Starting phenix.real_space_refine on Wed Jun 25 04:27:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wtb_32775/06_2025/7wtb_32775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtb_32775/06_2025/7wtb_32775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wtb_32775/06_2025/7wtb_32775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtb_32775/06_2025/7wtb_32775.map" model { file = "/net/cci-nas-00/data/ceres_data/7wtb_32775/06_2025/7wtb_32775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtb_32775/06_2025/7wtb_32775.cif" } resolution = 3.7 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 172 5.16 5 C 18014 2.51 5 N 4957 2.21 5 O 5325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 1.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28480 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" 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: "B" 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: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "D" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'ACO': 1, 'ANP': 1, 'BTI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'ACO': 1, 'ANP': 1, 'BTI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.59, per 1000 atoms: 0.72 Number of scatterers: 28480 At special positions: 0 Unit cell: (160.6, 161.7, 137.5, 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 172 16.00 P 12 15.00 O 5325 8.00 N 4957 7.00 C 18014 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=2.04 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.03 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.03 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.80 Conformation dependent library (CDL) restraints added in 5.6 seconds 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6738 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 28 sheets defined 46.8% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.91 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.648A pdb=" N THR A 72 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.638A pdb=" N ILE A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 removed outlier: 3.831A pdb=" N ALA A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.967A pdb=" N ALA A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 210 through 227 removed outlier: 3.740A pdb=" N GLU A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 303 Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 343 through 354 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 435 through 450 Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.595A pdb=" N LEU A 462 " --> pdb=" O ASN A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.667A pdb=" N GLY A 474 " --> pdb=" O GLN A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 4.222A pdb=" N ILE A 481 " --> pdb=" O THR A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 540 through 549 removed outlier: 4.208A 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 577 Processing helix chain 'A' and resid 583 through 597 removed outlier: 3.852A pdb=" N LEU A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 3.687A 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 618 Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.584A pdb=" N GLU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.569A pdb=" N VAL A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.603A 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 763 removed outlier: 4.085A pdb=" N ARG A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 789 removed outlier: 3.915A pdb=" N ALA A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 Processing helix chain 'A' and resid 809 through 817 Processing helix chain 'A' and resid 827 through 843 removed outlier: 4.059A pdb=" N VAL A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 867 through 869 No H-bonds generated for 'chain 'A' and resid 867 through 869' Processing helix chain 'A' and resid 870 through 882 Processing helix chain 'A' and resid 886 through 901 removed outlier: 3.569A pdb=" N LYS A 891 " --> pdb=" O PHE A 887 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) removed outlier: 3.630A 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 927 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: 3.991A pdb=" N SER A 981 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 998 removed outlier: 3.664A 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 46 through 59 removed outlier: 3.642A pdb=" N ILE B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 4.306A pdb=" N GLN B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 124 through 134 removed outlier: 3.701A pdb=" N ALA B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 Processing helix chain 'B' and resid 151 through 162 removed outlier: 3.873A pdb=" N ALA B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 209 through 228 removed outlier: 3.588A pdb=" N GLU B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 303 Processing helix chain 'B' and resid 332 through 341 removed outlier: 3.954A pdb=" N THR B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 354 removed outlier: 3.645A pdb=" N ALA B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 435 through 450 Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 468 through 474 removed outlier: 3.531A pdb=" N LEU B 472 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 474 " --> pdb=" O GLN B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 481 removed outlier: 4.310A pdb=" N ILE B 481 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.636A pdb=" N PHE B 488 " --> pdb=" O PRO B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 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: 4.450A pdb=" N GLN B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 590 through 598 Processing helix chain 'B' and resid 608 through 618 Processing helix chain 'B' and resid 622 through 632 removed outlier: 3.551A pdb=" N LEU B 630 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU B 632 " --> pdb=" O GLN B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 682 through 697 Processing helix chain 'B' and resid 719 through 734 Processing helix chain 'B' and resid 748 through 762 removed outlier: 4.367A 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: 3.691A pdb=" N LEU B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 843 removed outlier: 3.993A pdb=" N VAL B 831 " --> pdb=" O PRO B 827 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP B 838 " --> pdb=" O TYR B 834 " (cutoff:3.500A) removed outlier: 3.896A 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 850 through 855 removed outlier: 4.179A pdb=" N LYS B 855 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 882 Processing helix chain 'B' and resid 886 through 893 removed outlier: 3.517A pdb=" N VAL B 890 " --> pdb=" O LYS B 886 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 891 " --> pdb=" O PHE B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 902 Processing helix chain 'B' and resid 908 through 925 Processing helix chain 'B' and resid 927 through 934 removed outlier: 3.624A pdb=" N GLN B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 950 Processing helix chain 'B' and resid 960 through 969 removed outlier: 3.542A pdb=" N ARG B 964 " --> pdb=" O PRO B 960 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 969 " --> pdb=" O SER B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 982 removed outlier: 3.749A pdb=" N SER B 981 " --> pdb=" O ARG B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 999 removed outlier: 3.756A pdb=" N GLU B 991 " --> pdb=" O LEU B 987 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 992 " --> pdb=" O GLN B 988 " (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 496 through 510 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: 4.329A pdb=" N GLN C 575 " --> pdb=" O ARG C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 588 removed outlier: 3.637A pdb=" N LEU C 587 " --> pdb=" O ARG C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 598 Processing helix chain 'C' and resid 608 through 618 Processing helix chain 'C' and resid 622 through 632 removed outlier: 3.677A pdb=" N LEU C 630 " --> pdb=" O ARG C 626 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU C 632 " --> pdb=" O GLN C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 670 removed outlier: 3.544A pdb=" N GLY C 670 " --> pdb=" O ALA C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 697 removed outlier: 3.644A pdb=" N MET C 686 " --> pdb=" O TYR C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 734 removed outlier: 3.697A pdb=" N LEU C 726 " --> pdb=" O TYR C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 760 Processing helix chain 'C' and resid 778 through 790 Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.635A pdb=" N SER C 802 " --> pdb=" O ASP C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 817 removed outlier: 3.635A pdb=" N LEU C 813 " --> pdb=" O SER C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 843 removed outlier: 4.049A pdb=" N VAL C 831 " --> pdb=" O PRO C 827 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 849 removed outlier: 4.928A pdb=" N ALA C 847 " --> pdb=" O LEU C 844 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP C 849 " --> pdb=" O ALA C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 855 Processing helix chain 'C' and resid 860 through 865 removed outlier: 4.100A pdb=" N ASN C 864 " --> pdb=" O ASP C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 869 No H-bonds generated for 'chain 'C' and resid 867 through 869' Processing helix chain 'C' and resid 870 through 882 Processing helix chain 'C' and resid 886 through 893 removed outlier: 3.519A pdb=" N VAL C 890 " --> pdb=" O LYS C 886 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 891 " --> pdb=" O PHE C 887 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 893 " --> pdb=" O GLU C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 