Starting phenix.real_space_refine on Sat Mar 7 01:19:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x2j_22009/03_2026/6x2j_22009_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x2j_22009/03_2026/6x2j_22009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x2j_22009/03_2026/6x2j_22009_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x2j_22009/03_2026/6x2j_22009_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x2j_22009/03_2026/6x2j_22009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x2j_22009/03_2026/6x2j_22009.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 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: 7 Type Number sf(0) Gaussians Br 4 7.06 5 S 140 5.16 5 C 11692 2.51 5 N 2952 2.21 5 O 3056 1.98 5 F 4 1.80 5 H 18108 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 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: 35956 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8961 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 539} 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: 8961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8961 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 539} 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: 8961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8961 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 539} 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: 8961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8961 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 539} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ULJ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ULJ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ULJ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'ULJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.88, per 1000 atoms: 0.16 Number of scatterers: 35956 At special positions: 0 Unit cell: (111, 110, 143, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 4 34.99 S 140 16.00 F 4 9.00 O 3056 8.00 N 2952 7.00 C 11692 6.00 H 18108 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: 2.70 Conformation dependent library (CDL) restraints added in 977.5 milliseconds 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 8 sheets defined 77.1% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 458 through 469 removed outlier: 3.635A pdb=" N ILE A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 removed outlier: 4.029A pdb=" N LEU A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 516 through 525 Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 538 through 541 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 604 through 611 removed outlier: 3.748A pdb=" N ILE A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.835A pdb=" N PHE A 640 " --> pdb=" O VAL A 636 " (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: 4.463A 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 767 through 788 Processing helix chain 'A' and resid 804 through 818 removed outlier: 4.061A pdb=" N ILE A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 827 through 845 removed outlier: 3.637A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 853 through 892 removed outlier: 4.830A pdb=" N ILE A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 860 " --> pdb=" O CYS A 856 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL A 876 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHE A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.598A pdb=" N SER A 899 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 912 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 970 removed outlier: 3.503A pdb=" N ASP A 966 " --> pdb=" O GLY A 962 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 990 removed outlier: 3.744A 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: 3.768A pdb=" N ILE A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU A1045 " --> pdb=" O GLU A1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 Processing helix chain 'B' and resid 458 through 469 removed outlier: 3.751A pdb=" N GLN B 467 " --> pdb=" O GLN B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 494 through 504 removed outlier: 3.596A pdb=" N GLN B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 525 Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 538 through 541 removed outlier: 3.871A pdb=" N THR B 541 " --> pdb=" O LEU B 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 541' Processing helix chain 'B' and resid 550 through 559 removed outlier: 3.588A 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 590 Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 604 through 611 removed outlier: 4.032A pdb=" N LYS B 610 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 630 through 640 removed outlier: 3.780A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (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: 4.458A 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 767 through 788 Processing helix chain 'B' and resid 804 through 819 removed outlier: 4.132A pdb=" N ILE B 817 " --> pdb=" O THR B 813 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 823 Processing helix chain 'B' and resid 827 through 851 removed outlier: 3.682A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 851 " --> pdb=" O LEU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 892 removed outlier: 4.613A pdb=" N ILE B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N PHE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL B 876 " --> pdb=" O ARG B 872 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N PHE B 879 " --> pdb=" O VAL B 875 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 880 " --> pdb=" O VAL B 876 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 884 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 3.614A 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 911 Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' 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 Processing helix chain 'B' and resid 950 through 970 removed outlier: 3.529A pdb=" N ALA B 965 " --> pdb=" O VAL B 961 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 966 " --> pdb=" O GLY B 962 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 990 removed outlier: 4.416A pdb=" N ILE B 976 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 999 Processing helix chain 'B' and resid 1040 through 1072 removed outlier: 3.755A pdb=" N ILE B1044 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU B1045 " --> pdb=" O GLU B1041 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B1063 " --> pdb=" O GLU B1059 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B1064 " --> pdb=" O LYS B1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 456 Processing helix chain 'C' and resid 458 through 466 removed outlier: 4.433A pdb=" N ARG C 464 " --> pdb=" O ASN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 494 through 504 Processing helix chain 'C' and resid 516 through 525 removed outlier: 3.538A pdb=" N HIS C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 535 Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 550 through 559 removed outlier: 3.582A 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 590 Processing helix chain 'C' and resid 592 through 601 Processing helix chain 'C' and resid 604 through 611 removed outlier: 3.921A pdb=" N LYS C 610 " --> pdb=" O ASP C 606 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 630 Processing helix chain 'C' and resid 630 through 640 removed outlier: 3.783A pdb=" N PHE C 640 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 692 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: 4.465A 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 767 through 788 Processing helix chain 'C' and resid 804 through 820 removed outlier: 3.867A pdb=" N TRP C 809 " --> pdb=" O ASN C 805 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE C 817 " --> pdb=" O THR C 813 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 827 through 846 removed outlier: 3.529A pdb=" N TYR C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 851 Processing helix chain 'C' and resid 853 through 892 removed outlier: 4.465A pdb=" N ILE C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N PHE C 859 " --> pdb=" O ASN C 855 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 860 " --> pdb=" O CYS C 856 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL C 875 " --> pdb=" O LEU C 871 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL C 876 " --> pdb=" O ARG C 872 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE C 879 " --> pdb=" O VAL C 875 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 880 " --> pdb=" O VAL C 876 " (cutoff:3.500A) removed outlier: 3.962A 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 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 969 removed outlier: 3.523A pdb=" N ASP C 966 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 990 removed outlier: 4.361A 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: 3.909A pdb=" N ILE C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU C1045 " --> pdb=" O GLU C1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 456 Processing helix chain 'D' and resid 458 through 469 removed outlier: 4.278A pdb=" N ARG D 464 " --> pdb=" O ASN D 460 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 493 removed outlier: 3.549A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 504 Processing helix chain 'D' and resid 516 through 525 Processing helix chain 'D' and resid 526 through 535 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.838A pdb=" N THR D 541 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP D 542 " --> pdb=" O LYS D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 559 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 582 through 590 Processing helix chain 'D' and resid 592 through 601 Processing helix chain 'D' and resid 604 through 609 Processing helix chain 'D' and resid 621 through 630 Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.763A 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: 3.623A pdb=" N ASN D 722 " --> pdb=" O ALA D 718 " (cutoff:3.500A) removed outlier: 4.359A 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 767 through 788 Processing helix chain 'D' and resid 804 through 820 removed outlier: 3.531A pdb=" N TRP D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE D 817 " --> pdb=" O THR D 813 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 819 " --> pdb=" O GLY D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 827 through 845 removed outlier: 3.531A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 851 Processing helix chain 'D' and resid 853 through 892 removed outlier: 4.456A pdb=" N ILE D 858 " --> pdb=" O GLU D 854 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N PHE D 859 " --> pdb=" O ASN D 855 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL D 876 " --> pdb=" O ARG D 872 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 877 " --> pdb=" O SER D 873 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE D 879 " --> pdb=" O VAL D 875 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 880 " --> pdb=" O VAL D 876 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE D 884 " --> pdb=" O LEU D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.522A pdb=" N SER D 899 " --> pdb=" O ASP D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 912 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: 3.574A pdb=" N PHE D 938 " --> pdb=" O PRO D 934 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 968 removed outlier: 3.512A pdb=" N ASP D 966 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 990 removed outlier: 4.233A pdb=" N ILE D 976 " --> pdb=" O SER D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 999 Processing helix chain 'D' and resid 1040 through 1072 removed outlier: 3.830A pdb=" N ILE D1044 " --> pdb=" O LEU D1040 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU D1045 " --> pdb=" O GLU D1041 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 656 through 659 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 removed outlier: 3.575A pdb=" N GLU B 657 " --> pdb=" O LEU B 643 " (cutoff:3.500A) 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 removed outlier: 3.757A pdb=" N GLU C 657 " --> pdb=" O LEU C 643 " (cutoff:3.500A) 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 1108 hydrogen bonds defined for protein. 