Starting phenix.real_space_refine on Wed Jun 18 09:51:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xl9_38442/06_2025/8xl9_38442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xl9_38442/06_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_38442/06_2025/8xl9_38442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xl9_38442/06_2025/8xl9_38442.map" model { file = "/net/cci-nas-00/data/ceres_data/8xl9_38442/06_2025/8xl9_38442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xl9_38442/06_2025/8xl9_38442.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 12.05, per 1000 atoms: 0.57 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: 5.06 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.90 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: 7.80 Time building geometry restraints manager: 5.96 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.680 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: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 48.860 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.003 TRP D 607 HIS 0.008 0.001 HIS C 574 PHE 0.020 0.003 PHE C1077 TYR 0.017 0.002 TYR C 837 ARG 0.003 0.000 ARG D 496 Details of bonding type rmsd hydrogen bonds : bond 0.13957 ( 908) hydrogen bonds : angle 7.67337 ( 2628) covalent geometry : bond 0.00616 (21520) covalent geometry : angle 0.86894 (29172) 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 : 2.300 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: 0.6698 (tpt) REVERT: B 543 ASP cc_start: 0.7052 (m-30) cc_final: 0.6812 (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: 1.6670 time to fit residues: 667.2038 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 : 2.292 ------------------------------------------------------------------------------- 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 229 optimal weight: 4.9990 chunk 206 optimal weight: 0.2980 chunk 114 optimal weight: 8.9990 chunk 70 optimal weight: 0.0370 chunk 139 optimal weight: 0.0670 chunk 110 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- 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 A1040 GLN 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 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 = 0.4369 r_free = 0.4369 target = 0.209754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.167882 restraints weight = 24078.702| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.82 r_work: 0.3814 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21524 Z= 0.122 Angle : 0.583 8.387 29172 Z= 0.303 Chirality : 0.043 0.209 3260 Planarity : 0.005 0.064 3820 Dihedral : 6.272 48.989 3044 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.00 % Favored : 95.85 % Rotamer: Outliers : 2.31 % Allowed : 13.99 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.15), residues: 2724 helix: -0.41 (0.14), residues: 1196 sheet: -0.57 (0.27), residues: 372 loop : -2.23 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 838 HIS 0.008 0.001 HIS A1019 PHE 0.021 0.002 PHE A 612 TYR 0.015 0.002 TYR A 837 ARG 0.002 0.000 ARG A 715 Details of bonding type rmsd hydrogen bonds : bond 0.04605 ( 908) hydrogen bonds : angle 5.48071 ( 2628) covalent geometry : bond 0.00262 (21520) covalent geometry : angle 0.58276 (29172) Misc. bond : bond 0.00011 ( 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 325 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 273 time to evaluate : 2.417 Fit side-chains REVERT: A 543 ASP cc_start: 0.7337 (m-30) cc_final: 0.6929 (m-30) REVERT: A 544 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7258 (tp) REVERT: A 836 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8158 (tm-30) REVERT: A 1143 MET cc_start: 0.6981 (tpp) cc_final: 0.6704 (tpt) REVERT: B 543 ASP cc_start: 0.7346 (m-30) cc_final: 0.6936 (m-30) REVERT: B 836 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: B 881 MET cc_start: 0.7726 (mtp) cc_final: 0.7092 (mtt) REVERT: B 1146 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6347 (mm-30) REVERT: C 543 ASP cc_start: 0.7344 (m-30) cc_final: 0.6918 (m-30) REVERT: C 836 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: C 1143 MET cc_start: 0.6941 (tpp) cc_final: 0.6661 (tpt) REVERT: D 543 ASP cc_start: 0.7360 (m-30) cc_final: 0.6925 (m-30) REVERT: D 836 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: D 881 MET cc_start: 0.7717 (mtp) cc_final: 0.7100 (mtt) REVERT: D 1146 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6342 (mm-30) outliers start: 52 outliers final: 15 residues processed: 299 average time/residue: 1.6317 time to fit residues: 540.7835 Evaluate side-chains 269 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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 1146 GLU 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 1146 GLU 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 2 optimal weight: 0.0470 chunk 253 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- 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 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 HIS A1073 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 923 GLN D 923 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.208084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.166311 restraints weight = 24176.207| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.86 r_work: 0.3789 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21524 Z= 0.148 Angle : 0.598 8.764 29172 Z= 0.309 Chirality : 0.044 0.215 3260 Planarity : 0.005 0.046 3820 Dihedral : 5.612 47.991 3024 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.66 % Favored : 95.19 % Rotamer: Outliers : 2.93 % Allowed : 14.03 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2724 helix: 0.38 (0.15), residues: 1172 sheet: -0.26 (0.27), residues: 364 loop : -1.81 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 838 HIS 0.007 0.001 HIS D 574 PHE 0.019 0.002 PHE C1077 TYR 0.017 0.002 TYR D 837 ARG 0.003 0.000 ARG A 762 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 908) hydrogen bonds : angle 5.29389 ( 2628) covalent geometry : bond 0.00335 (21520) covalent geometry : angle 0.59809 (29172) Misc. bond : bond 0.00034 ( 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 343 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 277 time to evaluate : 2.603 Fit side-chains REVERT: A 543 ASP cc_start: 0.7350 (m-30) cc_final: 0.6948 (m-30) REVERT: A 544 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7303 (tp) REVERT: A 836 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8170 (tm-30) REVERT: A 1079 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 1143 MET cc_start: 0.7007 (tpp) cc_final: 0.6505 (tpp) REVERT: A 1169 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.5990 (pp20) REVERT: B 543 ASP cc_start: 0.7480 (m-30) cc_final: 0.7072 (m-30) REVERT: B 836 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: B 1079 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7403 (tm-30) REVERT: B 1145 MET cc_start: 0.6713 (ttp) cc_final: 0.6453 (ttp) REVERT: C 543 ASP cc_start: 0.7479 (m-30) cc_final: 0.7065 (m-30) REVERT: C 836 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: C 1079 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7441 (tm-30) REVERT: C 1143 MET cc_start: 0.7095 (tpp) cc_final: 0.6686 (tpp) REVERT: C 1145 MET cc_start: 0.6563 (ttp) cc_final: 0.6253 (ttp) REVERT: C 1169 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.6034 (pp20) REVERT: D 543 ASP cc_start: 0.7506 (m-30) cc_final: 0.7077 (m-30) REVERT: D 836 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: D 881 MET cc_start: 0.7887 (mtp) cc_final: 0.7236 (mtt) REVERT: D 1079 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7422 (tm-30) REVERT: D 1145 MET cc_start: 0.6736 (ttp) cc_final: 0.6474 (ttp) REVERT: D 1169 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5995 (pp20) outliers start: 66 outliers final: 25 residues processed: 324 average time/residue: 1.5809 time to fit residues: 570.9956 Evaluate side-chains 284 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 251 time to evaluate : 2.320 ------------------------------------------------------------------------------- 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 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 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 870 GLN Chi-restraints excluded: chain B residue 1153 MET 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 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 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 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 193 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 134 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 151 optimal weight: 0.0470 overall best weight: 0.9884 ------------------------------------------------------------------------------- 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 807 GLN A 923 GLN A1073 GLN B 807 GLN B 923 GLN C 736 HIS C 807 GLN C 923 GLN D 807 GLN D 923 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.209207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.167148 restraints weight = 24483.866| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.16 r_work: 0.3796 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21524 Z= 0.117 Angle : 0.549 8.800 29172 Z= 0.284 Chirality : 0.043 0.206 3260 Planarity : 0.004 0.039 3820 Dihedral : 5.263 46.289 3024 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.11 % Favored : 95.74 % Rotamer: Outliers : 2.75 % Allowed : 15.10 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 2724 helix: 0.73 (0.15), residues: 1192 sheet: -0.25 (0.28), residues: 372 loop : -1.58 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 838 HIS 0.006 0.001 HIS A 574 PHE 0.015 0.001 PHE A1077 TYR 0.017 0.002 TYR B 837 ARG 0.003 0.000 ARG A 762 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 908) hydrogen bonds : angle 5.13598 ( 2628) covalent geometry : bond 0.00256 (21520) covalent geometry : angle 0.54923 (29172) Misc. bond : bond 0.00005 ( 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 344 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 282 time to evaluate : 2.385 Fit side-chains REVERT: A 543 ASP cc_start: 0.7368 (m-30) cc_final: 0.6951 (m-30) REVERT: A 548 GLU cc_start: 0.7046 (pt0) cc_final: 0.6721 (tp30) REVERT: A 605 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7212 (pp20) REVERT: A 839 GLU cc_start: 0.7150 (tp30) cc_final: 0.6864 (tp30) REVERT: A 854 MET cc_start: 0.7410 (ttm) cc_final: 0.6914 (ttm) REVERT: A 881 MET cc_start: 0.7960 (mtp) cc_final: 0.7254 (mtt) REVERT: A 1079 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7447 (tm-30) REVERT: A 1143 MET cc_start: 0.6996 (tpp) cc_final: 0.6504 (tpp) REVERT: A 1169 GLU cc_start: 0.6376 (pp20) cc_final: 0.6042 (pp20) REVERT: B 543 ASP cc_start: 0.7520 (m-30) cc_final: 0.7092 (m-30) REVERT: B 605 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7124 (pp20) REVERT: B 839 GLU cc_start: 0.7140 (tp30) cc_final: 0.6893 (tp30) REVERT: B 1079 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 1145 MET cc_start: 0.6563 (ttp) cc_final: 0.6028 (ttp) REVERT: B 1146 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6349 (mm-30) REVERT: C 543 ASP cc_start: 0.7389 (m-30) cc_final: 0.6948 (m-30) REVERT: C 605 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7115 (pp20) REVERT: C 839 GLU cc_start: 0.7129 (tp30) cc_final: 0.6893 (tp30) REVERT: C 1079 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 1143 MET cc_start: 0.7091 (tpp) cc_final: 0.6687 (tpp) REVERT: C 1145 MET cc_start: 0.6505 (ttp) cc_final: 0.6279 (ttp) REVERT: C 1169 GLU cc_start: 0.6369 (pp20) cc_final: 0.5970 (pp20) REVERT: D 543 ASP cc_start: 0.7413 (m-30) cc_final: 0.6945 (m-30) REVERT: D 605 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7193 (pp20) REVERT: D 839 GLU cc_start: 0.7129 (tp30) cc_final: 0.6887 (tp30) REVERT: D 881 MET cc_start: 0.7840 (mtp) cc_final: 0.7188 (mtt) REVERT: D 1079 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7415 (tm-30) REVERT: D 1145 MET cc_start: 0.6564 (ttp) cc_final: 0.6064 (ttp) REVERT: D 1146 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6345 (mm-30) REVERT: D 1169 GLU cc_start: 0.6374 (pp20) cc_final: 0.5977 (pp20) outliers start: 62 outliers final: 24 residues processed: 326 average time/residue: 1.5539 time to fit residues: 564.3822 Evaluate side-chains 291 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 2.494 ------------------------------------------------------------------------------- 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 870 GLN 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 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 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 813 LEU Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 1153 MET 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 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 1175 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 73 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 67 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 B 788 GLN B 923 GLN C 736 HIS C 788 GLN D 736 HIS D 788 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.205878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.164041 restraints weight = 24291.818| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.21 r_work: 0.3745 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21524 Z= 0.193 Angle : 0.634 9.578 29172 Z= 0.327 Chirality : 0.046 0.235 3260 Planarity : 0.005 0.046 3820 Dihedral : 5.663 49.140 3024 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.52 % Favored : 95.34 % Rotamer: Outliers : 3.29 % Allowed : 16.34 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2724 helix: 0.67 (0.15), residues: 1192 sheet: -0.07 (0.28), residues: 348 loop : -1.54 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 838 HIS 0.009 0.001 HIS B 574 PHE 0.023 0.002 PHE A1077 TYR 0.017 0.002 TYR B 722 ARG 0.009 0.001 ARG C 547 Details of bonding type rmsd hydrogen bonds : bond 0.05504 ( 908) hydrogen bonds : angle 5.28309 ( 2628) covalent geometry : bond 0.00444 (21520) covalent geometry : angle 0.63369 (29172) Misc. bond : bond 0.00009 ( 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 331 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 257 time to evaluate : 2.584 Fit side-chains REVERT: A 543 ASP cc_start: 0.7376 (m-30) cc_final: 0.6952 (m-30) REVERT: A 605 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7258 (pp20) REVERT: A 836 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: A 854 MET cc_start: 0.7519 (ttm) cc_final: 0.7005 (ttm) REVERT: A 881 MET cc_start: 0.8095 (mtp) cc_final: 0.7344 (mtm) REVERT: A 1006 ASP cc_start: 0.8020 (m-30) cc_final: 0.7799 (t0) REVERT: A 1012 MET cc_start: 0.7601 (mmm) cc_final: 0.7369 (mmp) REVERT: A 1079 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7540 (tm-30) REVERT: A 1095 MET cc_start: 0.0331 (pmm) cc_final: -0.0727 (ppp) REVERT: A 1143 MET cc_start: 0.7098 (tpp) cc_final: 0.6814 (tpp) REVERT: A 1169 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.6064 (pp20) REVERT: B 543 ASP cc_start: 0.7523 (m-30) cc_final: 0.7081 (m-30) REVERT: B 605 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7291 (pp20) REVERT: B 836 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: B 881 MET cc_start: 0.8048 (mtp) cc_final: 0.7267 (mtt) REVERT: B 1012 MET cc_start: 0.7727 (mmm) cc_final: 0.7495 (mmp) REVERT: B 1051 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7280 (tp30) REVERT: B 1079 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7533 (tm-30) REVERT: B 1095 MET cc_start: 0.0155 (pmm) cc_final: -0.0653 (ppp) REVERT: B 1145 MET cc_start: 0.6758 (ttp) cc_final: 0.6173 (ttp) REVERT: B 1146 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6236 (mm-30) REVERT: C 543 ASP cc_start: 0.7523 (m-30) cc_final: 0.7066 (m-30) REVERT: C 605 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7284 (pp20) REVERT: C 836 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: C 881 MET cc_start: 0.8042 (mtp) cc_final: 0.7288 (mtm) REVERT: C 1079 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7589 (tm-30) REVERT: C 1095 MET cc_start: -0.0425 (pmm) cc_final: -0.1261 (ppp) REVERT: C 1143 MET cc_start: 0.7126 (tpp) cc_final: 0.6921 (tpp) REVERT: C 1145 MET cc_start: 0.6618 (ttp) cc_final: 0.6308 (ttp) REVERT: C 1169 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6020 (pp20) REVERT: D 543 ASP cc_start: 0.7533 (m-30) cc_final: 