902 Processing helix chain 'C' and resid 910 through 925 removed outlier: 4.024A pdb=" N VAL C 914 " --> pdb=" O SER C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 934 Processing helix chain 'C' and resid 941 through 950 Processing helix chain 'C' and resid 960 through 969 removed outlier: 3.512A pdb=" N ARG C 964 " --> pdb=" O PRO C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 982 removed outlier: 3.683A pdb=" N SER C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 999 removed outlier: 3.541A pdb=" N GLU C 991 " --> pdb=" O LEU C 987 " (cutoff:3.500A) removed outlier: 3.629A 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 1028 removed outlier: 3.527A pdb=" N THR C1026 " --> pdb=" O ASP C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1041 Processing helix chain 'D' and resid 496 through 511 Processing helix chain 'D' and resid 541 through 548 removed outlier: 3.624A 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 577 removed outlier: 3.637A pdb=" N GLN D 575 " --> pdb=" O ARG D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 3.743A pdb=" N LEU D 587 " --> pdb=" O ARG D 583 " (cutoff:3.500A) removed outlier: 3.725A 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: 3.533A pdb=" N PHE D 612 " --> pdb=" O GLY D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 655 through 670 removed outlier: 3.574A pdb=" N VAL D 659 " --> pdb=" O PRO D 655 " (cutoff:3.500A) removed outlier: 3.530A 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 removed outlier: 3.609A pdb=" N TYR D 723 " --> pdb=" O SER D 719 " (cutoff:3.500A) 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: 3.729A 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: 3.823A pdb=" N VAL D 831 " --> pdb=" O PRO D 827 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 849 removed outlier: 5.294A pdb=" N ALA D 847 " --> pdb=" O LEU D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 855 Processing helix chain 'D' and resid 860 through 865 Processing helix chain 'D' and resid 867 through 869 No H-bonds generated for 'chain 'D' and resid 867 through 869' Processing helix chain 'D' and resid 870 through 881 Processing helix chain 'D' and resid 883 through 885 No H-bonds generated for 'chain 'D' and resid 883 through 885' Processing helix chain 'D' and resid 886 through 891 Processing helix chain 'D' and resid 893 through 901 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 removed outlier: 3.521A pdb=" N VAL D 945 " --> pdb=" O PRO D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 960 through 969 Processing helix chain 'D' and resid 977 through 982 removed outlier: 3.874A pdb=" N SER D 981 " --> pdb=" O ARG D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 998 Processing helix chain 'D' and resid 1003 through 1013 removed outlier: 3.996A pdb=" N VAL D1007 " --> pdb=" O THR D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1028 Processing helix chain 'D' and resid 1034 through 1040 Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 removed outlier: 3.665A pdb=" N GLU A 82 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 42 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE A 66 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS A 39 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N HIS A 115 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET A 41 " --> pdb=" O HIS A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 207 removed outlier: 3.801A pdb=" N ILE A 192 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 236 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 264 removed outlier: 6.909A pdb=" N GLN A 248 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU A 262 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU A 246 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 324 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.713A pdb=" N CYS A 372 " --> pdb=" O HIS A 432 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N HIS A 432 " --> pdb=" O CYS A 372 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 374 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE A 430 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS A 376 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS A 428 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 378 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.759A pdb=" N GLN A 388 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 396 through 398 Processing sheet with id=AA7, first strand: chain 'A' and resid 564 through 567 removed outlier: 8.982A pdb=" N GLU A 605 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP A 567 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N MET A 604 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU A 642 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 700 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N CYS A 739 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA A 702 " --> pdb=" O CYS A 739 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS A 741 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 704 " --> pdb=" O LYS A 741 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 738 " --> pdb=" O HIS A 769 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N HIS A 771 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 740 " --> pdb=" O HIS A 771 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU A 768 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ASP A 795 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE A 770 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 564 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL A 796 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N MET A 566 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1047 through 1051 removed outlier: 5.533A pdb=" N ALA A1062 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A1064 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLN A1075 " --> pdb=" O SER A1066 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A1068 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN A1073 " --> pdb=" O LEU A1068 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1146 through 1150 removed outlier: 4.098A pdb=" N CYS A1138 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU A1137 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A1123 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A1139 " --> pdb=" O ILE A1121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1130 through 1131 removed outlier: 6.953A pdb=" N GLU A1176 " --> pdb=" O ARG A1158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 85 removed outlier: 3.517A pdb=" N GLU B 82 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 66 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS B 39 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N HIS B 115 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N MET B 41 " --> pdb=" O HIS B 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 204 through 207 Processing sheet with id=AB4, first strand: chain 'B' and resid 257 through 264 removed outlier: 7.070A pdb=" N GLN B 248 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU B 262 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU B 246 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 324 " --> pdb=" O GLU B 311 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 275 through 277 removed outlier: 4.047A pdb=" N VAL B 427 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 381 through 382 removed outlier: 3.715A pdb=" N GLN B 388 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 564 through 567 removed outlier: 8.793A pdb=" N GLU B 605 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASP B 567 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N TRP B 607 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU B 642 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE B 639 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ARG B 675 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET B 641 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE B 677 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B 643 " --> pdb=" O PHE B 677 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE B 674 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA B 703 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 676 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N SER B 705 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 700 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N CYS B 739 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 702 " --> pdb=" O CYS B 739 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS B 741 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 704 " --> pdb=" O LYS B 741 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N HIS B 771 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE B 740 " --> pdb=" O HIS B 771 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 768 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASP B 795 " --> pdb=" O LEU B 768 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE B 770 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU B 564 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL B 796 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N MET B 566 " --> pdb=" O VAL B 796 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 7.008A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1112 through 1113 removed outlier: 6.812A pdb=" N ILE B1112 " --> pdb=" O ILE B1174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1146 through 1150 removed outlier: 4.145A pdb=" N CYS B1138 " --> pdb=" O VAL B1149 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU B1137 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE B1123 " --> pdb=" O LEU B1137 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B1139 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1130 through 1131 Processing sheet with id=AC3, first strand: chain 'C' and resid 564 through 567 removed outlier: 7.224A pdb=" N LEU C 565 " --> pdb=" O SER C 603 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N GLU C 605 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ASP C 567 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET C 604 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU C 642 " --> pdb=" O MET C 604 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE C 639 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG C 675 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET C 641 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N PHE C 677 " --> pdb=" O MET C 641 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 643 " --> pdb=" O PHE C 677 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 700 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N CYS C 739 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA C 702 " --> pdb=" O CYS C 739 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS C 741 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE C 704 " --> pdb=" O LYS C 741 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 738 " --> pdb=" O HIS C 769 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS C 771 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 740 " --> pdb=" O HIS C 771 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU C 768 " --> pdb=" O VAL C 793 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ASP C 795 " --> pdb=" O LEU C 768 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE C 770 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU C 564 " --> pdb=" O VAL C 794 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL C 796 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N MET C 566 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1047 through 1049 removed outlier: 6.005A pdb=" N ALA C1062 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C1064 " --> pdb=" O PHE C1077 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1112 through 1113 removed outlier: 3.541A pdb=" N ILE C1112 " --> pdb=" O LEU C1175 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU C1175 " --> pdb=" O ILE C1112 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ILE C1174 " --> pdb=" O VAL C1160 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL C1160 " --> pdb=" O ILE C1174 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU C1176 " --> pdb=" O ARG C1158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1146 through 1150 removed outlier: 3.784A pdb=" N CYS C1138 " --> pdb=" O VAL C1149 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LEU C1137 " --> pdb=" O ILE C1123 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE C1123 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C1139 " --> pdb=" O ILE C1121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 564 through 567 removed outlier: 7.345A pdb=" N LEU D 565 " --> pdb=" O SER D 603 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N GLU D 605 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASP D 567 " --> pdb=" O GLU D 605 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE D 639 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ARG D 675 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N MET D 641 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE D 677 " --> pdb=" O MET D 641 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU D 643 " --> pdb=" O PHE D 677 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE D 674 " --> pdb=" O GLU D 701 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA D 703 " --> pdb=" O PHE D 674 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL D 676 " --> pdb=" O ALA D 703 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N SER D 705 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU D 768 " --> pdb=" O VAL D 793 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASP D 795 " --> pdb=" O LEU D 768 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE D 770 " --> pdb=" O ASP D 795 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 564 " --> pdb=" O VAL D 794 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL D 796 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N MET D 566 " --> pdb=" O VAL D 796 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 1047 through 1050 removed outlier: 6.854A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 1111 through 1113 removed outlier: 7.632A pdb=" N ILE D1112 " --> pdb=" O ILE D1174 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE D1174 " --> pdb=" O VAL D1160 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL D1160 " --> pdb=" O ILE D1174 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU D1176 " --> pdb=" O ARG D1158 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA D1129 " --> pdb=" O VAL D1157 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 1146 through 1150 removed outlier: 4.192A pdb=" N CYS D1138 " --> pdb=" O VAL D1149 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU D1137 " --> pdb=" O ILE D1123 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE D1123 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL D1139 " --> pdb=" O ILE D1121 " (cutoff:3.500A) 1181 hydrogen bonds defined for protein. 3426 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: 15.56 Time building geometry restraints manager: 9.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4817 1.31 - 1.43: 7272 1.43 - 1.56: 16671 1.56 - 1.69: 50 1.69 - 1.82: 300 Bond restraints: 29110 Sorted by residual: bond pdb=" C6 BTI C1900 " pdb=" S1 BTI C1900 " ideal model delta sigma weight residual 1.811 1.442 0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C6 BTI D1900 " pdb=" S1 BTI D1900 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C6 BTI B2002 " pdb=" S1 BTI B2002 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C6 BTI A1201 " pdb=" S1 BTI A1201 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C2' ANP A1202 " pdb=" C3' ANP A1202 " ideal model delta sigma weight residual 1.520 1.225 0.295 2.00e-02 2.50e+03 2.17e+02 ... (remaining 29105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.89: 39426 6.89 - 13.77: 42 13.77 - 20.66: 4 20.66 - 27.54: 2 27.54 - 34.43: 5 Bond angle restraints: 39479 Sorted by residual: angle pdb=" C10 BTI B2002 " pdb=" C11 BTI B2002 " pdb=" O11 BTI B2002 " ideal model delta sigma weight residual 125.49 91.06 34.43 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C10 BTI C1900 " pdb=" C11 BTI C1900 " pdb=" O11 BTI C1900 " ideal model delta sigma weight residual 125.49 93.15 32.34 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C1' ANP A1202 " pdb=" N9 ANP A1202 " pdb=" C8 ANP A1202 " ideal model delta sigma weight residual 128.35 98.16 30.19 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C1' ANP B2003 " pdb=" N9 ANP B2003 " pdb=" C8 ANP B2003 " ideal model delta sigma weight residual 128.35 98.48 29.87 3.00e+00 1.11e-01 9.91e+01 angle pdb=" C10 BTI A1201 " pdb=" C11 BTI A1201 " pdb=" O11 BTI A1201 " ideal model delta sigma weight residual 125.49 97.93 27.56 3.00e+00 1.11e-01 8.44e+01 ... (remaining 39474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.19: 15986 18.19 - 36.37: 1365 36.37 - 54.56: 274 54.56 - 72.75: 96 72.75 - 90.93: 34 Dihedral angle restraints: 17755 sinusoidal: 7258 harmonic: 10497 Sorted by residual: dihedral pdb=" CB CYS C 752 " pdb=" SG CYS C 752 " pdb=" SG CYS C 786 " pdb=" CB CYS C 786 " ideal model delta sinusoidal sigma weight residual 93.00 179.42 -86.42 1 1.00e+01 1.00e-02 9.00e+01 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 93.00 173.64 -80.64 1 1.00e+01 1.00e-02 8.04e+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 93.00 154.11 -61.11 1 1.00e+01 1.00e-02 4.96e+01 ... (remaining 17752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3945 0.084 - 0.168: 401 0.168 - 0.251: 35 0.251 - 0.335: 1 0.335 - 0.419: 4 Chirality restraints: 4386 Sorted by residual: chirality pdb=" CA ARG C1036 " pdb=" N ARG C1036 " pdb=" C ARG C1036 " pdb=" CB ARG C1036 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA THR C1035 " pdb=" N THR C1035 " pdb=" C THR C1035 " pdb=" CB THR C1035 " both_signs ideal model delta sigma weight residual False 2.53 2.92 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C2' ANP B2003 " pdb=" C1' ANP B2003 " pdb=" C3' ANP B2003 " pdb=" O2' ANP B2003 " both_signs ideal model delta sigma weight residual False -2.72 -2.35 -0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 4383 not shown) Planarity restraints: 5173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 511 " 0.033 2.00e-02 2.50e+03 6.57e-02 4.31e+01 pdb=" C GLY D 511 " -0.114 2.00e-02 2.50e+03 pdb=" O GLY D 511 " 0.040 2.00e-02 2.50e+03 pdb=" N PRO D 512 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 508 " 0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C MET D 508 " -0.087 2.00e-02 2.50e+03 pdb=" O MET D 508 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL D 509 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C1038 " 0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C PHE C1038 " -0.086 2.00e-02 2.50e+03 pdb=" O PHE C1038 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU C1039 " 0.030 2.00e-02 2.50e+03 ... (remaining 5170 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 469 2.67 - 3.23: 27126 3.23 - 3.78: 44178 3.78 - 4.34: 56620 4.34 - 4.90: 93898 Nonbonded interactions: 222291 Sorted by model distance: nonbonded pdb=" C8 ANP B2003 " pdb=" O4' ANP B2003 " model vdw 2.109 2.608 nonbonded pdb=" O ALA C1132 " pdb=" OG SER C1151 " model vdw 2.125 3.040 nonbonded pdb=" O THR B1156 " pdb=" NH1 ARG B1158 " model vdw 2.190 3.120 nonbonded pdb=" ND2 ASN B 44 " pdb=" O PRO B 116 " model vdw 2.192 3.120 nonbonded pdb=" OD1 ASN A1069 " pdb=" N ARG A1070 " model vdw 2.192 3.120 ... (remaining 222286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 1178) selection = (chain 'B' and resid 33 through 1178) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 63.660 