 optimal weight: 20.0000 chunk 120 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 GLN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1059 HIS ** D 348 GLN ** 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 = 0.3855 r_free = 0.3855 target = 0.078380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.060509 restraints weight = 123552.460| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 5.89 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27773 Z= 0.145 Angle : 0.637 11.963 37685 Z= 0.316 Chirality : 0.043 0.330 4166 Planarity : 0.004 0.055 4955 Dihedral : 6.764 55.809 3961 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.06 % Allowed : 16.58 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3485 helix: 1.03 (0.14), residues: 1488 sheet: -0.40 (0.23), residues: 529 loop : -1.60 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 838 HIS 0.006 0.001 HIS C 259 PHE 0.015 0.001 PHE B 920 TYR 0.016 0.001 TYR C 118 ARG 0.009 0.000 ARG C1070 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 1106) hydrogen bonds : angle 4.89092 ( 3225) SS BOND : bond 0.00394 ( 4) SS BOND : angle 1.76811 ( 8) covalent geometry : bond 0.00328 (27768) covalent geometry : angle 0.63628 (37677) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 209 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 MET cc_start: 0.7907 (ppp) cc_final: 0.7202 (ppp) REVERT: A 822 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7244 (pp) REVERT: A 848 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8209 (p90) REVERT: B 566 MET cc_start: 0.8478 (ppp) cc_final: 0.8067 (ppp) REVERT: B 612 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: B 641 MET cc_start: 0.8778 (ppp) cc_final: 0.8255 (ppp) REVERT: B 686 MET cc_start: 0.9045 (mpp) cc_final: 0.8436 (mpp) REVERT: B 823 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: B 1073 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.6198 (mp10) REVERT: C 149 MET cc_start: 0.8482 (mmp) cc_final: 0.7976 (mmt) REVERT: C 204 MET cc_start: 0.7058 (mtp) cc_final: 0.6597 (mmp) REVERT: C 377 ARG cc_start: 0.7345 (ptt90) cc_final: 0.6953 (ptt90) REVERT: C 395 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7496 (mt-10) REVERT: C 401 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7098 (mm-30) REVERT: C 625 ARG cc_start: 0.9260 (mmm-85) cc_final: 0.8658 (mmm160) REVERT: C 663 CYS cc_start: 0.8980 (m) cc_final: 0.8739 (m) REVERT: C 724 MET cc_start: 0.9191 (mmp) cc_final: 0.8247 (mmm) REVERT: C 759 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9201 (mm) REVERT: C 828 MET cc_start: 0.8452 (ppp) cc_final: 0.8140 (ppp) REVERT: C 1058 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8160 (pp) REVERT: C 1067 ASP cc_start: 0.9366 (m-30) cc_final: 0.8833 (t0) REVERT: C 1096 LYS cc_start: 0.9370 (ptpp) cc_final: 0.9090 (ptpp) REVERT: C 1098 MET cc_start: 0.8451 (tpp) cc_final: 0.8119 (tpp) REVERT: C 1143 MET cc_start: 0.6143 (ppp) cc_final: 0.5596 (ppp) REVERT: C 1153 MET cc_start: 0.1071 (ppp) cc_final: 0.0851 (ppp) REVERT: D 75 MET cc_start: 0.8163 (tpt) cc_final: 0.7797 (tpt) REVERT: D 423 ASP cc_start: 0.7704 (t0) cc_final: 0.7451 (t0) REVERT: D 430 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.6875 (tp) REVERT: D 443 MET cc_start: 0.8060 (ttt) cc_final: 0.7794 (ttp) REVERT: D 471 PHE cc_start: 0.8433 (t80) cc_final: 0.8146 (t80) REVERT: D 848 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7416 (p90) REVERT: D 886 LYS cc_start: 0.9062 (mptt) cc_final: 0.8844 (ptmm) REVERT: D 1095 MET cc_start: 0.7082 (tmm) cc_final: 0.6819 (tmm) REVERT: D 1145 MET cc_start: 0.6108 (ppp) cc_final: 0.4680 (mmt) outliers start: 59 outliers final: 40 residues processed: 254 average time/residue: 0.3951 time to fit residues: 163.8318 Evaluate side-chains 252 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 739 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 848 PHE Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1073 GLN Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1026 THR Chi-restraints excluded: chain C residue 1031 ASP Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1080 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 39 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 135 optimal weight: 0.4980 chunk 189 optimal weight: 3.9990 chunk 337 optimal weight: 0.0570 chunk 162 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.078636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.060630 restraints weight = 124312.946| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 6.03 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27773 