Starting phenix.real_space_refine on Sat Mar 7 02:13:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wj5_21688/03_2026/6wj5_21688_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wj5_21688/03_2026/6wj5_21688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wj5_21688/03_2026/6wj5_21688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wj5_21688/03_2026/6wj5_21688.map" model { file = "/net/cci-nas-00/data/ceres_data/6wj5_21688/03_2026/6wj5_21688_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wj5_21688/03_2026/6wj5_21688_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.036 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: 6 Type Number sf(0) Gaussians S 144 5.16 5 C 11812 2.51 5 N 2972 2.21 5 O 3092 1.98 5 F 32 1.80 5 H 18268 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36320 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9039 Classifications: {'peptide': 562} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 9039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9039 Classifications: {'peptide': 562} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 9039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9039 Classifications: {'peptide': 562} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 9039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9039 Classifications: {'peptide': 562} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'LXY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'LXY': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'LXY': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'LXY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.00, per 1000 atoms: 0.17 Number of scatterers: 36320 At special positions: 0 Unit cell: (109.935, 108.888, 146.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 F 32 9.00 O 3092 8.00 N 2972 7.00 C 11812 6.00 H 18268 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 807.3 milliseconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4304 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 8 sheets defined 74.6% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 448 through 456 removed outlier: 3.632A pdb=" N PHE A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 466 removed outlier: 3.707A pdb=" N ARG A 464 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.714A pdb=" N GLN A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'A' and resid 526 through 538 Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 550 through 558 removed outlier: 3.944A pdb=" N PHE A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 621 through 630 removed outlier: 3.985A pdb=" N GLU A 628 " --> pdb=" O THR A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.990A pdb=" N PHE A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 692 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'A' and resid 700 through 714 Processing helix chain 'A' and resid 714 through 739 removed outlier: 4.412A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 766 through 788 removed outlier: 3.520A pdb=" N CYS A 786 " --> pdb=" O ILE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 816 removed outlier: 3.889A pdb=" N TRP A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 827 through 845 removed outlier: 3.665A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.576A pdb=" N GLN A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 892 removed outlier: 3.764A pdb=" N ILE A 860 " --> pdb=" O CYS A 856 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 Processing helix chain 'A' and resid 900 through 911 Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 917 through 922 Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 933 through 948 Processing helix chain 'A' and resid 950 through 988 removed outlier: 3.918A pdb=" N ASP A 966 " --> pdb=" O GLY A 962 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 969 " --> pdb=" O ALA A 965 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 999 Processing helix chain 'A' and resid 1040 through 1072 removed outlier: 3.549A pdb=" N ILE A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU A1045 " --> pdb=" O GLU A1041 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A1064 " --> pdb=" O LYS A1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 Processing helix chain 'B' and resid 458 through 466 removed outlier: 4.467A pdb=" N ARG B 464 " --> pdb=" O ASN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.586A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 526 through 538 Processing helix chain 'B' and resid 550 through 558 removed outlier: 3.669A pdb=" N PHE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 621 through 630 removed outlier: 3.500A pdb=" N GLU B 625 " --> pdb=" O CYS B 621 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU B 628 " --> pdb=" O THR B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.761A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 692 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 714 Processing helix chain 'B' and resid 714 through 739 removed outlier: 4.509A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 766 through 788 removed outlier: 3.555A pdb=" N CYS B 786 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 816 removed outlier: 3.881A pdb=" N TRP B 809 " --> pdb=" O ASN B 805 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 814 " --> pdb=" O ILE B 810 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 816 " --> pdb=" O TYR B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 823 Processing helix chain 'B' and resid 827 through 845 removed outlier: 3.634A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 851 removed outlier: 3.546A pdb=" N GLN B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 892 removed outlier: 4.718A pdb=" N ILE B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N PHE B 879 " --> pdb=" O VAL B 875 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 880 " --> pdb=" O VAL B 876 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 883 " --> pdb=" O PHE B 879 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 890 " --> pdb=" O LEU B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 Processing helix chain 'B' and resid 900 through 912 Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 922 through 927 Processing helix chain 'B' and resid 933 through 948 removed outlier: 3.507A pdb=" N ALA B 939 " --> pdb=" O VAL B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 990 removed outlier: 3.703A pdb=" N ILE B 957 " --> pdb=" O MET B 953 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 966 " --> pdb=" O GLY B 962 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 969 " --> pdb=" O ALA B 965 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 removed outlier: 3.765A pdb=" N LEU B 995 " --> pdb=" O PRO B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1072 