0.7080 (m-30) REVERT: D 605 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7299 (pp20) REVERT: D 836 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: D 881 MET cc_start: 0.7985 (mtp) cc_final: 0.7393 (mtm) REVERT: D 1079 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7565 (tm-30) REVERT: D 1095 MET cc_start: 0.0135 (pmm) cc_final: -0.0676 (ppp) REVERT: D 1145 MET cc_start: 0.6766 (ttp) cc_final: 0.6198 (ttp) REVERT: D 1146 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6298 (mm-30) REVERT: D 1169 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.6010 (pp20) outliers start: 74 outliers final: 29 residues processed: 309 average time/residue: 1.6987 time to fit residues: 580.8582 Evaluate side-chains 294 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 251 time to evaluate : 2.532 ------------------------------------------------------------------------------- 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 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 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 1051 GLU Chi-restraints excluded: chain B residue 1146 GLU Chi-restraints excluded: chain B residue 1153 MET 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 870 GLN 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 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 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 77 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 A 736 HIS A 788 GLN A 923 GLN A1073 GLN B 736 HIS B 923 GLN C 506 HIS C 736 HIS D 736 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.208015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.166467 restraints weight = 24173.895| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.85 r_work: 0.3795 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2104 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= 0.121 Angle : 0.559 9.429 29172 Z= 0.290 Chirality : 0.043 0.207 3260 Planarity : 0.005 0.047 3820 Dihedral : 5.307 47.479 3024 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.70 % Rotamer: Outliers : 3.02 % Allowed : 17.05 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2724 helix: 0.99 (0.15), residues: 1184 sheet: -0.32 (0.28), residues: 364 loop : -1.38 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 838 HIS 0.005 0.001 HIS C 574 PHE 0.016 0.001 PHE A1077 TYR 0.017 0.002 TYR D 837 ARG 0.008 0.000 ARG C 547 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 908) hydrogen bonds : angle 5.10866 ( 2628) covalent geometry : bond 0.00266 (21520) covalent geometry : angle 0.55945 (29172) Misc. bond : bond 0.00001 ( 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 331 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 263 time to evaluate : 2.233 Fit side-chains REVERT: A 543 ASP cc_start: 0.7352 (m-30) cc_final: 0.6915 (m-30) REVERT: A 548 GLU cc_start: 0.7036 (pt0) cc_final: 0.6745 (tp30) REVERT: A 605 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7164 (pp20) REVERT: A 788 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: A 836 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: A 839 GLU cc_start: 0.7089 (tp30) cc_final: 0.6833 (tp30) REVERT: A 854 MET cc_start: 0.7523 (ttm) cc_final: 0.6999 (ttm) REVERT: A 881 MET cc_start: 0.8036 (mtp) cc_final: 0.7323 (mtm) REVERT: A 1079 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 1143 MET cc_start: 0.7065 (tpp) cc_final: 0.6832 (tpp) REVERT: A 1169 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.6040 (pp20) REVERT: B 543 ASP cc_start: 0.7504 (m-30) cc_final: 0.7071 (m-30) REVERT: B 544 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7570 (tp) REVERT: B 605 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7198 (pp20) REVERT: B 836 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: B 839 GLU cc_start: 0.7128 (tp30) cc_final: 0.6876 (tp30) REVERT: B 854 MET cc_start: 0.7405 (ttt) cc_final: 0.7035 (ttm) REVERT: B 881 MET cc_start: 0.7943 (mtp) cc_final: 0.7180 (mtt) REVERT: B 1079 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7456 (tm-30) REVERT: B 1145 MET cc_start: 0.6707 (ttp) cc_final: 0.6175 (ttp) REVERT: B 1146 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6212 (mm-30) REVERT: C 543 ASP cc_start: 0.7560 (m-30) cc_final: 0.7109 (m-30) REVERT: C 605 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7185 (pp20) REVERT: C 836 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: C 839 GLU cc_start: 0.7119 (tp30) cc_final: 0.6870 (tp30) REVERT: C 881 MET cc_start: 0.7999 (mtp) cc_final: 0.7304 (mtm) REVERT: C 1012 MET cc_start: 0.7534 (mmm) cc_final: 0.7245 (mmp) REVERT: C 1051 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7165 (tp30) REVERT: C 1079 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7490 (tm-30) REVERT: C 1095 MET cc_start: -0.0491 (pmm) cc_final: -0.1264 (ppp) REVERT: C 1143 MET cc_start: 0.7123 (tpp) cc_final: 0.6842 (tpp) REVERT: C 1145 MET cc_start: 0.6512 (ttp) cc_final: 0.6290 (ttp) REVERT: C 1169 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.6053 (pp20) REVERT: D 543 ASP cc_start: 0.7562 (m-30) cc_final: 0.7125 (m-30) REVERT: D 544 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7522 (tp) REVERT: D 605 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7178 (pp20) REVERT: D 836 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: D 839 GLU cc_start: 0.7106 (tp30) cc_final: 0.6859 (tp30) REVERT: D 881 MET cc_start: 0.7779 (mtp) cc_final: 0.7198 (mtm) REVERT: D 1012 MET cc_start: 0.7524 (mmm) cc_final: 