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: 0.040 Extract box with map and model: 1.100 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 80.670 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.180 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:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.369 29118 Z= 0.451 Angle : 0.919 34.430 39487 Z= 0.490 Chirality : 0.049 0.419 4386 Planarity : 0.005 0.076 5173 Dihedral : 14.936 90.932 11005 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.90 % Favored : 92.88 % Rotamer: Outliers : 1.76 % Allowed : 0.73 % Favored : 97.51 % 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: 0.09 (0.14), residues: 3653 helix: 1.66 (0.14), residues: 1444 sheet: 0.15 (0.23), residues: 533 loop : -1.47 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 607 HIS 0.010 0.001 HIS A 271 PHE 0.023 0.001 PHE A 387 TYR 0.017 0.001 TYR A 261 ARG 0.013 0.001 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.16090 ( 1181) hydrogen bonds : angle 6.49773 ( 3426) SS BOND : bond 0.00458 ( 4) SS BOND : angle 3.26692 ( 8) covalent geometry : bond 0.00849 (29110) covalent geometry : angle 0.91766 (39479) Misc. bond : bond 0.00068 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 552 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8050 (mtm) cc_final: 0.7718 (mtm) REVERT: A 783 MET cc_start: 0.8721 (mmt) cc_final: 0.8387 (mmp) REVERT: A 1098 MET cc_start: 0.3768 (tmm) cc_final: 0.2484 (tpt) REVERT: B 149 MET cc_start: 0.6869 (mmp) cc_final: 0.6586 (tmm) REVERT: B 395 GLU cc_start: 0.7426 (mp0) cc_final: 0.7202 (mp0) REVERT: B 428 LYS cc_start: 0.8555 (mtmt) cc_final: 0.7824 (tttt) REVERT: B 471 PHE cc_start: 0.8640 (t80) cc_final: 0.8417 (t80) REVERT: B 743 MET cc_start: 0.8468 (pmm) cc_final: 0.8213 (pmm) REVERT: B 836 GLU cc_start: 0.8836 (tp30) cc_final: 0.8542 (tp30) REVERT: B 1006 ASP cc_start: 0.9221 (m-30) cc_final: 0.9009 (m-30) REVERT: C 519 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7481 (mmmt) REVERT: C 584 THR cc_start: 0.8741 (m) cc_final: 0.8516 (p) REVERT: C 671 MET cc_start: 0.4761 (tpt) cc_final: 0.4392 (tpp) REVERT: C 739 CYS cc_start: 0.7302 (t) cc_final: 0.7040 (t) REVERT: C 1012 MET cc_start: 0.8271 (mmm) cc_final: 0.8045 (mmt) REVERT: C 1038 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7332 (p90) REVERT: C 1048 PHE cc_start: 0.5958 (OUTLIER) cc_final: 0.5204 (p90) REVERT: C 1164 LYS cc_start: 0.8506 (tmtt) cc_final: 0.8304 (tptp) REVERT: C 1165 ASP cc_start: 0.8489 (m-30) cc_final: 0.8109 (m-30) REVERT: D 566 MET cc_start: 0.6876 (ttp) cc_final: 0.6267 (ptm) REVERT: D 873 ASN cc_start: 0.7998 (m110) cc_final: 0.7747 (m-40) REVERT: D 1153 MET cc_start: 0.7279 (ptt) cc_final: 0.6816 (pmm) REVERT: D 1171 ASP cc_start: 0.8938 (m-30) cc_final: 0.8258 (m-30) outliers start: 53 outliers final: 9 residues processed: 592 average time/residue: 0.4445 time to fit residues: 399.3563 Evaluate side-chains 325 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 313 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1053 GLU Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain D residue 496 ARG Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1056 LYS Chi-restraints excluded: chain D residue 1059 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 5.9990 chunk 275 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 330 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS A1073 GLN A1093 GLN A1135 GLN ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 306 ASN B 317 HIS B 348 GLN B 375 GLN B 769 HIS B 873 ASN B 879 HIS B 956 HIS C 506 HIS ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 HIS C 879 HIS C1059 HIS ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN ** D 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 ASN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.075670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.057802 restraints weight = 159763.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.059436 restraints weight = 104565.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.060542 restraints weight = 77112.368| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 : 0.006 0.083 29118 Z= 0.289 Angle : 0.791 8.728 39487 Z= 0.410 Chirality : 0.047 0.336 4386 Planarity : 0.006 0.061 5173 Dihedral : 8.796 65.507 4242 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.09 % Favored : 92.80 % Rotamer: Outliers : 3.25 % Allowed : 11.25 % Favored : 85.50 % 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: -0.26 (0.14), residues: 3653 helix: 1.31 (0.13), residues: 1462 sheet: -0.08 (0.23), residues: 522 loop : -1.60 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 838 HIS 0.011 0.002 HIS B 282 PHE 0.038 0.002 PHE A1100 TYR 0.023 0.002 TYR C 593 ARG 0.012 0.001 ARG C 625 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 1181) hydrogen bonds : angle 5.49513 ( 3426) SS BOND : bond 0.00553 ( 4) SS BOND : angle 2.04786 ( 8) covalent geometry : bond 0.00598 (29110) covalent geometry : angle 0.79069 (39479) Misc. bond : bond 0.00144 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 308 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7801 (mtm) cc_final: 0.7598 (mtm) REVERT: A 275 VAL cc_start: 0.8877 (t) cc_final: 0.8581 (p) REVERT: A 501 LEU cc_start: 0.9636 (mm) cc_final: 0.9366 (mm) REVERT: A 508 MET cc_start: 0.8905 (mmp) cc_final: 0.8364 (mmm) REVERT: A 607 TRP cc_start: 0.7998 (OUTLIER) cc_final: 0.7264 (t60) REVERT: A 822 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8641 (pp) REVERT: A 881 MET cc_start: 0.8687 (tmm) cc_final: 0.8390 (tmm) REVERT: A 921 MET cc_start: 0.9461 (OUTLIER) cc_final: 0.9142 (mtp) REVERT: A 946 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8844 (mm-30) REVERT: A 1054 ARG cc_start: 0.7912 (ptt90) cc_final: 0.7433 (ptt90) REVERT: B 41 MET cc_start: 0.8363 (ttp) cc_final: 0.7431 (tmm) REVERT: B 149 MET cc_start: 0.7064 (mmp) cc_final: 0.6816 (tmm) REVERT: B 377 ARG cc_start: 0.7580 (mtm-85) cc_final: 0.7098 (mtm180) REVERT: B 395 GLU cc_start: 0.7442 (mp0) cc_final: 0.7148 (mp0) REVERT: B 428 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8276 (tttt) REVERT: B 477 ASP cc_start: 0.8260 (p0) cc_final: 0.7835 (p0) REVERT: B 743 MET cc_start: 0.8611 (pmm) cc_final: 0.8287 (pmm) REVERT: B 801 MET cc_start: 0.9342 (mtt) cc_final: 0.9053 (mtm) REVERT: B 804 MET cc_start: 0.7586 (tpp) cc_final: 0.7071 (mmm) REVERT: B 854 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6442 (tpt) REVERT: B 994 LEU cc_start: 0.9443 (mt) cc_final: 0.9087 (pp) REVERT: B 1006 ASP cc_start: 0.9439 (m-30) cc_final: 0.9096 (m-30) REVERT: B 1101 HIS cc_start: 0.7498 (m-70) cc_final: 0.7216 (m90) REVERT: B 1116 MET cc_start: 0.8286 (ttt) cc_final: 0.7925 (ttt) REVERT: B 1145 MET cc_start: 0.7056 (pmm) cc_final: 0.6289 (ptp) REVERT: B 1162 VAL cc_start: 0.6956 (p) cc_final: 0.6615 (p) REVERT: C 519 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7692 (mmtm) REVERT: C 616 MET cc_start: 0.8964 (mmm) cc_final: 0.8662 (mmp) REVERT: C 1038 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7690 (p90) REVERT: C 1143 MET cc_start: 0.2208 (ptp) cc_final: 0.1831 (ptp) REVERT: D 566 MET cc_start: 0.7413 (ttp) cc_final: 0.6297 (ptm) REVERT: D 604 MET cc_start: 0.8327 (tpp) cc_final: 0.8066 (tpp) REVERT: D 641 MET cc_start: 0.8973 (tpp) cc_final: 0.8745 (tpp) REVERT: D 783 MET cc_start: 0.9310 (mmt) cc_final: 0.9070 (mmp) REVERT: D 836 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8568 (mt-10) REVERT: D 1085 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7930 (mpt-90) REVERT: D 1143 MET cc_start: -0.0709 (ttp) cc_final: -0.1465 (ttp) REVERT: D 1153 MET cc_start: 0.8330 (ptt) cc_final: 0.8011 (pmm) outliers start: 98 outliers final: 68 residues processed: 379 average time/residue: 0.4855 time to fit residues: 290.1713 Evaluate side-chains 330 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 255 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1034 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1086 SER Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 SER Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1145 MET Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain D residue 496 ARG Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 896 GLU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1059 HIS Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1085 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 268 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 0.0060 chunk 23 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 295 optimal weight: 0.6980 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN A 998 HIS A1135 GLN ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN C 495 ASN C 498 GLN C 506 HIS D 923 GLN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.076474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.058636 restraints weight = 155717.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.060224 restraints weight = 100990.