removed outlier: 5.451A pdb=" N LEU B1045 " --> pdb=" O GLU B1041 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B1057 " --> pdb=" O ASP B1053 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B1063 " --> pdb=" O GLU B1059 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B1064 " --> pdb=" O LYS B1060 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B1067 " --> pdb=" O GLU B1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 Processing helix chain 'C' and resid 458 through 466 removed outlier: 4.530A pdb=" N ARG C 464 " --> pdb=" O ASN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 516 through 524 Processing helix chain 'C' and resid 526 through 534 Processing helix chain 'C' and resid 535 through 536 No H-bonds generated for 'chain 'C' and resid 535 through 536' Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.746A pdb=" N PHE C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 621 through 630 removed outlier: 3.827A pdb=" N GLU C 628 " --> pdb=" O THR C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.942A pdb=" N PHE C 640 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 692 removed outlier: 3.529A pdb=" N ALA C 688 " --> pdb=" O THR C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 699 Processing helix chain 'C' and resid 700 through 714 Processing helix chain 'C' and resid 714 through 739 removed outlier: 3.626A pdb=" N TYR C 726 " --> pdb=" O ASN C 722 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 766 through 788 removed outlier: 4.160A pdb=" N CYS C 786 " --> pdb=" O ILE C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 816 removed outlier: 4.128A pdb=" N TRP C 809 " --> pdb=" O ASN C 805 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 814 " --> pdb=" O ILE C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 823 Processing helix chain 'C' and resid 827 through 851 removed outlier: 3.689A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 892 removed outlier: 3.830A pdb=" N ILE C 860 " --> pdb=" O CYS C 856 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 873 " --> pdb=" O THR C 869 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N PHE C 879 " --> pdb=" O VAL C 875 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 880 " --> pdb=" O VAL C 876 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 884 " --> pdb=" O LEU C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 Processing helix chain 'C' and resid 900 through 912 removed outlier: 3.767A pdb=" N MET C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 922 through 927 Processing helix chain 'C' and resid 933 through 948 Processing helix chain 'C' and resid 950 through 968 removed outlier: 3.757A pdb=" N ASP C 966 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 990 removed outlier: 4.352A pdb=" N ILE C 976 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 999 Processing helix chain 'C' and resid 1040 through 1072 removed outlier: 5.393A pdb=" N LEU C1045 " --> pdb=" O GLU C1041 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C1063 " --> pdb=" O GLU C1059 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C1064 " --> pdb=" O LYS C1060 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU C1067 " --> pdb=" O GLU C1063 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 456 Processing helix chain 'D' and resid 458 through 466 removed outlier: 4.413A pdb=" N ARG D 464 " --> pdb=" O ASN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.566A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 516 through 524 Processing helix chain 'D' and resid 526 through 535 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.939A pdb=" N THR D 541 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP D 542 " --> pdb=" O LYS D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 558 removed outlier: 3.927A pdb=" N PHE D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 582 through 589 Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'D' and resid 621 through 630 removed outlier: 3.967A pdb=" N GLU D 628 " --> pdb=" O THR D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.945A pdb=" N PHE D 640 " --> pdb=" O VAL D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 692 Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'D' and resid 700 through 714 Processing helix chain 'D' and resid 714 through 739 removed outlier: 3.547A pdb=" N TYR D 726 " --> pdb=" O ASN D 722 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 766 through 788 removed outlier: 3.693A pdb=" N CYS D 786 " --> pdb=" O ILE D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 816 removed outlier: 3.918A pdb=" N TRP D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR D 814 " --> pdb=" O ILE D 810 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 816 " --> pdb=" O TYR D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 823 Processing helix chain 'D' and resid 827 through 845 removed outlier: 3.711A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 851 removed outlier: 3.587A pdb=" N GLN D 851 " --> pdb=" O LEU D 847 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 892 removed outlier: 3.686A pdb=" N ILE D 860 " --> pdb=" O CYS D 856 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE D 879 " --> pdb=" O VAL D 875 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU D 880 " --> pdb=" O VAL D 876 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE D 884 " --> pdb=" O LEU D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 Processing helix chain 'D' and resid 900 through 911 Processing helix chain 'D' and resid 912 through 914 No H-bonds generated for 'chain 'D' and resid 912 through 914' Processing helix chain 'D' and resid 917 through 922 Processing helix chain 'D' and resid 922 through 927 Processing helix chain 'D' and resid 933 through 948 removed outlier: 3.600A pdb=" N SER D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 990 removed outlier: 3.768A pdb=" N ASP D 966 " --> pdb=" O GLY D 962 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS D 969 " --> pdb=" O ALA D 965 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS D 970 " --> pdb=" O ASP D 966 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 removed outlier: 3.569A pdb=" N LEU D 995 " --> pdb=" O PRO D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1072 removed outlier: 5.457A pdb=" N LEU D1045 " --> pdb=" O GLU D1041 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D1063 " --> pdb=" O GLU D1059 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D1064 " --> pdb=" O LYS D1060 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 642 through 644 Processing sheet with id=AA2, first strand: chain 'A' and resid 746 through 747 Processing sheet with id=AA3, first strand: chain 'B' and resid 642 through 644 Processing sheet with id=AA4, first strand: chain 'B' and resid 746 through 747 Processing sheet with id=AA5, first strand: chain 'C' and resid 642 through 644 Processing sheet with id=AA6, first strand: chain 'C' and resid 746 through 747 Processing sheet with id=AA7, first strand: chain 'D' and resid 642 through 644 Processing sheet with id=AA8, first strand: chain 'D' and resid 746 through 747 1056 hydrogen bonds defined for protein. 