0.7244 (mmp) REVERT: D 1051 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: D 1079 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7486 (tm-30) REVERT: D 1095 MET cc_start: 0.0210 (pmm) cc_final: -0.0678 (ppp) REVERT: D 1145 MET cc_start: 0.6698 (ttp) cc_final: 0.6203 (ttp) REVERT: D 1146 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6281 (mm-30) REVERT: D 1169 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.6038 (pp20) outliers start: 68 outliers final: 22 residues processed: 313 average time/residue: 1.6944 time to fit residues: 589.2641 Evaluate side-chains 297 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 2.475 ------------------------------------------------------------------------------- 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 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 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 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 1146 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 813 LEU Chi-restraints excluded: chain C residue 836 GLU Chi-restraints excluded: chain C residue 870 GLN Chi-restraints excluded: chain C residue 1051 GLU 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 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 1051 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 211 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 139 optimal weight: 0.0370 chunk 250 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 A1073 GLN B 506 HIS B 736 HIS B1069 ASN B1073 GLN C 506 HIS C 736 HIS C1069 ASN C1073 GLN D 506 HIS D 736 HIS D 873 ASN D1069 ASN D1073 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.209296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.168172 restraints weight = 24167.818| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.85 r_work: 0.3817 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2219 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= 0.108 Angle : 0.542 9.233 29172 Z= 0.281 Chirality : 0.043 0.202 3260 Planarity : 0.004 0.047 3820 Dihedral : 5.070 45.321 3024 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.22 % Favored : 95.63 % Rotamer: Outliers : 2.09 % Allowed : 18.07 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2724 helix: 1.20 (0.15), residues: 1188 sheet: -0.31 (0.28), residues: 364 loop : -1.30 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 838 HIS 0.004 0.001 HIS B 574 PHE 0.014 0.001 PHE B 920 TYR 0.017 0.001 TYR D 837 ARG 0.009 0.000 ARG D 547 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 908) hydrogen bonds : angle 5.03250 ( 2628) covalent geometry : bond 0.00233 (21520) covalent geometry : angle 0.54248 (29172) Misc. bond : bond 0.00001 ( 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 315 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 268 time to evaluate : 2.207 Fit side-chains REVERT: A 543 ASP cc_start: 0.7368 (m-30) cc_final: 0.6963 (m-30) REVERT: A 548 GLU cc_start: 0.6972 (pt0) cc_final: 0.6665 (tp30) REVERT: A 836 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: A 839 GLU cc_start: 0.7005 (tp30) cc_final: 0.6754 (tp30) REVERT: A 854 MET cc_start: 0.7478 (ttm) cc_final: 0.6951 (ttm) REVERT: A 881 MET cc_start: 0.7931 (mtp) cc_final: 0.7259 (mtm) REVERT: A 1079 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 1143 MET cc_start: 0.7032 (tpp) cc_final: 0.6812 (tpp) REVERT: A 1169 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6106 (pp20) REVERT: B 543 ASP cc_start: 0.7558 (m-30) cc_final: 0.7149 (m-30) REVERT: B 605 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7032 (pp20) REVERT: B 836 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: B 839 GLU cc_start: 0.7047 (tp30) cc_final: 0.6798 (tp30) REVERT: B 854 MET cc_start: 0.7400 (ttt) cc_final: 0.6993 (ttm) REVERT: B 881 MET cc_start: 0.7866 (mtp) cc_final: 0.7122 (mtt) REVERT: B 906 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7666 (mttt) REVERT: B 1012 MET cc_start: 0.7530 (mmm) cc_final: 0.7256 (mmp) REVERT: B 1079 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 1145 MET cc_start: 0.6662 (ttp) cc_final: 0.6079 (ttp) REVERT: B 1146 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6308 (mm-30) REVERT: C 543 ASP cc_start: 0.7554 (m-30) cc_final: 0.7116 (m-30) REVERT: C 544 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7506 (tp) REVERT: C 605 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7040 (pp20) REVERT: C 836 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: C 839 GLU cc_start: 0.7048 (tp30) cc_final: 0.6803 (tp30) REVERT: C 881 MET cc_start: 0.7947 (mtp) cc_final: 0.7264 (mtm) REVERT: C 1012 MET cc_start: 0.7467 (mmm) cc_final: 0.7216 (mmp) REVERT: C 1079 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7435 (tm-30) REVERT: C 1095 MET cc_start: -0.0546 (pmm) cc_final: -0.1244 (ppp) REVERT: C 1143 MET cc_start: 0.7070 (tpp) cc_final: 0.6829 (tpp) REVERT: C 1169 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.6074 (pp20) REVERT: D 543 ASP cc_start: 0.7541 (m-30) cc_final: 0.7091 (m-30) REVERT: D 544 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7513 (tp) REVERT: D 605 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7024 (pp20) REVERT: D 836 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: D 839 GLU cc_start: 0.7018 (tp30) cc_final: 0.6770 (tp30) REVERT: D 881 MET cc_start: 0.7689 (mtp) cc_final: 0.7142 (mtm) REVERT: D 906 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7662 (mttt) REVERT: D 1012 MET cc_start: 0.7491 (mmm) cc_final: 0.7251 (mmp) REVERT: D 1051 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: D 1079 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7412 (tm-30) REVERT: D 1095 MET cc_start: -0.0171 (pmm) cc_final: -0.0950 (ppp) REVERT: D 1145 MET cc_start: 0.6654 (ttp) cc_final: 0.6089 (ttp) REVERT: D 1146 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6305 (mm-30) REVERT: D 1169 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6099 (pp20) outliers start: 47 outliers final: 24 residues processed: 306 average time/residue: 1.6808 time to fit residues: 568.8495 Evaluate side-chains 295 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 254 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 607 TRP 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 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 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 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 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 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 1051 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 266 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 A 873 ASN B 736 HIS B 873 ASN B1073 GLN C 506 HIS C 873 ASN C1073 GLN D 506 HIS D 736 HIS D1073 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.209409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.167948 restraints weight = 24383.574| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.11 r_work: 0.3810 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21524 Z= 0.116 Angle : 0.550 9.255 29172 Z= 0.285 Chirality : 0.043 0.204 3260 Planarity : 0.004 0.048 3820 Dihedral : 4.978 43.707 3024 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.11 % Favored : 95.74 % Rotamer: Outliers : 2.04 % Allowed : 18.47 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2724 helix: 1.37 (0.15), residues: 1188 sheet: -0.28 (0.28), residues: 364 loop : -1.24 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 838 HIS 0.006 0.001 HIS A 574 PHE 0.017 0.001 PHE A1048 TYR 0.017 0.002 TYR D 837 ARG 0.009 0.000 ARG C 547 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 908) hydrogen bonds : angle 4.98206 ( 2628) covalent geometry : bond 0.00256 (21520) covalent geometry : angle 0.55049 (29172) Misc. bond : bond 0.00005 ( 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 304 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 2.264 Fit side-chains REVERT: A 543 ASP cc_start: 0.7383 (m-30) cc_final: 0.6935 (m-30) REVERT: A 836 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: A 839 GLU cc_start: 0.7078 (tp30) cc_final: 0.6824 (tp30) REVERT: A 854 MET cc_start: 0.7450 (ttm) cc_final: 0.6951 (ttm) REVERT: A 881 MET cc_start: 0.7940 (mtp) cc_final: 0.7275 (mtm) REVERT: A 1079 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 1095 MET cc_start: 0.0266 (pmm) cc_final: -0.0542 (ppp) REVERT: A 1143 MET cc_start: 0.6983 (tpp) cc_final: 0.6769 (tpp) REVERT: A 1169 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6260 (pp20) REVERT: B 543 ASP cc_start: 0.7562 (m-30) cc_final: 0.7139 (m-30) REVERT: B 544 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7426 (tp) REVERT: B 605 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7100 (pp20) REVERT: B 836 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: B 839 GLU cc_start: 0.7104 (tp30) cc_final: 0.6852 (tp30) REVERT: B 854 MET cc_start: 0.7504 (ttt) cc_final: 0.6944 (ttm) REVERT: B 881 MET cc_start: 0.7855 (mtp) cc_final: 0.7099 (mtt) REVERT: B 1079 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 1145 MET cc_start: 0.6661 (ttp) cc_final: 0.6063 (ttp) REVERT: B 1146 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6282 (mm-30) REVERT: C 543 ASP cc_start: 0.7542 (m-30) cc_final: 0.7114 (m-30) REVERT: C 544 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7542 (tp) REVERT: C 605 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: C 836 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: C 839 GLU cc_start: 0.7108 (tp30) cc_final: 0.6858 (tp30) REVERT: C 881 MET cc_start: 0.7959 (mtp) cc_final: 0.7290 (mtm) REVERT: C 1012 MET cc_start: 0.7398 (mmm) cc_final: 0.7186 (mmp) REVERT: C 1079 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7446 (tm-30) REVERT: C 1095 MET cc_start: -0.0651 (pmm) cc_final: -0.1273 (ppp) REVERT: C 1143 MET cc_start: 0.7069 (tpp) cc_final: 0.6837 (tpp) REVERT: C 1169 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.6255 (pp20) REVERT: D 543 ASP cc_start: 0.7547 (m-30) cc_final: 0.7099 (m-30) REVERT: D 544 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7531 (tp) REVERT: D 605 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7052 (pp20) REVERT: D 836 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: D 839 GLU cc_start: 0.7100 (tp30) cc_final: 0.6849 (tp30) REVERT: D 881 MET cc_start: 0.7717 (mtp) cc_final: 0.7281 (mtt) REVERT: D 1012 MET cc_start: 0.7331 (mmm) cc_final: 0.7125 (mmp) REVERT: D 1079 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7401 (tm-30) REVERT: D 1095 MET cc_start: -0.0161 (pmm) cc_final: -0.0910 (ppp) REVERT: D 1145 MET cc_start: 0.6659 (ttp) cc_final: 0.6053 (ttp) REVERT: D 1146 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6296 (mm-30) REVERT: D 1169 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6229 (pp20) outliers start: 46 outliers final: 26 residues processed: 296 average time/residue: 1.7152 time to fit residues: 562.4293 Evaluate side-chains 294 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 