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.061280 restraints weight = 74205.916| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29118 Z= 0.134 Angle : 0.621 9.934 39487 Z= 0.316 Chirality : 0.043 0.192 4386 Planarity : 0.004 0.061 5173 Dihedral : 7.994 70.310 4231 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.35 % Favored : 93.54 % Rotamer: Outliers : 3.02 % Allowed : 12.98 % Favored : 84.00 % 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: -0.00 (0.14), residues: 3653 helix: 1.62 (0.14), residues: 1473 sheet: -0.12 (0.23), residues: 532 loop : -1.51 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 607 HIS 0.010 0.001 HIS B 282 PHE 0.017 0.001 PHE B 461 TYR 0.014 0.001 TYR A 118 ARG 0.009 0.001 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 1181) hydrogen bonds : angle 5.06295 ( 3426) SS BOND : bond 0.00175 ( 4) SS BOND : angle 2.61482 ( 8) covalent geometry : bond 0.00302 (29110) covalent geometry : angle 0.61983 (39479) Misc. bond : bond 0.00029 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 289 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7882 (mtm) cc_final: 0.7647 (mtm) REVERT: A 275 VAL cc_start: 0.8854 (t) cc_final: 0.8562 (p) REVERT: A 508 MET cc_start: 0.8872 (mmp) cc_final: 0.8408 (mmm) REVERT: A 607 TRP cc_start: 0.7875 (OUTLIER) cc_final: 0.7216 (t60) REVERT: A 783 MET cc_start: 0.9056 (mmt) cc_final: 0.8820 (mmp) REVERT: A 881 MET cc_start: 0.8554 (tmm) cc_final: 0.8268 (tmm) REVERT: A 900 MET cc_start: 0.8521 (mmp) cc_final: 0.8314 (mmp) REVERT: A 908 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7883 (t) REVERT: A 921 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8952 (mtp) REVERT: A 1031 ASP cc_start: 0.6662 (t0) cc_final: 0.6456 (t70) REVERT: B 41 MET cc_start: 0.8422 (ttp) cc_final: 0.7691 (tmm) REVERT: B 47 GLU cc_start: 0.7714 (pm20) cc_final: 0.7107 (pm20) REVERT: B 149 MET cc_start: 0.7089 (mmp) cc_final: 0.6847 (tmm) REVERT: B 377 ARG cc_start: 0.7592 (mtm-85) cc_final: 0.7377 (mtm180) REVERT: B 395 GLU cc_start: 0.7520 (mp0) cc_final: 0.7272 (mp0) REVERT: B 408 ASP cc_start: 0.8216 (m-30) cc_final: 0.8016 (m-30) REVERT: B 428 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8588 (mttt) REVERT: B 477 ASP cc_start: 0.8190 (p0) cc_final: 0.7714 (p0) REVERT: B 641 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8368 (ppp) REVERT: B 743 MET cc_start: 0.8632 (pmm) cc_final: 0.8253 (pmm) REVERT: B 754 MET cc_start: 0.9023 (ptp) cc_final: 0.8672 (ptp) REVERT: B 804 MET cc_start: 0.7656 (tpp) cc_final: 0.7160 (mmm) REVERT: B 874 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8488 (pp) REVERT: B 994 LEU cc_start: 0.9400 (mt) cc_final: 0.9087 (pp) REVERT: B 1006 ASP cc_start: 0.9453 (m-30) cc_final: 0.9076 (m-30) REVERT: C 519 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7774 (mmtm) REVERT: C 526 ASP cc_start: 0.8504 (p0) cc_final: 0.8227 (t0) REVERT: C 604 MET cc_start: 0.8264 (tmm) cc_final: 0.7928 (tmm) REVERT: C 616 MET cc_start: 0.9072 (mmm) cc_final: 0.8769 (mmp) REVERT: C 641 MET cc_start: 0.9066 (ppp) cc_final: 0.8775 (ppp) REVERT: C 804 MET cc_start: 0.9130 (tpp) cc_final: 0.8636 (mmp) REVERT: C 873 ASN cc_start: 0.8820 (m-40) cc_final: 0.8446 (p0) REVERT: D 566 MET cc_start: 0.7402 (ttp) cc_final: 0.6579 (tmm) REVERT: D 683 LEU cc_start: 0.9268 (mp) cc_final: 0.8840 (mm) REVERT: D 743 MET cc_start: 0.8775 (pmm) cc_final: 0.8505 (pmm) REVERT: D 783 MET cc_start: 0.9286 (mmt) cc_final: 0.8777 (mmm) REVERT: D 836 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8499 (mt-10) REVERT: D 923 GLN cc_start: 0.9558 (OUTLIER) cc_final: 0.9037 (tt0) REVERT: D 1143 MET cc_start: -0.0691 (ttp) cc_final: -0.1393 (ttp) REVERT: D 1153 MET cc_start: 0.8330 (ptt) cc_final: 0.8018 (pmm) outliers start: 91 outliers final: 54 residues processed: 351 average time/residue: 0.4146 time to fit residues: 232.7709 Evaluate side-chains 323 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 262 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1135 GLN Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1086 SER Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 739 CYS Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 923 GLN Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1068 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1116 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 171 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 340 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 316 optimal weight: 10.0000 chunk 107 optimal weight: 0.0050 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 268 optimal weight: 6.9990 chunk 293 optimal weight: 8.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 HIS ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 640 GLN ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 898 ASN D 956 HIS ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 ASN ** D1135 GLN ** 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 = 0.3748 r_free = 0.3748 target = 0.075550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.057801 restraints weight = 160040.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.059428 restraints weight = 103037.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.060581 restraints weight = 75631.630| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29118 Z= 0.142 Angle : 0.604 7.662 39487 Z= 0.307 Chirality : 0.043 0.216 4386 Planarity : 0.004 0.046 5173 Dihedral : 7.446 72.363 4225 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.14 % Favored : 92.75 % Rotamer: Outliers : 3.35 % Allowed : 14.54 % Favored : 82.11 % 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: 0.01 (0.14), residues: 3653 helix: 1.64 (0.14), residues: 1472 sheet: -0.14 (0.22), residues: 528 loop : -1.51 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 624 HIS 0.017 0.001 HIS D1059 PHE 0.026 0.001 PHE B 461 TYR 0.013 0.001 TYR A 118 ARG 0.010 0.000 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 1181) hydrogen bonds : angle 4.94937 ( 3426) SS BOND : bond 0.03067 ( 4) SS BOND : angle 2.47589 ( 8) covalent geometry : bond 0.00313 (29110) covalent geometry : angle 0.60267 (39479) Misc. bond : bond 0.00020 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 269 time to evaluate : 5.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 VAL cc_start: 0.8895 (t) cc_final: 0.8622 (p) REVERT: A 501 LEU cc_start: 0.9669 (mm) cc_final: 0.9417 (mm) REVERT: A 508 MET cc_start: 0.8794 (mmp) cc_final: 0.8346 (mmm) REVERT: A 822 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8680 (pp) REVERT: A 908 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7767 (t) REVERT: A 921 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9088 (mtp) REVERT: A 1031 ASP cc_start: 0.6540 (t0) cc_final: 0.6222 (t70) REVERT: A 1054 ARG cc_start: 0.7913 (ptt90) cc_final: 0.7384 (ptt90) REVERT: B 41 MET cc_start: 0.8595 (ttp) cc_final: 0.7902 (tmm) REVERT: B 149 MET cc_start: 0.7118 (mmp) cc_final: 0.6873 (tmm) REVERT: B 395 GLU cc_start: 0.7476 (mp0) cc_final: 0.7208 (mp0) REVERT: B 408 ASP cc_start: 0.8238 (m-30) cc_final: 0.7978 (m-30) REVERT: B 477 ASP cc_start: 0.8155 (p0) cc_final: 0.7705 (p0) REVERT: B 641 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8030 (ppp) REVERT: B 651 TYR cc_start: 0.7596 (m-80) cc_final: 0.6992 (m-10) REVERT: B 754 MET cc_start: 0.8992 (ptp) cc_final: 0.8677 (ptp) REVERT: B 804 MET cc_start: 0.7726 (tpp) cc_final: 0.7165 (mmm) REVERT: B 836 GLU cc_start: 0.9159 (tp30) cc_final: 0.8782 (tp30) REVERT: B 854 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6087 (tpt) REVERT: B 994 LEU cc_start: 0.9417 (mt) cc_final: 0.9121 (pp) REVERT: B 1006 ASP cc_start: 0.9440 (m-30) cc_final: 0.8985 (m-30) REVERT: B 1097 GLU cc_start: 0.2739 (OUTLIER) cc_final: 0.2441 (pm20) REVERT: B 1116 MET cc_start: 0.8624 (ttt) cc_final: 0.8311 (ttt) REVERT: C 519 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7904 (tptp) REVERT: C 526 ASP cc_start: 0.8555 (p0) cc_final: 0.8270 (t0) REVERT: C 604 MET cc_start: 0.8262 (tmm) cc_final: 0.8049 (tmm) REVERT: C 804 MET cc_start: 0.9215 (tpp) cc_final: 0.8806 (tpt) REVERT: C 873 ASN cc_start: 0.8772 (m-40) cc_final: 0.8431 (p0) REVERT: C 1012 MET cc_start: 0.8239 (mmm) cc_final: 0.8016 (mmm) REVERT: C 1036 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8270 (ttp80) REVERT: D 625 ARG cc_start: 0.8696 (mmt180) cc_final: 0.8105 (mmm160) REVERT: D 683 LEU cc_start: 0.9226 (mp) cc_final: 0.8922 (mm) REVERT: D 724 MET cc_start: 0.8815 (mmm) cc_final: 0.8477 (mmm) REVERT: D 743 MET cc_start: 0.8718 (pmm) cc_final: 0.8479 (pmm) REVERT: D 783 MET cc_start: 0.9292 (mmt) cc_final: 0.9054 (mmm) REVERT: D 836 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8474 (mt-10) REVERT: D 1054 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.6233 (mpp-170) REVERT: D 1143 MET cc_start: -0.0761 (ttp) cc_final: -0.1641 (ttp) REVERT: D 1153 MET cc_start: 0.8185 (ptt) cc_final: 0.7794 (pmm) outliers start: 101 outliers final: 72 residues processed: 338 average time/residue: 0.5089 time to fit residues: 279.4244 Evaluate side-chains 329 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 248 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 921 MET Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1097 GLU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 SER Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 739 CYS Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1053 GLU Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1165 ASP Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1068 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1116 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 342 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 127 optimal weight: 0.0040 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 898 ASN D 956 HIS ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** 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 = 0.3730 r_free = 0.3730 target = 0.074607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.056523 restraints weight = 158830.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.058147 restraints weight = 103066.