3084 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: 7.75 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 18216 1.13 - 1.30: 2900 1.30 - 1.48: 7116 1.48 - 1.65: 8260 1.65 - 1.82: 228 Bond restraints: 36720 Sorted by residual: bond pdb=" N HIS B 983 " pdb=" H HIS B 983 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LEU C 466 " pdb=" H LEU C 466 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N PHE C 783 " pdb=" H PHE C 783 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN B 917 " pdb=" H ASN B 917 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ILE D 905 " pdb=" H ILE D 905 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 36715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 57661 2.84 - 5.67: 6855 5.67 - 8.51: 1911 8.51 - 11.35: 42 11.35 - 14.19: 43 Bond angle restraints: 66512 Sorted by residual: angle pdb=" CA ASP B 511 " pdb=" CB ASP B 511 " pdb=" CG ASP B 511 " ideal model delta sigma weight residual 112.60 120.40 -7.80 1.00e+00 1.00e+00 6.09e+01 angle pdb=" CA ASP C 511 " pdb=" CB ASP C 511 " pdb=" CG ASP C 511 " ideal model delta sigma weight residual 112.60 120.03 -7.43 1.00e+00 1.00e+00 5.52e+01 angle pdb=" CA ASP A 511 " pdb=" CB ASP A 511 " pdb=" CG ASP A 511 " ideal model delta sigma weight residual 112.60 120.01 -7.41 1.00e+00 1.00e+00 5.50e+01 angle pdb=" CA ASN D 577 " pdb=" CB ASN D 577 " pdb=" CG ASN D 577 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" CA ASP D 511 " pdb=" CB ASP D 511 " pdb=" CG ASP D 511 " ideal model delta sigma weight residual 112.60 119.03 -6.43 1.00e+00 1.00e+00 4.13e+01 ... (remaining 66507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 15819 17.87 - 35.74: 903 35.74 - 53.60: 238 53.60 - 71.47: 235 71.47 - 89.34: 21 Dihedral angle restraints: 17216 sinusoidal: 9264 harmonic: 7952 Sorted by residual: dihedral pdb=" C VAL D 948 " pdb=" N VAL D 948 " pdb=" CA VAL D 948 " pdb=" CB VAL D 948 " ideal model delta harmonic sigma weight residual -122.00 -136.22 14.22 0 2.50e+00 1.60e-01 3.24e+01 dihedral pdb=" CA LYS B 787 " pdb=" C LYS B 787 " pdb=" N GLU B 788 " pdb=" CA GLU B 788 " ideal model delta harmonic sigma weight residual 180.00 152.28 27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ASP A 763 " pdb=" C ASP A 763 " pdb=" N THR A 764 " pdb=" CA THR A 764 " ideal model delta harmonic sigma weight residual -180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 17213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2066 0.098 - 0.197: 736 0.197 - 0.295: 117 0.295 - 0.393: 13 0.393 - 0.491: 4 Chirality restraints: 2936 Sorted by residual: chirality pdb=" CA VAL C 948 " pdb=" N VAL C 948 " pdb=" C VAL C 948 " pdb=" CB VAL C 948 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CA VAL A 948 " pdb=" N VAL A 948 " pdb=" C VAL A 948 " pdb=" CB VAL A 948 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" CA VAL D 948 " pdb=" N VAL D 948 " pdb=" C VAL D 948 " pdb=" CB VAL D 948 " both_signs ideal model delta sigma weight residual False 2.44 2.02 0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 2933 not shown) Planarity restraints: 5204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 458 " 0.324 9.50e-02 1.11e+02 1.56e-01 2.97e+02 pdb=" NE ARG B 458 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG B 458 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG B 458 " -0.077 2.00e-02 2.50e+03 pdb=" NH2 ARG B 458 " -0.003 2.00e-02 2.50e+03 pdb="HH11 ARG B 458 " -0.078 2.00e-02 2.50e+03 pdb="HH12 ARG B 458 " 0.233 2.00e-02 2.50e+03 pdb="HH21 ARG B 458 " 0.121 2.00e-02 2.50e+03 pdb="HH22 ARG B 458 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 458 " -0.328 9.50e-02 1.11e+02 1.53e-01 2.72e+02 pdb=" NE ARG D 458 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG D 458 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG D 458 " 0.081 2.00e-02 2.50e+03 pdb=" NH2 ARG D 458 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG D 458 " 0.083 2.00e-02 2.50e+03 pdb="HH12 ARG D 458 " -0.228 2.00e-02 2.50e+03 pdb="HH21 ARG D 458 " -0.097 2.00e-02 2.50e+03 pdb="HH22 ARG D 458 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 458 " 0.318 9.50e-02 1.11e+02 1.48e-01 2.51e+02 pdb=" NE ARG C 458 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG C 458 " -0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG C 458 " -0.083 2.00e-02 2.50e+03 pdb=" NH2 ARG C 458 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 458 " -0.050 2.00e-02 2.50e+03 pdb="HH12 ARG C 458 " 0.208 2.00e-02 2.50e+03 pdb="HH21 ARG C 458 " 0.121 2.00e-02 2.50e+03 pdb="HH22 ARG C 458 " -0.165 2.00e-02 2.50e+03 ... (remaining 5201 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 2370 2.23 - 2.82: 71279 2.82 - 3.41: 103748 3.41 - 4.01: 134462 4.01 - 4.60: 197980 Nonbonded interactions: 509839 Sorted by model distance: nonbonded pdb=" OE1 GLU D 808 " pdb=" HH TYR D 812 " model vdw 1.632 2.450 nonbonded pdb=" HB3 SER C 921 " pdb="HH12 ARG D 919 " model vdw 1.635 2.270 nonbonded pdb=" OE1 GLN D 664 " pdb=" HH TYR D 706 " model vdw 1.647 2.450 nonbonded pdb=" OE1 GLU A 808 " pdb=" HH TYR A 812 " model vdw 1.651 2.450 nonbonded pdb=" OE1 GLU B 808 " pdb=" HH TYR B 812 " model vdw 1.656 2.450 ... (remaining 509834 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 30.710 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 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 : 0.012 0.085 18452 Z= 0.716 Angle : 1.838 10.741 25028 Z= 1.233 Chirality : 0.097 0.491 2936 Planarity : 0.014 0.142 3044 Dihedral : 13.447 89.341 6720 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.50 % Allowed : 3.85 % Favored : 95.65 % Rotamer: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.16), residues: 2208 helix: -2.01 (0.10), residues: 1620 sheet: 0.93 (0.66), residues: 60 loop : 0.08 (0.31), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 464 TYR 0.189 0.025 TYR D 785 PHE 0.061 0.011 PHE C 898 TRP 0.076 0.016 TRP C 993 HIS 0.017 0.005 HIS D 553 Details of bonding type rmsd covalent geometry : bond 0.01188 (18452) covalent geometry : angle 1.83844 (25028) hydrogen bonds : bond 0.18302 ( 1056) hydrogen bonds : angle 7.35908 ( 3084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 597 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 596 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 509 LEU cc_start: 0.8363 (mt) cc_final: 0.8147 (mt) REVERT: A 603 LYS cc_start: 0.9319 (mttt) cc_final: 0.9058 (pttt) REVERT: A 705 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7379 (mm-30) REVERT: A 720 MET cc_start: 0.7784 (mmm) cc_final: 