Starting phenix.real_space_refine on Sun Aug 24 15:51:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xl9_38442/08_2025/8xl9_38442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xl9_38442/08_2025/8xl9_38442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xl9_38442/08_2025/8xl9_38442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xl9_38442/08_2025/8xl9_38442.map" model { file = "/net/cci-nas-00/data/ceres_data/8xl9_38442/08_2025/8xl9_38442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xl9_38442/08_2025/8xl9_38442.cif" } resolution = 2.61 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= 0.001 sd= 0.147 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 13376 2.51 5 N 3612 2.21 5 O 3908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21044 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5246 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 45, 'TRANS': 637} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: B, C, D Time building chain proxies: 5.20, per 1000 atoms: 0.25 Number of scatterers: 21044 At special positions: 0 Unit cell: (160.518, 98.0343, 128.199, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 3908 8.00 N 3612 7.00 C 13376 6.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 919.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5024 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 47.9% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.601A pdb=" N LEU A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 559 removed outlier: 4.091A pdb=" N ILE A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Proline residue: A 550 - end of helix Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 583 through 589 removed outlier: 3.584A pdb=" N LEU A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 598 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 655 through 670 removed outlier: 3.645A pdb=" N VAL A 659 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 removed outlier: 3.582A pdb=" N ALA A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 Processing helix chain 'A' and resid 748 through 763 Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 798 through 802 removed outlier: 3.865A pdb=" N SER A 802 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 Processing helix chain 'A' and resid 827 through 843 removed outlier: 3.677A pdb=" N VAL A 831 " --> pdb=" O PRO A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 853 removed outlier: 5.319A pdb=" N ALA A 847 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP A 849 " --> pdb=" O ALA A 846 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N CYS A 850 " --> pdb=" O ALA A 847 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR A 851 " --> pdb=" O PHE A 848 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 852 " --> pdb=" O ASP A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 867 through 880 Processing helix chain 'A' and resid 886 through 901 Processing helix chain 'A' and resid 908 through 924 Processing helix chain 'A' and resid 927 through 934 Processing helix chain 'A' and resid 941 through 950 Processing helix chain 'A' and resid 960 through 968 removed outlier: 3.500A pdb=" N LEU A 968 " --> pdb=" O ARG A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 996 removed outlier: 3.888A pdb=" N ASP A 996 " --> pdb=" O LYS A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1013 Processing helix chain 'A' and resid 1013 through 1027 Processing helix chain 'A' and resid 1029 through 1033 removed outlier: 4.195A pdb=" N SER A1032 " --> pdb=" O PRO A1029 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A1033 " --> pdb=" O LEU A1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1029 through 1033' Processing helix chain 'A' and resid 1034 through 1041 Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.601A pdb=" N LEU B 500 " --> pdb=" O ARG B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 559 removed outlier: 4.090A pdb=" N ILE B 544 " --> pdb=" O GLY B 540 " (cutoff:3.500A) Proline residue: B 550 - end of helix Processing helix chain 'B' and resid 571 through 578 Processing helix chain 'B' and resid 583 through 589 removed outlier: 3.584A pdb=" N LEU B 587 " --> pdb=" O ARG B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 598 Processing helix chain 'B' and resid 610 through 618 Processing helix chain 'B' and resid 622 through 634 Processing helix chain 'B' and resid 655 through 670 removed outlier: 3.644A pdb=" N VAL B 659 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 696 removed outlier: 3.583A pdb=" N ALA B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 733 Processing helix chain 'B' and resid 748 through 763 Processing helix chain 'B' and resid 778 through 790 Processing helix chain 'B' and resid 798 through 802 removed outlier: 3.865A pdb=" N SER B 802 " --> pdb=" O ASP B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 816 Processing helix chain 'B' and resid 827 through 843 removed outlier: 3.677A pdb=" N VAL B 831 " --> pdb=" O PRO B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 853 removed outlier: 5.319A pdb=" N ALA B 847 " --> pdb=" O LEU B 844 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP B 849 " --> pdb=" O ALA B 846 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N CYS B 850 " --> pdb=" O ALA B 847 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR B 851 " --> pdb=" O PHE B 848 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 852 " --> pdb=" O ASP B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 865 Processing helix chain 'B' and resid 867 through 880 Processing helix chain 'B' and resid 886 through 901 Processing helix chain 'B' and resid 908 through 924 Processing helix chain 'B' and resid 927 through 934 Processing helix chain 'B' and resid 941 through 950 Processing helix chain 'B' and resid 960 through 968 removed outlier: 3.500A pdb=" N LEU B 968 " --> pdb=" O ARG B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 996 removed outlier: 3.888A pdb=" N ASP B 996 " --> pdb=" O LYS B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1013 Processing helix chain 'B' and resid 1013 through 1027 Processing helix chain 'B' and resid 1029 through 1033 removed outlier: 4.195A pdb=" N SER B1032 " --> pdb=" O PRO B1029 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B1033 " --> pdb=" O LEU B1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1029 through 1033' Processing helix chain 'B' and resid 1034 through 1041 Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.602A pdb=" N LEU C 500 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 559 removed outlier: 4.091A pdb=" N ILE C 544 " --> pdb=" O GLY C 540 " (cutoff:3.500A) Proline residue: C 550 - end of helix Processing helix chain 'C' and resid 571 through 578 Processing helix chain 'C' and resid 583 through 589 removed outlier: 3.584A pdb=" N LEU C 587 " --> pdb=" O ARG C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 598 Processing helix chain 'C' and resid 610 through 618 Processing helix chain 'C' and resid 622 through 634 Processing helix chain 'C' and resid 655 through 670 removed outlier: 3.644A pdb=" N VAL C 659 " --> pdb=" O PRO C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 696 removed outlier: 3.582A pdb=" N ALA C 696 " --> pdb=" O ALA C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 733 Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'C' and resid 778 through 790 Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.865A pdb=" N SER C 802 " --> pdb=" O ASP C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 816 Processing helix chain 'C' and resid 827 through 843 removed outlier: 3.677A pdb=" N VAL C 831 " --> pdb=" O PRO C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 853 removed outlier: 5.319A pdb=" N ALA C 847 " --> pdb=" O LEU C 844 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 849 " --> pdb=" O ALA C 846 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N CYS C 850 " --> pdb=" O ALA C 847 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR C 851 " --> pdb=" O PHE C 848 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 852 " --> pdb=" O ASP C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 865 Processing helix chain 'C' and resid 867 through 880 Processing helix chain 'C' and resid 886 through 901 Processing helix chain 'C' and resid 908 through 924 Processing helix chain 'C' and resid 927 through 934 Processing helix chain 'C' and resid 941 through 950 Processing helix chain 'C' and resid 960 through 968 removed outlier: 3.501A pdb=" N LEU C 968 " --> pdb=" O ARG C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 996 removed outlier: 3.888A pdb=" N ASP C 996 " --> pdb=" O LYS C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1013 Processing helix chain 'C' and resid 1013 through 1027 Processing helix chain 'C' and resid 1029 through 1033 removed outlier: 4.195A pdb=" N SER C1032 " --> pdb=" O PRO C1029 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C1033 " --> pdb=" O LEU C1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1029 through 1033' Processing helix chain 'C' and resid 1034 through 1041 Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.602A pdb=" N LEU D 500 " --> pdb=" O ARG D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 559 removed outlier: 4.091A pdb=" N ILE D 544 " --> pdb=" O GLY D 540 " (cutoff:3.500A) Proline residue: D 550 - end of helix Processing helix chain 'D' and resid 571 through 578 Processing helix chain 'D' and resid 583 through 589 removed outlier: 3.584A pdb=" N LEU D 587 " --> pdb=" O ARG D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 598 Processing helix chain 'D' and resid 610 through 618 Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 655 through 670 removed outlier: 3.644A pdb=" N VAL D 659 " --> pdb=" O PRO D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 696 removed outlier: 3.582A pdb=" N ALA D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 733 Processing helix chain 'D' and resid 748 through 763 Processing helix chain 'D' and resid 778 through 790 Processing helix chain 'D' and resid 798 through 802 removed outlier: 3.864A pdb=" N SER D 802 " --> pdb=" O ASP D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 816 Processing helix chain 'D' and resid 827 through 843 removed outlier: 3.677A pdb=" N VAL D 831 " --> pdb=" O PRO D 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 853 removed outlier: 5.318A pdb=" N ALA D 847 " --> pdb=" O LEU D 844 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 849 " --> pdb=" O ALA D 846 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N CYS D 850 " --> pdb=" O ALA D 847 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR D 851 " --> pdb=" O PHE D 848 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 852 " --> pdb=" O ASP D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 865 Processing helix chain 'D' and resid 867 through 880 Processing helix chain 'D' and resid 886 through 901 Processing helix chain 'D' and resid 908 through 924 Processing helix chain 'D' and resid 927 through 934 Processing helix chain 'D' and resid 941 through 950 Processing helix chain 'D' and resid 960 through 968 removed outlier: 3.500A pdb=" N LEU D 968 " --> pdb=" O ARG D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 996 removed outlier: 3.889A pdb=" N ASP D 996 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1003 through 1013 Processing helix chain 'D' and resid 1013 through 1027 Processing helix chain 'D' and resid 1029 through 1033 removed outlier: 4.195A pdb=" N SER D1032 " --> pdb=" O PRO D1029 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D1033 " --> pdb=" O LEU D1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1029 through 1033' Processing helix chain 'D' and resid 1034 through 1041 Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 567 removed outlier: 8.567A pdb=" N GLU A 605 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP A 567 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N TRP A 607 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N MET A 604 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU A 642 " --> pdb=" O MET A 604 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ASN A 606 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 13.654A pdb=" N ARG A 644 " --> pdb=" O ASN A 606 " (cutoff:3.500A) removed outlier: 11.181A pdb=" N GLY A 608 " --> pdb=" O ARG A 644 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE A 639 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG A 675 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET A 641 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE A 677 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 643 " --> pdb=" O PHE A 677 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE A 674 " --> pdb=" O GLU A 701 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 703 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 676 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER A 705 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 738 " --> pdb=" O HIS A 769 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N HIS A 771 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE A 740 " --> pdb=" O HIS A 771 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 795 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR A 772 " --> pdb=" O ASP A 795 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 564 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL A 796 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N MET A 566 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1048 through 1051 removed outlier: 5.633A pdb=" N ALA A1062 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A1064 " --> pdb=" O PHE A1077 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1111 through 1113 removed outlier: 3.644A pdb=" N GLU A1176 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A1159 " --> pdb=" O GLU A1176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1119 through 1123 removed outlier: 5.685A pdb=" N VAL A1120 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A1141 " --> pdb=" O VAL A1120 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A1122 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS A1138 " --> pdb=" O VAL A1149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1130 through 1131 removed outlier: 3.581A pdb=" N VAL A1131 " --> pdb=" O GLY A1155 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY A1155 " --> pdb=" O VAL A1131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 564 through 567 removed outlier: 8.566A pdb=" N GLU B 605 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP B 567 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N TRP B 607 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N MET B 604 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU B 642 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ASN B 606 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 13.654A pdb=" N ARG B 644 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 11.181A pdb=" N GLY B 608 " --> pdb=" O ARG B 644 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE B 639 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG B 675 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET B 641 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE B 677 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 643 " --> pdb=" O PHE B 677 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE B 674 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA B 703 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 676 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER B 705 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 738 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N HIS B 771 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE B 740 " --> pdb=" O HIS B 771 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B 795 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR B 772 " --> pdb=" O ASP B 795 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 564 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL B 796 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N MET B 566 " --> pdb=" O VAL B 796 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1048 through 1051 removed outlier: 5.633A pdb=" N ALA B1062 " --> pdb=" O GLU B1079 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU B1079 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B1064 " --> pdb=" O PHE B1077 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1111 through 1113 removed outlier: 3.644A pdb=" N GLU B1176 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B1159 " --> pdb=" O GLU B1176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1119 through 1123 removed outlier: 5.684A pdb=" N VAL B1120 " --> pdb=" O SER B1141 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER B1141 " --> pdb=" O VAL B1120 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B1122 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS B1138 " --> pdb=" O VAL B1149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1130 through 1131 removed outlier: 3.581A pdb=" N VAL B1131 " --> pdb=" O GLY B1155 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY B1155 " --> pdb=" O VAL B1131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 564 through 567 removed outlier: 8.566A pdb=" N GLU C 605 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP C 567 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N TRP C 607 " --> pdb=" O ASP C 567 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N MET C 604 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU C 642 " --> pdb=" O MET C 604 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ASN C 606 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 13.654A pdb=" N ARG C 644 " --> pdb=" O ASN C 606 " (cutoff:3.500A) removed outlier: 11.180A pdb=" N GLY C 608 " --> pdb=" O ARG C 644 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE C 639 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG C 675 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET C 641 " --> pdb=" O ARG C 675 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE C 677 " --> pdb=" O MET C 641 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU C 643 " --> pdb=" O PHE C 677 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE C 674 " --> pdb=" O GLU C 701 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA C 703 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL C 676 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER C 705 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 738 " --> pdb=" O HIS C 769 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N HIS C 771 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE C 740 " --> pdb=" O HIS C 771 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 795 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR C 772 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU C 564 " --> pdb=" O VAL C 794 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL C 796 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N MET C 566 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1048 through 1051 removed outlier: 5.633A pdb=" N ALA C1062 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C1064 " --> pdb=" O PHE C1077 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1111 through 1113 removed outlier: 3.645A pdb=" N GLU C1176 " --> pdb=" O LYS C1159 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS C1159 " --> pdb=" O GLU C1176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1119 through 1123 removed outlier: 5.685A pdb=" N VAL C1120 " --> pdb=" O SER C1141 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER C1141 " --> pdb=" O VAL C1120 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C1122 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS C1138 " --> pdb=" O VAL C1149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1130 through 1131 removed outlier: 3.581A pdb=" N VAL C1131 " --> pdb=" O GLY C1155 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY C1155 " --> pdb=" O VAL C1131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 564 through 567 removed outlier: 8.567A pdb=" N GLU D 605 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP D 567 " --> pdb=" O GLU D 605 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N TRP D 607 " --> pdb=" O ASP D 567 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 13.653A pdb=" N ARG D 644 " --> pdb=" O ASN D 606 " (cutoff:3.500A) removed outlier: 11.181A pdb=" N GLY D 608 " --> pdb=" O ARG D 644 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE D 639 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG D 675 " --> pdb=" O PHE D 639 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET D 641 " --> pdb=" O ARG D 675 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE D 677 " --> pdb=" O MET D 641 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU D 643 " --> pdb=" O PHE D 677 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE D 674 " --> pdb=" O GLU D 701 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA D 703 " --> pdb=" O PHE D 674 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL D 676 " --> pdb=" O ALA D 703 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER D 705 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU D 738 " --> pdb=" O HIS D 769 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N HIS D 771 " --> pdb=" O LEU D 738 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE D 740 " --> pdb=" O HIS D 771 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 795 " --> pdb=" O ILE D 770 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR D 772 " --> pdb=" O ASP D 795 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU D 564 " --> pdb=" O VAL D 794 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL D 796 " --> pdb=" O LEU D 564 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N MET D 566 " --> pdb=" O VAL D 796 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1048 through 1051 removed outlier: 5.633A pdb=" N ALA D1062 " --> pdb=" O GLU D1079 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLU D1079 " --> pdb=" O ALA D1062 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D1064 " --> pdb=" O PHE D1077 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1111 through 1113 removed outlier: 3.644A pdb=" N GLU D1176 " --> pdb=" O LYS D1159 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS D1159 " --> pdb=" O GLU D1176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 1119 through 1123 removed outlier: 5.685A pdb=" N VAL D1120 " --> pdb=" O SER D1141 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER D1141 " --> pdb=" O VAL D1120 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP D1122 " --> pdb=" O VAL D1139 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS D1138 " --> pdb=" O VAL D1149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1130 through 1131 removed outlier: 3.581A pdb=" N VAL D1131 " --> pdb=" O GLY D1155 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY D1155 " --> pdb=" O VAL D1131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 908 hydrogen bonds defined for protein. 2628 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: 4.03 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3572 1.31 - 1.44: 5332 1.44 - 1.56: 12352 1.56 - 1.68: 4 1.68 - 1.81: 260 Bond restraints: 21520 Sorted by residual: bond pdb=" C3 BTN D1201 " pdb=" O3 BTN D1201 " ideal model delta sigma weight residual 1.220 1.395 -0.175 2.00e-02 2.50e+03 7.64e+01 bond pdb=" C3 BTN B1201 " pdb=" O3 BTN B1201 " ideal model delta sigma weight residual 1.220 1.394 -0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" C3 BTN A1201 " pdb=" O3 BTN A1201 " ideal model delta sigma weight residual 1.220 1.394 -0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" C3 BTN C1201 " pdb=" O3 BTN C1201 " ideal model delta sigma weight residual 1.220 1.394 -0.174 2.00e-02 2.50e+03 7.57e+01 bond pdb=" C2 BTN C1201 " pdb=" S1 BTN C1201 " ideal model delta sigma weight residual 1.824 1.664 0.160 2.00e-02 2.50e+03 6.37e+01 ... (remaining 21515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 28461 2.38 - 4.76: 607 4.76 - 7.14: 76 7.14 - 9.52: 16 9.52 - 11.90: 12 Bond angle restraints: 29172 Sorted by residual: angle pdb=" N LYS D 906 " pdb=" CA LYS D 906 " pdb=" C LYS D 906 " ideal model delta sigma weight residual 107.99 119.89 -11.90 1.76e+00 3.23e-01 4.57e+01 angle pdb=" N LYS B 906 " pdb=" CA LYS B 906 " pdb=" C LYS B 906 " ideal model delta sigma weight residual 107.99 119.89 -11.90 1.76e+00 3.23e-01 4.57e+01 angle pdb=" N LYS A 906 " pdb=" CA LYS A 906 " pdb=" C LYS A 906 " ideal model delta sigma weight residual 107.99 119.89 -11.90 1.76e+00 3.23e-01 4.57e+01 angle pdb=" N LYS C 906 " pdb=" CA LYS C 906 " pdb=" C LYS C 906 " ideal model delta sigma weight residual 107.99 119.88 -11.89 1.76e+00 3.23e-01 4.57e+01 angle pdb=" N TYR A 894 " pdb=" CA TYR A 894 " pdb=" C TYR A 894 " ideal model delta sigma weight residual 111.14 105.11 6.03 1.08e+00 8.57e-01 3.11e+01 ... (remaining 29167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11788 18.00 - 36.00: 1048 36.00 - 54.00: 196 54.00 - 72.00: 44 72.00 - 90.00: 24 Dihedral angle restraints: 13100 sinusoidal: 5276 harmonic: 7824 Sorted by residual: dihedral pdb=" CA GLY D 803 " pdb=" C GLY D 803 " pdb=" N MET D 804 " pdb=" CA MET D 804 " ideal model delta harmonic sigma weight residual 180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA GLY C 803 " pdb=" C GLY C 803 " pdb=" N MET C 804 " pdb=" CA MET C 804 " ideal model delta harmonic sigma weight residual -180.00 -159.86 -20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA GLY B 803 " pdb=" C GLY B 803 " pdb=" N MET B 804 " pdb=" CA MET B 804 " ideal model delta harmonic sigma weight residual -180.00 -159.86 -20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 13097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2562 0.061 - 0.122: 583 0.122 - 0.183: 95 0.183 - 0.245: 12 0.245 - 0.306: 8 Chirality restraints: 3260 Sorted by residual: chirality pdb=" C2 BTN C1201 " pdb=" C4 BTN C1201 " pdb=" C7 BTN C1201 " pdb=" S1 BTN C1201 " both_signs ideal model delta sigma weight residual False 3.08 2.78 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C2 BTN D1201 " pdb=" C4 BTN D1201 " pdb=" C7 BTN D1201 " pdb=" S1 BTN D1201 " both_signs ideal model delta sigma weight residual False 3.08 2.78 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C2 BTN A1201 " pdb=" C4 BTN A1201 " pdb=" C7 BTN A1201 " pdb=" S1 BTN A1201 " both_signs ideal model delta sigma weight residual False 3.08 2.78 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 3257 not shown) Planarity restraints: 3820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTN C1201 " 0.022 2.00e-02 2.50e+03 5.14e-02 3.96e+01 pdb=" C4 BTN C1201 " -0.038 2.00e-02 2.50e+03 pdb=" C5 BTN C1201 " -0.047 2.00e-02 2.50e+03 pdb=" N1 BTN C1201 " 0.065 2.00e-02 2.50e+03 pdb=" N2 BTN C1201 " 0.060 2.00e-02 2.50e+03 pdb=" O3 BTN C1201 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTN B1201 " 0.022 2.00e-02 2.50e+03 5.13e-02 3.94e+01 pdb=" C4 BTN B1201 " -0.037 2.00e-02 2.50e+03 pdb=" C5 BTN B1201 " -0.047 2.00e-02 2.50e+03 pdb=" N1 BTN B1201 " 0.065 2.00e-02 2.50e+03 pdb=" N2 BTN B1201 " 0.060 2.00e-02 2.50e+03 pdb=" O3 BTN B1201 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTN A1201 " -0.022 2.00e-02 2.50e+03 5.13e-02 3.94e+01 pdb=" C4 BTN A1201 " 0.037 2.00e-02 2.50e+03 pdb=" C5 BTN A1201 " 0.047 2.00e-02 2.50e+03 pdb=" N1 BTN A1201 " -0.065 2.00e-02 2.50e+03 pdb=" N2 BTN A1201 " -0.060 2.00e-02 2.50e+03 pdb=" O3 BTN A1201 " 0.062 2.00e-02 2.50e+03 ... (remaining 3817 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5711 2.81 - 3.33: 17792 3.33 - 3.85: 36118 3.85 - 4.38: 41988 4.38 - 4.90: 72012 Nonbonded interactions: 173621 Sorted by model distance: nonbonded pdb=" OD2 ASP C 586 " pdb=" OH TYR C 845 " model vdw 2.283 3.040 nonbonded pdb=" OD2 ASP A 586 " pdb=" OH TYR A 845 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP B 586 " pdb=" OH TYR B 845 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP D 586 " pdb=" OH TYR D 845 " model vdw 2.284 3.040 nonbonded pdb=" NE2 GLN C 870 " pdb=" OH TYR C 894 " model vdw 2.311 3.120 ... (remaining 173616 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: 0.06 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: 1.100 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.490 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.006 0.175 21524 Z= 0.353 Angle : 0.869 11.900 29172 Z= 0.486 Chirality : 0.055 0.306 3260 Planarity : 0.008 0.074 3820 Dihedral : 14.706 90.000 8076 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.85 % Favored : 94.71 % Rotamer: Outliers : 0.53 % Allowed : 5.33 % Favored : 94.14 % 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 aren not related in a simple way. whole: -3.36 (0.13), residues: 2724 helix: -2.22 (0.11), residues: 1156 sheet: -0.91 (0.26), residues: 348 loop : -2.57 (0.15), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 496 TYR 0.017 0.002 TYR C 837 PHE 0.020 0.003 PHE C1077 TRP 0.021 0.003 TRP D 607 HIS 0.008 0.001 HIS C 574 Details of bonding type rmsd covalent geometry : bond 0.00616 (21520) covalent geometry : angle 0.86894 (29172) hydrogen bonds : bond 0.13957 ( 908) hydrogen bonds : angle 7.67337 ( 2628) Misc. bond : bond 0.11913 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 349 time to evaluate : 0.836 Fit side-chains REVERT: A 543 ASP cc_start: 0.7028 (m-30) cc_final: 0.6772 (m-30) REVERT: A 641 MET cc_start: 0.8211 (ptm) cc_final: 0.7983 (ptm) REVERT: A 881 MET cc_start: 0.7006 (mtp) cc_final: 0.6359 (mtm) REVERT: A 1143 MET cc_start: 0.6960 (tpp) cc_final: 0.6699 (tpt) REVERT: B 543 ASP cc_start: 0.7052 (m-30) cc_final: 0.6813 (m-30) REVERT: C 543 ASP cc_start: 0.7049 (m-30) cc_final: 0.6809 (m-30) REVERT: C 881 MET cc_start: 0.6993 (mtp) cc_final: 0.6362 (mtm) REVERT: C 1143 MET cc_start: 0.6996 (tpp) cc_final: 0.6685 (tpt) REVERT: D 543 ASP cc_start: 0.7056 (m-30) cc_final: 0.6817 (m-30) outliers start: 12 outliers final: 12 residues processed: 361 average time/residue: 0.8535 time to fit residues: 340.2795 Evaluate side-chains 267 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 255 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 870 GLN Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 906 LYS Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 906 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0040 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS A 560 HIS ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS A 870 GLN A 919 GLN ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 GLN A 949 GLN A 998 HIS A1019 HIS B 506 HIS B 560 HIS B 736 HIS B 870 GLN B 919 GLN B 934 GLN B 949 GLN B 998 HIS B1019 HIS B1059 HIS B1073 GLN C 506 HIS C 560 HIS C 736 HIS C 870 GLN C 919 GLN ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 GLN C 949 GLN C 998 HIS C1019 HIS C1073 GLN D 506 HIS D 560 HIS D 736 HIS D 870 GLN D 919 GLN ** D 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 934 GLN D 949 GLN D 998 HIS D1019 HIS D1073 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.208291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.166143 restraints weight = 24156.925| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.83 r_work: 0.3786 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21524 Z= 0.145 Angle : 0.609 8.349 29172 Z= 0.317 Chirality : 0.044 0.215 3260 Planarity : 0.006 0.063 3820 Dihedral : 6.500 52.795 3044 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.48 % Favored : 95.37 % Rotamer: Outliers : 2.22 % Allowed : 14.25 % Favored : 83.53 % 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 aren not related in a simple way. whole: -1.86 (0.15), residues: 2724 helix: -0.50 (0.14), residues: 1196 sheet: -0.64 (0.29), residues: 324 loop : -2.14 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 626 TYR 0.015 0.002 TYR A 837 PHE 0.021 0.002 PHE A1077 TRP 0.015 0.002 TRP D 838 HIS 0.007 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00319 (21520) covalent geometry : angle 0.60875 (29172) hydrogen bonds : bond 0.05090 ( 908) hydrogen bonds : angle 5.56231 ( 2628) Misc. bond : bond 0.00070 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.823 Fit side-chains REVERT: A 543 ASP cc_start: 0.7348 (m-30) cc_final: 0.6958 (m-30) REVERT: A 544 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7267 (tp) REVERT: A 836 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: A 1143 MET cc_start: 0.7025 (tpp) cc_final: 0.6775 (tpt) REVERT: B 543 ASP cc_start: 0.7347 (m-30) cc_final: 0.6940 (m-30) REVERT: B 836 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: B 881 MET cc_start: 0.7815 (mtp) cc_final: 0.7230 (mtm) REVERT: B 1079 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7526 (tm-30) REVERT: C 543 ASP cc_start: 0.7334 (m-30) cc_final: 0.6926 (m-30) REVERT: C 836 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: C 1079 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7579 (tm-30) REVERT: C 1143 MET cc_start: 0.7011 (tpp) cc_final: 0.6774 (tpt) REVERT: D 543 ASP cc_start: 0.7369 (m-30) cc_final: 0.6929 (m-30) REVERT: D 836 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: D 881 MET cc_start: 0.7803 (mtp) cc_final: 0.7226 (mtm) REVERT: D 1079 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7560 (tm-30) outliers start: 50 outliers final: 15 residues processed: 293 average time/residue: 0.8755 time to fit residues: 282.8869 Evaluate side-chains 264 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 244 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 788 GLN Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 870 GLN Chi-restraints excluded: chain B residue 1153 MET Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 788 GLN Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 714 SER Chi-restraints excluded: chain D residue 788 GLN Chi-restraints excluded: chain D residue 836 GLU Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 1153 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 123 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 185 optimal weight: 0.0020 chunk 133 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 GLN A 923 GLN A1019 HIS A1073 GLN B 807 GLN B 923 GLN B1019 HIS C 807 GLN C 923 GLN C1019 HIS D 807 GLN D 923 GLN D1019 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.208783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167234 restraints weight = 24330.573| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.84 r_work: 0.3802 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21524 Z= 0.129 Angle : 0.580 8.777 29172 Z= 0.300 Chirality : 0.044 0.210 3260 Planarity : 0.005 0.060 3820 Dihedral : 5.572 48.878 3024 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.41 % Favored : 95.45 % Rotamer: Outliers : 3.24 % Allowed : 14.56 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.15), residues: 2724 helix: 0.41 (0.15), residues: 1172 sheet: -0.36 (0.27), residues: 372 loop : -1.82 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 762 TYR 0.017 0.002 TYR C 837 PHE 0.018 0.002 PHE A1077 TRP 0.013 0.002 TRP D 838 HIS 0.006 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00283 (21520) covalent geometry : angle 0.58032 (29172) hydrogen bonds : bond 0.04550 ( 908) hydrogen bonds : angle 5.23826 ( 2628) Misc. bond : bond 0.00038 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 280 time to evaluate : 0.826 Fit side-chains REVERT: A 543 ASP cc_start: 0.7337 (m-30) cc_final: 0.6950 (m-30) REVERT: A 544 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7324 (tp) REVERT: A 850 CYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7435 (p) REVERT: A 1079 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 1143 MET cc_start: 0.7018 (tpp) cc_final: 0.6520 (tpp) REVERT: A 1169 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5934 (pp20) REVERT: B 543 ASP cc_start: 0.7469 (m-30) cc_final: 0.7054 (m-30) REVERT: B 836 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: B 1146 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6339 (mm-30) REVERT: B 1169 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5914 (pp20) REVERT: C 543 ASP cc_start: 0.7473 (m-30) cc_final: 0.7068 (m-30) REVERT: C 836 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: C 1143 MET cc_start: 0.7065 (tpp) cc_final: 0.6564 (tpp) REVERT: C 1169 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.5928 (pp20) REVERT: D 543 ASP cc_start: 0.7497 (m-30) cc_final: 