607 TRP 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 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 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 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 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 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 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 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 238 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 788 GLN A1069 ASN B1075 GLN D 506 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.206652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.164322 restraints weight = 24065.136| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.10 r_work: 0.3765 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21524 Z= 0.173 Angle : 0.615 9.497 29172 Z= 0.318 Chirality : 0.046 0.223 3260 Planarity : 0.005 0.050 3820 Dihedral : 5.326 46.345 3024 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.19 % Favored : 95.67 % Rotamer: Outliers : 2.40 % Allowed : 17.76 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2724 helix: 1.17 (0.15), residues: 1188 sheet: -0.32 (0.28), residues: 364 loop : -1.24 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 838 HIS 0.009 0.001 HIS D 574 PHE 0.020 0.002 PHE C1077 TYR 0.017 0.002 TYR D 837 ARG 0.009 0.001 ARG D 547 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 908) hydrogen bonds : angle 5.13045 ( 2628) covalent geometry : bond 0.00397 (21520) covalent geometry : angle 0.61481 (29172) Misc. bond : bond 0.00002 ( 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 304 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 250 time to evaluate : 2.893 Fit side-chains REVERT: A 543 ASP cc_start: 0.7337 (m-30) cc_final: 0.6907 (m-30) REVERT: A 788 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7722 (mp10) REVERT: A 836 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: A 1079 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7506 (tm-30) REVERT: A 1095 MET cc_start: 0.0285 (pmm) cc_final: -0.0457 (ppp) REVERT: A 1143 MET cc_start: 0.6903 (tpp) cc_final: 0.6565 (tpp) REVERT: A 1169 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6304 (pp20) REVERT: B 543 ASP cc_start: 0.7564 (m-30) cc_final: 0.7162 (m-30) REVERT: B 544 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7579 (tp) REVERT: B 605 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7318 (pp20) REVERT: B 788 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: B 836 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: B 854 MET cc_start: 0.7528 (ttt) cc_final: 0.7095 (ttm) REVERT: B 1079 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7501 (tm-30) REVERT: B 1095 MET cc_start: 0.0332 (pmm) cc_final: -0.0498 (ppp) REVERT: B 1145 MET cc_start: 0.6737 (ttp) cc_final: 0.6184 (ttp) REVERT: B 1146 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6230 (mm-30) REVERT: B 1169 GLU cc_start: 0.6420 (pp20) cc_final: 0.6001 (pp20) REVERT: C 543 ASP cc_start: 0.7544 (m-30) cc_final: 0.7112 (m-30) REVERT: C 605 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7307 (pp20) REVERT: C 788 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7753 (mp10) REVERT: C 836 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: C 881 MET cc_start: 0.8158 (mtp) cc_final: 0.7457 (mtt) REVERT: C 1012 MET cc_start: 0.7491 (mmm) cc_final: 0.7190 (mmp) REVERT: C 1079 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 1095 MET cc_start: -0.0744 (pmm) cc_final: -0.1289 (ppp) REVERT: C 1169 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6324 (pp20) REVERT: D 543 ASP cc_start: 0.7549 (m-30) cc_final: 0.7122 (m-30) REVERT: D 605 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7289 (pp20) REVERT: D 788 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7745 (mp10) REVERT: D 836 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: D 881 MET cc_start: 0.8024 (mtp) cc_final: 0.7454 (mtm) REVERT: D 1012 MET cc_start: 0.7490 (mmm) cc_final: 0.7202 (mmp) REVERT: D 1051 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: D 1079 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7527 (tm-30) REVERT: D 1095 MET cc_start: -0.0133 (pmm) cc_final: -0.0837 (ppp) REVERT: D 1145 MET cc_start: 0.6747 (ttp) cc_final: 0.6169 (ttp) REVERT: D 1146 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6208 (mm-30) REVERT: D 1169 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6320 (pp20) outliers start: 54 outliers final: 29 residues processed: 293 average time/residue: 2.0733 time to fit residues: 676.4781 Evaluate side-chains 289 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 607 TRP 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 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 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 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 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 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 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 1169 GLU Chi-restraints excluded: chain D residue 1175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 98 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 117 optimal weight: 0.0050 chunk 87 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 62 optimal weight: 0.0050 chunk 157 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.0370 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 870 GLN B 870 GLN C 870 GLN D 506 HIS D 870 