0.7262 (mmt) REVERT: A 721 MET cc_start: 0.7016 (ttm) cc_final: 0.6752 (ttt) REVERT: A 774 MET cc_start: 0.8333 (mtm) cc_final: 0.7805 (mtp) REVERT: A 825 GLU cc_start: 0.8278 (tt0) cc_final: 0.7757 (pm20) REVERT: A 904 SER cc_start: 0.9357 (t) cc_final: 0.9111 (t) REVERT: A 915 ASP cc_start: 0.7627 (t0) cc_final: 0.7262 (p0) REVERT: A 969 LYS cc_start: 0.8818 (tttt) cc_final: 0.8379 (ttmt) REVERT: A 978 MET cc_start: 0.8382 (mtm) cc_final: 0.8110 (mtp) REVERT: A 1042 MET cc_start: 0.7685 (ppp) cc_final: 0.7121 (tmm) REVERT: A 1073 GLU cc_start: 0.8233 (tt0) cc_final: 0.7679 (tt0) REVERT: B 640 PHE cc_start: 0.8169 (m-80) cc_final: 0.7741 (m-10) REVERT: B 705 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6879 (mm-30) REVERT: B 717 ARG cc_start: 0.7159 (ttt180) cc_final: 0.6915 (ttm170) REVERT: B 720 MET cc_start: 0.7894 (mmm) cc_final: 0.7442 (mmt) REVERT: B 721 MET cc_start: 0.7053 (ttm) cc_final: 0.6829 (ttt) REVERT: B 825 GLU cc_start: 0.8150 (tt0) cc_final: 0.7620 (pm20) REVERT: B 904 SER cc_start: 0.9330 (t) cc_final: 0.9088 (t) REVERT: B 915 ASP cc_start: 0.7851 (t0) cc_final: 0.7570 (p0) REVERT: B 996 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7995 (ttm110) REVERT: B 1042 MET cc_start: 0.7675 (ppp) cc_final: 0.6536 (tmm) REVERT: B 1046 LYS cc_start: 0.7083 (ttmt) cc_final: 0.6738 (ttmt) REVERT: B 1056 PHE cc_start: 0.7899 (t80) cc_final: 0.7684 (t80) REVERT: B 1073 GLU cc_start: 0.8253 (tt0) cc_final: 0.7500 (tt0) REVERT: C 591 LYS cc_start: 0.8789 (mttt) cc_final: 0.8432 (mttp) REVERT: C 628 GLU cc_start: 0.8408 (tt0) cc_final: 0.8185 (tm-30) REVERT: C 705 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6953 (mm-30) REVERT: C 720 MET cc_start: 0.7993 (mmm) cc_final: 0.7599 (mmt) REVERT: C 721 MET cc_start: 0.7012 (ttm) cc_final: 0.6768 (ttt) REVERT: C 825 GLU cc_start: 0.8331 (tt0) cc_final: 0.7746 (pm20) REVERT: C 904 SER cc_start: 0.9351 (t) cc_final: 0.9146 (t) REVERT: C 915 ASP cc_start: 0.7743 (t0) cc_final: 0.7432 (t0) REVERT: C 1042 MET cc_start: 0.7827 (ppp) cc_final: 0.7062 (tmm) REVERT: C 1046 LYS cc_start: 0.6853 (ttmt) cc_final: 0.6611 (ttmt) REVERT: C 1059 GLU cc_start: 0.7510 (tp30) cc_final: 0.7031 (tt0) REVERT: C 1073 GLU cc_start: 0.8118 (tt0) cc_final: 0.7538 (tt0) REVERT: D 591 LYS cc_start: 0.8854 (mttt) cc_final: 0.8470 (mttp) REVERT: D 709 MET cc_start: 0.7972 (tmt) cc_final: 0.7710 (tmm) REVERT: D 720 MET cc_start: 0.7886 (mmm) cc_final: 0.7471 (mmt) REVERT: D 721 MET cc_start: 0.7058 (ttm) cc_final: 0.6845 (ttt) REVERT: D 744 MET cc_start: 0.8144 (mmp) cc_final: 0.7898 (mmt) REVERT: D 825 GLU cc_start: 0.8168 (tt0) cc_final: 0.7619 (pm20) REVERT: D 904 SER cc_start: 0.9394 (t) cc_final: 0.9157 (t) REVERT: D 978 MET cc_start: 0.8384 (mtm) cc_final: 0.8131 (mtp) REVERT: D 987 GLU cc_start: 0.7001 (tt0) cc_final: 0.6628 (tt0) REVERT: D 1042 MET cc_start: 0.7326 (ppp) cc_final: 0.7011 (tpp) REVERT: D 1073 GLU cc_start: 0.8184 (tt0) cc_final: 0.7854 (tt0) outliers start: 1 outliers final: 0 residues processed: 596 average time/residue: 0.3016 time to fit residues: 273.4672 Evaluate side-chains 361 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN A 549 ASN A 766 ASN A 831 GLN A 893 ASN B 549 ASN B 831 GLN C 476 ASN C 492 ASN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C 831 GLN C 917 ASN C1047 GLN D 831 GLN D 940 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.128034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.102741 restraints weight = 72670.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.107170 restraints weight = 29489.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.109912 restraints weight = 16915.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.111514 restraints weight = 12096.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.112531 restraints weight = 9896.058| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18452 Z= 0.155 Angle : 0.649 7.404 25028 Z= 0.347 Chirality : 0.041 0.178 2936 Planarity : 0.005 0.068 3044 Dihedral : 6.504 54.505 2496 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.97 % Allowed : 8.90 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2208 helix: -0.51 (0.12), residues: 1640 sheet: -0.05 (0.70), residues: 68 loop : 0.14 (0.31), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 601 TYR 0.022 0.002 TYR C 785 PHE 0.016 0.001 PHE C 823 TRP 0.014 0.001 TRP A 711 HIS 0.006 0.001 HIS D 512 Details of bonding type rmsd covalent geometry : bond 0.00330 (18452) covalent geometry : angle 0.64896 (25028) hydrogen bonds : bond 0.05448 ( 1056) hydrogen bonds : angle 4.90139 ( 3084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 400 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 381 time to evaluate : 0.936 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: A 589 HIS cc_start: 0.7271 (m170) cc_final: 0.6781 (m170) REVERT: A 615 ASN cc_start: 0.8087 (m110) cc_final: 0.7832 (m-40) REVERT: A 693 ASN cc_start: 0.8732 (t0) cc_final: 0.8408 (t0) REVERT: A 705 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 720 MET cc_start: 0.8027 (mmm) cc_final: 0.7697 (mmt) REVERT: A 721 MET cc_start: 0.7142 (ttm) cc_final: 0.6909 (ttt) REVERT: A 774 MET cc_start: 0.8335 (mtm) cc_final: 0.8029 (mtp) REVERT: A 969 LYS cc_start: 0.8856 (tttt) cc_final: 0.8595 (ttmt) REVERT: A 1042 MET cc_start: 0.7579 (ppp) cc_final: 0.7051 (tmm) REVERT: B 1042 MET cc_start: 0.7804 (ppp) cc_final: 0.6712 (tmm) REVERT: B 1059 GLU cc_start: 0.7624 (tp30) cc_final: 0.7314 (mt-10) REVERT: C 720 MET cc_start: 0.7920 (mmm) cc_final: 0.7522 (mmt) REVERT: C 852 ARG cc_start: 0.8390 (mtt90) cc_final: 0.7642 (mtt180) REVERT: C 870 LEU cc_start: 0.8782 (tp) cc_final: 0.8562 (tp) REVERT: C 1042 MET cc_start: 0.7890 (ppp) cc_final: 0.6979 (tmm) REVERT: C 1059 GLU cc_start: 0.7579 (tp30) cc_final: 0.7216 (mt-10) REVERT: D 709 MET cc_start: 0.8235 (tmt) cc_final: 0.7834 (tmm) REVERT: D 720 MET cc_start: 0.8002 (mmm) cc_final: 0.7751 (mmt) REVERT: D 721 MET cc_start: 0.7139 (ttm) cc_final: 0.6911 (ttt) REVERT: D 864 GLU cc_start: 0.7291 (mt-10) cc_final: 0.7003 (mm-30) REVERT: D 987 GLU cc_start: 0.6781 (tt0) cc_final: 0.6490 (tt0) REVERT: D 1059 GLU cc_start: 0.7675 (tp30) cc_final: 0.7215 (mt-10) outliers start: 19 outliers final: 12 residues processed: 391 average time/residue: 0.2811 time to fit residues: 173.5335 Evaluate side-chains 311 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 299 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain D residue 810 ILE Chi-restraints excluded: chain D residue 875 VAL Chi-restraints excluded: chain D residue 920 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 78 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 197 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 940 GLN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN C 917 ASN C 940 GLN C1047 GLN D 537 ASN D 940 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.141871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.117318 restraints weight = 72453.