3258 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: 8.50 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 7035 1.03 - 1.25: 13477 1.25 - 1.46: 5815 1.46 - 1.68: 9797 1.68 - 1.89: 228 Bond restraints: 36352 Sorted by residual: bond pdb=" N ILE D 803 " pdb=" H ILE D 803 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" N ILE A 803 " pdb=" H ILE A 803 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" N ILE C 803 " pdb=" H ILE C 803 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.10e+01 bond pdb=" N ILE B 803 " pdb=" H ILE B 803 " ideal model delta sigma weight residual 0.860 1.028 -0.168 2.00e-02 2.50e+03 7.08e+01 bond pdb=" CD1 PHE A 841 " pdb=" HD1 PHE A 841 " ideal model delta sigma weight residual 0.930 1.088 -0.158 2.00e-02 2.50e+03 6.21e+01 ... (remaining 36347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 59073 3.10 - 6.19: 5600 6.19 - 9.29: 1106 9.29 - 12.39: 36 12.39 - 15.49: 21 Bond angle restraints: 65836 Sorted by residual: angle pdb=" CA THR C 516 " pdb=" C THR C 516 " pdb=" O THR C 516 " ideal model delta sigma weight residual 121.89 113.22 8.67 1.17e+00 7.31e-01 5.50e+01 angle pdb=" N VAL D 564 " pdb=" CA VAL D 564 " pdb=" C VAL D 564 " ideal model delta sigma weight residual 110.72 104.15 6.57 1.01e+00 9.80e-01 4.23e+01 angle pdb=" N GLN D 833 " pdb=" CA GLN D 833 " pdb=" C GLN D 833 " ideal model delta sigma weight residual 111.40 103.50 7.90 1.22e+00 6.72e-01 4.19e+01 angle pdb=" N LYS B 578 " pdb=" CA LYS B 578 " pdb=" C LYS B 578 " ideal model delta sigma weight residual 113.01 105.48 7.53 1.20e+00 6.94e-01 3.94e+01 angle pdb=" CA VAL B 595 " pdb=" C VAL B 595 " pdb=" O VAL B 595 " ideal model delta sigma weight residual 120.85 114.29 6.56 1.06e+00 8.90e-01 3.84e+01 ... (remaining 65831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15552 17.99 - 35.98: 910 35.98 - 53.97: 260 53.97 - 71.96: 215 71.96 - 89.95: 63 Dihedral angle restraints: 17000 sinusoidal: 9108 harmonic: 7892 Sorted by residual: dihedral pdb=" CA LYS A 787 " pdb=" C LYS A 787 " pdb=" N GLU A 788 " pdb=" CA GLU A 788 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+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 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 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 -135.43 13.43 0 2.50e+00 1.60e-01 2.89e+01 ... (remaining 16997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1638 0.068 - 0.136: 820 0.136 - 0.204: 338 0.204 - 0.272: 72 0.272 - 0.340: 20 Chirality restraints: 2888 Sorted by residual: chirality pdb=" CA PHE C 877 " pdb=" N PHE C 877 " pdb=" C PHE C 877 " pdb=" CB PHE C 877 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLU A 546 " pdb=" N GLU A 546 " pdb=" C GLU A 546 " pdb=" CB GLU A 546 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+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 2.11 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 2885 not shown) Planarity restraints: 5160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 590 " 0.131 2.00e-02 2.50e+03 4.83e-01 3.51e+03 pdb=" CG ASN C 590 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN C 590 " -0.128 2.00e-02 2.50e+03 pdb=" ND2 ASN C 590 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 590 " 0.831 2.00e-02 2.50e+03 pdb="HD22 ASN C 590 " -0.824 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 590 " 0.174 2.00e-02 2.50e+03 4.78e-01 3.43e+03 pdb=" CG ASN D 590 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN D 590 " -0.169 2.00e-02 2.50e+03 pdb=" ND2 ASN D 590 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN D 590 " 0.815 2.00e-02 2.50e+03 pdb="HD22 ASN D 590 " -0.805 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 917 " 0.266 2.00e-02 2.50e+03 4.53e-01 3.08e+03 pdb=" CG ASN C 917 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 917 " -0.262 2.00e-02 2.50e+03 pdb=" ND2 ASN C 917 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 917 " -0.729 2.00e-02 2.50e+03 pdb="HD22 ASN C 917 " 0.747 2.00e-02 2.50e+03 ... (remaining 5157 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.25: 2551 2.25 - 2.86: 79256 2.86 - 3.47: 107745 3.47 - 4.09: 142436 4.09 - 4.70: 218740 Nonbonded interactions: 550728 Sorted by model distance: nonbonded pdb=" OE1 GLU D 808 " pdb=" HH TYR D 812 " model vdw 1.635 2.450 nonbonded pdb=" OE1 GLU B 808 " pdb=" HH TYR B 812 " model vdw 1.645 2.450 nonbonded pdb=" OE1 GLU C 808 " pdb=" HH TYR C 812 " model vdw 1.650 2.450 nonbonded pdb=" HG SER A1039 " pdb=" OE1 GLU A1043 " model vdw 1.651 2.450 nonbonded pdb=" HG SER C1076 " pdb=" OE2 GLU C1077 " model vdw 1.651 2.450 ... (remaining 550723 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: 0.02 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.470 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 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 : 0.014 0.085 18244 Z= 0.936 Angle : 1.847 9.101 24712 Z= 1.278 Chirality : 0.093 0.340 2888 Planarity : 0.014 0.174 3020 Dihedral : 13.593 88.454 6596 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.70 % Favored : 95.98 % Rotamer: Outliers : 1.34 % Allowed : 5.37 % Favored : 93.29 % 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: -2.17 (0.16), residues: 2188 helix: -1.67 (0.10), residues: 1648 sheet: 3.69 (0.79), residues: 20 loop : -0.02 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 919 TYR 0.174 0.020 TYR D 785 PHE 0.047 0.008 PHE D 746 TRP 0.088 0.014 TRP B 711 HIS 0.018 0.002 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.01395 (18244) covalent geometry : angle 1.84731 (24712) hydrogen bonds : bond 0.21254 ( 1108) hydrogen bonds : angle 7.77602 ( 3258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 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 741 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 715 time to evaluate : 0.717 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: A 496 LYS cc_start: 0.7225 (mttt) cc_final: 0.7008 (mmmt) REVERT: A 523 MET cc_start: 0.7714 (tpt) cc_final: 0.7423 (tpt) REVERT: A 528 GLN cc_start: 0.6952 (mm-40) cc_final: 0.6143 (mm-40) REVERT: A 544 LEU cc_start: 0.8326 (mt) cc_final: 0.7955 (mm) REVERT: A 547 ASP cc_start: 0.7390 (t0) cc_final: 0.6909 (t0) REVERT: A 558 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6308 (mp0) REVERT: A 562 LYS cc_start: 0.7610 (mmtt) cc_final: 0.7117 (mtmm) REVERT: A 575 VAL cc_start: 0.7905 (p) cc_final: 0.7705 (m) REVERT: A 589 HIS cc_start: 0.7630 (m170) cc_final: 0.7337 (m-70) REVERT: A 590 ASN cc_start: 0.7451 (m-40) cc_final: 0.7119 (m110) REVERT: A 594 GLU cc_start: 0.7168 (tp30) cc_final: 0.6964 (tp30) REVERT: A 597 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6359 (mt) REVERT: A 603 LYS cc_start: 0.8138 (mttt) cc_final: 0.7846 (tttm) REVERT: A 606 ASP cc_start: 0.7724 (m-30) cc_final: 0.7448 (m-30) REVERT: A 607 GLU cc_start: 0.6398 (tt0) cc_final: 0.6036 (tt0) REVERT: A 628 GLU cc_start: 0.7154 (tt0) cc_final: 0.6289 (tm-30) REVERT: A 634 MET cc_start: 0.7431 (tpt) cc_final: 0.6982 (tpt) REVERT: A 640 PHE cc_start: 0.6765 (m-80) cc_final: 0.6085 (m-10) REVERT: A 642 MET cc_start: 0.6864 (mtp) cc_final: 0.6457 (mtm) REVERT: A 716 PHE cc_start: 0.7496 (t80) cc_final: 0.7231 (t80) REVERT: A 717 ARG cc_start: 0.6742 (ttt180) cc_final: 0.5690 (ttp80) REVERT: A 720 MET cc_start: 0.6817 (mmm) cc_final: 0.6025 (mpm) REVERT: A 721 MET cc_start: 0.6499 (ttm) cc_final: 0.6191 (tpt) REVERT: A 727 CYS cc_start: 0.7666 (t) cc_final: 0.6829 (m) REVERT: A 731 ILE cc_start: 0.7477 (mt) cc_final: 0.7157 (mm) REVERT: A 744 MET cc_start: 0.7052 (mmt) cc_final: 0.6835 (mmm) REVERT: A 845 ASN cc_start: 0.8824 (t0) cc_final: 0.8534 (t0) REVERT: A 864 GLU cc_start: 0.6283 (tt0) cc_final: 0.5337 (tm-30) REVERT: A 868 LYS cc_start: 0.6919 (mttm) cc_final: 0.6325 (mtpm) REVERT: A 875 VAL cc_start: 0.8204 (t) cc_final: 0.7965 (p) REVERT: A 877 PHE cc_start: 0.7074 (m-10) cc_final: 0.6676 (m-80) REVERT: A 882 LEU cc_start: 0.8272 (tp) cc_final: 0.8070 (tp) REVERT: A 930 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6546 (mt-10) REVERT: A 981 GLU cc_start: 0.7727 (tp30) cc_final: 0.7387 (tt0) REVERT: A 993 TRP cc_start: 0.7409 (p-90) cc_final: 0.7196 (p-90) REVERT: A 1001 LYS cc_start: 0.6894 (mmtp) cc_final: 0.6586 (mtmm) REVERT: A 1050 ARG cc_start: 0.6936 (ttm-80) cc_final: 0.6622 (ttm-80) REVERT: B 503 LYS cc_start: 0.6536 (tttt) cc_final: 0.6242 (tppp) REVERT: B 528 GLN cc_start: 0.6829 (mm-40) cc_final: 0.6471 (mm-40) REVERT: B 544 LEU cc_start: 0.7444 (mt) cc_final: 0.6969 (mm) REVERT: B 558 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6715 (mp0) REVERT: B 575 VAL cc_start: 0.8640 (p) cc_final: 0.8326 (m) REVERT: B 594 GLU cc_start: 0.6832 (tp30) cc_final: 0.6577 (mm-30) REVERT: B 607 GLU cc_start: 0.6367 (tt0) cc_final: 0.5972 (tt0) REVERT: B 628 GLU cc_start: 0.7245 (tt0) cc_final: 0.6642 (tm-30) REVERT: B 629 TYR cc_start: 0.7732 (m-80) cc_final: 0.7366 (m-80) REVERT: B 634 MET cc_start: 0.7324 (tpt) cc_final: 0.7085 (tpt) REVERT: B 640 PHE cc_start: 0.7022 (m-80) cc_final: 0.6472 (m-10) REVERT: B 642 MET cc_start: 0.7062 (mtp) cc_final: 0.6596 (mtm) REVERT: B 687 ASN cc_start: 0.7481 (m-40) cc_final: 0.6823 (m-40) REVERT: B 689 MET cc_start: 0.7879 (mtt) cc_final: 0.7522 (mtm) REVERT: B 693 ASN cc_start: 0.7569 (m-40) cc_final: 0.7356 (t0) REVERT: B 695 ILE cc_start: 0.7228 (tt) cc_final: 0.6519 (tp) REVERT: B 699 ASN cc_start: 0.7297 (m-40) cc_final: 0.6599 (m110) REVERT: B 704 LYS cc_start: 0.6563 (mttt) cc_final: 0.5685 (mmtm) REVERT: B 717 ARG cc_start: 0.6681 (ttt180) cc_final: 0.5857 (mtp85) REVERT: B 720 MET cc_start: 0.6715 (mmm) cc_final: 0.6482 (mmp) REVERT: B 721 MET cc_start: 0.6447 (ttm) cc_final: 0.6108 (tpt) REVERT: B 727 CYS cc_start: 0.7974 (t) cc_final: 0.6842 (m) REVERT: B 845 ASN cc_start: 0.8747 (t0) cc_final: 0.8345 (t0) REVERT: B 864 GLU cc_start: 0.6499 (tt0) cc_final: 0.5697 (mm-30) REVERT: B 868 LYS cc_start: 0.6759 (mttm) cc_final: 0.6226 (mtpm) REVERT: B 882 LEU cc_start: 0.8099 (tp) cc_final: 0.7834 (tp) REVERT: B 896 ASP cc_start: 0.7734 (m-30) cc_final: 0.7456 (m-30) REVERT: B 930 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6790 (mt-10) REVERT: B 966 ASP cc_start: 0.5289 (m-30) cc_final: 0.4961 (m-30) REVERT: B 972 SER cc_start: 0.7941 (t) cc_final: 0.7425 (p) REVERT: B 1001 LYS cc_start: 0.7463 (mmtp) cc_final: 0.6821 (mtmm) REVERT: B 1052 LYS cc_start: 0.6731 (ttmt) cc_final: 0.6359 (tttp) REVERT: B 1063 GLU cc_start: 0.7627 (tp30) cc_final: 0.7013 (mm-30) REVERT: B 1070 GLN cc_start: 0.7665 (tt0) cc_final: 0.7458 (tt0) REVERT: C 460 ASN cc_start: 0.7273 (t0) cc_final: 0.6995 (t0) REVERT: C 467 GLN cc_start: 0.7496 (tt0) cc_final: 0.7130 (mm-40) REVERT: C 496 LYS cc_start: 0.7384 (mttt) cc_final: 0.7073 (mptp) REVERT: C 558 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7166 (mp0) REVERT: C 626 MET cc_start: 0.7464 (mtp) cc_final: 0.7205 (ttm) REVERT: C 628 GLU cc_start: 0.7116 (tt0) cc_final: 0.6439 (tt0) REVERT: C 629 TYR cc_start: 0.7639 (m-80) cc_final: 0.7225 (m-80) REVERT: C 635 LYS cc_start: 0.6359 (ttpt) cc_final: 0.5775 (tptp) REVERT: C 640 PHE cc_start: 0.6659 (m-80) cc_final: 0.6211 (m-10) REVERT: C 687 ASN cc_start: 0.7772 (m-40) cc_final: 0.7182 (m110) REVERT: C 691 GLN cc_start: 0.7499 (mt0) cc_final: 0.7040 (mm-40) REVERT: C 695 ILE cc_start: 0.7224 (tt) cc_final: 0.6970 (tp) REVERT: C 699 ASN cc_start: 0.7130 (m-40) cc_final: 0.6711 (m110) REVERT: C 705 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6517 (mm-30) REVERT: C 721 MET cc_start: 0.6444 (ttm) cc_final: 0.5856 (tpp) REVERT: C 727 CYS cc_start: 0.7684 (t) cc_final: 0.6816 (m) REVERT: C 731 ILE cc_start: 0.7766 (mt) cc_final: 0.7526 (mm) REVERT: C 735 ILE cc_start: 0.8101 (mt) cc_final: 0.7885 (mm) REVERT: C 751 ILE cc_start: 0.6233 (mt) cc_final: 0.5973 (mt) REVERT: C 819 VAL cc_start: 0.8815 (t) cc_final: 0.8614 (m) REVERT: C 833 GLN cc_start: 0.7235 (tt0) cc_final: 0.6964 (tm-30) REVERT: C 842 TYR cc_start: 0.7965 (m-80) cc_final: 0.7715 (m-80) REVERT: C 845 ASN cc_start: 0.8669 (t0) cc_final: 0.8444 (t0) REVERT: C 864 GLU cc_start: 0.6678 (tt0) cc_final: 0.5794 (mm-30) REVERT: C 868 LYS cc_start: 0.6653 (mttm) cc_final: 0.5948 (mtmm) REVERT: C 896 ASP cc_start: 0.7928 (m-30) cc_final: 0.7698 (m-30) REVERT: C 930 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6900 (mt-10) REVERT: C 972 SER cc_start: 0.7691 (t) cc_final: 0.7181 (p) REVERT: C 978 MET cc_start: 0.7906 (mtm) cc_final: 0.7669 (mtp) REVERT: C 981 GLU cc_start: 0.7678 (tp30) cc_final: 0.7327 (tt0) REVERT: C 1001 LYS cc_start: 0.7261 (mmtp) cc_final: 0.6713 (mtmm) REVERT: C 1048 LYS cc_start: 0.6145 (ttmm) cc_final: 0.5851 (ttpp) REVERT: C 1049 TYR cc_start: 0.7221 (m-80) cc_final: 0.6808 (m-80) REVERT: C 1052 LYS cc_start: 0.6719 (ttmt) cc_final: 0.6295 (tttp) REVERT: D 504 LYS cc_start: 0.6514 (mmtm) cc_final: 0.6222 (mtpp) REVERT: D 558 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6673 (mp0) REVERT: D 562 LYS cc_start: 0.7608 (mttt) cc_final: 0.7233 (mtpm) REVERT: D 575 VAL cc_start: 0.8607 (p) cc_final: 0.8286 (m) REVERT: D 593 LYS cc_start: 0.7069 (ttpt) cc_final: 0.6798 (tttm) REVERT: D 594 GLU cc_start: 0.6943 (tp30) cc_final: 0.6523 (mm-30) REVERT: D 603 LYS cc_start: 0.8244 (mttt) cc_final: 0.7992 (tttm) REVERT: D 607 GLU cc_start: 0.6342 (tt0) cc_final: 0.5918 (tt0) REVERT: D 628 GLU cc_start: 0.7109 (tt0) cc_final: 0.6377 (tt0) REVERT: D 640 PHE cc_start: 0.6258 (m-80) cc_final: 0.5780 (m-10) REVERT: D 664 GLN cc_start: 0.7923 (pt0) cc_final: 0.7397 (mt0) REVERT: D 693 ASN cc_start: 0.7248 (m-40) cc_final: 0.7002 (t0) REVERT: D 705 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6260 (mm-30) REVERT: D 717 ARG cc_start: 0.6569 (ttt180) cc_final: 0.5769 (ttp80) REVERT: D 720 MET cc_start: 0.6589 (mmm) cc_final: 0.6051 (mmp) REVERT: D 868 LYS cc_start: 0.6644 (mttm) cc_final: 0.6126 (mtpm) REVERT: D 882 LEU cc_start: 0.8087 (tp) cc_final: 0.7867 (tp) REVERT: D 966 ASP cc_start: 0.4986 (m-30) cc_final: 0.4773 (m-30) REVERT: D 972 SER cc_start: 0.7630 (t) cc_final: 0.7137 (p) REVERT: D 989 LYS cc_start: 0.6879 (mtmt) cc_final: 0.6656 (mtpm) REVERT: D 1001 LYS cc_start: 0.6615 (mmtp) cc_final: 0.6244 (mppt) REVERT: D 1050 ARG cc_start: 0.6730 (ttm-80) cc_final: 0.6337 (ttm-80) REVERT: D 1052 LYS cc_start: 0.6973 (ttmt) cc_final: 0.6632 (tttm) outliers start: 26 outliers final: 8 residues processed: 724 average time/residue: 0.9864 time to fit residues: 825.4012 Evaluate side-chains 539 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 530 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 PRO Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain B residue 449 PRO Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain C residue 535 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain D residue 485 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN A1070 GLN B 463 GLN B 487 HIS B 492 ASN B 829 HIS C 494 HIS C 590 ASN C 831 GLN C 851 GLN C 893 ASN C1061 GLN D 487 HIS D 590 ASN D 829 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.156929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.128674 restraints weight = 58993.565| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.89 r_work: 0.3180 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18244 Z= 0.167 Angle : 0.622 7.495 24712 Z= 0.325 Chirality : 0.039 0.180 2888 Planarity : 0.004 0.062 3020 Dihedral : 5.351 51.523 2423 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.17 % Allowed : 14.31 % Favored : 83.52 % 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: -0.10 (0.17), residues: 2188 helix: 0.04 (0.12), residues: 1648 sheet: -0.77 (0.72), residues: 48 loop : 0.23 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C1050 TYR 0.017 0.002 TYR B 840 PHE 0.015 0.001 PHE B 746 TRP 0.018 0.002 TRP C 832 HIS 0.008 0.001 HIS D 520 Details of bonding type rmsd covalent geometry : bond 0.00383 (18244) covalent geometry : angle 0.62166 (24712) hydrogen bonds : bond 0.05276 ( 1108) hydrogen bonds : angle 4.75658 ( 3258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 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 573 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 531 time to evaluate : 0.933 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 547 ASP cc_start: 0.8208 (t0) cc_final: 0.7626 (t0) REVERT: A 591 LYS cc_start: 0.8612 (mttt) cc_final: 0.8212 (mttm) REVERT: A 597 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7870 (mt) REVERT: A 606 ASP cc_start: 0.8028 (m-30) cc_final: 0.7006 (p0) REVERT: A 628 GLU cc_start: 0.8244 (tt0) cc_final: 0.7979 (tt0) REVERT: A 634 MET cc_start: 0.8781 (tpt) cc_final: 0.8352 (tpt) REVERT: A 640 PHE cc_start: 0.7054 (m-80) cc_final: 0.6480 (m-10) REVERT: A 642 MET cc_start: 0.7074 (mtp) cc_final: 0.6811 (mtm) REVERT: A 699 ASN cc_start: 0.8101 (m-40) cc_final: 0.7726 (m110) REVERT: A 704 LYS cc_start: 0.7808 (mttt) cc_final: 0.6866 (mmpt) REVERT: A 720 MET cc_start: 0.7649 (mmm) cc_final: 0.7199 (mmp) REVERT: A 721 MET cc_start: 0.7438 (ttm) cc_final: 0.6993 (tpt) REVERT: A 727 CYS cc_start: 0.8233 (t) cc_final: 0.7870 (m) REVERT: A 731 ILE cc_start: 0.8357 (mt) cc_final: 0.8130 (mm) REVERT: A 739 ASN cc_start: 0.8004 (m-40) cc_final: 0.7665 (m-40) REVERT: A 808 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6942 (mt-10) REVERT: A 844 MET cc_start: 0.8982 (mmm) cc_final: 0.8777 (tpp) REVERT: A 845 ASN cc_start: 0.9207 (t0) cc_final: 0.8740 (t0) REVERT: A 852 ARG cc_start: 0.7776 (mmt90) cc_final: 0.7341 (mmt-90) REVERT: A 864 GLU cc_start: 0.7711 (tt0) cc_final: 0.7375 (mm-30) REVERT: A 868 LYS cc_start: 0.8095 (mttm) cc_final: 0.7655 (mtpm) REVERT: A 877 PHE cc_start: 0.7807 (m-10) cc_final: 0.6916 (m-80) REVERT: A 930 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7502 (mm-30) REVERT: A 986 LEU cc_start: 0.7722 (mm) cc_final: 0.7488 (mm) REVERT: A 995 LEU cc_start: 0.8241 (mm) cc_final: 0.8040 (mm) REVERT: A 1001 LYS cc_start: 0.7639 (mmtp) cc_final: 0.7385 (mtmm) REVERT: A 1047 GLN cc_start: 0.7950 (tp40) cc_final: 0.7739 (tt0) REVERT: B 575 VAL cc_start: 0.8640 (p) cc_final: 0.8353 (m) REVERT: B 593 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8247 (tttm) REVERT: B 594 GLU cc_start: 0.8033 (tp30) cc_final: 0.7657 (mm-30) REVERT: B 628 GLU cc_start: 0.8098 (tt0) cc_final: 0.7488 (tm-30) REVERT: B 629 TYR cc_start: 0.8891 (m-80) cc_final: 0.8673 (m-80) REVERT: B 634 MET cc_start: 0.8740 (tpt) cc_final: 0.8461 (tpt) REVERT: B 640 PHE cc_start: 0.6884 (m-80) cc_final: 0.6302 (m-80) REVERT: B 642 MET cc_start: 0.7379 (mtp) cc_final: 0.7119 (mtm) REVERT: B 687 ASN cc_start: 0.8612 (m-40) cc_final: 0.8026 (m110) REVERT: B 693 ASN cc_start: 0.8100 (m-40) cc_final: 0.7800 (t0) REVERT: B 698 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7632 (mt) REVERT: B 699 ASN cc_start: 0.8063 (m-40) cc_final: 0.7690 (m-40) REVERT: B 704 LYS cc_start: 0.7828 (mttt) cc_final: 0.7055 (mmtp) REVERT: B 721 MET cc_start: 0.7593 (ttm) cc_final: 0.7275 (tpt) REVERT: B 727 CYS cc_start: 0.8342 (t) cc_final: 0.7767 (m) REVERT: B 731 ILE cc_start: 0.8514 (mt) cc_final: 0.8277 (mm) REVERT: B 851 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7367 (mt0) REVERT: B 864 GLU cc_start: 0.7999 (tt0) cc_final: 0.7375 (mm-30) REVERT: B 868 LYS cc_start: 0.8161 (mttm) cc_final: 0.7735 (mtpm) REVERT: B 909 PHE cc_start: 0.8512 (t80) cc_final: 0.8153 (t80) REVERT: B 930 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7576 (mt-10) REVERT: B 972 SER cc_start: 0.8357 (t) cc_final: 0.8085 (p) REVERT: B 981 GLU cc_start: 0.8213 (tp30) cc_final: 0.7929 (mt-10) REVERT: B 1001 LYS cc_start: 0.7724 (mmtp) cc_final: 0.7465 (mtmm) REVERT: B 1042 MET cc_start: 0.6306 (pp-130) cc_final: 0.6046 (pp-130) REVERT: B 1052 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8036 (ptmm) REVERT: B 1053 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.8001 (m-30) REVERT: C 571 ASN cc_start: 0.7946 (m110) cc_final: 0.7721 (t0) REVERT: C 584 LEU cc_start: 0.9003 (tm) cc_final: 0.8781 (tp) REVERT: C 628 GLU cc_start: 0.7887 (tt0) cc_final: 0.7584 (tt0) REVERT: C 635 LYS cc_start: 0.7581 (ttpt) cc_final: 0.7369 (tttm) REVERT: C 720 MET cc_start: 0.7630 (mmm) cc_final: 0.7145 (mmp) REVERT: C 721 MET cc_start: 0.7595 (ttm) cc_final: 0.7029 (tpp) REVERT: C 727 CYS cc_start: 0.8017 (t) cc_final: 0.7473 (m) REVERT: C 731 ILE cc_start: 0.8762 (mt) cc_final: 0.8516 (mm) REVERT: C 751 ILE cc_start: 0.6603 (mt) cc_final: 0.6389 (mt) REVERT: C 808 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7072 (mt-10) REVERT: C 833 GLN cc_start: 0.8013 (tt0) cc_final: 0.7668 (tt0) REVERT: C 864 GLU cc_start: 0.7978 (tt0) cc_final: 0.7388 (mm-30) REVERT: C 868 LYS cc_start: 0.7996 (mttm) cc_final: 0.7534 (mtmp) REVERT: C 920 GLU cc_start: 0.7746 (tt0) cc_final: 0.7466 (tt0) REVERT: C 930 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7610 (mt-10) REVERT: C 972 SER cc_start: 0.8391 (t) cc_final: 0.8011 (p) REVERT: C 981 GLU cc_start: 0.8269 (tp30) cc_final: 0.8042 (tt0) REVERT: C 1001 LYS cc_start: 0.7805 (mmtp) cc_final: 0.7485 (mtmm) REVERT: C 1048 LYS cc_start: 0.7904 (ttmm) cc_final: 0.7628 (ttpp) REVERT: C 1052 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8162 (ttpp) REVERT: D 504 LYS cc_start: 0.7739 (mmtm) cc_final: 0.7419 (mtpp) REVERT: D 575 VAL cc_start: 0.8673 (p) cc_final: 0.8406 (m) REVERT: D 585 HIS cc_start: 0.8438 (m170) cc_final: 0.8149 (m-70) REVERT: D 593 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8355 (tttm) REVERT: D 607 GLU cc_start: 0.6834 (tt0) cc_final: 0.6474 (tt0) REVERT: D 628 GLU cc_start: 0.7990 (tt0) cc_final: 0.7427 (tm-30) REVERT: D 693 ASN cc_start: 0.7919 (m-40) cc_final: 0.7689 (t0) REVERT: D 699 ASN cc_start: 0.8006 (m-40) cc_final: 0.7591 (m-40) REVERT: D 705 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7429 (mm-30) REVERT: D 720 MET cc_start: 0.7665 (mmm) cc_final: 0.7060 (mmp) REVERT: D 727 CYS cc_start: 0.7916 (t) cc_final: 0.7591 (m) REVERT: D 733 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7940 (tpp) REVERT: D 852 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7133 (mmt90) REVERT: D 864 GLU cc_start: 0.7247 (tp30) cc_final: 0.6911 (tp30) REVERT: D 868 LYS cc_start: 0.8165 (mttm) cc_final: 0.7753 (mtpm) REVERT: D 966 ASP cc_start: 0.7425 (m-30) cc_final: 0.7131 (m-30) REVERT: D 972 SER cc_start: 0.8084 (t) cc_final: 0.7860 (p) REVERT: D 981 GLU cc_start: 0.8340 (tp30) cc_final: 0.7991 (tt0) REVERT: D 986 LEU cc_start: 0.7970 (mt) cc_final: 0.7620 (mp) REVERT: D 989 LYS cc_start: 0.7392 (mtmt) cc_final: 0.7167 (mtpm) REVERT: D 1001 LYS cc_start: 0.7462 (mmtp) cc_final: 0.7210 (mtmm) REVERT: D 1052 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8270 (tttm) outliers start: 42 outliers final: 12 residues processed: 554 average time/residue: 1.0459 time to fit residues: 666.7665 Evaluate side-chains 473 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 455 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 851 GLN Chi-restraints excluded: chain B residue 872 ARG Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN B 644 HIS B 700 HIS ** B1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1070 GLN C 590 ASN ** C 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 GLN D 460 ASN D 494 HIS D 664 GLN ** D 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN D 829 HIS D1047 GLN ** D1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.151090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.123300 restraints weight = 57248.643| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.81 r_work: 0.3125 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18244 Z= 0.179 Angle : 0.582 5.524 24712 Z= 0.303 Chirality : 0.039 0.188 2888 Planarity : 0.004 0.059 3020 Dihedral : 4.614 43.992 2409 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.15 % Allowed : 17.20 % Favored : 79.65 % 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: 2188 helix: 0.71 (0.12), residues: 1648 sheet: -1.06 (0.67), residues: 48 loop : 0.12 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.020 0.002 TYR C 842 PHE 0.012 0.002 PHE C 877 TRP 0.015 0.001 TRP C 711 HIS 0.006 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00414 (18244) covalent geometry : angle 0.58227 (24712) hydrogen bonds : bond 0.04840 ( 1108) hydrogen bonds : angle 4.41474 ( 3258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 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 539 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 478 time to evaluate : 0.882 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 547 ASP cc_start: 0.8229 (t0) cc_final: 0.7562 (t0) REVERT: A 591 LYS cc_start: 0.8653 (mttt) cc_final: 0.8317 (mttm) REVERT: A 606 ASP cc_start: 0.8009 (m-30) cc_final: 0.7072 (p0) REVERT: A 628 GLU cc_start: 0.8087 (tt0) cc_final: 0.7556 (tm-30) REVERT: A 634 MET cc_start: 0.8708 (tpt) cc_final: 0.8391 (tpt) REVERT: A 640 PHE cc_start: 0.7148 (m-80) cc_final: 0.6507 (m-10) REVERT: A 642 MET cc_start: 0.7184 (mtp) cc_final: 0.6948 (mtm) REVERT: A 693 ASN cc_start: 0.7952 (m-40) cc_final: 