Z= 0.133 Angle : 0.639 12.559 37685 Z= 0.315 Chirality : 0.043 0.339 4166 Planarity : 0.004 0.051 4955 Dihedral : 6.652 55.392 3959 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.95 % Allowed : 17.10 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3485 helix: 1.05 (0.14), residues: 1488 sheet: -0.40 (0.23), residues: 530 loop : -1.59 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 838 HIS 0.005 0.001 HIS B 574 PHE 0.015 0.001 PHE D 387 TYR 0.017 0.001 TYR C 118 ARG 0.011 0.000 ARG C1070 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 1106) hydrogen bonds : angle 4.85492 ( 3225) SS BOND : bond 0.00364 ( 4) SS BOND : angle 1.69161 ( 8) covalent geometry : bond 0.00301 (27768) covalent geometry : angle 0.63865 (37677) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 3.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 MET cc_start: 0.7919 (ppp) cc_final: 0.7176 (ppp) REVERT: A 822 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7201 (pp) REVERT: A 848 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8162 (p90) REVERT: B 566 MET cc_start: 0.8463 (ppp) cc_final: 0.8057 (ppp) REVERT: B 612 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: B 641 MET cc_start: 0.8723 (ppp) cc_final: 0.8175 (ppp) REVERT: B 671 MET cc_start: 0.8492 (tpp) cc_final: 0.8220 (tpp) REVERT: B 686 MET cc_start: 0.9056 (mpp) cc_final: 0.8440 (mpp) REVERT: B 801 MET cc_start: 0.8389 (mpp) cc_final: 0.8017 (mpp) REVERT: B 823 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: C 149 MET cc_start: 0.8546 (mmp) cc_final: 0.8055 (mmt) REVERT: C 204 MET cc_start: 0.7132 (mtp) cc_final: 0.6650 (mmp) REVERT: C 377 ARG cc_start: 0.7403 (ptt90) cc_final: 0.7020 (ptt90) REVERT: C 395 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7495 (mt-10) REVERT: C 401 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7001 (mm-30) REVERT: C 625 ARG cc_start: 0.9239 (mmm-85) cc_final: 0.8641 (mmm160) REVERT: C 663 CYS cc_start: 0.8981 (m) cc_final: 0.8743 (m) REVERT: C 686 MET cc_start: 0.8970 (mmt) cc_final: 0.8765 (mmt) REVERT: C 724 MET cc_start: 0.9213 (mmp) cc_final: 0.8270 (mmm) REVERT: C 743 MET cc_start: 0.7263 (mmm) cc_final: 0.6917 (mmm) REVERT: C 759 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9209 (mm) REVERT: C 828 MET cc_start: 0.8445 (ppp) cc_final: 0.8131 (ppp) REVERT: C 1058 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8142 (pp) REVERT: C 1067 ASP cc_start: 0.9376 (m-30) cc_final: 0.8841 (t0) REVERT: C 1096 LYS cc_start: 0.9389 (ptpp) cc_final: 0.9112 (ptpp) REVERT: C 1098 MET cc_start: 0.8441 (tpp) cc_final: 0.8118 (tpp) REVERT: C 1143 MET cc_start: 0.6186 (ppp) cc_final: 0.5653 (ppp) REVERT: C 1153 MET cc_start: 0.0818 (ppp) cc_final: 0.0575 (ppp) REVERT: D 75 MET cc_start: 0.8159 (tpt) cc_final: 0.7894 (tpt) REVERT: D 423 ASP cc_start: 0.7615 (t0) cc_final: 0.7379 (t0) REVERT: D 471 PHE cc_start: 0.8421 (t80) cc_final: 0.8145 (t80) REVERT: D 848 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.7423 (p90) REVERT: D 886 LYS cc_start: 0.9090 (mptt) cc_final: 0.8843 (ptmm) REVERT: D 1095 MET cc_start: 0.7145 (tmm) cc_final: 0.6891 (tmm) REVERT: D 1145 MET cc_start: 0.6253 (ppp) cc_final: 0.5045 (mmt) outliers start: 56 outliers final: 40 residues processed: 250 average time/residue: 0.3852 time to fit residues: 156.4443 Evaluate side-chains 247 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 739 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 848 PHE Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1006 ASP Chi-restraints excluded: chain C residue 1026 THR Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1080 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 210 optimal weight: 0.1980 chunk 146 optimal weight: 8.9990 chunk 271 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 333 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 346 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.079352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.061523 restraints weight = 123086.819| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 5.97 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27773 Z= 0.117 Angle : 0.642 12.713 37685 Z= 0.314 Chirality : 0.043 0.321 4166 Planarity : 0.004 0.051 4955 Dihedral : 6.545 59.608 3959 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.67 % Allowed : 17.42 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3485 helix: 1.13 (0.14), residues: 1483 sheet: -0.31 (0.23), residues: 528 loop : -1.56 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 838 HIS 0.005 0.001 HIS B 574 PHE 0.036 0.001 PHE C 183 TYR 0.018 0.001 TYR C 118 ARG 0.026 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 1106) hydrogen bonds : angle 4.78456 ( 3225) SS BOND : bond 0.00326 ( 4) SS BOND : angle 1.71358 ( 8) covalent geometry : bond 0.00268 (27768) covalent geometry : angle 0.64127 (37677) Misc. bond : bond 0.00072 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6970 Ramachandran restraints generated. 