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122019 restraints weight = 27919.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.124852 restraints weight = 15527.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126503 restraints weight = 10931.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127346 restraints weight = 8893.029| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18452 Z= 0.161 Angle : 0.567 7.004 25028 Z= 0.305 Chirality : 0.038 0.150 2936 Planarity : 0.004 0.052 3044 Dihedral : 5.912 51.599 2496 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.12 % Allowed : 11.61 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.18), residues: 2208 helix: 0.09 (0.13), residues: 1636 sheet: 0.20 (0.75), residues: 68 loop : 0.06 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 601 TYR 0.015 0.001 TYR A 654 PHE 0.019 0.001 PHE D 823 TRP 0.012 0.001 TRP A 832 HIS 0.005 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00367 (18452) covalent geometry : angle 0.56658 (25028) hydrogen bonds : bond 0.04642 ( 1056) hydrogen bonds : angle 4.52863 ( 3084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 320 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 PHE cc_start: 0.8912 (m-80) cc_final: 0.8668 (m-80) REVERT: A 721 MET cc_start: 0.7123 (ttm) cc_final: 0.6922 (ttt) REVERT: A 774 MET cc_start: 0.8307 (mtm) cc_final: 0.7995 (mtp) REVERT: A 917 ASN cc_start: 0.8301 (m110) cc_final: 0.7942 (m-40) REVERT: A 940 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7507 (mm-40) REVERT: A 1042 MET cc_start: 0.7607 (ppp) cc_final: 0.6732 (tmm) REVERT: B 1042 MET cc_start: 0.7782 (ppp) cc_final: 0.6527 (tmm) REVERT: B 1059 GLU cc_start: 0.7758 (tp30) cc_final: 0.7261 (tt0) REVERT: C 852 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7692 (mtt180) REVERT: C 870 LEU cc_start: 0.8882 (tp) cc_final: 0.8626 (tp) REVERT: C 1042 MET cc_start: 0.7873 (ppp) cc_final: 0.6823 (tmm) REVERT: C 1050 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7543 (ttm110) REVERT: C 1059 GLU cc_start: 0.7693 (tp30) cc_final: 0.7288 (mt-10) REVERT: D 535 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7736 (t0) REVERT: D 627 ILE cc_start: 0.9105 (mt) cc_final: 0.8884 (mt) REVERT: D 940 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7391 (mm-40) REVERT: D 946 ILE cc_start: 0.8898 (mt) cc_final: 0.8551 (mt) REVERT: D 987 GLU cc_start: 0.7107 (tt0) cc_final: 0.6767 (tt0) REVERT: D 1051 LEU cc_start: 0.8424 (tp) cc_final: 0.8013 (tt) REVERT: D 1055 THR cc_start: 0.8627 (t) cc_final: 0.8380 (m) REVERT: D 1059 GLU cc_start: 0.7652 (tp30) cc_final: 0.7249 (mt-10) outliers start: 22 outliers final: 13 residues processed: 332 average time/residue: 0.3102 time to fit residues: 157.7864 Evaluate side-chains 300 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 284 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 882 LEU Chi-restraints excluded: chain D residue 940 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 73 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 160 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 917 ASN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.131320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105469 restraints weight = 72513.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.110280 restraints weight = 27746.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.113216 restraints weight = 15390.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114936 restraints weight = 10795.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.115975 restraints weight = 8750.245| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18452 Z= 0.166 Angle : 0.548 7.136 25028 Z= 0.292 Chirality : 0.038 0.139 2936 Planarity : 0.004 0.050 3044 Dihedral : 5.707 52.541 2496 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.07 % Allowed : 12.01 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2208 helix: 0.36 (0.13), residues: 1636 sheet: 0.58 (0.85), residues: 48 loop : 0.15 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 601 TYR 0.011 0.001 TYR B 840 PHE 0.018 0.001 PHE D 612 TRP 0.010 0.001 TRP C 832 HIS 0.004 0.001 HIS B1062 Details of bonding type rmsd covalent geometry : bond 0.00380 (18452) covalent geometry : angle 0.54826 (25028) hydrogen bonds : bond 0.04370 ( 1056) hydrogen bonds : angle 4.43426 ( 3084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 323 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 302 time to evaluate : 0.989 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 535 ASP cc_start: 0.8085 (t0) cc_final: 0.7687 (t0) REVERT: A 785 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.6517 (m-10) REVERT: A 969 LYS cc_start: 0.8842 (tttt) cc_final: 0.8598 (ttmt) REVERT: A 1042 MET cc_start: 0.7627 (ppp) cc_final: 0.6765 (tmm) REVERT: A 1050 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7292 (ttm110) REVERT: B 495 ASP cc_start: 0.7878 (p0) cc_final: 0.7659 (p0) REVERT: B 523 MET cc_start: 0.8531 (tpt) cc_final: 0.8128 (tpt) REVERT: B 601 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8452 (mtp85) REVERT: B 864 GLU cc_start: 0.7185 (tt0) cc_final: 0.6983 (tt0) REVERT: B 1042 MET cc_start: 0.7826 (ppp) cc_final: 0.6481 (tmm) REVERT: B 1059 GLU cc_start: 0.7720 (tp30) cc_final: 0.7417 (tp30) REVERT: C 852 ARG cc_start: 0.8378 (mtt90) cc_final: 0.7666 (mtt180) REVERT: C 870 LEU cc_start: 0.8791 (tp) cc_final: 0.8566 (tp) REVERT: C 1042 MET cc_start: 0.7986 (ppp) cc_final: 0.6761 (tmm) REVERT: C 1059 GLU cc_start: 0.7693 (tp30) cc_final: 0.7247 (mt-10) REVERT: D 535 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7794 (t0) REVERT: D 774 MET cc_start: 0.8120 (mmm) cc_final: 0.7842 (mmm) REVERT: D 785 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6755 (m-10) REVERT: D 987 GLU cc_start: 0.7687 (tt0) cc_final: 0.7332 (tt0) REVERT: D 1055 THR cc_start: 0.8538 (t) cc_final: 0.8292 (m) REVERT: D 1059 GLU cc_start: 0.7682 (tp30) cc_final: 0.7195 (mt-10) outliers start: 21 outliers final: 15 residues processed: 315 average time/residue: 0.2818 time to fit residues: 140.8126 Evaluate side-chains 301 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 283 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 112 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 917 ASN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 893 ASN C 917 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.139280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114941 restraints weight = 72031.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119540 restraints weight = 27974.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122307 restraints weight = 15658.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123942 restraints weight = 11079.