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.210826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.170034 restraints weight = 24360.831| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.84 r_work: 0.3847 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21524 Z= 0.102 Angle : 0.548 9.176 29172 Z= 0.283 Chirality : 0.042 0.195 3260 Planarity : 0.004 0.048 3820 Dihedral : 4.816 43.240 3024 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.85 % Favored : 96.00 % Rotamer: Outliers : 2.09 % Allowed : 18.43 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2724 helix: 1.51 (0.15), residues: 1192 sheet: -0.27 (0.28), residues: 364 loop : -1.16 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 838 HIS 0.004 0.001 HIS D 506 PHE 0.014 0.001 PHE C 920 TYR 0.016 0.001 TYR D 837 ARG 0.012 0.000 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 908) hydrogen bonds : angle 4.93522 ( 2628) covalent geometry : bond 0.00216 (21520) covalent geometry : angle 0.54814 (29172) Misc. bond : bond 0.00003 ( 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 308 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 2.275 Fit side-chains REVERT: A 543 ASP cc_start: 0.7213 (m-30) cc_final: 0.6783 (m-30) REVERT: A 870 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6142 (tp40) REVERT: A 881 MET cc_start: 0.7865 (mtp) cc_final: 0.7175 (mtm) REVERT: A 906 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7748 (mttt) REVERT: A 1079 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 1095 MET cc_start: 0.0263 (pmm) cc_final: -0.0563 (ppp) REVERT: B 543 ASP cc_start: 0.7480 (m-30) cc_final: 0.7131 (m-30) REVERT: B 544 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7528 (tp) REVERT: B 854 MET cc_start: 0.7478 (ttt) cc_final: 0.6886 (ttm) REVERT: B 870 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6127 (tp40) REVERT: B 881 MET cc_start: 0.7744 (mtp) cc_final: 0.7110 (mtm) REVERT: B 906 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7777 (mttt) REVERT: B 1079 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7373 (tm-30) REVERT: B 1095 MET cc_start: 0.0255 (pmm) cc_final: -0.0556 (ppp) REVERT: B 1145 MET cc_start: 0.6595 (ttp) cc_final: 0.6334 (ttp) REVERT: B 1169 GLU cc_start: 0.6636 (pp20) cc_final: 0.6361 (pp20) REVERT: C 543 ASP cc_start: 0.7527 (m-30) cc_final: 0.7111 (m-30) REVERT: C 854 MET cc_start: 0.7332 (ttt) cc_final: 0.6969 (ttm) REVERT: C 870 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6146 (tp40) REVERT: C 881 MET cc_start: 0.7822 (mtp) cc_final: 0.7184 (mtm) REVERT: C 906 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7786 (mttt) REVERT: C 1079 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7378 (tm-30) REVERT: C 1095 MET cc_start: -0.0709 (pmm) cc_final: -0.1327 (ppp) REVERT: C 1169 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6284 (pp20) REVERT: D 543 ASP cc_start: 0.7525 (m-30) cc_final: 0.7105 (m-30) REVERT: D 870 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6148 (tp40) REVERT: D 881 MET cc_start: 0.7676 (mtp) cc_final: 0.7154 (mtm) REVERT: D 906 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7787 (mttt) REVERT: D 1051 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7136 (tp30) REVERT: D 1079 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7363 (tm-30) REVERT: D 1095 MET cc_start: -0.0173 (pmm) cc_final: -0.0913 (ppp) REVERT: D 1145 MET cc_start: 0.6611 (ttp) cc_final: 0.6087 (ttp) REVERT: D 1146 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6248 (mm-30) outliers start: 47 outliers final: 12 residues processed: 298 average time/residue: 1.6297 time to fit residues: 538.6650 Evaluate side-chains 271 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 906 LYS 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 813 LEU Chi-restraints excluded: chain B residue 870 GLN Chi-restraints excluded: chain B residue 906 LYS Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 580 THR 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 1169 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain D residue 580 THR 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 1051 GLU Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 268 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 788 GLN A1059 HIS B1069 ASN C1069 ASN C1075 GLN D 506 HIS D1069 ASN D1075 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.207329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165120 restraints weight = 24276.049| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.19 r_work: 0.3761 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21524 Z= 0.192 Angle : 0.632 10.693 29172 Z= 0.326 Chirality : 0.046 0.228 3260 Planarity : 0.005 0.051 3820 Dihedral : 5.252 42.724 3024 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.15 % Favored : 95.70 % Rotamer: Outliers : 1.60 % Allowed : 18.69 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2724 helix: 1.19 (0.15), residues: 1192 sheet: -0.35 (0.27), residues: 364 loop : -1.19 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 838 HIS 0.010 0.001 HIS C 574 PHE 0.020 0.002 PHE C1077 TYR 0.017 0.002 TYR D 837 ARG 0.011 0.001 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.05255 ( 908) hydrogen bonds : angle 5.14261 ( 2628) covalent geometry : bond 0.00445 (21520) covalent geometry : angle 0.63173 (29172) Misc. bond : bond 0.00001 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18959.67 seconds wall clock time: 323 minutes 54.48 seconds (19434.48 seconds total)