0.7063 (m-30) REVERT: D 836 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: D 1146 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6315 (mm-30) REVERT: D 1169 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5905 (pp20) outliers start: 73 outliers final: 25 residues processed: 326 average time/residue: 0.8046 time to fit residues: 291.1195 Evaluate side-chains 282 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 850 CYS Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 788 GLN Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 870 GLN Chi-restraints excluded: chain B residue 1146 GLU Chi-restraints excluded: chain B residue 1153 MET Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 788 GLN Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain C residue 1169 GLU Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 714 SER Chi-restraints excluded: chain D residue 788 GLN Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 836 GLU Chi-restraints excluded: chain D residue 854 MET Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1153 MET Chi-restraints excluded: chain D residue 1169 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 247 optimal weight: 7.9990 chunk 201 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS A 923 GLN A1073 GLN B 736 HIS B 923 GLN C 506 HIS C 736 HIS C 923 GLN D 506 HIS D 736 HIS D 923 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.209077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.167211 restraints weight = 24373.929| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.16 r_work: 0.3794 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21524 Z= 0.119 Angle : 0.555 8.937 29172 Z= 0.287 Chirality : 0.043 0.207 3260 Planarity : 0.004 0.039 3820 Dihedral : 5.312 46.648 3024 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.22 % Favored : 95.63 % Rotamer: Outliers : 3.11 % Allowed : 14.83 % Favored : 82.06 % 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 aren not related in a simple way. whole: -0.53 (0.16), residues: 2724 helix: 0.86 (0.15), residues: 1168 sheet: -0.28 (0.27), residues: 372 loop : -1.62 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 547 TYR 0.017 0.002 TYR C 837 PHE 0.015 0.001 PHE A1077 TRP 0.012 0.002 TRP D 838 HIS 0.006 0.001 HIS C 574 Details of bonding type rmsd covalent geometry : bond 0.00260 (21520) covalent geometry : angle 0.55478 (29172) hydrogen bonds : bond 0.04243 ( 908) hydrogen bonds : angle 5.16676 ( 2628) Misc. bond : bond 0.00008 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 280 time to evaluate : 0.934 Fit side-chains REVERT: A 543 ASP cc_start: 0.7358 (m-30) cc_final: 0.6929 (m-30) REVERT: A 548 GLU cc_start: 0.7077 (pt0) cc_final: 0.6718 (tp30) REVERT: A 836 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8065 (tm-30) REVERT: A 839 GLU cc_start: 0.7191 (tp30) cc_final: 0.6917 (tp30) REVERT: A 1079 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7443 (tm-30) REVERT: A 1143 MET cc_start: 0.6984 (tpp) cc_final: 0.6492 (tpp) REVERT: A 1169 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6039 (pp20) REVERT: B 543 ASP cc_start: 0.7511 (m-30) cc_final: 0.7088 (m-30) REVERT: B 1079 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7378 (tm-30) REVERT: B 1145 MET cc_start: 0.6017 (ttp) cc_final: 0.5686 (ttp) REVERT: B 1146 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6368 (mm-30) REVERT: B 1169 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6013 (pp20) REVERT: C 543 ASP cc_start: 0.7415 (m-30) cc_final: 0.6971 (m-30) REVERT: C 1079 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7398 (tm-30) REVERT: C 1143 MET cc_start: 0.7015 (tpp) cc_final: 0.6628 (tpp) REVERT: C 1169 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.6012 (pp20) REVERT: D 543 ASP cc_start: 0.7429 (m-30) cc_final: 0.6968 (m-30) REVERT: D 881 MET cc_start: 0.7964 (mtp) cc_final: 0.7166 (mtt) REVERT: D 1079 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7388 (tm-30) REVERT: D 1146 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6382 (mm-30) REVERT: D 1169 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6003 (pp20) outliers start: 70 outliers final: 31 residues processed: 329 average time/residue: 0.7924 time to fit residues: 289.9493 Evaluate side-chains 297 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 259 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 1153 MET Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 870 GLN Chi-restraints excluded: chain B residue 1146 GLU Chi-restraints excluded: chain B residue 1153 MET Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain C residue 1169 GLU Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 605 GLU Chi-restraints excluded: chain D residue 607 TRP Chi-restraints excluded: chain D residue 714 SER Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1153 MET Chi-restraints excluded: chain D residue 1169 GLU Chi-restraints excluded: chain D residue 1175 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 159 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 131 optimal weight: 30.0000 chunk 132 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 241 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 HIS A 923 GLN A1073 GLN B 736 HIS C 506 HIS C 736 HIS D 506 HIS D 736 HIS D 923 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.207187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165289 restraints weight = 24128.616| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.85 r_work: 0.3781 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21524 Z= 0.157 Angle : 0.594 9.478 29172 Z= 0.307 Chirality : 0.045 0.224 3260 Planarity : 0.005 0.048 3820 Dihedral : 5.458 47.650 3024 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.37 % Favored : 95.48 % Rotamer: Outliers : 3.11 % Allowed : 16.21 % Favored : 80.68 % 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 aren not related in a simple way. whole: -0.41 (0.16), residues: 2724 helix: 0.93 (0.15), residues: 1168 sheet: -0.32 (0.27), residues: 372 loop : -1.48 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 547 TYR 0.017 0.002 TYR C 837 PHE 0.020 0.002 PHE A1077 TRP 0.012 0.002 TRP C 838 HIS 0.008 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00357 (21520) covalent geometry : angle 0.59438 (29172) hydrogen bonds : bond 0.04906 ( 908) hydrogen bonds : angle 5.19043 ( 2628) Misc. bond : bond 0.00006 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 262 time to evaluate : 0.853 Fit side-chains REVERT: A 543 ASP cc_start: 0.7356 (m-30) cc_final: 0.6971 (m-30) REVERT: A 544 ILE cc_start: 0.7435 (tp) cc_final: 0.7179 (tp) REVERT: A 836 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: A 906 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7731 (mttt) REVERT: A 1079 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 1095 MET cc_start: 0.0312 (pmm) cc_final: -0.0701 (ppp) REVERT: A 1143 MET cc_start: 0.7115 (tpp) cc_final: 0.6746 (tpp) REVERT: A 1169 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6167 (pp20) REVERT: B 543 ASP cc_start: 0.7504 (m-30) cc_final: 0.7049 (m-30) REVERT: B 836 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: B 906 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7724 (mttt) REVERT: B 1079 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7465 (tm-30) REVERT: B 1095 MET cc_start: 0.0143 (pmm) cc_final: -0.0681 (ppp) REVERT: B 1145 MET cc_start: 0.6090 (ttp) cc_final: 0.5721 (ttp) REVERT: B 1146 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6294 (mm-30) REVERT: B 1169 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.6155 (pp20) REVERT: C 543 ASP cc_start: 0.7540 (m-30) cc_final: 0.7092 (m-30) REVERT: C 836 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: C 906 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7735 (mttt) REVERT: C 1079 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7495 (tm-30) REVERT: C 1095 MET cc_start: 0.0134 (pmm) cc_final: -0.0721 (ppp) REVERT: C 1143 MET cc_start: 0.7109 (tpp) cc_final: 0.6852 (tpp) REVERT: C 1169 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6156 (pp20) REVERT: D 543 ASP cc_start: 0.7541 (m-30) cc_final: 0.7087 (m-30) REVERT: D 836 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: D 881 MET cc_start: 0.7981 (mtp) cc_final: 0.7220 (mtt) REVERT: D 906 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7743 (mttt) REVERT: D 1079 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7490 (tm-30) REVERT: D 1095 MET cc_start: 0.0148 (pmm) cc_final: -0.0687 (ppp) REVERT: D 1146 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6300 (mm-30) REVERT: D 1169 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6160 (pp20) outliers start: 70 outliers final: 32 residues processed: 312 average time/residue: 0.8027 time to fit residues: 276.8461 Evaluate side-chains 298 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 1153 MET Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 870 GLN Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 1146 GLU Chi-restraints excluded: chain B residue 1153 MET Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 906 LYS Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain C residue 1169 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 605 GLU Chi-restraints excluded: chain D residue 607 TRP Chi-restraints excluded: chain D residue 714 SER Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 836 GLU Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 906 LYS Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1153 MET Chi-restraints excluded: chain D residue 1169 GLU Chi-restraints excluded: chain D residue 1175 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 225 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 271 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 ASN A 736 HIS A 788 GLN A1075 GLN B 736 HIS B 788 GLN B1075 GLN C 506 HIS C 736 HIS C 788 GLN C1069 ASN C1075 GLN D 506 HIS D 736 HIS D 788 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.204391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.162006 restraints weight = 24028.718| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.88 r_work: 0.3735 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21524 Z= 0.242 Angle : 0.690 10.036 29172 Z= 0.357 Chirality : 0.049 0.245 3260 Planarity : 0.005 0.051 3820 Dihedral : 6.038 53.501 3024 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.92 % Favored : 94.93 % Rotamer: Outliers : 3.37 % Allowed : 17.36 % Favored : 79.26 % 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 aren not related in a simple way. whole: -0.59 (0.16), residues: 2724 helix: 0.62 (0.15), residues: 1184 sheet: -0.28 (0.28), residues: 328 loop : -1.43 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 547 TYR 0.020 0.003 TYR B 722 PHE 0.026 0.003 PHE A1077 TRP 0.016 0.003 TRP A 607 HIS 0.012 0.002 HIS C 574 Details of bonding type rmsd covalent geometry : bond 0.00561 (21520) covalent geometry : angle 0.68997 (29172) hydrogen bonds : bond 0.06161 ( 908) hydrogen bonds : angle 5.38289 ( 2628) Misc. bond : bond 0.00008 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 256 time to evaluate : 0.787 Fit side-chains REVERT: A 543 ASP cc_start: 0.7361 (m-30) cc_final: 0.6922 (m-30) REVERT: A 836 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: A 854 MET cc_start: 0.7521 (ttt) cc_final: 0.7089 (ttm) REVERT: A 1012 MET cc_start: 0.7703 (mmm) cc_final: 0.7436 (mmp) REVERT: A 1095 MET cc_start: 0.0205 (pmm) cc_final: -0.0713 (ppp) REVERT: A 1143 MET cc_start: 0.6992 (tpp) cc_final: 0.6727 (tpp) REVERT: A 1169 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6244 (pp20) REVERT: B 543 ASP cc_start: 0.7492 (m-30) cc_final: 0.7079 (m-30) REVERT: B 836 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: B 1012 MET cc_start: 0.7705 (mmm) cc_final: 0.7495 (mmp) REVERT: B 1051 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: B 1079 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7628 (tm-30) REVERT: B 1095 MET cc_start: -0.0028 (pmm) cc_final: -0.0688 (ppp) REVERT: B 1145 MET cc_start: 0.6222 (ttp) cc_final: 0.5857 (ttp) REVERT: B 1146 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6359 (mm-30) REVERT: B 1169 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6194 (pp20) REVERT: C 543 ASP cc_start: 0.7551 (m-30) cc_final: 0.7122 (m-30) REVERT: C 836 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: C 1012 MET cc_start: 0.7715 (mmm) cc_final: 0.7505 (mmp) REVERT: C 1051 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7325 (tp30) REVERT: C 1079 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7592 (tm-30) REVERT: C 1095 MET cc_start: 0.0001 (pmm) cc_final: -0.0679 (ppp) REVERT: C 1143 MET cc_start: 0.6991 (tpp) cc_final: 0.6735 (tpp) REVERT: C 1169 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6152 (pp20) REVERT: D 543 ASP cc_start: 0.7562 (m-30) cc_final: 0.7116 (m-30) REVERT: D 836 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: D 1012 MET cc_start: 0.7715 (mmm) cc_final: 0.7504 (mmp) REVERT: D 1051 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7325 (tp30) REVERT: D 1079 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7632 (tm-30) REVERT: D 1095 MET cc_start: -0.0042 (pmm) cc_final: -0.0700 (ppp) REVERT: D 1146 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6386 (mm-30) REVERT: D 1169 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6255 (pp20) outliers start: 76 outliers final: 41 residues processed: 308 average time/residue: 0.6882 time to fit residues: 235.1491 Evaluate side-chains 307 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 1153 MET Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 714 SER Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 788 GLN Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 870 GLN Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 1051 GLU Chi-restraints excluded: chain B residue 1146 GLU Chi-restraints excluded: chain B residue 1153 MET Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 714 SER Chi-restraints excluded: chain C residue 788 GLN Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 906 LYS Chi-restraints excluded: chain C residue 1051 GLU Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain C residue 1169 GLU Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 605 GLU Chi-restraints excluded: chain D residue 607 TRP Chi-restraints excluded: chain D residue 714 SER Chi-restraints excluded: chain D residue 788 GLN Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 836 GLU Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 906 LYS Chi-restraints excluded: chain D residue 1051 GLU Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1153 MET Chi-restraints excluded: chain D residue 1169 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 112 optimal weight: 0.3980 chunk 173 optimal weight: 0.9990 chunk 262 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS B 506 HIS C 506 HIS D 506 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.207528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165861 restraints weight = 24134.817| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.86 r_work: 0.3790 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21524 Z= 0.126 Angle : 0.578 9.838 29172 Z= 0.300 Chirality : 0.044 0.212 3260 Planarity : 0.005 0.050 3820 Dihedral : 5.522 49.308 3024 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.30 % Favored : 95.56 % Rotamer: Outliers : 2.75 % Allowed : 18.34 % Favored : 78.91 % 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 aren not related in a simple way. whole: -0.27 (0.16), residues: 2724 helix: 0.97 (0.15), residues: 1188 sheet: -0.41 (0.28), residues: 336 loop : -1.28 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 547 TYR 0.017 0.002 TYR C 837 PHE 0.016 0.002 PHE D1077 TRP 0.013 0.002 TRP C 838 HIS 0.005 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00278 (21520) covalent geometry : angle 0.57842 (29172) hydrogen bonds : bond 0.04454 ( 908) hydrogen bonds : angle 5.11894 ( 2628) Misc. bond : bond 0.00002 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 258 time to evaluate : 0.796 Fit side-chains REVERT: A 543 ASP cc_start: 0.7343 (m-30) cc_final: 0.6909 (m-30) REVERT: A 548 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6191 (pm20) REVERT: A 836 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: A 854 MET cc_start: 0.7507 (ttt) cc_final: 0.7016 (ttm) REVERT: A 906 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7758 (mttt) REVERT: A 1051 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7128 (tp30) REVERT: A 1079 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 1095 MET cc_start: -0.0103 (pmm) cc_final: -0.0925 (ppp) REVERT: A 1143 MET cc_start: 0.6881 (tpp) cc_final: 0.6518 (tpp) REVERT: A 1169 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6225 (pp20) REVERT: B 543 ASP cc_start: 0.7537 (m-30) cc_final: 0.7125 (m-30) REVERT: B 836 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: B 906 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7747 (mttt) REVERT: B 1079 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7416 (tm-30) REVERT: B 1095 MET cc_start: -0.0135 (pmm) cc_final: -0.0889 (ppp) REVERT: B 1145 MET cc_start: 0.6047 (ttp) cc_final: 0.5701 (ttp) REVERT: B 1146 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6317 (mm-30) REVERT: B 1169 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6265 (pp20) REVERT: C 543 ASP cc_start: 0.7540 (m-30) cc_final: 0.7126 (m-30) REVERT: C 544 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7589 (tp) REVERT: C 836 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: C 906 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7767 (mttt) REVERT: C 1079 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7419 (tm-30) REVERT: C 1095 MET cc_start: -0.0110 (pmm) cc_final: -0.0912 (ppp) REVERT: C 1143 MET cc_start: 0.6921 (tpp) cc_final: 0.6682 (tpp) REVERT: C 1169 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6200 (pp20) REVERT: D 543 ASP cc_start: 0.7564 (m-30) cc_final: 0.7136 (m-30) REVERT: D 544 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7586 (tp) REVERT: D 836 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: D 854 MET cc_start: 0.7374 (ttt) cc_final: 0.7023 (ttm) REVERT: D 881 MET cc_start: 0.7825 (mtp) cc_final: 0.7155 (mtm) REVERT: D 906 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7752 (mttt) REVERT: D 1079 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7420 (tm-30) REVERT: D 1095 MET cc_start: -0.0115 (pmm) cc_final: -0.0898 (ppp) REVERT: D 1146 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6289 (mm-30) REVERT: D 1169 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6211 (pp20) outliers start: 62 outliers final: 21 residues processed: 304 average time/residue: 0.6647 time to fit residues: 223.3288 Evaluate side-chains 294 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 255 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 870 GLN Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 1146 GLU Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 906 LYS Chi-restraints excluded: chain C residue 1169 GLU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 605 GLU Chi-restraints excluded: chain D residue 607 TRP Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 836 GLU Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 906 LYS Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1169 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 115 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS A 736 HIS A1069 ASN B 506 HIS B 736 HIS B1069 ASN C 506 HIS C 736 HIS D 506 HIS D 736 HIS D1069 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.206984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.165374 restraints weight = 24049.204| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.84 r_work: 0.3780 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21524 Z= 0.171 Angle : 0.613 9.922 29172 Z= 0.318 Chirality : 0.046 0.224 3260 Planarity : 0.005 0.051 3820 Dihedral : 5.606 50.641 3024 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.70 % Rotamer: Outliers : 2.66 % Allowed : 18.38 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.16), residues: 2724 helix: 0.95 (0.15), residues: 1188 sheet: -0.26 (0.29), residues: 308 loop : -1.29 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 547 TYR 0.017 0.002 TYR B 837 PHE 0.021 0.002 PHE A1077 TRP 0.014 0.003 TRP D 838 HIS 0.009 0.001 HIS B 574 Details of bonding type rmsd covalent geometry : bond 0.00391 (21520) covalent geometry : angle 0.61326 (29172) hydrogen bonds : bond 0.05138 ( 908) hydrogen bonds : angle 5.17635 ( 2628) Misc. bond : bond 0.00001 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 257 time to evaluate : 0.829 Fit side-chains REVERT: A 543 ASP cc_start: 0.7361 (m-30) cc_final: 0.6917 (m-30) REVERT: A 548 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6267 (pm20) REVERT: A 788 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: A 836 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: A 854 MET cc_start: 0.7506 (ttt) cc_final: 0.7057 (ttm) REVERT: A 906 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7772 (mttt) REVERT: A 1051 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: A 1079 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 1095 MET cc_start: -0.0137 (pmm) cc_final: -0.0881 (ppp) REVERT: A 1143 MET cc_start: 0.6850 (tpp) cc_final: 0.6589 (tpp) REVERT: A 1169 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6232 (pp20) REVERT: B 543 ASP cc_start: 0.7596 (m-30) cc_final: 0.7179 (m-30) REVERT: B 544 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7571 (tp) REVERT: B 788 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: B 836 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: B 854 MET cc_start: 0.7466 (ttt) cc_final: 0.7025 (ttm) REVERT: B 1079 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7492 (tm-30) REVERT: B 1095 MET cc_start: -0.0205 (pmm) cc_final: -0.0927 (ppp) REVERT: B 1145 MET cc_start: 0.6048 (ttp) cc_final: 0.5706 (ttp) REVERT: B 1146 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6217 (mm-30) REVERT: B 1169 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6185 (pp20) REVERT: C 543 ASP cc_start: 0.7577 (m-30) cc_final: 0.7155 (m-30) REVERT: C 544 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7565 (tp) REVERT: C 788 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7640 (mp10) REVERT: C 836 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8172 (tm-30) REVERT: C 854 MET cc_start: 0.7453 (ttt) cc_final: 0.7020 (ttm) REVERT: C 1079 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7491 (tm-30) REVERT: C 1095 MET cc_start: -0.0169 (pmm) cc_final: -0.0920 (ppp) REVERT: C 1143 MET cc_start: 0.6877 (tpp) cc_final: 0.6627 (tpp) REVERT: C 1169 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6184 (pp20) REVERT: D 543 ASP cc_start: 0.7591 (m-30) cc_final: 0.7172 (m-30) REVERT: D 544 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7559 (tp) REVERT: D 788 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7593 (mp10) REVERT: D 836 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: D 854 MET cc_start: 0.7684 (ttt) cc_final: 0.7149 (ttm) REVERT: D 1079 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 1095 MET cc_start: -0.0125 (pmm) cc_final: -0.0874 (ppp) REVERT: D 1146 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6250 (mm-30) REVERT: D 1169 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6211 (pp20) outliers start: 60 outliers final: 30 residues processed: 296 average time/residue: 0.6787 time to fit residues: 222.3360 Evaluate side-chains 303 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 1051 GLU Chi-restraints excluded: chain A residue 1153 MET Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 788 GLN Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 870 GLN Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1146 GLU Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 788 GLN Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 906 LYS Chi-restraints excluded: chain C residue 1169 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 605 GLU Chi-restraints excluded: chain D residue 607 TRP Chi-restraints excluded: chain D residue 788 GLN Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 836 GLU Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 906 LYS Chi-restraints excluded: chain D residue 1125 VAL Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1169 GLU Chi-restraints excluded: chain D residue 1175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 80 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 220 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 268 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS B 506 HIS B1073 GLN C 506 HIS C1073 GLN D 506 HIS D1073 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.209901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168722 restraints weight = 24121.298| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.17 r_work: 0.3801 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21524 Z= 0.112 Angle : 0.552 9.659 29172 Z= 0.287 Chirality : 0.043 0.203 3260 Planarity : 0.005 0.049 3820 Dihedral : 5.160 46.998 3024 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.63 % Favored : 96.22 % Rotamer: Outliers : 2.18 % Allowed : 19.05 % Favored : 78.77 % 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 aren not related in a simple way. whole: 0.02 (0.16), residues: 2724 helix: 1.30 (0.15), residues: 1188 sheet: -0.31 (0.27), residues: 364 loop : -1.22 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 547 TYR 0.017 0.001 TYR A 837 PHE 0.015 0.001 PHE D1077 TRP 0.011 0.002 TRP B 838 HIS 0.005 0.001 HIS D 574 Details of bonding type rmsd covalent geometry : bond 0.00247 (21520) covalent geometry : angle 0.55202 (29172) hydrogen bonds : bond 0.04043 ( 908) hydrogen bonds : angle 4.98783 ( 2628) Misc. bond : bond 0.00007 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 0.535 Fit side-chains REVERT: A 543 ASP cc_start: 0.7299 (m-30) cc_final: 0.6814 (m-30) REVERT: A 548 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: A 788 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: A 836 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: A 839 GLU cc_start: 0.7153 (tp30) cc_final: 0.6897 (tp30) REVERT: A 854 MET cc_start: 0.7451 (ttt) cc_final: 0.7015 (ttm) REVERT: A 906 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7706 (mttt) REVERT: A 1079 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7300 (tm-30) REVERT: A 1095 MET cc_start: -0.0195 (pmm) cc_final: -0.0877 (ppp) REVERT: A 1169 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.6132 (pp20) REVERT: B 543 ASP cc_start: 0.7580 (m-30) cc_final: 0.7128 (m-30) REVERT: B 544 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7501 (tp) REVERT: B 788 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7439 (mp10) REVERT: B 836 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: B 839 GLU cc_start: 0.7141 (tp30) cc_final: 0.6877 (tp30) REVERT: B 854 MET cc_start: 0.7493 (ttt) cc_final: 0.6925 (ttm) REVERT: B 881 MET cc_start: 0.7834 (mtp) cc_final: 0.7180 (mtm) REVERT: B 906 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7686 (mttt) REVERT: B 1079 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7347 (tm-30) REVERT: B 1095 MET cc_start: -0.0193 (pmm) cc_final: -0.0864 (ppp) REVERT: B 1145 MET cc_start: 0.5975 (ttp) cc_final: 