0.7591 (t0) REVERT: A 699 ASN cc_start: 0.8131 (m-40) cc_final: 0.7586 (m110) REVERT: A 704 LYS cc_start: 0.7763 (mttt) cc_final: 0.7155 (mttm) REVERT: A 720 MET cc_start: 0.7573 (mmm) cc_final: 0.7112 (mmp) REVERT: A 721 MET cc_start: 0.7461 (ttm) cc_final: 0.6956 (tpt) REVERT: A 731 ILE cc_start: 0.8484 (mt) cc_final: 0.8259 (mm) REVERT: A 739 ASN cc_start: 0.8199 (m-40) cc_final: 0.7903 (m-40) REVERT: A 808 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6907 (mt-10) REVERT: A 852 ARG cc_start: 0.7830 (mmt90) cc_final: 0.7500 (mmt-90) REVERT: A 864 GLU cc_start: 0.7803 (tt0) cc_final: 0.7386 (mm-30) REVERT: A 868 LYS cc_start: 0.7964 (mttm) cc_final: 0.7525 (mtpm) REVERT: A 877 PHE cc_start: 0.7745 (m-10) cc_final: 0.6778 (m-80) REVERT: A 924 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7781 (mm-30) REVERT: A 930 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 986 LEU cc_start: 0.7924 (mm) cc_final: 0.7402 (mp) REVERT: A 1001 LYS cc_start: 0.7721 (mmtp) cc_final: 0.7321 (mtmm) REVERT: A 1047 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: B 544 LEU cc_start: 0.7934 (mt) cc_final: 0.7730 (mm) REVERT: B 546 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6834 (pp20) REVERT: B 547 ASP cc_start: 0.7807 (m-30) cc_final: 0.7530 (m-30) REVERT: B 575 VAL cc_start: 0.8916 (p) cc_final: 0.8651 (m) REVERT: B 593 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8222 (tttm) REVERT: B 594 GLU cc_start: 0.7958 (tp30) cc_final: 0.7555 (mm-30) REVERT: B 628 GLU cc_start: 0.8066 (tt0) cc_final: 0.7569 (tm-30) REVERT: B 634 MET cc_start: 0.8646 (tpt) cc_final: 0.8321 (tpt) REVERT: B 642 MET cc_start: 0.7454 (mtp) cc_final: 0.7130 (mtm) REVERT: B 687 ASN cc_start: 0.8464 (m-40) cc_final: 0.7816 (m110) REVERT: B 693 ASN cc_start: 0.8114 (m-40) cc_final: 0.7822 (t0) REVERT: B 698 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7923 (mt) REVERT: B 699 ASN cc_start: 0.8037 (m-40) cc_final: 0.7651 (m110) REVERT: B 704 LYS cc_start: 0.7890 (mttt) cc_final: 0.7113 (mmtp) REVERT: B 721 MET cc_start: 0.7602 (ttm) cc_final: 0.7161 (tpt) REVERT: B 727 CYS cc_start: 0.8367 (t) cc_final: 0.7875 (m) REVERT: B 731 ILE cc_start: 0.8536 (mt) cc_final: 0.8327 (mm) REVERT: B 808 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6877 (mt-10) REVERT: B 864 GLU cc_start: 0.8092 (tt0) cc_final: 0.7446 (mm-30) REVERT: B 868 LYS cc_start: 0.8117 (mttm) cc_final: 0.7695 (mtpm) REVERT: B 972 SER cc_start: 0.8387 (t) cc_final: 0.8153 (p) REVERT: B 1001 LYS cc_start: 0.7807 (mmtp) cc_final: 0.7495 (mtmm) REVERT: B 1052 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8026 (ptmt) REVERT: C 481 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7234 (m-70) REVERT: C 584 LEU cc_start: 0.8953 (tm) cc_final: 0.8714 (tt) REVERT: C 606 ASP cc_start: 0.7711 (m-30) cc_final: 0.6885 (p0) REVERT: C 628 GLU cc_start: 0.7838 (tt0) cc_final: 0.7466 (tt0) REVERT: C 634 MET cc_start: 0.8699 (tpt) cc_final: 0.7698 (tpt) REVERT: C 635 LYS cc_start: 0.7553 (ttpt) cc_final: 0.7078 (tttp) REVERT: C 693 ASN cc_start: 0.7950 (m-40) cc_final: 0.7728 (t0) REVERT: C 720 MET cc_start: 0.7525 (mmm) cc_final: 0.7026 (mmp) REVERT: C 721 MET cc_start: 0.7482 (ttm) cc_final: 0.6929 (tpp) REVERT: C 727 CYS cc_start: 0.8158 (t) cc_final: 0.7653 (m) REVERT: C 731 ILE cc_start: 0.8794 (mt) cc_final: 0.8569 (mm) REVERT: C 778 PHE cc_start: 0.7721 (t80) cc_final: 0.7515 (t80) REVERT: C 808 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7052 (mt-10) REVERT: C 864 GLU cc_start: 0.7955 (tt0) cc_final: 0.7326 (mm-30) REVERT: C 868 LYS cc_start: 0.8021 (mttm) cc_final: 0.7559 (mtmp) REVERT: C 930 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 972 SER cc_start: 0.8397 (t) cc_final: 0.8019 (p) REVERT: C 987 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7218 (mm-30) REVERT: C 1001 LYS cc_start: 0.7868 (mmtp) cc_final: 0.7487 (mtmm) REVERT: C 1048 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7791 (ttpp) REVERT: C 1059 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: D 504 LYS cc_start: 0.7797 (mmtm) cc_final: 0.7571 (mtpp) REVERT: D 575 VAL cc_start: 0.8737 (p) cc_final: 0.8484 (m) REVERT: D 593 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8413 (tttm) REVERT: D 603 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8125 (tmtm) REVERT: D 606 ASP cc_start: 0.7795 (m-30) cc_final: 0.6658 (p0) REVERT: D 607 GLU cc_start: 0.6845 (tt0) cc_final: 0.6410 (tt0) REVERT: D 628 GLU cc_start: 0.8022 (tt0) cc_final: 0.7453 (tm-30) REVERT: D 693 ASN cc_start: 0.7947 (m-40) cc_final: 0.7723 (t0) REVERT: D 699 ASN cc_start: 0.8028 (m-40) cc_final: 0.7431 (m-40) REVERT: D 704 LYS cc_start: 0.7726 (mttt) cc_final: 0.6725 (mmpt) REVERT: D 720 MET cc_start: 0.7587 (mmm) cc_final: 0.6952 (mmp) REVERT: D 727 CYS cc_start: 0.8035 (t) cc_final: 0.7817 (m) REVERT: D 852 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7134 (mmt90) REVERT: D 853 PHE cc_start: 0.8604 (m-80) cc_final: 0.8162 (m-80) REVERT: D 864 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6811 (tp30) REVERT: D 868 LYS cc_start: 0.8161 (mttm) cc_final: 0.7748 (mtpm) REVERT: D 930 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7357 (mt-10) REVERT: D 966 ASP cc_start: 0.7661 (m-30) cc_final: 0.7401 (m-30) REVERT: D 972 SER cc_start: 0.8162 (t) cc_final: 0.7892 (p) REVERT: D 981 GLU cc_start: 0.8256 (tp30) cc_final: 0.7941 (tt0) REVERT: D 986 LEU cc_start: 0.7900 (mt) cc_final: 0.7474 (mp) REVERT: D 989 LYS cc_start: 0.7439 (mtmt) cc_final: 0.7204 (mtpm) REVERT: D 1001 LYS cc_start: 0.7591 (mmtp) cc_final: 0.7320 (mtmm) REVERT: D 1052 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8162 (tttm) outliers start: 61 outliers final: 26 residues processed: 513 average time/residue: 1.0417 time to fit residues: 615.2466 Evaluate side-chains 476 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 442 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 872 ARG Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 589 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain C residue 1059 GLU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 900 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 183 optimal weight: 1.9990 chunk 143 optimal weight: 0.0980 chunk 217 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS A 700 HIS B1047 GLN B1061 GLN C 691 GLN C 739 ASN D 664 GLN D 687 ASN D1047 GLN D1061 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.150706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.122804 restraints weight = 57144.748| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.82 r_work: 0.3112 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18244 Z= 0.164 Angle : 0.537 5.442 24712 Z= 0.276 Chirality : 0.038 0.173 2888 Planarity : 0.004 0.054 3020 Dihedral : 4.209 33.953 2406 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.94 % Allowed : 19.11 % Favored : 77.94 % 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: 1.20 (0.18), residues: 2188 helix: 1.13 (0.13), residues: 1652 sheet: -1.18 (0.68), residues: 48 loop : 0.17 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 458 TYR 0.019 0.002 TYR C 842 PHE 0.013 0.001 PHE C 877 TRP 0.011 0.001 TRP A 711 HIS 0.005 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00376 (18244) covalent geometry : angle 0.53677 (24712) hydrogen bonds : bond 0.04437 ( 1108) hydrogen bonds : angle 4.23537 ( 3258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 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 509 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 452 time to evaluate : 0.932 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 466 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8243 (mm) REVERT: A 528 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7563 (mm-40) REVERT: A 547 ASP cc_start: 0.8183 (t0) cc_final: 0.7425 (t0) REVERT: A 591 LYS cc_start: 0.8652 (mttt) cc_final: 0.8313 (mttm) REVERT: A 606 ASP cc_start: 0.7983 (m-30) cc_final: 0.7048 (p0) REVERT: A 628 GLU cc_start: 0.8040 (tt0) cc_final: 0.7524 (tm-30) REVERT: A 634 MET cc_start: 0.8645 (tpt) cc_final: 0.8407 (tpt) REVERT: A 693 ASN cc_start: 0.7965 (m-40) cc_final: 0.7565 (t0) REVERT: A 699 ASN cc_start: 0.8113 (m-40) cc_final: 0.7590 (m110) REVERT: A 704 LYS cc_start: 0.7802 (mttt) cc_final: 0.6818 (mmpt) REVERT: A 720 MET cc_start: 0.7590 (mmm) cc_final: 0.7100 (mmp) REVERT: A 721 MET cc_start: 0.7484 (ttm) cc_final: 0.6994 (tpt) REVERT: A 731 ILE cc_start: 0.8639 (mt) cc_final: 0.8367 (mm) REVERT: A 808 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 864 GLU cc_start: 0.7769 (tt0) cc_final: 0.7421 (mm-30) REVERT: A 868 LYS cc_start: 0.7971 (mttm) cc_final: 0.7580 (mtpm) REVERT: A 877 PHE cc_start: 0.7712 (m-10) cc_final: 0.6711 (m-80) REVERT: A 930 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7258 (mm-30) REVERT: A 986 LEU cc_start: 0.8142 (mm) cc_final: 0.7580 (mp) REVERT: A 987 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7370 (mm-30) REVERT: A 1001 LYS cc_start: 0.7767 (mmtp) cc_final: 0.7387 (mtmm) REVERT: A 1046 LYS cc_start: 0.8445 (ttmt) cc_final: 0.7987 (mtpp) REVERT: A 1047 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: A 1052 LYS cc_start: 0.8429 (tttp) cc_final: 0.8021 (mtpp) REVERT: B 528 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7687 (mm110) REVERT: B 544 LEU cc_start: 0.7925 (mt) cc_final: 0.7720 (mm) REVERT: B 575 VAL cc_start: 0.8829 (p) cc_final: 0.8524 (m) REVERT: B 593 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8272 (tttm) REVERT: B 594 GLU cc_start: 0.7992 (tp30) cc_final: 0.7610 (mm-30) REVERT: B 628 GLU cc_start: 0.8012 (tt0) cc_final: 0.7569 (tm-30) REVERT: B 634 MET cc_start: 0.8702 (tpt) cc_final: 0.8444 (tpt) REVERT: B 642 MET cc_start: 0.7386 (mtp) cc_final: 0.7124 (mtm) REVERT: B 687 ASN cc_start: 0.8476 (m-40) cc_final: 0.7823 (m110) REVERT: B 693 ASN cc_start: 0.8075 (m-40) cc_final: 0.7793 (t0) REVERT: B 699 ASN cc_start: 0.8037 (m-40) cc_final: 0.7724 (m110) REVERT: B 704 LYS cc_start: 0.7835 (mttt) cc_final: 0.7084 (mmtp) REVERT: B 721 MET cc_start: 0.7577 (ttm) cc_final: 0.7143 (tpt) REVERT: B 727 CYS cc_start: 0.8427 (t) cc_final: 0.7931 (m) REVERT: B 808 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6844 (mt-10) REVERT: B 864 GLU cc_start: 0.8109 (tt0) cc_final: 0.7421 (mm-30) REVERT: B 868 LYS cc_start: 0.8131 (mttm) cc_final: 0.7693 (mtpm) REVERT: B 972 SER cc_start: 0.8344 (t) cc_final: 0.8138 (p) REVERT: B 1001 LYS cc_start: 0.7790 (mmtp) cc_final: 0.7494 (mtmm) REVERT: B 1052 LYS cc_start: 0.8331 (ttmt) cc_final: 0.8048 (ttmm) REVERT: C 481 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.7244 (m-70) REVERT: C 528 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7656 (mm-40) REVERT: C 584 LEU cc_start: 0.8909 (tm) cc_final: 0.8678 (tt) REVERT: C 606 ASP cc_start: 0.7824 (m-30) cc_final: 0.6965 (p0) REVERT: C 628 GLU cc_start: 0.7843 (tt0) cc_final: 0.7394 (tm-30) REVERT: C 635 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7033 (tttp) REVERT: C 639 ASP cc_start: 0.8233 (m-30) cc_final: 0.8031 (m-30) REVERT: C 689 MET cc_start: 0.8738 (mtt) cc_final: 0.8488 (mtt) REVERT: C 693 ASN cc_start: 0.7938 (m-40) cc_final: 0.7732 (t0) REVERT: C 720 MET cc_start: 0.7489 (mmm) cc_final: 0.7003 (mmp) REVERT: C 721 MET cc_start: 0.7510 (ttm) cc_final: 0.6986 (tpp) REVERT: C 727 CYS cc_start: 0.8195 (t) cc_final: 0.7654 (m) REVERT: C 731 ILE cc_start: 0.8816 (mt) cc_final: 0.8572 (mm) REVERT: C 778 PHE cc_start: 0.7711 (t80) cc_final: 0.7451 (t80) REVERT: C 808 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7029 (mt-10) REVERT: C 853 PHE cc_start: 0.8809 (m-80) cc_final: 0.8564 (m-80) REVERT: C 864 GLU cc_start: 0.8010 (tt0) cc_final: 0.7423 (tp30) REVERT: C 868 LYS cc_start: 0.7990 (mttm) cc_final: 0.7537 (mtmp) REVERT: C 972 SER cc_start: 0.8356 (t) cc_final: 0.7977 (p) REVERT: C 987 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7260 (mm-30) REVERT: C 1001 LYS cc_start: 0.7891 (mmtp) cc_final: 0.7500 (mtmm) REVERT: C 1046 LYS cc_start: 0.8323 (ttmt) cc_final: 0.7928 (mtpp) REVERT: C 1048 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7664 (ttpp) REVERT: C 1050 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7990 (ttt-90) REVERT: D 575 VAL cc_start: 0.8717 (p) cc_final: 0.8454 (m) REVERT: D 593 LYS cc_start: 0.8660 (ttpt) cc_final: 0.8446 (tttm) REVERT: D 606 ASP cc_start: 0.8015 (m-30) cc_final: 0.6894 (p0) REVERT: D 628 GLU cc_start: 0.7988 (tt0) cc_final: 0.7421 (tm-30) REVERT: D 693 ASN cc_start: 0.7933 (m-40) cc_final: 0.7662 (t0) REVERT: D 699 ASN cc_start: 0.7985 (m-40) cc_final: 0.7466 (m-40) REVERT: D 704 LYS cc_start: 0.7722 (mttt) cc_final: 0.6717 (mmpt) REVERT: D 720 MET cc_start: 0.7641 (mmm) cc_final: 0.6940 (mmp) REVERT: D 727 CYS cc_start: 0.8135 (t) cc_final: 0.7810 (m) REVERT: D 852 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7118 (mmt90) REVERT: D 853 PHE cc_start: 0.8541 (m-80) cc_final: 0.8110 (m-80) REVERT: D 864 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6718 (tp30) REVERT: D 868 LYS cc_start: 0.8125 (mttm) cc_final: 0.7709 (mtpm) REVERT: D 930 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7194 (mm-30) REVERT: D 972 SER cc_start: 0.8180 (t) cc_final: 0.7897 (p) REVERT: D 981 GLU cc_start: 0.8261 (tp30) cc_final: 0.7993 (tt0) REVERT: D 986 LEU cc_start: 0.7856 (mt) cc_final: 0.7410 (mp) REVERT: D 989 LYS cc_start: 0.7446 (mtmt) cc_final: 0.7212 (mttm) REVERT: D 995 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7933 (mm) REVERT: D 1001 LYS cc_start: 0.7540 (mmtp) cc_final: 0.7305 (mtmm) REVERT: D 1004 ILE cc_start: 0.8095 (mp) cc_final: 0.7655 (mt) REVERT: D 1052 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8116 (ttmm) outliers start: 57 outliers final: 29 residues processed: 486 average time/residue: 1.0694 time to fit residues: 595.6279 Evaluate side-chains 480 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 444 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 589 HIS Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 589 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Chi-restraints excluded: chain D residue 995 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 195 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 691 GLN ** C 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 845 ASN C1047 GLN D 664 GLN D 687 ASN ** D 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.151755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.123011 restraints weight = 57238.188| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.87 r_work: 0.3106 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18244 Z= 0.151 Angle : 0.523 5.695 24712 Z= 0.268 Chirality : 0.037 0.162 2888 Planarity : 0.004 0.059 3020 Dihedral : 4.081 32.607 2406 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.63 % Allowed : 19.73 % Favored : 77.63 % 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: 1.48 (0.18), residues: 2188 helix: 1.34 (0.13), residues: 1652 sheet: -1.23 (0.67), residues: 48 loop : 0.22 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 464 TYR 0.014 0.001 TYR C 842 PHE 0.011 0.001 PHE C 877 TRP 0.010 0.001 TRP C 711 HIS 0.004 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00348 (18244) covalent geometry : angle 0.52262 (24712) hydrogen bonds : bond 0.04269 ( 1108) hydrogen bonds : angle 4.15398 ( 3258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 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 502 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 451 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8236 (mm) REVERT: A 528 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7573 (mm-40) REVERT: A 591 LYS cc_start: 0.8648 (mttt) cc_final: 0.8336 (mttm) REVERT: A 606 ASP cc_start: 0.8046 (m-30) cc_final: 0.7079 (p0) REVERT: A 628 GLU cc_start: 0.8032 (tt0) cc_final: 0.7559 (tm-30) REVERT: A 693 ASN cc_start: 0.8004 (m-40) cc_final: 0.7600 (t0) REVERT: A 699 ASN cc_start: 0.8193 (m-40) cc_final: 0.7665 (m110) REVERT: A 704 LYS cc_start: 0.7856 (mttt) cc_final: 0.7227 (mttm) REVERT: A 720 MET cc_start: 0.7618 (mmm) cc_final: 0.7147 (mmp) REVERT: A 721 MET cc_start: 0.7493 (ttm) cc_final: 0.7027 (tpt) REVERT: A 731 ILE cc_start: 0.8705 (mt) cc_final: 0.8442 (mm) REVERT: A 739 ASN cc_start: 0.8315 (m-40) cc_final: 0.8057 (m-40) REVERT: A 808 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6783 (mt-10) REVERT: A 864 GLU cc_start: 0.7879 (tt0) cc_final: 0.7522 (tp30) REVERT: A 868 LYS cc_start: 0.7979 (mttm) cc_final: 0.7573 (mtpm) REVERT: A 877 PHE cc_start: 0.7771 (m-10) cc_final: 0.6762 (m-80) REVERT: A 930 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7202 (mm-30) REVERT: A 986 LEU cc_start: 0.8094 (mm) cc_final: 0.7500 (mp) REVERT: A 987 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7450 (mm-30) REVERT: A 1001 LYS cc_start: 0.7787 (mmtp) cc_final: 0.7375 (mtmm) REVERT: A 1046 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8052 (mtpp) REVERT: A 1047 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: A 1052 LYS cc_start: 0.8419 (tttp) cc_final: 0.8031 (mtpp) REVERT: B 528 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7707 (mm110) REVERT: B 544 LEU cc_start: 0.7959 (mt) cc_final: 0.7747 (mm) REVERT: B 575 VAL cc_start: 0.8875 (p) cc_final: 0.8590 (m) REVERT: B 584 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8802 (tt) REVERT: B 593 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8254 (tttm) REVERT: B 594 GLU cc_start: 0.7983 (tp30) cc_final: 0.7626 (mm-30) REVERT: B 628 GLU cc_start: 0.8070 (tt0) cc_final: 0.7603 (tm-30) REVERT: B 634 MET cc_start: 0.8725 (tpt) cc_final: 0.8482 (tpt) REVERT: B 639 ASP cc_start: 0.8173 (m-30) cc_final: 0.7961 (m-30) REVERT: B 642 MET cc_start: 0.7337 (mtp) cc_final: 0.7099 (mtm) REVERT: B 687 ASN cc_start: 0.8509 (m-40) cc_final: 0.7855 (m110) REVERT: B 693 ASN cc_start: 0.8049 (m-40) cc_final: 0.7769 (t0) REVERT: B 699 ASN cc_start: 0.8040 (m-40) cc_final: 0.7579 (m110) REVERT: B 704 LYS cc_start: 0.7832 (mttt) cc_final: 0.7079 (mmtm) REVERT: B 721 MET cc_start: 0.7602 (ttm) cc_final: 0.7157 (tpt) REVERT: B 727 CYS cc_start: 0.8447 (t) cc_final: 0.7867 (m) REVERT: B 808 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6876 (mt-10) REVERT: B 842 TYR cc_start: 0.8698 (m-80) cc_final: 0.8455 (m-80) REVERT: B 864 GLU cc_start: 0.8155 (tt0) cc_final: 0.7504 (tp30) REVERT: B 868 LYS cc_start: 0.8150 (mttm) cc_final: 0.7742 (mtpm) REVERT: B 972 SER cc_start: 0.8394 (t) cc_final: 0.8172 (p) REVERT: B 1001 LYS cc_start: 0.7752 (mmtp) cc_final: 0.7453 (mtmm) REVERT: B 1047 GLN cc_start: 0.7738 (tt0) cc_final: 0.7493 (mt0) REVERT: B 1052 LYS cc_start: 0.8312 (ttmt) cc_final: 0.8035 (tttp) REVERT: C 481 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.7255 (m-70) REVERT: C 528 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7755 (mm-40) REVERT: C 584 LEU cc_start: 0.8913 (tm) cc_final: 0.8694 (tt) REVERT: C 606 ASP cc_start: 0.7918 (m-30) cc_final: 0.7015 (p0) REVERT: C 628 GLU cc_start: 0.7727 (tt0) cc_final: 0.7293 (tm-30) REVERT: C 639 ASP cc_start: 0.8249 (m-30) cc_final: 0.8041 (m-30) REVERT: C 689 MET cc_start: 0.8747 (mtt) cc_final: 0.8509 (mtt) REVERT: C 693 ASN cc_start: 0.7943 (m-40) cc_final: 0.7728 (t0) REVERT: C 720 MET cc_start: 0.7617 (mmm) cc_final: 0.7114 (mmp) REVERT: C 721 MET cc_start: 0.7582 (ttm) cc_final: 0.7038 (tpp) REVERT: C 727 CYS cc_start: 0.8290 (t) cc_final: 0.7728 (m) REVERT: C 731 ILE cc_start: 0.8843 (mt) cc_final: 0.8622 (mm) REVERT: C 778 PHE cc_start: 0.7653 (t80) cc_final: 0.7427 (t80) REVERT: C 853 PHE cc_start: 0.8794 (m-80) cc_final: 0.8563 (m-80) REVERT: C 864 GLU cc_start: 0.8001 (tt0) cc_final: 0.7441 (tp30) REVERT: C 868 LYS cc_start: 0.8008 (mttm) cc_final: 0.7568 (mtmp) REVERT: C 920 GLU cc_start: 0.7865 (tt0) cc_final: 0.7389 (tm-30) REVERT: C 930 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 972 SER cc_start: 0.8385 (t) cc_final: 0.8004 (p) REVERT: C 987 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7365 (mm-30) REVERT: C 1001 LYS cc_start: 0.7841 (mmtp) cc_final: 0.7470 (mtmm) REVERT: C 1046 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7870 (mtpp) REVERT: C 1047 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: C 1048 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7752 (ttpp) REVERT: C 1050 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8031 (ttt-90) REVERT: D 575 VAL cc_start: 0.8734 (p) cc_final: 0.8482 (m) REVERT: D 579 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: D 593 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8493 (tttm) REVERT: D 606 ASP cc_start: 0.8013 (m-30) cc_final: 0.6910 (p0) REVERT: D 628 GLU cc_start: 0.8052 (tt0) cc_final: 0.7484 (tm-30) REVERT: D 693 ASN cc_start: 0.7918 (m-40) cc_final: 0.7679 (t0) REVERT: D 699 ASN cc_start: 0.7992 (m-40) cc_final: 0.7469 (m-40) REVERT: D 704 LYS cc_start: 0.7752 (mttt) cc_final: 0.6769 (mmpt) REVERT: D 720 MET cc_start: 0.7645 (mmm) cc_final: 0.6942 (mmp) REVERT: D 727 CYS cc_start: 0.8181 (t) cc_final: 0.7844 (m) REVERT: D 852 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7428 (mmt90) REVERT: D 853 PHE cc_start: 0.8540 (m-80) cc_final: 0.8145 (m-80) REVERT: D 864 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6716 (tp30) REVERT: D 868 LYS cc_start: 0.8181 (mttm) cc_final: 0.7801 (mtpm) REVERT: D 930 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7348 (mm-30) REVERT: D 966 ASP cc_start: 0.7606 (m-30) cc_final: 0.7385 (m-30) REVERT: D 972 SER cc_start: 0.8261 (t) cc_final: 0.8006 (p) REVERT: D 981 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: D 986 LEU cc_start: 0.7930 (mt) cc_final: 0.7519 (mp) REVERT: D 987 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7300 (mm-30) REVERT: D 989 LYS cc_start: 0.7350 (mtmt) cc_final: 0.7109 (mttm) REVERT: D 1001 LYS cc_start: 0.7609 (mmtp) cc_final: 0.7355 (mtmm) REVERT: D 1004 ILE cc_start: 0.8125 (mp) cc_final: 0.7685 (mt) REVERT: D 1052 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8140 (ttmm) outliers start: 51 outliers final: 26 residues processed: 483 average time/residue: 1.0284 time to fit residues: 573.3007 Evaluate side-chains 474 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 438 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 589 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 1047 GLN Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 579 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 182 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 218 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 700 HIS ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN D 687 ASN D 700 HIS ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.152887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.125067 restraints weight = 57232.318| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.79 r_work: 0.3121 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18244 Z= 0.140 Angle : 0.516 7.625 24712 Z= 0.263 Chirality : 0.037 0.157 2888 Planarity : 0.004 0.063 3020 Dihedral : 3.900 22.287 2404 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.69 % Allowed : 20.35 % Favored : 76.96 % 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: 1.60 (0.18), residues: 2188 helix: 1.47 (0.13), residues: 1656 sheet: -1.21 (0.68), residues: 48 loop : 0.13 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 464 TYR 0.017 0.001 TYR C 842 PHE 0.012 0.001 PHE C 877 TRP 0.009 0.001 TRP C 711 HIS 0.004 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00323 (18244) covalent geometry : angle 0.51593 (24712) hydrogen bonds : bond 0.04137 ( 1108) hydrogen bonds : angle 4.09139 ( 3258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 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 495 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 443 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8261 (mm) REVERT: A 591 LYS cc_start: 0.8664 (mttt) cc_final: 0.8355 (mttm) REVERT: A 606 ASP cc_start: 0.8032 (m-30) cc_final: 0.7097 (p0) REVERT: A 628 GLU cc_start: 0.8011 (tt0) cc_final: 0.7586 (tm-30) REVERT: A 693 ASN cc_start: 0.8010 (m-40) cc_final: 0.7619 (t0) REVERT: A 699 ASN cc_start: 0.8188 (m-40) cc_final: 0.7680 (m110) REVERT: A 704 LYS cc_start: 0.7888 (mttt) cc_final: 0.6891 (mmpt) REVERT: A 720 MET cc_start: 0.7644 (mmm) cc_final: 0.7141 (mmp) REVERT: A 721 MET cc_start: 0.7516 (ttm) cc_final: 0.7064 (tpt) REVERT: A 731 ILE cc_start: 0.8683 (mt) cc_final: 0.8419 (mm) REVERT: A 808 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6773 (mt-10) REVERT: A 864 GLU cc_start: 0.7869 (tt0) cc_final: 0.7559 (tp30) REVERT: A 868 LYS cc_start: 0.7970 (mttm) cc_final: 0.7572 (mtpm) REVERT: A 877 PHE cc_start: 0.7773 (m-10) cc_final: 0.6703 (m-80) REVERT: A 930 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7181 (mm-30) REVERT: A 986 LEU cc_start: 0.8188 (mm) cc_final: 0.7579 (mp) REVERT: A 987 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7383 (mm-30) REVERT: A 1001 LYS cc_start: 0.7785 (mmtp) cc_final: 