3485 Oldfield, 0 Emsley, 3485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 MET cc_start: 0.8005 (ppp) cc_final: 0.7289 (ppp) REVERT: A 822 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7219 (pp) REVERT: A 848 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8210 (p90) REVERT: B 566 MET cc_start: 0.8466 (ppp) cc_final: 0.8070 (ppp) REVERT: B 612 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: B 641 MET cc_start: 0.8725 (ppp) cc_final: 0.8190 (ppp) REVERT: B 671 MET cc_start: 0.8550 (tpp) cc_final: 0.8329 (tpp) REVERT: B 686 MET cc_start: 0.9055 (mpp) cc_final: 0.8437 (mpp) REVERT: B 801 MET cc_start: 0.8348 (mpp) cc_final: 0.7982 (mpp) REVERT: B 823 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7764 (m-30) REVERT: C 149 MET cc_start: 0.8588 (mmp) cc_final: 0.8117 (mmt) REVERT: C 204 MET cc_start: 0.7199 (mtp) cc_final: 0.6725 (mmp) REVERT: C 377 ARG cc_start: 0.7375 (ptt90) cc_final: 0.6948 (ptt90) REVERT: C 395 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 401 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6936 (mm-30) REVERT: C 663 CYS cc_start: 0.8955 (m) cc_final: 0.8706 (m) REVERT: C 724 MET cc_start: 0.9217 (mmp) cc_final: 0.8291 (mmm) REVERT: C 759 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9216 (mm) REVERT: C 828 MET cc_start: 0.8400 (ppp) cc_final: 0.8111 (ppp) REVERT: C 1058 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8116 (pp) REVERT: C 1067 ASP cc_start: 0.9356 (m-30) cc_final: 0.8789 (t0) REVERT: C 1096 LYS cc_start: 0.9391 (ptpp) cc_final: 0.9105 (ptpp) REVERT: C 1098 MET cc_start: 0.8431 (tpp) cc_final: 0.8055 (tpp) REVERT: C 1143 MET cc_start: 0.6258 (ppp) cc_final: 0.5738 (ppp) REVERT: C 1153 MET cc_start: 0.0960 (ppp) cc_final: 0.0662 (ppp) REVERT: D 75 MET cc_start: 0.8183 (tpt) cc_final: 0.7892 (tpt) REVERT: D 423 ASP cc_start: 0.7701 (t0) cc_final: 0.7420 (t0) REVERT: D 471 PHE cc_start: 0.8411 (t80) cc_final: 0.8150 (t80) REVERT: D 848 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.7485 (p90) REVERT: D 886 LYS cc_start: 0.9102 (mptt) cc_final: 0.8833 (ptmm) REVERT: D 1095 MET cc_start: 0.7162 (tmm) cc_final: 0.6917 (tmm) REVERT: D 1145 MET cc_start: 0.6338 (ppp) cc_final: 0.5173 (mmt) outliers start: 48 outliers final: 37 residues processed: 251 average time/residue: 0.4004 time to fit residues: 164.4595 Evaluate side-chains 244 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 739 CYS Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 848 PHE Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 876 PHE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain B residue 823 ASP Chi-restraints excluded: chain B residue 848 PHE Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 649 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1080 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 242 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 228 optimal weight: 20.0000 chunk 167 optimal weight: 0.7980 chunk 344 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 255 optimal weight: 9.9990 chunk 301 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.080134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.062206 restraints weight = 123241.342| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 6.11 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27773 Z= 0.110 Angle : 0.642 12.971 37685 Z= 0.312 Chirality : 0.043 0.321 4166 Planarity : 0.004 0.049 4955 Dihedral : 6.422 57.808 3959 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.53 % Allowed : 17.87 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3485 helix: 1.18 (0.14), residues: 1476 sheet: -0.24 (0.23), residues: 528 loop : -1.54 (0.15), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 838 HIS 0.005 0.001 HIS A 879 PHE 0.017 0.001 PHE B 832 TYR 0.019 0.001 TYR C 118 ARG 0.021 0.000 ARG A1070 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 1106) hydrogen bonds : angle 4.69426 ( 3225) SS BOND : bond 0.00308 ( 4) SS BOND : angle 1.70851 ( 8) covalent geometry : bond 0.00251 (27768) covalent geometry : angle 0.64142 (37677) Misc. bond : bond 0.00054 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13450.39 seconds wall clock time: 235 minutes 24.29 seconds (14124.29 seconds total)