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.059241 restraints weight = 75786.292| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29118 Z= 0.136 Angle : 0.604 15.257 39487 Z= 0.304 Chirality : 0.042 0.199 4386 Planarity : 0.005 0.154 5173 Dihedral : 7.206 71.230 4225 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.12 % Favored : 92.77 % Rotamer: Outliers : 3.39 % Allowed : 15.67 % 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: 0.04 (0.14), residues: 3653 helix: 1.63 (0.14), residues: 1482 sheet: -0.11 (0.23), residues: 526 loop : -1.49 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 607 HIS 0.034 0.001 HIS D 956 PHE 0.019 0.001 PHE B 461 TYR 0.019 0.001 TYR B 651 ARG 0.006 0.000 ARG B1070 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 1181) hydrogen bonds : angle 4.83511 ( 3426) SS BOND : bond 0.00711 ( 4) SS BOND : angle 2.27886 ( 8) covalent geometry : bond 0.00304 (29110) covalent geometry : angle 0.60311 (39479) Misc. bond : bond 0.00018 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 262 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 VAL cc_start: 0.8904 (t) cc_final: 0.8632 (p) REVERT: A 501 LEU cc_start: 0.9694 (mm) cc_final: 0.9437 (mm) REVERT: A 508 MET cc_start: 0.8788 (mmp) cc_final: 0.8397 (mmm) REVERT: A 577 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8826 (mm) REVERT: A 686 MET cc_start: 0.9251 (mtm) cc_final: 0.8875 (mmm) REVERT: A 724 MET cc_start: 0.8696 (mmm) cc_final: 0.8176 (tpp) REVERT: A 810 MET cc_start: 0.9680 (ptm) cc_final: 0.9480 (ptp) REVERT: A 822 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8659 (pp) REVERT: A 1054 ARG cc_start: 0.7960 (ptt90) cc_final: 0.7513 (ptt90) REVERT: B 41 MET cc_start: 0.8649 (ttp) cc_final: 0.8103 (tmm) REVERT: B 408 ASP cc_start: 0.8214 (m-30) cc_final: 0.7949 (m-30) REVERT: B 477 ASP cc_start: 0.8151 (p0) cc_final: 0.7717 (p0) REVERT: B 754 MET cc_start: 0.8991 (ptp) cc_final: 0.8652 (ptp) REVERT: B 994 LEU cc_start: 0.9403 (mt) cc_final: 0.9080 (pp) REVERT: B 1006 ASP cc_start: 0.9440 (m-30) cc_final: 0.8969 (m-30) REVERT: B 1097 GLU cc_start: 0.2744 (OUTLIER) cc_final: 0.2064 (pm20) REVERT: B 1116 MET cc_start: 0.8533 (ttt) cc_final: 0.8167 (ttt) REVERT: C 519 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7863 (mmtm) REVERT: C 526 ASP cc_start: 0.8528 (p0) cc_final: 0.8276 (t70) REVERT: C 616 MET cc_start: 0.9048 (mmm) cc_final: 0.8831 (mmp) REVERT: C 641 MET cc_start: 0.8889 (ppp) cc_final: 0.8671 (ppp) REVERT: C 804 MET cc_start: 0.9213 (tpp) cc_final: 0.8854 (tpt) REVERT: C 854 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6462 (tmm) REVERT: C 873 ASN cc_start: 0.8807 (m-40) cc_final: 0.8426 (p0) REVERT: C 1036 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8345 (ttp80) REVERT: D 508 MET cc_start: 0.8666 (tpp) cc_final: 0.8382 (tpp) REVERT: D 566 MET cc_start: 0.7202 (ttp) cc_final: 0.6523 (tmm) REVERT: D 625 ARG cc_start: 0.8729 (mmt180) cc_final: 0.8089 (mmm160) REVERT: D 683 LEU cc_start: 0.9184 (mp) cc_final: 0.8942 (mm) REVERT: D 724 MET cc_start: 0.8886 (mmm) cc_final: 0.8460 (mmm) REVERT: D 743 MET cc_start: 0.8731 (pmm) cc_final: 0.8514 (pmm) REVERT: D 836 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8475 (mt-10) REVERT: D 1054 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6255 (mpp-170) REVERT: D 1143 MET cc_start: -0.0800 (ttp) cc_final: -0.1702 (ttp) REVERT: D 1153 MET cc_start: 0.8264 (ptt) cc_final: 0.7954 (pmm) outliers start: 102 outliers final: 77 residues processed: 331 average time/residue: 0.3906 time to fit residues: 207.7719 Evaluate side-chains 332 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 248 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1086 SER Chi-restraints excluded: chain B residue 1097 GLU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 521 SER Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 739 CYS Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1165 ASP Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1116 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 146 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 346 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 234 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 348 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 898 ASN ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** 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 = 0.3730 r_free = 0.3730 target = 0.074624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.056742 restraints weight = 157248.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.058322 restraints weight = 102271.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.059405 restraints weight = 75225.145| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29118 Z= 0.116 Angle : 0.593 12.969 39487 Z= 0.296 Chirality : 0.042 0.191 4386 Planarity : 0.004 0.094 5173 Dihedral : 7.024 71.979 4225 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.90 % Favored : 92.99 % Rotamer: Outliers : 3.22 % Allowed : 16.59 % Favored : 80.19 % 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: 0.08 (0.14), residues: 3653 helix: 1.67 (0.14), residues: 1482 sheet: -0.14 (0.23), residues: 539 loop : -1.46 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 838 HIS 0.016 0.001 HIS D 956 PHE 0.017 0.001 PHE B 461 TYR 0.013 0.001 TYR B 261 ARG 0.006 0.000 ARG B1070 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 1181) hydrogen bonds : angle 4.73684 ( 3426) SS BOND : bond 0.00203 ( 4) SS BOND : angle 2.45587 ( 8) covalent geometry : bond 0.00262 (29110) covalent geometry : angle 0.59217 (39479) Misc. bond : bond 0.00015 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 258 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 VAL cc_start: 0.8888 (t) cc_final: 0.8618 (p) REVERT: A 501 LEU cc_start: 0.9692 (mm) cc_final: 0.9442 (mm) REVERT: A 577 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8799 (mm) REVERT: A 616 MET cc_start: 0.7839 (mmp) cc_final: 0.7549 (mmp) REVERT: A 686 MET cc_start: 0.9273 (mtm) cc_final: 0.8831 (mmm) REVERT: A 724 MET cc_start: 0.8731 (mmm) cc_final: 0.8221 (tpp) REVERT: A 822 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8656 (pp) REVERT: A 854 MET cc_start: 0.7798 (mmt) cc_final: 0.7543 (mmt) REVERT: A 1054 ARG cc_start: 0.8008 (ptt90) cc_final: 0.7510 (ptt90) REVERT: B 41 MET cc_start: 0.8651 (ttp) cc_final: 0.7376 (tmm) REVERT: B 47 GLU cc_start: 0.7733 (pm20) cc_final: 0.7087 (pm20) REVERT: B 149 MET cc_start: 0.8241 (tmm) cc_final: 0.7828 (mmp) REVERT: B 234 PHE cc_start: 0.8659 (m-10) cc_final: 0.8440 (m-10) REVERT: B 408 ASP cc_start: 0.8242 (m-30) cc_final: 0.8002 (m-30) REVERT: B 428 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8586 (mttt) REVERT: B 477 ASP cc_start: 0.8135 (p0) cc_final: 0.7706 (p0) REVERT: B 566 MET cc_start: 0.7665 (tpt) cc_final: 0.7461 (tpp) REVERT: B 641 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8142 (ppp) REVERT: B 754 MET cc_start: 0.9007 (ptp) cc_final: 0.8656 (ptp) REVERT: B 854 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6438 (tpt) REVERT: B 921 MET cc_start: 0.8882 (mtp) cc_final: 0.8598 (mtp) REVERT: B 994 LEU cc_start: 0.9425 (mt) cc_final: 0.9049 (pp) REVERT: B 1006 ASP cc_start: 0.9458 (m-30) cc_final: 0.8987 (m-30) REVERT: B 1097 GLU cc_start: 0.2658 (OUTLIER) cc_final: 0.0887 (pm20) REVERT: B 1116 MET cc_start: 0.8533 (ttt) cc_final: 0.8187 (ttt) REVERT: B 1166 MET cc_start: 0.8989 (tpt) cc_final: 0.8665 (ppp) REVERT: C 519 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7862 (mmtm) REVERT: C 604 MET cc_start: 0.8124 (tmm) cc_final: 0.7877 (tmm) REVERT: C 873 ASN cc_start: 0.8797 (m-40) cc_final: 0.8412 (p0) REVERT: C 1036 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8521 (tmm-80) REVERT: D 508 MET cc_start: 0.8705 (tpp) cc_final: 0.8281 (mmp) REVERT: D 566 MET cc_start: 0.7188 (ttp) cc_final: 0.6555 (tmm) REVERT: D 625 ARG cc_start: 0.8735 (mmt180) cc_final: 0.8088 (mmm160) REVERT: D 724 MET cc_start: 0.8946 (mmm) cc_final: 0.8443 (mmm) REVERT: D 743 MET cc_start: 0.8713 (pmm) cc_final: 0.8481 (pmm) REVERT: D 783 MET cc_start: 0.9301 (mmt) cc_final: 0.9088 (mmm) REVERT: D 836 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8513 (mp0) REVERT: D 1054 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6269 (mpp-170) REVERT: D 1143 MET cc_start: -0.0888 (ttp) cc_final: -0.1659 (ttp) REVERT: D 1153 MET cc_start: 0.8319 (ptt) cc_final: 0.8022 (pmm) outliers start: 97 outliers final: 68 residues processed: 330 average time/residue: 0.3909 time to fit residues: 208.2084 Evaluate side-chains 319 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 243 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1086 SER Chi-restraints excluded: chain B residue 1097 GLU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 739 CYS Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1053 GLU Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1116 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 51 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 188 optimal weight: 0.3980 chunk 36 optimal weight: 6.9990 chunk 311 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 HIS D 898 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.073743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.055886 restraints weight = 159805.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.057512 restraints weight = 103068.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.058608 restraints weight = 75745.020| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29118 Z= 0.131 Angle : 0.608 11.909 39487 Z= 0.303 Chirality : 0.042 0.227 4386 Planarity : 0.004 0.063 5173 Dihedral : 6.922 71.901 4225 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.34 % Favored : 92.55 % Rotamer: Outliers : 3.45 % Allowed : 17.09 % Favored : 79.46 % 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: 0.08 (0.14), residues: 3653 helix: 1.67 (0.14), residues: 1482 sheet: -0.14 (0.23), residues: 535 loop : -1.45 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 624 HIS 0.011 0.001 HIS D 956 PHE 0.014 0.001 PHE B 461 TYR 0.014 0.001 TYR A 118 ARG 0.006 0.000 ARG B1070 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 1181) hydrogen bonds : angle 4.72269 ( 3426) SS BOND : bond 0.02250 ( 4) SS BOND : angle 2.78210 ( 8) covalent geometry : bond 0.00292 (29110) covalent geometry : angle 0.60717 (39479) Misc. bond : bond 0.00018 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 251 time to evaluate : 3.