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124856 restraints weight = 9018.180| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18452 Z= 0.227 Angle : 0.582 7.538 25028 Z= 0.310 Chirality : 0.039 0.144 2936 Planarity : 0.004 0.047 3044 Dihedral : 5.690 51.977 2496 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.43 % Allowed : 12.32 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2208 helix: 0.33 (0.13), residues: 1636 sheet: 0.52 (0.86), residues: 48 loop : 0.04 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 601 TYR 0.014 0.001 TYR B 840 PHE 0.016 0.002 PHE D 612 TRP 0.012 0.001 TRP C 832 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd covalent geometry : bond 0.00530 (18452) covalent geometry : angle 0.58161 (25028) hydrogen bonds : bond 0.04556 ( 1056) hydrogen bonds : angle 4.52619 ( 3084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 325 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 785 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6573 (m-10) REVERT: A 849 TYR cc_start: 0.8424 (m-80) cc_final: 0.8187 (m-10) REVERT: A 1042 MET cc_start: 0.7634 (ppp) cc_final: 0.6853 (tmm) REVERT: A 1050 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7173 (ttm110) REVERT: B 523 MET cc_start: 0.8504 (tpt) cc_final: 0.8114 (tpt) REVERT: B 849 TYR cc_start: 0.8426 (m-80) cc_final: 0.8142 (m-10) REVERT: B 1042 MET cc_start: 0.7807 (ppp) cc_final: 0.6997 (tmm) REVERT: B 1059 GLU cc_start: 0.7749 (tp30) cc_final: 0.7397 (mt-10) REVERT: C 495 ASP cc_start: 0.7868 (p0) cc_final: 0.7497 (p0) REVERT: C 523 MET cc_start: 0.8541 (tpt) cc_final: 0.8190 (tpt) REVERT: C 849 TYR cc_start: 0.8426 (m-80) cc_final: 0.8032 (m-10) REVERT: C 852 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7657 (mtt180) REVERT: C 870 LEU cc_start: 0.8978 (tp) cc_final: 0.8718 (tp) REVERT: C 1042 MET cc_start: 0.7972 (ppp) cc_final: 0.6722 (tmm) REVERT: C 1059 GLU cc_start: 0.7623 (tp30) cc_final: 0.7292 (mt-10) REVERT: D 535 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7822 (t0) REVERT: D 774 MET cc_start: 0.8097 (mmm) cc_final: 0.7800 (mmm) REVERT: D 785 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6763 (m-10) REVERT: D 849 TYR cc_start: 0.8320 (m-80) cc_final: 0.7970 (m-10) REVERT: D 987 GLU cc_start: 0.7804 (tt0) cc_final: 0.7580 (tt0) REVERT: D 1055 THR cc_start: 0.8723 (t) cc_final: 0.8479 (m) REVERT: D 1059 GLU cc_start: 0.7691 (tp30) cc_final: 0.7286 (mt-10) outliers start: 28 outliers final: 20 residues processed: 318 average time/residue: 0.2764 time to fit residues: 139.4316 Evaluate side-chains 302 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 279 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 904 SER Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 5.9990 chunk 210 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 917 ASN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.116412 restraints weight = 71516.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.121124 restraints weight = 27280.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123925 restraints weight = 15049.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125570 restraints weight = 10575.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126495 restraints weight = 8583.369| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18452 Z= 0.112 Angle : 0.505 6.689 25028 Z= 0.265 Chirality : 0.037 0.144 2936 Planarity : 0.004 0.048 3044 Dihedral : 5.266 55.272 2496 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.12 % Allowed : 13.29 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 2208 helix: 0.66 (0.13), residues: 1636 sheet: 1.05 (0.87), residues: 48 loop : 0.08 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 601 TYR 0.009 0.001 TYR B 840 PHE 0.014 0.001 PHE D 612 TRP 0.009 0.001 TRP C 711 HIS 0.002 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00249 (18452) covalent geometry : angle 0.50531 (25028) hydrogen bonds : bond 0.03865 ( 1056) hydrogen bonds : angle 4.19142 ( 3084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 333 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 311 time to evaluate : 1.002 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: A 785 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.6343 (m-10) REVERT: A 849 TYR cc_start: 0.8385 (m-80) cc_final: 0.8055 (m-10) REVERT: A 1042 MET cc_start: 0.7631 (ppp) cc_final: 0.6787 (tmm) REVERT: A 1050 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7308 (ttm110) REVERT: B 523 MET cc_start: 0.8431 (tpt) cc_final: 0.8059 (tpt) REVERT: B 601 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8501 (mtp85) REVERT: B 849 TYR cc_start: 0.8464 (m-80) cc_final: 0.8133 (m-10) REVERT: B 1042 MET cc_start: 0.7757 (ppp) cc_final: 0.6829 (tmm) REVERT: B 1059 GLU cc_start: 0.7731 (tp30) cc_final: 0.7360 (mt-10) REVERT: C 464 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7530 (ttp-170) REVERT: C 495 ASP cc_start: 0.7852 (p0) cc_final: 0.7485 (p0) REVERT: C 852 ARG cc_start: 0.8242 (mtt90) cc_final: 0.7649 (mtt180) REVERT: C 1042 MET cc_start: 0.7856 (ppp) cc_final: 0.6561 (tmm) REVERT: C 1059 GLU cc_start: 0.7590 (tp30) cc_final: 0.7235 (mt-10) REVERT: D 535 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7771 (t0) REVERT: D 785 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6660 (m-10) REVERT: D 946 ILE cc_start: 0.8900 (mt) cc_final: 0.8596 (mt) REVERT: D 987 GLU cc_start: 0.7783 (tt0) cc_final: 0.7512 (tt0) REVERT: D 1055 THR cc_start: 0.8747 (t) cc_final: 0.8501 (m) REVERT: D 1059 GLU cc_start: 0.7680 (tp30) cc_final: 0.7244 (mt-10) outliers start: 22 outliers final: 14 residues processed: 325 average time/residue: 0.2877 time to fit residues: 147.5756 Evaluate side-chains 297 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 280 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 917 ASN ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115230 restraints weight = 72009.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119860 restraints weight = 27830.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122625 restraints weight = 15469.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124251 restraints weight = 10927.