0.5673 (ttp) REVERT: B 1146 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6187 (mm-30) REVERT: B 1169 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6136 (pp20) REVERT: C 543 ASP cc_start: 0.7557 (m-30) cc_final: 0.7090 (m-30) REVERT: C 788 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: C 836 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: C 839 GLU cc_start: 0.7168 (tp30) cc_final: 0.6907 (tp30) REVERT: C 854 MET cc_start: 0.7505 (ttt) cc_final: 0.6937 (ttm) REVERT: C 906 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7695 (mttt) REVERT: C 1079 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7339 (tm-30) REVERT: C 1095 MET cc_start: -0.0271 (pmm) cc_final: -0.0965 (ppp) REVERT: C 1143 MET cc_start: 0.6798 (tpp) cc_final: 0.6561 (tpp) REVERT: C 1169 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6129 (pp20) REVERT: D 543 ASP cc_start: 0.7579 (m-30) cc_final: 0.7135 (m-30) REVERT: D 788 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7419 (mp10) REVERT: D 836 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: D 839 GLU cc_start: 0.7140 (tp30) cc_final: 0.6875 (tp30) REVERT: D 854 MET cc_start: 0.7608 (ttt) cc_final: 0.7035 (ttm) REVERT: D 906 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7689 (mttt) REVERT: D 1079 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7322 (tm-30) REVERT: D 1095 MET cc_start: -0.0205 (pmm) cc_final: -0.0870 (ppp) REVERT: D 1146 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.6212 (mm-30) REVERT: D 1169 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6106 (pp20) outliers start: 49 outliers final: 23 residues processed: 303 average time/residue: 0.7358 time to fit residues: 246.6072 Evaluate side-chains 295 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 714 SER Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 GLU Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 788 GLN Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 870 GLN Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 1146 GLU Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 788 GLN Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 906 LYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1169 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 605 GLU Chi-restraints excluded: chain D residue 607 TRP Chi-restraints excluded: chain D residue 788 GLN Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 836 GLU Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 906 LYS Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1169 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 25 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 246 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 197 optimal weight: 0.0020 chunk 196 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS A 873 ASN B 506 HIS B 873 ASN C 506 HIS C 873 ASN C1069 ASN D 506 HIS D 873 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.210648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.169984 restraints weight = 24394.681| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.09 r_work: 0.3823 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21524 Z= 0.110 Angle : 0.546 9.398 29172 Z= 0.283 Chirality : 0.043 0.204 3260 Planarity : 0.005 0.049 3820 Dihedral : 4.961 44.128 3024 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.96 % Favored : 95.89 % Rotamer: Outliers : 2.09 % Allowed : 19.14 % Favored : 78.77 % 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 aren not related in a simple way. whole: 0.18 (0.16), residues: 2724 helix: 1.46 (0.15), residues: 1192 sheet: -0.30 (0.27), residues: 364 loop : -1.15 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 547 TYR 0.018 0.001 TYR A 837 PHE 0.015 0.001 PHE A1048 TRP 0.011 0.002 TRP B 838 HIS 0.005 0.001 HIS D 574 Details of bonding type rmsd covalent geometry : bond 0.00240 (21520) covalent geometry : angle 0.54599 (29172) hydrogen bonds : bond 0.03981 ( 908) hydrogen bonds : angle 4.94764 ( 2628) Misc. bond : bond 0.00002 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5448 Ramachandran restraints generated. 2724 Oldfield, 0 Emsley, 2724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 259 time to evaluate : 0.767 Fit side-chains REVERT: A 543 ASP cc_start: 0.7318 (m-30) cc_final: 0.6864 (m-30) REVERT: A 548 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6378 (pm20) REVERT: A 839 GLU cc_start: 0.7152 (tp30) cc_final: 0.6871 (tp30) REVERT: A 854 MET cc_start: 0.7459 (ttt) cc_final: 0.7039 (ttm) REVERT: A 906 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7680 (mttt) REVERT: A 1079 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 1095 MET cc_start: -0.0268 (pmm) cc_final: -0.0982 (ppp) REVERT: A 1169 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6115 (pp20) REVERT: B 543 ASP cc_start: 0.7590 (m-30) cc_final: 0.7122 (m-30) REVERT: B 544 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7492 (tp) REVERT: B 839 GLU cc_start: 0.7142 (tp30) cc_final: 0.6859 (tp30) REVERT: B 854 MET cc_start: 0.7576 (ttt) cc_final: 0.7016 (ttm) REVERT: B 906 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7679 (mttt) REVERT: B 1079 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7332 (tm-30) REVERT: B 1095 MET cc_start: -0.0226 (pmm) cc_final: -0.0965 (ppp) REVERT: B 1145 MET cc_start: 0.5885 (ttp) cc_final: 0.5576 (ttp) REVERT: B 1146 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6161 (mm-30) REVERT: B 1169 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6106 (pp20) REVERT: C 543 ASP cc_start: 0.7567 (m-30) cc_final: 0.7135 (m-30) REVERT: C 839 GLU cc_start: 0.7171 (tp30) cc_final: 0.6885 (tp30) REVERT: C 854 MET cc_start: 0.7463 (ttt) cc_final: 0.6908 (ttm) REVERT: C 906 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7688 (mttt) REVERT: C 1079 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7318 (tm-30) REVERT: C 1095 MET cc_start: -0.0242 (pmm) cc_final: -0.0976 (ppp) REVERT: C 1143 MET cc_start: 0.6966 (tpp) cc_final: 0.6753 (tpp) REVERT: C 1169 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6109 (pp20) REVERT: D 543 ASP cc_start: 0.7574 (m-30) cc_final: 0.7159 (m-30) REVERT: D 839 GLU cc_start: 0.7119 (tp30) cc_final: 0.6839 (tp30) REVERT: D 854 MET cc_start: 0.7582 (ttt) cc_final: 0.7004 (ttm) REVERT: D 881 MET cc_start: 0.7778 (mtp) cc_final: 0.7131 (mtm) REVERT: D 906 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7668 (mttt) REVERT: D 1079 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7313 (tm-30) REVERT: D 1095 MET cc_start: -0.0261 (pmm) cc_final: -0.0990 (ppp) REVERT: D 1146 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6185 (mm-30) REVERT: D 1169 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.6092 (pp20) outliers start: 47 outliers final: 20 residues processed: 295 average time/residue: 0.7292 time to fit residues: 238.1028 Evaluate side-chains 289 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 906 LYS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1169 GLU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 870 GLN Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 1146 GLU Chi-restraints excluded: chain B residue 1169 GLU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 906 LYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1169 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain D residue 580 THR Chi-restraints excluded: chain D residue 607 TRP Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 870 GLN Chi-restraints excluded: chain D residue 906 LYS Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1169 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 240 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 257 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 62 optimal weight: 0.0570 chunk 68 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS B 506 HIS B1069 ASN B1073 GLN C 506 HIS D 506 HIS D1069 ASN D1073 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.207733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.166376 restraints weight = 24156.372| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.83 r_work: 0.3795 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21524 Z= 0.161 Angle : 0.601 9.551 29172 Z= 0.312 Chirality : 0.045 0.221 3260 Planarity : 0.005 0.051 3820 Dihedral : 5.248 45.327 3024 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.19 % Favored : 95.67 % Rotamer: Outliers : 1.64 % Allowed : 19.72 % Favored : 78.64 % 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 aren not related in a simple way. whole: 0.04 (0.16), residues: 2724 helix: 1.29 (0.15), residues: 1192 sheet: -0.32 (0.27), residues: 364 loop : -1.17 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 547 TYR 0.017 0.002 TYR B 837 PHE 0.020 0.002 PHE C1077 TRP 0.014 0.003 TRP B 838 HIS 0.008 0.001 HIS C 574 Details of bonding type rmsd covalent geometry : bond 0.00369 (21520) covalent geometry : angle 0.60117 (29172) hydrogen bonds : bond 0.04879 ( 908) hydrogen bonds : angle 5.07493 ( 2628) Misc. bond : bond 0.00003 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8611.15 seconds wall clock time: 147 minutes 13.08 seconds (8833.08 seconds total)