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 VAL cc_start: 0.8922 (t) cc_final: 0.8670 (p) REVERT: A 324 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7227 (pt0) REVERT: A 501 LEU cc_start: 0.9703 (mm) cc_final: 0.9452 (mm) REVERT: A 508 MET cc_start: 0.9012 (mmm) cc_final: 0.8546 (mmm) REVERT: A 577 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8919 (mm) REVERT: A 616 MET cc_start: 0.7951 (mmp) cc_final: 0.7516 (mmp) REVERT: A 686 MET cc_start: 0.9275 (mtm) cc_final: 0.8887 (mmt) REVERT: A 724 MET cc_start: 0.8792 (mmm) cc_final: 0.8305 (tpp) REVERT: A 822 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8677 (pp) REVERT: A 854 MET cc_start: 0.7798 (mmt) cc_final: 0.7555 (mmt) REVERT: A 1054 ARG cc_start: 0.8010 (ptt90) cc_final: 0.7530 (ptt90) REVERT: B 41 MET cc_start: 0.8756 (ttp) cc_final: 0.7339 (tmm) REVERT: B 234 PHE cc_start: 0.8671 (m-10) cc_final: 0.8452 (m-10) REVERT: B 250 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8817 (mm) REVERT: B 408 ASP cc_start: 0.8277 (m-30) cc_final: 0.7981 (m-30) REVERT: B 477 ASP cc_start: 0.8144 (p0) cc_final: 0.7727 (p0) REVERT: B 566 MET cc_start: 0.7676 (tpt) cc_final: 0.7440 (tpp) REVERT: B 754 MET cc_start: 0.9065 (ptp) cc_final: 0.8728 (ptp) REVERT: B 804 MET cc_start: 0.7485 (mmm) cc_final: 0.6890 (tpp) REVERT: B 921 MET cc_start: 0.8973 (mtp) cc_final: 0.8728 (mtp) REVERT: B 994 LEU cc_start: 0.9388 (mt) cc_final: 0.9043 (pp) REVERT: B 1006 ASP cc_start: 0.9449 (m-30) cc_final: 0.9009 (m-30) REVERT: B 1097 GLU cc_start: 0.2659 (OUTLIER) cc_final: 0.1292 (pm20) REVERT: B 1116 MET cc_start: 0.8593 (ttt) cc_final: 0.8257 (ttt) REVERT: B 1165 ASP cc_start: 0.8968 (t0) cc_final: 0.8634 (m-30) REVERT: B 1166 MET cc_start: 0.9067 (tpt) cc_final: 0.8620 (ppp) REVERT: C 519 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7836 (mmtm) REVERT: C 604 MET cc_start: 0.8096 (tmm) cc_final: 0.7824 (tmm) REVERT: C 801 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8691 (mtm) REVERT: C 804 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8729 (tpt) REVERT: C 854 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6707 (tmm) REVERT: C 1036 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8414 (ttp80) REVERT: D 508 MET cc_start: 0.8739 (tpp) cc_final: 0.8474 (mmp) REVERT: D 566 MET cc_start: 0.7373 (ttp) cc_final: 0.6587 (tmm) REVERT: D 625 ARG cc_start: 0.8751 (mmt180) cc_final: 0.8168 (mmm160) REVERT: D 724 MET cc_start: 0.8972 (mmm) cc_final: 0.8445 (mmm) REVERT: D 743 MET cc_start: 0.8686 (pmm) cc_final: 0.8452 (pmm) REVERT: D 783 MET cc_start: 0.9294 (mmt) cc_final: 0.8952 (mmm) REVERT: D 836 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8517 (mp0) REVERT: D 1054 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6417 (mpp-170) REVERT: D 1143 MET cc_start: -0.0834 (ttp) cc_final: -0.1729 (ttp) REVERT: D 1153 MET cc_start: 0.8307 (ptt) cc_final: 0.8029 (pmm) outliers start: 104 outliers final: 71 residues processed: 325 average time/residue: 0.4056 time to fit residues: 212.0286 Evaluate side-chains 326 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 244 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 641 MET Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1097 GLU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1157 VAL Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 739 CYS Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1165 ASP Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1116 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 209 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 0.0020 chunk 91 optimal weight: 0.9990 chunk 292 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 HIS B 873 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 898 ASN D 923 GLN D1135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.074403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.056502 restraints weight = 158428.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.058167 restraints weight = 102319.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.059311 restraints weight = 74707.076| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 29118 Z= 0.108 Angle : 0.613 12.438 39487 Z= 0.303 Chirality : 0.042 0.231 4386 Planarity : 0.004 0.049 5173 Dihedral : 6.713 75.756 4223 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.57 % Favored : 93.35 % Rotamer: Outliers : 2.85 % Allowed : 17.79 % Favored : 79.36 % 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: 0.13 (0.14), residues: 3653 helix: 1.71 (0.14), residues: 1475 sheet: -0.07 (0.23), residues: 535 loop : -1.43 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 607 HIS 0.008 0.001 HIS D 574 PHE 0.017 0.001 PHE B 461 TYR 0.013 0.001 TYR B 261 ARG 0.008 0.000 ARG B1070 Details of bonding type rmsd hydrogen bonds : bond 0.02834 ( 1181) hydrogen bonds : angle 4.63586 ( 3426) SS BOND : bond 0.01230 ( 4) SS BOND : angle 2.65825 ( 8) covalent geometry : bond 0.00245 (29110) covalent geometry : angle 0.61193 (39479) Misc. bond : bond 0.00015 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 268 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 275 VAL cc_start: 0.8878 (t) cc_final: 0.8618 (p) REVERT: A 324 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7046 (pt0) REVERT: A 501 LEU cc_start: 0.9698 (mm) cc_final: 0.9451 (mm) REVERT: A 508 MET cc_start: 0.8932 (mmm) cc_final: 0.8272 (mmm) REVERT: A 577 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8868 (mm) REVERT: A 616 MET cc_start: 0.7939 (mmp) cc_final: 0.7513 (mmp) REVERT: A 686 MET cc_start: 0.9312 (mtm) cc_final: 0.8878 (mmt) REVERT: A 724 MET cc_start: 0.8772 (mmm) cc_final: 0.8279 (tpp) REVERT: A 822 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8650 (pp) REVERT: A 854 MET cc_start: 0.7676 (mmt) cc_final: 0.7451 (mmt) REVERT: A 1054 ARG cc_start: 0.7988 (ptt90) cc_final: 0.7512 (ptt90) REVERT: B 41 MET cc_start: 0.8707 (ttp) cc_final: 0.7522 (tmm) REVERT: B 149 MET cc_start: 0.8121 (tmm) cc_final: 0.7686 (mmp) REVERT: B 178 HIS cc_start: 0.9571 (m-70) cc_final: 0.9361 (m90) REVERT: B 234 PHE cc_start: 0.8669 (m-10) cc_final: 0.8444 (m-10) REVERT: B 408 ASP cc_start: 0.8240 (m-30) cc_final: 0.7955 (m-30) REVERT: B 477 ASP cc_start: 0.8101 (p0) cc_final: 0.7614 (p0) REVERT: B 566 MET cc_start: 0.7727 (tpt) cc_final: 0.7303 (tpp) REVERT: B 754 MET cc_start: 0.9053 (ptp) cc_final: 0.8706 (ptp) REVERT: B 804 MET cc_start: 0.8556 (mmm) cc_final: 0.8134 (tpp) REVERT: B 854 MET cc_start: 0.7792 (tpt) cc_final: 0.7389 (tpp) REVERT: B 921 MET cc_start: 0.8961 (mtp) cc_final: 0.8703 (mtp) REVERT: B 994 LEU cc_start: 0.9400 (mt) cc_final: 0.9042 (pp) REVERT: B 1006 ASP cc_start: 0.9437 (m-30) cc_final: 0.8972 (m-30) REVERT: B 1116 MET cc_start: 0.8600 (ttt) cc_final: 0.8236 (ttt) REVERT: B 1165 ASP cc_start: 0.8985 (t0) cc_final: 0.8703 (m-30) REVERT: B 1166 MET cc_start: 0.9036 (tpt) cc_final: 0.8630 (ppp) REVERT: C 519 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7815 (mmtm) REVERT: C 604 MET cc_start: 0.8156 (tmm) cc_final: 0.7904 (tmm) REVERT: C 801 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8591 (mtm) REVERT: C 804 MET cc_start: 0.9115 (tpt) cc_final: 0.8626 (tpt) REVERT: C 854 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6626 (tmm) REVERT: C 881 MET cc_start: 0.8945 (mmp) cc_final: 0.8684 (tpp) REVERT: C 921 MET cc_start: 0.8998 (tpp) cc_final: 0.8749 (tpp) REVERT: C 1036 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8409 (ptm-80) REVERT: C 1048 PHE cc_start: 0.4546 (OUTLIER) cc_final: 0.4320 (p90) REVERT: D 508 MET cc_start: 0.8745 (tpp) cc_final: 0.8521 (mmp) REVERT: D 566 MET cc_start: 0.7332 (ttp) cc_final: 0.6803 (tmm) REVERT: D 625 ARG cc_start: 0.8746 (mmt180) cc_final: 0.8248 (mmm160) REVERT: D 724 MET cc_start: 0.8955 (mmm) cc_final: 0.8397 (mmm) REVERT: D 743 MET cc_start: 0.8693 (pmm) cc_final: 0.8437 (pmm) REVERT: D 783 MET cc_start: 0.9276 (mmt) cc_final: 0.8952 (mmm) REVERT: D 833 ASP cc_start: 0.8793 (m-30) cc_final: 0.8578 (m-30) REVERT: D 836 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8586 (mp0) REVERT: D 1054 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6359 (mpp-170) REVERT: D 1143 MET cc_start: -0.0819 (ttp) cc_final: -0.1524 (ttp) REVERT: D 1153 MET cc_start: 0.8356 (ptt) cc_final: 0.8105 (pmm) outliers start: 86 outliers final: 60 residues processed: 331 average time/residue: 0.3906 time to fit residues: 206.3083 Evaluate side-chains 321 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 252 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 739 CYS Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1131 VAL Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1145 MET Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1116 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 75 optimal weight: 4.9990 chunk 266 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 217 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN A1135 GLN A1161 HIS ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 330 GLN B 873 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 873 ASN D 898 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.071062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.053350 restraints weight = 163765.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.054894 restraints weight = 105560.