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125157 restraints weight = 8891.255| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18452 Z= 0.197 Angle : 0.549 7.395 25028 Z= 0.291 Chirality : 0.038 0.146 2936 Planarity : 0.004 0.043 3044 Dihedral : 5.253 52.939 2496 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.43 % Allowed : 13.65 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 2208 helix: 0.63 (0.13), residues: 1640 sheet: 0.99 (0.86), residues: 48 loop : 0.03 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 601 TYR 0.013 0.001 TYR B 840 PHE 0.014 0.001 PHE D 823 TRP 0.010 0.001 TRP C 832 HIS 0.004 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00457 (18452) covalent geometry : angle 0.54918 (25028) hydrogen bonds : bond 0.04145 ( 1056) hydrogen bonds : angle 4.31389 ( 3084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 307 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 279 time to evaluate : 0.982 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: symmetry clash revert: symmetry clash REVERT: A 785 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6441 (m-10) REVERT: A 849 TYR cc_start: 0.8344 (m-80) cc_final: 0.7985 (m-10) REVERT: A 1042 MET cc_start: 0.7660 (ppp) cc_final: 0.6817 (tmm) REVERT: A 1050 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7283 (ttm110) REVERT: B 523 MET cc_start: 0.8463 (tpt) cc_final: 0.8094 (tpt) REVERT: B 717 ARG cc_start: 0.7458 (ttt180) cc_final: 0.7196 (ttm-80) REVERT: B 774 MET cc_start: 0.7961 (mmm) cc_final: 0.7653 (mmm) REVERT: B 849 TYR cc_start: 0.8435 (m-80) cc_final: 0.8086 (m-10) REVERT: B 1042 MET cc_start: 0.7731 (ppp) cc_final: 0.6834 (tmm) REVERT: B 1059 GLU cc_start: 0.7735 (tp30) cc_final: 0.7348 (mt-10) REVERT: C 464 ARG cc_start: 0.7965 (mtt-85) cc_final: 0.7503 (ttp-170) REVERT: C 495 ASP cc_start: 0.7905 (p0) cc_final: 0.7520 (p0) REVERT: C 849 TYR cc_start: 0.8385 (m-80) cc_final: 0.7898 (m-10) REVERT: C 852 ARG cc_start: 0.8210 (mtt90) cc_final: 0.7573 (mtt180) REVERT: C 1042 MET cc_start: 0.7856 (ppp) cc_final: 0.6995 (tmm) REVERT: C 1059 GLU cc_start: 0.7585 (tp30) cc_final: 0.7245 (mt-10) REVERT: D 535 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7821 (t0) REVERT: D 785 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6624 (m-10) REVERT: D 849 TYR cc_start: 0.8252 (m-80) cc_final: 0.7826 (m-10) REVERT: D 1055 THR cc_start: 0.8750 (t) cc_final: 0.8503 (m) REVERT: D 1059 GLU cc_start: 0.7661 (tp30) cc_final: 0.7267 (mt-10) outliers start: 28 outliers final: 20 residues processed: 300 average time/residue: 0.2860 time to fit residues: 134.7672 Evaluate side-chains 298 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 870 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 102 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 202 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 805 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.143170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.119110 restraints weight = 71026.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123802 restraints weight = 27098.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.126599 restraints weight = 15004.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128027 restraints weight = 10556.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.129121 restraints weight = 8761.952| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18452 Z= 0.103 Angle : 0.495 6.554 25028 Z= 0.258 Chirality : 0.036 0.144 2936 Planarity : 0.004 0.042 3044 Dihedral : 4.979 55.958 2496 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.12 % Allowed : 14.31 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.18), residues: 2208 helix: 0.91 (0.13), residues: 1640 sheet: 1.33 (0.86), residues: 48 loop : 0.08 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 601 TYR 0.010 0.001 TYR A 456 PHE 0.012 0.001 PHE D 823 TRP 0.008 0.001 TRP C 711 HIS 0.003 0.001 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.00227 (18452) covalent geometry : angle 0.49508 (25028) hydrogen bonds : bond 0.03631 ( 1056) hydrogen bonds : angle 4.05707 ( 3084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 314 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 292 time to evaluate : 0.823 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: A 483 MET cc_start: 0.8411 (mtp) cc_final: 0.7938 (mmt) REVERT: A 785 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.6169 (m-10) REVERT: A 825 GLU cc_start: 0.7134 (pm20) cc_final: 0.6888 (pm20) REVERT: A 1042 MET cc_start: 0.7616 (ppp) cc_final: 0.6740 (tmm) REVERT: A 1050 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7255 (ttm110) REVERT: B 483 MET cc_start: 0.8185 (mtp) cc_final: 0.7750 (mmt) REVERT: B 523 MET cc_start: 0.8409 (tpt) cc_final: 0.8066 (tpt) REVERT: B 774 MET cc_start: 0.7899 (mmm) cc_final: 0.7667 (mmm) REVERT: B 849 TYR cc_start: 0.8459 (m-80) cc_final: 0.8114 (m-10) REVERT: B 1042 MET cc_start: 0.7727 (ppp) cc_final: 0.6525 (tmm) REVERT: B 1059 GLU cc_start: 0.7711 (tp30) cc_final: 0.7316 (mt-10) REVERT: C 464 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7510 (ttp-170) REVERT: C 852 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7567 (mtt180) REVERT: C 946 ILE cc_start: 0.8780 (mt) cc_final: 0.8451 (mt) REVERT: C 1042 MET cc_start: 0.7856 (ppp) cc_final: 0.6944 (tmm) REVERT: C 1059 GLU cc_start: 0.7621 (tp30) cc_final: 0.7260 (mt-10) REVERT: D 483 MET cc_start: 0.8247 (mtp) cc_final: 0.7937 (mmt) REVERT: D 634 MET cc_start: 0.9012 (tpt) cc_final: 0.8409 (tpt) REVERT: D 785 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6437 (m-10) REVERT: D 946 ILE cc_start: 0.8911 (mt) cc_final: 0.8640 (mt) REVERT: D 1055 THR cc_start: 0.8703 (t) cc_final: 0.8461 (m) REVERT: D 1059 GLU cc_start: 0.7724 (tp30) cc_final: 0.7330 (mt-10) outliers start: 22 outliers final: 17 residues processed: 308 average time/residue: 0.2815 time to fit residues: 138.0309 Evaluate side-chains 293 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 274 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 120 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.139608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115544 restraints weight = 72058.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.120123 restraints weight = 27840.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122877 restraints weight = 15499.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124517 restraints weight = 10931.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.125452 restraints weight = 8862.520| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18452 Z= 0.198 Angle : 0.545 7.073 25028 Z= 0.289 Chirality : 0.038 0.154 2936 Planarity : 0.004 0.041 3044 Dihedral : 5.138 53.788 2496 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.02 % Allowed : 14.72 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.18), residues: 2208 helix: 0.81 (0.13), residues: 1644 sheet: 1.18 (0.85), residues: 48 loop : 0.00 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 458 TYR 0.012 0.001 TYR B 840 PHE 0.013 0.001 PHE D 823 TRP 0.011 0.001 TRP A 832 HIS 0.004 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00463 (18452) covalent geometry : angle 0.54487 (25028) hydrogen bonds : bond 0.04005 ( 1056) hydrogen bonds : angle 4.23799 ( 3084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 280 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.8435 (mtp) cc_final: 0.7958 (mmt) REVERT: A 785 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6359 (m-10) REVERT: A 849 TYR cc_start: 0.8385 (m-80) cc_final: 0.7967 (m-10) REVERT: A 1042 MET cc_start: 0.7576 (ppp) cc_final: 0.6759 (tmm) REVERT: A 1050 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7313 (ttm110) REVERT: B 483 MET cc_start: 0.8319 (mtp) cc_final: 0.7732 (mmt) REVERT: B 523 MET cc_start: 0.8455 (tpt) cc_final: 0.8120 (tpt) REVERT: B 717 ARG cc_start: 0.7472 (ttt180) cc_final: 0.7210 (ttm-80) REVERT: B 849 TYR cc_start: 0.8476 (m-80) cc_final: 0.8073 (m-10) REVERT: B 1042 MET cc_start: 0.7752 (ppp) cc_final: 0.7140 (tpp) REVERT: B 1059 GLU cc_start: 0.7719 (tp30) cc_final: 0.7340 (mt-10) REVERT: C 464 ARG cc_start: 0.7950 (mtt-85) cc_final: 0.7474 (ttp-170) REVERT: C 495 ASP cc_start: 0.7949 (p0) cc_final: 0.7620 (p0) REVERT: C 849 TYR cc_start: 0.8389 (m-80) cc_final: 0.7916 (m-10) REVERT: C 852 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7599 (mtt180) REVERT: C 1042 MET cc_start: 0.7831 (ppp) cc_final: 0.7097 (tpp) REVERT: C 1059 GLU cc_start: 0.7609 (tp30) cc_final: 0.7264 (mt-10) REVERT: D 483 MET cc_start: 0.8372 (mtp) cc_final: 0.7870 (mmt) REVERT: D 634 MET cc_start: 0.9023 (tpt) cc_final: 0.8405 (tpt) REVERT: D 785 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6552 (m-10) REVERT: D 849 TYR cc_start: 0.8250 (m-80) cc_final: 0.7803 (m-10) REVERT: D 996 ARG cc_start: 0.7987 (ttm170) cc_final: 0.7709 (ttm110) REVERT: D 1059 GLU cc_start: 0.7792 (tp30) cc_final: 0.7435 (mt-10) outliers start: 20 outliers final: 18 residues processed: 295 average time/residue: 0.2925 time to fit residues: 135.6534 Evaluate side-chains 291 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 271 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 816 ILE Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 93 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 212 optimal weight: 0.3980 chunk 129 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118014 restraints weight = 71453.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122699 restraints weight = 27522.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125504 restraints weight = 15243.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.127135 restraints weight = 10730.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128058 restraints weight = 8709.109| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18452 Z= 0.119 Angle : 0.509 7.075 25028 Z= 0.266 Chirality : 0.036 0.141 2936 Planarity : 0.004 0.040 3044 Dihedral : 4.963 55.425 2496 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.92 % Allowed : 14.88 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 2208 helix: 1.00 (0.13), residues: 1640 sheet: 1.40 (0.86), residues: 48 loop : 0.05 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 458 TYR 0.010 0.001 TYR A 456 PHE 0.014 0.001 PHE D 823 TRP 0.009 0.001 TRP C 711 HIS 0.003 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00270 (18452) covalent geometry : angle 0.50876 (25028) hydrogen bonds : bond 0.03666 ( 1056) hydrogen bonds : angle 4.06993 ( 3084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 470 is missing expected H atoms. Skipping. Residue LEU 538 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue THR 646 is missing expected H atoms. Skipping. Residue LYS 649 is missing expected H atoms. Skipping. Residue SER 650 is missing expected H atoms. Skipping. Residue LYS 997 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 282 time to evaluate : 0.939 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: A 483 MET cc_start: 0.8367 (mtp) cc_final: 0.7917 (mmt) REVERT: A 785 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.6198 (m-10) REVERT: A 849 TYR cc_start: 0.8341 (m-80) cc_final: 0.7946 (m-10) REVERT: A 852 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7948 (mmt90) REVERT: A 1042 MET cc_start: 0.7547 (ppp) cc_final: 0.6729 (tmm) REVERT: A 1050 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7279 (ttm110) REVERT: B 483 MET cc_start: 0.8245 (mtp) cc_final: 0.7743 (mmt) REVERT: B 523 MET cc_start: 0.8413 (tpt) cc_final: 0.8097 (tpt) REVERT: B 717 ARG cc_start: 0.7443 (ttt180) cc_final: 0.7188 (ttm-80) REVERT: B 849 TYR cc_start: 0.8457 (m-80) cc_final: 0.8056 (m-10) REVERT: B 1042 MET cc_start: 0.7715 (ppp) cc_final: 0.6951 (tpp) REVERT: B 1059 GLU cc_start: 0.7705 (tp30) cc_final: 0.7330 (mt-10) REVERT: C 464 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7472 (ttp-170) REVERT: C 495 ASP cc_start: 0.7912 (p0) cc_final: 0.7580 (p0) REVERT: C 852 ARG cc_start: 0.8203 (mtt90) cc_final: 0.7616 (mtt180) REVERT: C 1042 MET cc_start: 0.7652 (ppp) cc_final: 0.6999 (tpp) REVERT: C 1059 GLU cc_start: 0.7505 (tp30) cc_final: 0.7140 (mt-10) REVERT: D 483 MET cc_start: 0.8170 (mtp) cc_final: 0.7945 (mmt) REVERT: D 634 MET cc_start: 0.9016 (tpt) cc_final: 0.8375 (tpt) REVERT: D 785 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.6341 (m-10) REVERT: D 849 TYR cc_start: 0.8191 (m-80) cc_final: 0.7726 (m-10) REVERT: D 946 ILE cc_start: 0.8914 (mt) cc_final: 0.8624 (mt) REVERT: D 996 ARG cc_start: 0.7978 (ttm170) cc_final: 0.7708 (ttm110) REVERT: D 1059 GLU cc_start: 0.7772 (tp30) cc_final: 0.7439 (mt-10) REVERT: D 1072 MET cc_start: 0.8294 (ttp) cc_final: 0.8030 (ttp) outliers start: 18 outliers final: 16 residues processed: 296 average time/residue: 0.3001 time to fit residues: 140.0140 Evaluate side-chains 293 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 275 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 881 LEU Chi-restraints excluded: chain D residue 882 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 115 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118129 restraints weight = 71050.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.122772 restraints weight = 27341.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125583 restraints weight = 15196.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127246 restraints weight = 10686.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128116 restraints weight = 8648.477| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18452 Z= 0.124 Angle : 0.511 9.243 25028 Z= 0.266 Chirality : 0.037 0.139 2936 Planarity : 0.004 0.040 3044 Dihedral : 4.899 55.152 2496 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.97 % Allowed : 14.98 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.18), residues: 2208 helix: 1.03 (0.13), residues: 1648 sheet: 1.49 (0.86), residues: 48 loop : 0.06 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 458 TYR 0.010 0.001 TYR A 456 PHE 0.016 0.001 PHE D 823 TRP 0.009 0.001 TRP C 711 HIS 0.003 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00283 (18452) covalent geometry : angle 0.51061 (25028) hydrogen bonds : bond 0.03637 ( 1056) hydrogen bonds : angle 4.05411 ( 3084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5303.18 seconds wall clock time: 91 minutes 15.14 seconds (5475.14 seconds total)