0.7407 (mtmm) REVERT: A 1046 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8098 (mtpp) REVERT: A 1052 LYS cc_start: 0.8428 (tttp) cc_final: 0.8056 (mtpp) REVERT: B 528 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7703 (mm110) REVERT: B 544 LEU cc_start: 0.7920 (mt) cc_final: 0.7707 (mm) REVERT: B 575 VAL cc_start: 0.8868 (p) cc_final: 0.8590 (m) REVERT: B 593 LYS cc_start: 0.8526 (ttpt) cc_final: 0.8299 (tttm) REVERT: B 628 GLU cc_start: 0.8030 (tt0) cc_final: 0.7592 (tm-30) REVERT: B 634 MET cc_start: 0.8751 (tpt) cc_final: 0.8522 (tpt) REVERT: B 642 MET cc_start: 0.7325 (mtp) cc_final: 0.7013 (mtm) REVERT: B 687 ASN cc_start: 0.8606 (m-40) cc_final: 0.7910 (m110) REVERT: B 693 ASN cc_start: 0.8060 (m-40) cc_final: 0.7787 (t0) REVERT: B 699 ASN cc_start: 0.8049 (m-40) cc_final: 0.7610 (m110) REVERT: B 704 LYS cc_start: 0.7859 (mttt) cc_final: 0.7121 (mmtm) REVERT: B 721 MET cc_start: 0.7576 (ttm) cc_final: 0.7194 (tpt) REVERT: B 727 CYS cc_start: 0.8439 (t) cc_final: 0.7891 (m) REVERT: B 842 TYR cc_start: 0.8680 (m-80) cc_final: 0.8453 (m-80) REVERT: B 864 GLU cc_start: 0.8173 (tt0) cc_final: 0.7578 (tp30) REVERT: B 868 LYS cc_start: 0.8196 (mttm) cc_final: 0.7789 (mtpm) REVERT: B 972 SER cc_start: 0.8384 (t) cc_final: 0.8148 (p) REVERT: B 1001 LYS cc_start: 0.7764 (mmtp) cc_final: 0.7476 (mtmm) REVERT: B 1046 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7861 (mtpp) REVERT: B 1052 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8060 (ttmm) REVERT: C 481 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.7279 (m-70) REVERT: C 528 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7755 (mm-40) REVERT: C 584 LEU cc_start: 0.8890 (tm) cc_final: 0.8635 (tt) REVERT: C 606 ASP cc_start: 0.7905 (m-30) cc_final: 0.7005 (p0) REVERT: C 628 GLU cc_start: 0.7795 (tt0) cc_final: 0.7321 (tm-30) REVERT: C 639 ASP cc_start: 0.8249 (m-30) cc_final: 0.8047 (m-30) REVERT: C 689 MET cc_start: 0.8731 (mtt) cc_final: 0.8516 (mtt) REVERT: C 720 MET cc_start: 0.7592 (mmm) cc_final: 0.7086 (mmp) REVERT: C 721 MET cc_start: 0.7574 (ttm) cc_final: 0.7055 (tpp) REVERT: C 727 CYS cc_start: 0.8270 (t) cc_final: 0.7722 (m) REVERT: C 731 ILE cc_start: 0.8852 (mt) cc_final: 0.8643 (mm) REVERT: C 778 PHE cc_start: 0.7671 (t80) cc_final: 0.7425 (t80) REVERT: C 853 PHE cc_start: 0.8798 (m-80) cc_final: 0.8528 (m-80) REVERT: C 864 GLU cc_start: 0.8025 (tt0) cc_final: 0.7512 (tp30) REVERT: C 868 LYS cc_start: 0.7993 (mttm) cc_final: 0.7563 (mtmp) REVERT: C 920 GLU cc_start: 0.7865 (tt0) cc_final: 0.7404 (tm-30) REVERT: C 930 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7592 (mt-10) REVERT: C 972 SER cc_start: 0.8407 (t) cc_final: 0.8038 (p) REVERT: C 987 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7276 (mm-30) REVERT: C 1001 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7474 (mtmm) REVERT: C 1046 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7687 (mtpp) REVERT: C 1048 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7677 (ttpp) REVERT: C 1050 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8044 (ttt-90) REVERT: D 575 VAL cc_start: 0.8710 (p) cc_final: 0.8464 (m) REVERT: D 579 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7955 (mm110) REVERT: D 593 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8537 (tttm) REVERT: D 606 ASP cc_start: 0.7993 (m-30) cc_final: 0.6933 (p0) REVERT: D 628 GLU cc_start: 0.8012 (tt0) cc_final: 0.7496 (tm-30) REVERT: D 693 ASN cc_start: 0.7927 (m-40) cc_final: 0.7711 (t0) REVERT: D 699 ASN cc_start: 0.7946 (m-40) cc_final: 0.7457 (m-40) REVERT: D 704 LYS cc_start: 0.7825 (mttt) cc_final: 0.6817 (mmpt) REVERT: D 720 MET cc_start: 0.7614 (mmm) cc_final: 0.6910 (mmp) REVERT: D 727 CYS cc_start: 0.8192 (t) cc_final: 0.7898 (m) REVERT: D 852 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7440 (mmt90) REVERT: D 853 PHE cc_start: 0.8536 (m-80) cc_final: 0.8204 (m-80) REVERT: D 864 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6781 (tp30) REVERT: D 868 LYS cc_start: 0.8184 (mttm) cc_final: 0.7806 (mtpm) REVERT: D 930 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7421 (mm-30) REVERT: D 966 ASP cc_start: 0.7729 (m-30) cc_final: 0.7501 (m-30) REVERT: D 972 SER cc_start: 0.8270 (t) cc_final: 0.8036 (p) REVERT: D 981 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: D 986 LEU cc_start: 0.7952 (mt) cc_final: 0.7571 (mp) REVERT: D 989 LYS cc_start: 0.7308 (mtmt) cc_final: 0.7086 (mttm) REVERT: D 1001 LYS cc_start: 0.7618 (mmtp) cc_final: 0.7364 (mtmm) REVERT: D 1004 ILE cc_start: 0.8119 (mp) cc_final: 0.7688 (mt) REVERT: D 1052 LYS cc_start: 0.8431 (ttmt) cc_final: 0.8155 (ttmm) outliers start: 52 outliers final: 29 residues processed: 475 average time/residue: 1.0529 time to fit residues: 575.4039 Evaluate side-chains 470 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 434 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 872 ARG Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 579 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 632 GLU Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 103 optimal weight: 0.0050 chunk 187 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 119 optimal weight: 0.0050 overall best weight: 0.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN B1047 GLN C 691 GLN D 664 GLN D 687 ASN D1047 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.152744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.123883 restraints weight = 57457.414| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.89 r_work: 0.3122 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18244 Z= 0.121 Angle : 0.506 8.801 24712 Z= 0.257 Chirality : 0.036 0.152 2888 Planarity : 0.004 0.070 3020 Dihedral : 3.788 21.789 2404 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.58 % Allowed : 20.51 % Favored : 76.91 % 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: 1.84 (0.18), residues: 2188 helix: 1.62 (0.13), residues: 1664 sheet: -1.18 (0.67), residues: 48 loop : 0.23 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 464 TYR 0.016 0.001 TYR C 842 PHE 0.011 0.001 PHE C 877 TRP 0.009 0.001 TRP A 711 HIS 0.004 0.001 HIS C 700 Details of bonding type rmsd covalent geometry : bond 0.00278 (18244) covalent geometry : angle 0.50603 (24712) hydrogen bonds : bond 0.03925 ( 1108) hydrogen bonds : angle 4.01729 ( 3258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 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 499 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 449 time to evaluate : 0.988 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 591 LYS cc_start: 0.8655 (mttt) cc_final: 0.8356 (mttm) REVERT: A 606 ASP cc_start: 0.8044 (m-30) cc_final: 0.7066 (p0) REVERT: A 628 GLU cc_start: 0.8034 (tt0) cc_final: 0.7573 (tm-30) REVERT: A 632 GLU cc_start: 0.7528 (mp0) cc_final: 0.7289 (mp0) REVERT: A 693 ASN cc_start: 0.7995 (m-40) cc_final: 0.7603 (t0) REVERT: A 699 ASN cc_start: 0.8167 (m-40) cc_final: 0.7694 (m110) REVERT: A 704 LYS cc_start: 0.7849 (mttt) cc_final: 0.6850 (mmpt) REVERT: A 720 MET cc_start: 0.7628 (mmm) cc_final: 0.7119 (mmp) REVERT: A 721 MET cc_start: 0.7495 (ttm) cc_final: 0.7008 (tpt) REVERT: A 731 ILE cc_start: 0.8678 (mt) cc_final: 0.8428 (mm) REVERT: A 739 ASN cc_start: 0.8327 (m-40) cc_final: 0.8039 (m-40) REVERT: A 808 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6802 (mt-10) REVERT: A 864 GLU cc_start: 0.7889 (tt0) cc_final: 0.7524 (tp30) REVERT: A 868 LYS cc_start: 0.7949 (mttm) cc_final: 0.7525 (mtpm) REVERT: A 877 PHE cc_start: 0.7729 (m-10) cc_final: 0.6711 (m-80) REVERT: A 930 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7149 (mm-30) REVERT: A 986 LEU cc_start: 0.8184 (mm) cc_final: 0.7568 (mp) REVERT: A 987 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7394 (mm-30) REVERT: A 1001 LYS cc_start: 0.7742 (mmtp) cc_final: 0.7359 (mtmm) REVERT: A 1046 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8048 (mtpp) REVERT: A 1052 LYS cc_start: 0.8313 (tttp) cc_final: 0.7910 (mtpp) REVERT: B 528 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7689 (mt0) REVERT: B 544 LEU cc_start: 0.7959 (mt) cc_final: 0.7706 (mm) REVERT: B 575 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8593 (m) REVERT: B 593 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8233 (tttm) REVERT: B 594 GLU cc_start: 0.8006 (tp30) cc_final: 0.7658 (mm-30) REVERT: B 628 GLU cc_start: 0.8028 (tt0) cc_final: 0.7561 (tm-30) REVERT: B 642 MET cc_start: 0.7320 (mtp) cc_final: 0.7032 (mtm) REVERT: B 687 ASN cc_start: 0.8606 (m-40) cc_final: 0.7910 (m110) REVERT: B 693 ASN cc_start: 0.8066 (m-40) cc_final: 0.7790 (t0) REVERT: B 699 ASN cc_start: 0.8028 (m-40) cc_final: 0.7586 (m110) REVERT: B 704 LYS cc_start: 0.7876 (mttt) cc_final: 0.7091 (mmtm) REVERT: B 721 MET cc_start: 0.7583 (ttm) cc_final: 0.7160 (tpt) REVERT: B 727 CYS cc_start: 0.8419 (t) cc_final: 0.7905 (m) REVERT: B 842 TYR cc_start: 0.8627 (m-80) cc_final: 0.8410 (m-80) REVERT: B 864 GLU cc_start: 0.8171 (tt0) cc_final: 0.7547 (tp30) REVERT: B 868 LYS cc_start: 0.8154 (mttm) cc_final: 0.7741 (mtpm) REVERT: B 972 SER cc_start: 0.8364 (t) cc_final: 0.8129 (p) REVERT: B 981 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7693 (tp30) REVERT: B 1001 LYS cc_start: 0.7760 (mmtp) cc_final: 0.7445 (mtmm) REVERT: B 1046 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7821 (mtpp) REVERT: B 1052 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8011 (ttmm) REVERT: C 481 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.7277 (m-70) REVERT: C 528 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7768 (mt0) REVERT: C 584 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8632 (tt) REVERT: C 597 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8090 (mp) REVERT: C 606 ASP cc_start: 0.7917 (m-30) cc_final: 0.6986 (p0) REVERT: C 628 GLU cc_start: 0.7772 (tt0) cc_final: 0.7288 (tm-30) REVERT: C 689 MET cc_start: 0.8712 (mtt) cc_final: 0.8500 (mtt) REVERT: C 699 ASN cc_start: 0.8101 (m110) cc_final: 0.7839 (m110) REVERT: C 720 MET cc_start: 0.7602 (mmm) cc_final: 0.7068 (mmp) REVERT: C 721 MET cc_start: 0.7561 (ttm) cc_final: 0.7015 (tpp) REVERT: C 727 CYS cc_start: 0.8267 (t) cc_final: 0.7689 (m) REVERT: C 778 PHE cc_start: 0.7637 (t80) cc_final: 0.7404 (t80) REVERT: C 853 PHE cc_start: 0.8753 (m-80) cc_final: 0.8509 (m-80) REVERT: C 864 GLU cc_start: 0.8015 (tt0) cc_final: 0.7448 (tp30) REVERT: C 868 LYS cc_start: 0.7998 (mttm) cc_final: 0.7557 (mtmp) REVERT: C 920 GLU cc_start: 0.7886 (tt0) cc_final: 0.7459 (tt0) REVERT: C 972 SER cc_start: 0.8394 (t) cc_final: 0.8014 (p) REVERT: C 984 THR cc_start: 0.8766 (p) cc_final: 0.8555 (m) REVERT: C 987 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7172 (mm-30) REVERT: C 1001 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7502 (mtmm) REVERT: C 1046 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7827 (mtpp) REVERT: C 1048 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7641 (ttpp) REVERT: C 1050 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8034 (ttt-90) REVERT: D 575 VAL cc_start: 0.8700 (p) cc_final: 0.8445 (m) REVERT: D 579 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: D 593 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8483 (tttm) REVERT: D 606 ASP cc_start: 0.7993 (m-30) cc_final: 0.6895 (p0) REVERT: D 628 GLU cc_start: 0.8014 (tt0) cc_final: 0.7447 (tm-30) REVERT: D 632 GLU cc_start: 0.7791 (mp0) cc_final: 0.7433 (mp0) REVERT: D 693 ASN cc_start: 0.7937 (m-40) cc_final: 0.7712 (t0) REVERT: D 699 ASN cc_start: 0.7914 (m-40) cc_final: 0.7462 (m-40) REVERT: D 704 LYS cc_start: 0.7810 (mttt) cc_final: 0.6762 (mmpt) REVERT: D 720 MET cc_start: 0.7657 (mmm) cc_final: 0.6899 (mmp) REVERT: D 727 CYS cc_start: 0.8183 (t) cc_final: 0.7880 (m) REVERT: D 852 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7464 (mmt-90) REVERT: D 853 PHE cc_start: 0.8490 (m-80) cc_final: 0.8130 (m-80) REVERT: D 864 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: D 868 LYS cc_start: 0.8121 (mttm) cc_final: 0.7748 (mtpm) REVERT: D 930 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7473 (mm-30) REVERT: D 966 ASP cc_start: 0.7641 (m-30) cc_final: 0.7414 (m-30) REVERT: D 972 SER cc_start: 0.8253 (t) cc_final: 0.8009 (p) REVERT: D 981 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: D 986 LEU cc_start: 0.7922 (mt) cc_final: 0.7588 (mp) REVERT: D 989 LYS cc_start: 0.7308 (mtmt) cc_final: 0.7066 (mttm) REVERT: D 1001 LYS cc_start: 0.7624 (mmtp) cc_final: 0.7330 (mtmm) REVERT: D 1004 ILE cc_start: 0.8100 (mp) cc_final: 0.7686 (mt) REVERT: D 1052 LYS cc_start: 0.8408 (ttmt) cc_final: 0.8118 (ttmm) outliers start: 50 outliers final: 26 residues processed: 478 average time/residue: 1.0598 time to fit residues: 584.2685 Evaluate side-chains 472 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 437 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 1047 GLN Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 589 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 579 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 212 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN D 687 ASN ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.154821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.127553 restraints weight = 56135.854| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.78 r_work: 0.3145 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18244 Z= 0.136 Angle : 0.522 8.899 24712 Z= 0.265 Chirality : 0.036 0.154 2888 Planarity : 0.004 0.077 3020 Dihedral : 3.783 21.926 2404 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.32 % Allowed : 21.33 % Favored : 76.34 % 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: 1.88 (0.18), residues: 2188 helix: 1.66 (0.13), residues: 1664 sheet: -1.13 (0.68), residues: 48 loop : 0.23 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 464 TYR 0.016 0.001 TYR C 842 PHE 0.012 0.001 PHE C 877 TRP 0.019 0.001 TRP A 711 HIS 0.004 0.001 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.00316 (18244) covalent geometry : angle 0.52156 (24712) hydrogen bonds : bond 0.03984 ( 1108) hydrogen bonds : angle 4.02185 ( 3258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 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 483 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 438 time to evaluate : 0.698 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 569 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8427 (m) REVERT: A 591 LYS cc_start: 0.8706 (mttt) cc_final: 0.8434 (mttm) REVERT: A 606 ASP cc_start: 0.8042 (m-30) cc_final: 0.7082 (p0) REVERT: A 628 GLU cc_start: 0.8034 (tt0) cc_final: 0.7637 (tm-30) REVERT: A 632 GLU cc_start: 0.7560 (mp0) cc_final: 0.7308 (mp0) REVERT: A 639 ASP cc_start: 0.8162 (m-30) cc_final: 0.7922 (m-30) REVERT: A 693 ASN cc_start: 0.7960 (m-40) cc_final: 0.7594 (t0) REVERT: A 699 ASN cc_start: 0.8216 (m-40) cc_final: 0.7712 (m110) REVERT: A 704 LYS cc_start: 0.7901 (mttt) cc_final: 0.6910 (mmpt) REVERT: A 720 MET cc_start: 0.7665 (mmm) cc_final: 0.7116 (mmp) REVERT: A 721 MET cc_start: 0.7562 (ttm) cc_final: 0.7107 (tpt) REVERT: A 731 ILE cc_start: 0.8716 (mt) cc_final: 0.8502 (mm) REVERT: A 808 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6776 (mt-10) REVERT: A 864 GLU cc_start: 0.7851 (tt0) cc_final: 0.7548 (tp30) REVERT: A 868 LYS cc_start: 0.7977 (mttm) cc_final: 0.7547 (mtpm) REVERT: A 877 PHE cc_start: 0.7735 (m-10) cc_final: 0.6685 (m-80) REVERT: A 930 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7247 (mm-30) REVERT: A 986 LEU cc_start: 0.8151 (mm) cc_final: 0.7537 (mp) REVERT: A 987 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7360 (mm-30) REVERT: A 1001 LYS cc_start: 0.7678 (mmtp) cc_final: 0.7334 (mtmm) REVERT: A 1046 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7983 (mtpp) REVERT: A 1052 LYS cc_start: 0.8340 (tttp) cc_final: 0.7944 (mtpp) REVERT: B 528 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7723 (mt0) REVERT: B 575 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8670 (m) REVERT: B 593 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8331 (tttm) REVERT: B 628 GLU cc_start: 0.7996 (tt0) cc_final: 0.7584 (tm-30) REVERT: B 635 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7503 (tmmm) REVERT: B 642 MET cc_start: 0.7403 (mtp) cc_final: 0.7198 (mtm) REVERT: B 687 ASN cc_start: 0.8647 (m-40) cc_final: 0.7945 (m110) REVERT: B 693 ASN cc_start: 0.8022 (m-40) cc_final: 0.7782 (t0) REVERT: B 699 ASN cc_start: 0.8069 (m-40) cc_final: 0.7625 (m110) REVERT: B 704 LYS cc_start: 0.7912 (mttt) cc_final: 0.7147 (mmtm) REVERT: B 721 MET cc_start: 0.7698 (ttm) cc_final: 0.7323 (tpt) REVERT: B 727 CYS cc_start: 0.8477 (t) cc_final: 0.7994 (m) REVERT: B 864 GLU cc_start: 0.8205 (tt0) cc_final: 0.7515 (mm-30) REVERT: B 868 LYS cc_start: 0.8183 (mttm) cc_final: 0.7798 (mtpm) REVERT: B 972 SER cc_start: 0.8399 (t) cc_final: 0.8145 (p) REVERT: B 1001 LYS cc_start: 0.7744 (mmtp) cc_final: 0.7450 (mtmm) REVERT: B 1046 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7990 (mtpp) REVERT: B 1052 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8095 (ttmm) REVERT: C 481 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7350 (m-70) REVERT: C 528 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7723 (mt0) REVERT: C 530 MET cc_start: 0.8805 (mtm) cc_final: 0.8183 (mtp) REVERT: C 584 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8664 (tt) REVERT: C 597 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8149 (mp) REVERT: C 606 ASP cc_start: 0.7911 (m-30) cc_final: 0.7035 (p0) REVERT: C 628 GLU cc_start: 0.7734 (tt0) cc_final: 0.7316 (tm-30) REVERT: C 689 MET cc_start: 0.8648 (mtt) cc_final: 0.8437 (mtt) REVERT: C 699 ASN cc_start: 0.8032 (m110) cc_final: 0.7770 (m110) REVERT: C 720 MET cc_start: 0.7607 (mmm) cc_final: 0.7080 (mmp) REVERT: C 721 MET cc_start: 0.7474 (ttm) cc_final: 0.6973 (tpp) REVERT: C 727 CYS cc_start: 0.8229 (t) cc_final: 0.7587 (m) REVERT: C 778 PHE cc_start: 0.7652 (t80) cc_final: 0.7442 (t80) REVERT: C 853 PHE cc_start: 0.8745 (m-80) cc_final: 0.8500 (m-80) REVERT: C 864 GLU cc_start: 0.8087 (tt0) cc_final: 0.7503 (tp30) REVERT: C 868 LYS cc_start: 0.7995 (mttm) cc_final: 0.7570 (mtmp) REVERT: C 920 GLU cc_start: 0.7877 (tt0) cc_final: 0.7473 (tt0) REVERT: C 972 SER cc_start: 0.8405 (t) cc_final: 0.8043 (p) REVERT: C 984 THR cc_start: 0.8788 (p) cc_final: 0.8546 (m) REVERT: C 987 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7224 (mm-30) REVERT: C 1001 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7523 (mtmm) REVERT: C 1046 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7828 (mtpp) REVERT: C 1048 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7754 (ttpp) REVERT: C 1050 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8050 (ttt-90) REVERT: D 575 VAL cc_start: 0.8740 (p) cc_final: 0.8504 (m) REVERT: D 579 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7940 (mm110) REVERT: D 593 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8530 (tttm) REVERT: D 606 ASP cc_start: 0.8031 (m-30) cc_final: 0.6941 (p0) REVERT: D 628 GLU cc_start: 0.8000 (tt0) cc_final: 0.7525 (tm-30) REVERT: D 693 ASN cc_start: 0.7939 (m-40) cc_final: 0.7736 (t0) REVERT: D 699 ASN cc_start: 0.7931 (m-40) cc_final: 0.7509 (m-40) REVERT: D 704 LYS cc_start: 0.7874 (mttt) cc_final: 0.6849 (mmpt) REVERT: D 720 MET cc_start: 0.7695 (mmm) cc_final: 0.6921 (mmp) REVERT: D 727 CYS cc_start: 0.8161 (t) cc_final: 0.7876 (m) REVERT: D 852 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7535 (mmt-90) REVERT: D 853 PHE cc_start: 0.8507 (m-80) cc_final: 0.8145 (m-80) REVERT: D 864 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6777 (tp30) REVERT: D 868 LYS cc_start: 0.8196 (mttm) cc_final: 0.7827 (mtpm) REVERT: D 930 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7500 (mm-30) REVERT: D 966 ASP cc_start: 0.7647 (m-30) cc_final: 0.7445 (m-30) REVERT: D 972 SER cc_start: 0.8277 (t) cc_final: 0.8043 (p) REVERT: D 981 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: D 986 LEU cc_start: 0.7987 (mt) cc_final: 0.7665 (mp) REVERT: D 989 LYS cc_start: 0.7188 (mtmt) cc_final: 0.6959 (mttm) REVERT: D 1001 LYS cc_start: 0.7656 (mmtp) cc_final: 0.7351 (mtmm) REVERT: D 1004 ILE cc_start: 0.8146 (mp) cc_final: 0.7730 (mt) REVERT: D 1052 LYS cc_start: 0.8454 (ttmt) cc_final: 0.8185 (ttmm) outliers start: 45 outliers final: 24 residues processed: 467 average time/residue: 1.0838 time to fit residues: 582.0043 Evaluate side-chains 467 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 432 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 589 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 579 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 165 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 845 ASN B1047 GLN C 691 GLN D 664 GLN D 687 ASN D1047 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.152600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.125388 restraints weight = 55997.891| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.77 r_work: 0.3133 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18244 Z= 0.173 Angle : 0.551 9.239 24712 Z= 0.282 Chirality : 0.038 0.160 2888 Planarity : 0.004 0.082 3020 Dihedral : 3.916 22.478 2404 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.27 % Allowed : 21.75 % Favored : 75.98 % 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: 1.75 (0.18), residues: 2188 helix: 1.56 (0.13), residues: 1664 sheet: -1.10 (0.69), residues: 48 loop : 0.21 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 464 TYR 0.033 0.002 TYR B 842 PHE 0.014 0.001 PHE C 877 TRP 0.013 0.001 TRP A 711 HIS 0.004 0.001 HIS B 553 Details of bonding type rmsd covalent geometry : bond 0.00402 (18244) covalent geometry : angle 0.55115 (24712) hydrogen bonds : bond 0.04229 ( 1108) hydrogen bonds : angle 4.08710 ( 3258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 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 471 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 427 time to evaluate : 0.933 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 569 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8439 (m) REVERT: A 591 LYS cc_start: 0.8716 (mttt) cc_final: 0.8450 (mttm) REVERT: A 606 ASP cc_start: 0.8056 (m-30) cc_final: 0.7108 (p0) REVERT: A 628 GLU cc_start: 0.8008 (tt0) cc_final: 0.7635 (tm-30) REVERT: A 632 GLU cc_start: 0.7553 (mp0) cc_final: 0.7086 (mp0) REVERT: A 693 ASN cc_start: 0.7998 (m-40) cc_final: 0.7607 (t0) REVERT: A 699 ASN cc_start: 0.8255 (m-40) cc_final: 0.7748 (m110) REVERT: A 704 LYS cc_start: 0.7936 (mttt) cc_final: 0.6979 (mmpt) REVERT: A 720 MET cc_start: 0.7650 (mmm) cc_final: 0.7140 (mmp) REVERT: A 721 MET cc_start: 0.7600 (ttm) cc_final: 0.7140 (tpt) REVERT: A 808 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6778 (mt-10) REVERT: A 864 GLU cc_start: 0.7859 (tt0) cc_final: 0.7575 (tp30) REVERT: A 868 LYS cc_start: 0.7956 (mttm) cc_final: 0.7552 (mtpm) REVERT: A 877 PHE cc_start: 0.7676 (m-10) cc_final: 0.6622 (m-80) REVERT: A 930 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7210 (mm-30) REVERT: A 986 LEU cc_start: 0.8243 (mm) cc_final: 0.7659 (mp) REVERT: A 987 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7379 (mm-30) REVERT: A 1001 LYS cc_start: 0.7687 (mmtp) cc_final: 0.7374 (mtmm) REVERT: A 1046 LYS cc_start: 0.8472 (ttmt) cc_final: 0.8037 (mtpp) REVERT: A 1052 LYS cc_start: 0.8373 (tttp) cc_final: 0.7976 (mtpp) REVERT: B 481 HIS cc_start: 0.7167 (OUTLIER) cc_final: 0.6602 (m-70) REVERT: B 528 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7730 (mt0) REVERT: B 575 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8685 (m) REVERT: B 593 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8412 (tttm) REVERT: B 628 GLU cc_start: 0.8009 (tt0) cc_final: 0.7619 (tm-30) REVERT: B 642 MET cc_start: 0.7404 (mtp) cc_final: 0.7198 (mtm) REVERT: B 687 ASN cc_start: 0.8675 (m-40) cc_final: 0.7973 (m110) REVERT: B 693 ASN cc_start: 0.7983 (m-40) cc_final: 0.7751 (t0) REVERT: B 699 ASN cc_start: 0.8129 (m-40) cc_final: 0.7678 (m110) REVERT: B 704 LYS cc_start: 0.7949 (mttt) cc_final: 0.7206 (mmtm) REVERT: B 721 MET cc_start: 0.7730 (ttm) cc_final: 0.7286 (tpt) REVERT: B 727 CYS cc_start: 0.8473 (t) cc_final: 0.8049 (m) REVERT: B 864 GLU cc_start: 0.8235 (tt0) cc_final: 0.7621 (tp30) REVERT: B 868 LYS cc_start: 0.8185 (mttm) cc_final: 0.7797 (mtpm) REVERT: B 972 SER cc_start: 0.8413 (t) cc_final: 0.8146 (p) REVERT: B 981 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7770 (tp30) REVERT: B 1001 LYS cc_start: 0.7757 (mmtp) cc_final: 0.7464 (mtmm) REVERT: B 1046 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7782 (mtpp) REVERT: B 1052 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8128 (ttmm) REVERT: C 481 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7510 (m-70) REVERT: C 528 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7723 (mt0) REVERT: C 584 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8698 (tt) REVERT: C 597 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8182 (mp) REVERT: C 606 ASP cc_start: 0.7891 (m-30) cc_final: 0.7019 (p0) REVERT: C 628 GLU cc_start: 0.7755 (tt0) cc_final: 0.7345 (tm-30) REVERT: C 639 ASP cc_start: 0.8280 (m-30) cc_final: 0.8065 (m-30) REVERT: C 689 MET cc_start: 0.8692 (mtt) cc_final: 0.8469 (mtt) REVERT: C 704 LYS cc_start: 0.7891 (mttt) cc_final: 0.7160 (mmtt) REVERT: C 720 MET cc_start: 0.7642 (mmm) cc_final: 0.7111 (mmp) REVERT: C 721 MET cc_start: 0.7524 (ttm) cc_final: 0.7050 (tpp) REVERT: C 727 CYS cc_start: 0.8262 (t) cc_final: 0.7658 (m) REVERT: C 853 PHE cc_start: 0.8787 (m-80) cc_final: 0.8538 (m-80) REVERT: C 864 GLU cc_start: 0.8081 (tt0) cc_final: 0.7530 (tp30) REVERT: C 868 LYS cc_start: 0.7995 (mttm) cc_final: 0.7577 (mtmp) REVERT: C 972 SER cc_start: 0.8419 (t) cc_final: 0.8069 (p) REVERT: C 987 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7291 (mm-30) REVERT: C 1001 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7565 (mtmm) REVERT: C 1046 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7930 (mtpp) REVERT: C 1048 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7949 (ttpp) REVERT: C 1050 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8037 (ttt-90) REVERT: D 575 VAL cc_start: 0.8770 (p) cc_final: 0.8542 (m) REVERT: D 579 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7955 (mm110) REVERT: D 593 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8573 (tttm) REVERT: D 628 GLU cc_start: 0.8003 (tt0) cc_final: 0.7520 (tm-30) REVERT: D 632 GLU cc_start: 0.7683 (mp0) cc_final: 0.7235 (mp0) REVERT: D 699 ASN cc_start: 0.8036 (m-40) cc_final: 0.7566 (m-40) REVERT: D 704 LYS cc_start: 0.7851 (mttt) cc_final: 0.6882 (mmpt) REVERT: D 720 MET cc_start: 0.7770 (mmm) cc_final: 0.6991 (mmp) REVERT: D 727 CYS cc_start: 0.8163 (t) cc_final: 0.7894 (m) REVERT: D 852 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7480 (mmt90) REVERT: D 853 PHE cc_start: 0.8570 (m-80) cc_final: 0.8217 (m-80) REVERT: D 855 ASN cc_start: 0.7804 (p0) cc_final: 0.7513 (p0) REVERT: D 864 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6672 (tp30) REVERT: D 868 LYS cc_start: 0.8183 (mttm) cc_final: 0.7826 (mtpm) REVERT: D 930 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7553 (mm-30) REVERT: D 966 ASP cc_start: 0.7740 (m-30) cc_final: 0.7520 (m-30) REVERT: D 972 SER cc_start: 0.8288 (t) cc_final: 0.8081 (p) REVERT: D 981 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: D 986 LEU cc_start: 0.8016 (mt) cc_final: 0.7676 (mp) REVERT: D 989 LYS cc_start: 0.7186 (mtmt) cc_final: 0.6904 (mtpp) REVERT: D 1001 LYS cc_start: 0.7699 (mmtp) cc_final: 0.7399 (mtmm) REVERT: D 1004 ILE cc_start: 0.8165 (mp) cc_final: 0.7757 (mt) REVERT: D 1052 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8189 (ttmm) outliers start: 44 outliers final: 23 residues processed: 454 average time/residue: 1.0966 time to fit residues: 571.1123 Evaluate side-chains 457 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 423 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 579 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 105 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 664 GLN D 687 ASN ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.151670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.122825 restraints weight = 56855.978| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.89 r_work: 0.3111 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18244 Z= 0.144 Angle : 0.537 9.758 24712 Z= 0.274 Chirality : 0.037 0.154 2888 Planarity : 0.004 0.084 3020 Dihedral : 3.832 22.294 2404 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.81 % Allowed : 22.47 % Favored : 75.72 % 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: 2.04 (0.18), residues: 2188 helix: 1.75 (0.13), residues: 1640 sheet: -1.04 (0.70), residues: 48 loop : 0.46 (0.31), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 464 TYR 0.028 0.001 TYR B 842 PHE 0.011 0.001 PHE A 508 TRP 0.014 0.001 TRP A 711 HIS 0.004 0.001 HIS D 494 Details of bonding type rmsd covalent geometry : bond 0.00335 (18244) covalent geometry : angle 0.53667 (24712) hydrogen bonds : bond 0.04024 ( 1108) hydrogen bonds : angle 4.07630 ( 3258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 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 460 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 425 time to evaluate : 0.961 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 569 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8433 (m) REVERT: A 591 LYS cc_start: 0.8664 (mttt) cc_final: 0.8383 (mttm) REVERT: A 606 ASP cc_start: 0.8073 (m-30) cc_final: 0.7076 (p0) REVERT: A 628 GLU cc_start: 0.7989 (tt0) cc_final: 0.7551 (tm-30) REVERT: A 632 GLU cc_start: 0.7463 (mp0) cc_final: 0.7000 (mp0) REVERT: A 693 ASN cc_start: 0.8018 (m-40) cc_final: 0.7607 (t0) REVERT: A 699 ASN cc_start: 0.8161 (m-40) cc_final: 0.7642 (m110) REVERT: A 704 LYS cc_start: 0.7882 (mttt) cc_final: 0.6862 (mmpt) REVERT: A 720 MET cc_start: 0.7540 (mmm) cc_final: 0.7007 (mmp) REVERT: A 721 MET cc_start: 0.7516 (ttm) cc_final: 0.7030 (tpt) REVERT: A 808 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6771 (mt-10) REVERT: A 864 GLU cc_start: 0.7925 (tt0) cc_final: 0.7518 (tp30) REVERT: A 868 LYS cc_start: 0.7906 (mttm) cc_final: 0.7476 (mtpm) REVERT: A 877 PHE cc_start: 0.7584 (m-10) cc_final: 0.6570 (m-80) REVERT: A 924 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7783 (tp30) REVERT: A 930 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7159 (mm-30) REVERT: A 986 LEU cc_start: 0.8106 (mm) cc_final: 0.7503 (mp) REVERT: A 987 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7339 (mm-30) REVERT: A 1001 LYS cc_start: 0.7780 (mmtp) cc_final: 0.7385 (mtmm) REVERT: A 1046 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8034 (mtpp) REVERT: A 1052 LYS cc_start: 0.8306 (tttp) cc_final: 0.7901 (mtpp) REVERT: B 528 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7715 (mt0) REVERT: B 575 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8624 (m) REVERT: B 593 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8334 (tttm) REVERT: B 628 GLU cc_start: 0.8007 (tt0) cc_final: 0.7552 (tm-30) REVERT: B 634 MET cc_start: 0.8678 (tpt) cc_final: 0.8448 (tpt) REVERT: B 687 ASN cc_start: 0.8577 (m-40) cc_final: 0.7868 (m110) REVERT: B 693 ASN cc_start: 0.7993 (m-40) cc_final: 0.7737 (t0) REVERT: B 699 ASN cc_start: 0.8047 (m-40) cc_final: 0.7591 (m110) REVERT: B 704 LYS cc_start: 0.7884 (mttt) cc_final: 0.7116 (mmtm) REVERT: B 721 MET cc_start: 0.7596 (ttm) cc_final: 0.7125 (tpt) REVERT: B 727 CYS cc_start: 0.8368 (t) cc_final: 0.7967 (m) REVERT: B 864 GLU cc_start: 0.8226 (tt0) cc_final: 0.7552 (tp30) REVERT: B 868 LYS cc_start: 0.8143 (mttm) cc_final: 0.7730 (mtpm) REVERT: B 972 SER cc_start: 0.8350 (t) cc_final: 0.8076 (p) REVERT: B 981 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7804 (tp30) REVERT: B 1001 LYS cc_start: 0.7770 (mmtp) cc_final: 0.7449 (mtmm) REVERT: B 1046 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7763 (mtpp) REVERT: B 1052 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8003 (ttmm) REVERT: C 481 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7372 (m-70) REVERT: C 483 MET cc_start: 0.8745 (mmm) cc_final: 0.7682 (mtm) REVERT: C 528 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7698 (mt0) REVERT: C 530 MET cc_start: 0.8800 (mtm) cc_final: 0.8294 (mtp) REVERT: C 584 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8647 (tt) REVERT: C 597 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8045 (mp) REVERT: C 606 ASP cc_start: 0.7872 (m-30) cc_final: 0.6953 (p0) REVERT: C 628 GLU cc_start: 0.7820 (tt0) cc_final: 0.7318 (tm-30) REVERT: C 639 ASP cc_start: 0.8234 (m-30) cc_final: 0.8015 (m-30) REVERT: C 704 LYS cc_start: 0.7764 (mttt) cc_final: 0.7040 (mmtt) REVERT: C 720 MET cc_start: 0.7666 (mmm) cc_final: 0.7122 (mmp) REVERT: C 721 MET cc_start: 0.7474 (ttm) cc_final: 0.6967 (tpp) REVERT: C 727 CYS cc_start: 0.8190 (t) cc_final: 0.7568 (m) REVERT: C 853 PHE cc_start: 0.8700 (m-80) cc_final: 0.8475 (m-80) REVERT: C 864 GLU cc_start: 0.8005 (tt0) cc_final: 0.7450 (tp30) REVERT: C 868 LYS cc_start: 0.7935 (mttm) cc_final: 0.7509 (mtmp) REVERT: C 920 GLU cc_start: 0.7862 (tt0) cc_final: 0.7436 (tt0) REVERT: C 972 SER cc_start: 0.8384 (t) cc_final: 0.8037 (p) REVERT: C 987 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7241 (mm-30) REVERT: C 1001 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7544 (mtmm) REVERT: C 1042 MET cc_start: 0.6657 (ppp) cc_final: 0.6329 (pp-130) REVERT: C 1046 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7889 (mtpp) REVERT: C 1050 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7983 (ttt-90) REVERT: D 575 VAL cc_start: 0.8757 (p) cc_final: 0.8517 (m) REVERT: D 579 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7988 (mm110) REVERT: D 593 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8516 (tttm) REVERT: D 628 GLU cc_start: 0.8030 (tt0) cc_final: 0.7438 (tm-30) REVERT: D 632 GLU cc_start: 0.7646 (mp0) cc_final: 0.7259 (mp0) REVERT: D 699 ASN cc_start: 0.7958 (m-40) cc_final: 0.7485 (m-40) REVERT: D 704 LYS cc_start: 0.7773 (mttt) cc_final: 0.6760 (mmpt) REVERT: D 720 MET cc_start: 0.7672 (mmm) cc_final: 0.6860 (mmp) REVERT: D 727 CYS cc_start: 0.8079 (t) cc_final: 0.7801 (m) REVERT: D 852 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7533 (mmt-90) REVERT: D 853 PHE cc_start: 0.8487 (m-80) cc_final: 0.8120 (m-80) REVERT: D 864 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6620 (tp30) REVERT: D 868 LYS cc_start: 0.8076 (mttm) cc_final: 0.7713 (mtpm) REVERT: D 930 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7508 (mm-30) REVERT: D 966 ASP cc_start: 0.7727 (m-30) cc_final: 0.7519 (m-30) REVERT: D 972 SER cc_start: 0.8270 (t) cc_final: 0.8053 (p) REVERT: D 981 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: D 989 LYS cc_start: 0.7189 (mtmt) cc_final: 0.6976 (mtpp) REVERT: D 1001 LYS cc_start: 0.7683 (mmtp) cc_final: 0.7357 (mtmm) REVERT: D 1004 ILE cc_start: 0.8107 (mp) cc_final: 0.7697 (mt) REVERT: D 1052 LYS cc_start: 0.8391 (ttmt) cc_final: 0.8116 (ttmm) outliers start: 35 outliers final: 23 residues processed: 447 average time/residue: 1.0786 time to fit residues: 553.7570 Evaluate side-chains 453 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 420 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 582 SER Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 921 SER Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 481 HIS Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 584 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 733 MET Chi-restraints excluded: chain C residue 900 SER Chi-restraints excluded: chain C residue 921 SER Chi-restraints excluded: chain C residue 1050 ARG Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 579 GLN Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 852 ARG Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 921 SER Chi-restraints excluded: chain D residue 981 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 169 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 109 optimal weight: 0.9990 chunk 217 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 208 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 691 GLN D 664 GLN D 687 ASN D 693 ASN ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.153071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.124361 restraints weight = 56928.534| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.88 r_work: 0.3129 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18244 Z= 0.118 Angle : 0.516 9.077 24712 Z= 0.262 Chirality : 0.036 0.149 2888 Planarity : 0.004 0.083 3020 Dihedral : 3.699 21.560 2404 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.96 % Allowed : 22.57 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.28 (0.18), residues: 2188 helix: 1.91 (0.13), residues: 1644 sheet: -0.85 (0.71), residues: 48 loop : 0.59 (0.32), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 464 TYR 0.026 0.001 TYR B 842 PHE 0.010 0.001 PHE A 508 TRP 0.013 0.001 TRP A 711 HIS 0.004 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00275 (18244) covalent geometry : angle 0.51635 (24712) hydrogen bonds : bond 0.03766 ( 1108) hydrogen bonds : angle 3.99178 ( 3258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13631.37 seconds wall clock time: 230 minutes 21.30 seconds (13821.30 seconds total)