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.055975 restraints weight = 77846.751| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29118 Z= 0.210 Angle : 0.698 13.068 39487 Z= 0.352 Chirality : 0.044 0.228 4386 Planarity : 0.005 0.051 5173 Dihedral : 6.906 79.318 4223 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.69 % Favored : 92.23 % Rotamer: Outliers : 2.66 % Allowed : 18.69 % Favored : 78.66 % 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: -0.09 (0.14), residues: 3653 helix: 1.44 (0.14), residues: 1489 sheet: -0.17 (0.23), residues: 532 loop : -1.48 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 607 HIS 0.010 0.001 HIS D 574 PHE 0.020 0.002 PHE A 461 TYR 0.022 0.002 TYR A 118 ARG 0.017 0.001 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 1181) hydrogen bonds : angle 4.91137 ( 3426) SS BOND : bond 0.00564 ( 4) SS BOND : angle 2.59772 ( 8) covalent geometry : bond 0.00451 (29110) covalent geometry : angle 0.69673 (39479) Misc. bond : bond 0.00036 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 246 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7513 (tm-30) REVERT: A 501 LEU cc_start: 0.9731 (mm) cc_final: 0.9517 (mm) REVERT: A 508 MET cc_start: 0.8951 (mmm) cc_final: 0.8518 (mmm) REVERT: A 607 TRP cc_start: 0.7798 (OUTLIER) cc_final: 0.6917 (t60) REVERT: A 616 MET cc_start: 0.8254 (mmp) cc_final: 0.7785 (mmp) REVERT: A 686 MET cc_start: 0.9298 (mtm) cc_final: 0.8888 (mmt) REVERT: A 724 MET cc_start: 0.8923 (mmm) cc_final: 0.8371 (tpp) REVERT: A 759 LEU cc_start: 0.9735 (OUTLIER) cc_final: 0.9494 (mm) REVERT: A 822 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8646 (pp) REVERT: A 854 MET cc_start: 0.8052 (mmt) cc_final: 0.7808 (mmt) REVERT: B 41 MET cc_start: 0.8903 (ttp) cc_final: 0.7517 (tmm) REVERT: B 149 MET cc_start: 0.8116 (tmm) cc_final: 0.7493 (mmp) REVERT: B 178 HIS cc_start: 0.9570 (m-70) cc_final: 0.9364 (m90) REVERT: B 408 ASP cc_start: 0.8325 (m-30) cc_final: 0.8062 (m-30) REVERT: B 428 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8701 (mtmt) REVERT: B 477 ASP cc_start: 0.8096 (p0) cc_final: 0.7654 (p0) REVERT: B 566 MET cc_start: 0.7588 (tpt) cc_final: 0.7307 (tpp) REVERT: B 754 MET cc_start: 0.9139 (ptp) cc_final: 0.8793 (ptp) REVERT: B 836 GLU cc_start: 0.9130 (tp30) cc_final: 0.8650 (tp30) REVERT: B 921 MET cc_start: 0.9008 (mtp) cc_final: 0.8758 (mtp) REVERT: B 994 LEU cc_start: 0.9412 (mt) cc_final: 0.9082 (pp) REVERT: B 1006 ASP cc_start: 0.9434 (m-30) cc_final: 0.9045 (m-30) REVERT: B 1116 MET cc_start: 0.8626 (ttt) cc_final: 0.8236 (tmm) REVERT: B 1165 ASP cc_start: 0.8942 (t0) cc_final: 0.8653 (m-30) REVERT: B 1166 MET cc_start: 0.9059 (tpt) cc_final: 0.8622 (ppp) REVERT: C 519 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7963 (tptp) REVERT: C 801 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8687 (mtm) REVERT: C 881 MET cc_start: 0.8978 (mmp) cc_final: 0.8686 (tpp) REVERT: C 1036 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8340 (ptm-80) REVERT: D 625 ARG cc_start: 0.8794 (mmt180) cc_final: 0.8352 (mmm160) REVERT: D 671 MET cc_start: 0.8471 (tpp) cc_final: 0.8234 (tpt) REVERT: D 724 MET cc_start: 0.9092 (mmm) cc_final: 0.8790 (mmm) REVERT: D 743 MET cc_start: 0.8770 (pmm) cc_final: 0.8455 (pmm) REVERT: D 783 MET cc_start: 0.9301 (mmt) cc_final: 0.8950 (mmm) REVERT: D 836 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8562 (mp0) REVERT: D 881 MET cc_start: 0.8673 (tpp) cc_final: 0.8417 (ttm) REVERT: D 1054 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6322 (mpp-170) REVERT: D 1143 MET cc_start: 0.0044 (ttp) cc_final: -0.0384 (ttp) REVERT: D 1153 MET cc_start: 0.8217 (ptt) cc_final: 0.7923 (pmm) outliers start: 80 outliers final: 60 residues processed: 302 average time/residue: 0.4265 time to fit residues: 208.5744 Evaluate side-chains 305 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 238 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1135 GLN Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1070 ARG Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 739 CYS Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1131 VAL Chi-restraints excluded: chain C residue 1145 MET Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 804 MET Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1116 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 251 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 275 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 256 optimal weight: 8.9990 chunk 295 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 226 optimal weight: 0.4980 chunk 141 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 898 ASN ** D1073 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 = 0.3675 r_free = 0.3675 target = 0.071863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.054101 restraints weight = 161301.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.055736 restraints weight = 102850.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.056864 restraints weight = 75005.449| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29118 Z= 0.133 Angle : 0.661 15.910 39487 Z= 0.328 Chirality : 0.043 0.230 4386 Planarity : 0.004 0.044 5173 Dihedral : 6.783 79.948 4219 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.82 % Favored : 93.10 % Rotamer: Outliers : 2.12 % Allowed : 19.48 % Favored : 78.39 % 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: -0.01 (0.14), residues: 3653 helix: 1.52 (0.14), residues: 1490 sheet: -0.14 (0.23), residues: 524 loop : -1.44 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 607 HIS 0.006 0.001 HIS B 574 PHE 0.015 0.001 PHE B 461 TYR 0.015 0.001 TYR A 118 ARG 0.008 0.000 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 1181) hydrogen bonds : angle 4.77086 ( 3426) SS BOND : bond 0.01189 ( 4) SS BOND : angle 3.87255 ( 8) covalent geometry : bond 0.00301 (29110) covalent geometry : angle 0.65916 (39479) Misc. bond : bond 0.00017 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 245 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 MET cc_start: 0.9007 (mmm) cc_final: 0.8510 (mmm) REVERT: A 616 MET cc_start: 0.8162 (mmp) cc_final: 0.7740 (mmp) REVERT: A 686 MET cc_start: 0.9330 (mtm) cc_final: 0.8861 (mmt) REVERT: A 724 MET cc_start: 0.8916 (mmm) cc_final: 0.8371 (tpp) REVERT: A 759 LEU cc_start: 0.9741 (OUTLIER) cc_final: 0.9516 (mm) REVERT: A 822 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8622 (pp) REVERT: A 1054 ARG cc_start: 0.8059 (ptt90) cc_final: 0.7790 (ptt90) REVERT: B 41 MET cc_start: 0.8866 (ttp) cc_final: 0.7551 (tmm) REVERT: B 149 MET cc_start: 0.8119 (tmm) cc_final: 0.7568 (mmp) REVERT: B 178 HIS cc_start: 0.9567 (m-70) cc_final: 0.9351 (m90) REVERT: B 408 ASP cc_start: 0.8363 (m-30) cc_final: 0.8095 (m-30) REVERT: B 428 LYS cc_start: 0.9057 (mtmt) cc_final: 0.8645 (mtmt) REVERT: B 477 ASP cc_start: 0.8067 (p0) cc_final: 0.7634 (p0) REVERT: B 566 MET cc_start: 0.7567 (tpt) cc_final: 0.7294 (tpp) REVERT: B 686 MET cc_start: 0.8645 (mmt) cc_final: 0.8243 (mmt) REVERT: B 754 MET cc_start: 0.9131 (ptp) cc_final: 0.8742 (ptp) REVERT: B 804 MET cc_start: 0.8798 (mmm) cc_final: 0.7950 (tpp) REVERT: B 854 MET cc_start: 0.8000 (tpt) cc_final: 0.7452 (tpp) REVERT: B 921 MET cc_start: 0.9006 (mtp) cc_final: 0.8731 (mtp) REVERT: B 994 LEU cc_start: 0.9424 (mt) cc_final: 0.9069 (pp) REVERT: B 1006 ASP cc_start: 0.9439 (m-30) cc_final: 0.9022 (m-30) REVERT: B 1116 MET cc_start: 0.8667 (ttt) cc_final: 0.8284 (ttt) REVERT: B 1165 ASP cc_start: 0.8989 (t0) cc_final: 0.8720 (m-30) REVERT: B 1166 MET cc_start: 0.9063 (tpt) cc_final: 0.8651 (ppp) REVERT: C 519 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7955 (tptp) REVERT: C 801 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8705 (mtt) REVERT: C 881 MET cc_start: 0.8977 (mmp) cc_final: 0.8679 (tpp) REVERT: C 1036 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8670 (ptm-80) REVERT: D 625 ARG cc_start: 0.8790 (mmt180) cc_final: 0.8323 (mmm160) REVERT: D 724 MET cc_start: 0.9043 (mmm) cc_final: 0.8754 (mmm) REVERT: D 743 MET cc_start: 0.8875 (pmm) cc_final: 0.8465 (pmm) REVERT: D 783 MET cc_start: 0.9284 (mmt) cc_final: 0.8942 (mmm) REVERT: D 836 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8629 (mp0) REVERT: D 1143 MET cc_start: -0.0510 (ttp) cc_final: -0.1460 (ttp) REVERT: D 1153 MET cc_start: 0.8354 (ptt) cc_final: 0.8082 (pmm) outliers start: 64 outliers final: 55 residues processed: 293 average time/residue: 0.4094 time to fit residues: 192.1605 Evaluate side-chains 299 residues out of total 3013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 239 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 701 GLU Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1070 ARG Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 739 CYS Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1036 ARG Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1131 VAL Chi-restraints excluded: chain C residue 1145 MET Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1116 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 92 optimal weight: 0.2980 chunk 166 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 293 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 343 optimal weight: 0.0040 chunk 316 optimal weight: 9.9990 chunk 270 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1075 GLN ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 898 ASN D1059 HIS ** D1073 GLN ** 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 = 0.3676 r_free = 0.3676 target = 0.071883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.054245 restraints weight = 160348.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.055814 restraints weight = 102075.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.056916 restraints weight = 74597.022| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29118 Z= 0.130 Angle : 0.659 15.320 39487 Z= 0.325 Chirality : 0.043 0.228 4386 Planarity : 0.005 0.207 5173 Dihedral : 6.730 81.915 4219 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.09 % Favored : 92.83 % Rotamer: Outliers : 2.09 % Allowed : 19.48 % Favored : 78.43 % 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: -0.00 (0.14), residues: 3653 helix: 1.55 (0.14), residues: 1486 sheet: -0.20 (0.23), residues: 524 loop : -1.43 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 607 HIS 0.006 0.001 HIS B 574 PHE 0.014 0.001 PHE A 387 TYR 0.015 0.001 TYR A 118 ARG 0.018 0.001 ARG A 942 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 1181) hydrogen bonds : angle 4.71551 ( 3426) SS BOND : bond 0.00899 ( 4) SS BOND : angle 3.61394 ( 8) covalent geometry : bond 0.00296 (29110) covalent geometry : angle 0.65694 (39479) Misc. bond : bond 0.00019 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11254.89 seconds wall clock time: 199 minutes 29.83 seconds (11969.83 seconds total)