Starting phenix.real_space_refine on Sun Mar 17 02:10:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4q_0341/03_2024/6n4q_0341_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4q_0341/03_2024/6n4q_0341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4q_0341/03_2024/6n4q_0341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4q_0341/03_2024/6n4q_0341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4q_0341/03_2024/6n4q_0341_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4q_0341/03_2024/6n4q_0341_neut.pdb" } resolution = 3.6 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= 0.002 sd= 0.010 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 120 5.16 5 C 10638 2.51 5 N 2624 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 788": "NH1" <-> "NH2" Residue "A ARG 823": "NH1" <-> "NH2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "A ARG 829": "NH1" <-> "NH2" Residue "B ARG 826": "NH1" <-> "NH2" Residue "C ARG 788": "NH1" <-> "NH2" Residue "C ARG 823": "NH1" <-> "NH2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 829": "NH1" <-> "NH2" Residue "D ARG 826": "NH1" <-> "NH2" Residue "I PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 56": "NH1" <-> "NH2" Residue "J ARG 87": "NH1" <-> "NH2" Residue "K PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "L ARG 87": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16358 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2136 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 252} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2150 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 8, 'TRANS': 253} Chain: "E" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 262 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "F" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 262 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "C" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2136 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 252} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2150 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 8, 'TRANS': 253} Chain: "G" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 262 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "H" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 262 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "I" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1649 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "J" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1720 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1649 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "L" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1720 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 8.31, per 1000 atoms: 0.51 Number of scatterers: 16358 At special positions: 0 Unit cell: (146.4, 147.6, 201.6, 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 120 16.00 O 2976 8.00 N 2624 7.00 C 10638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.04 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 21 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 25 " distance=2.03 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 16 " distance=2.04 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 21 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 25 " distance=2.03 Simple disulfide: pdb=" SG CYS G 2 " - pdb=" SG CYS G 16 " distance=2.04 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 21 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 25 " distance=2.03 Simple disulfide: pdb=" SG CYS H 2 " - pdb=" SG CYS H 16 " distance=2.04 Simple disulfide: pdb=" SG CYS H 9 " - pdb=" SG CYS H 21 " distance=2.03 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 25 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 149 " - pdb=" SG CYS J 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 149 " - pdb=" SG CYS L 204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.7 seconds 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 26 sheets defined 44.2% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 732 through 752 removed outlier: 3.826A pdb=" N THR A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N MET A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 785 removed outlier: 3.581A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 793 removed outlier: 3.729A pdb=" N PHE A 792 " --> pdb=" O ILE A 789 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 793 " --> pdb=" O SER A 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 789 through 793' Processing helix chain 'A' and resid 795 through 813 removed outlier: 3.834A pdb=" N LEU A 811 " --> pdb=" O SER A 807 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 813 " --> pdb=" O VAL A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 removed outlier: 3.971A pdb=" N LEU A 822 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 830 removed outlier: 3.558A pdb=" N VAL A 830 " --> pdb=" O LEU A 827 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 827 through 830' Processing helix chain 'A' and resid 831 through 837 removed outlier: 3.648A pdb=" N THR A 835 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 849 Processing helix chain 'A' and resid 850 through 853 Processing helix chain 'A' and resid 854 through 876 removed outlier: 3.795A pdb=" N ILE A 858 " --> pdb=" O MET A 854 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 885 removed outlier: 3.664A pdb=" N PHE A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 899 removed outlier: 3.590A pdb=" N THR A 899 " --> pdb=" O PHE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 912 removed outlier: 3.593A pdb=" N LEU A 911 " --> pdb=" O ILE A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 945 Proline residue: A 924 - end of helix removed outlier: 3.535A pdb=" N PHE A 927 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 930 " --> pdb=" O ILE A 926 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 940 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 977 removed outlier: 3.714A pdb=" N GLU A 959 " --> pdb=" O HIS A 955 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 967 " --> pdb=" O HIS A 963 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASN A 969 " --> pdb=" O ASP A 965 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU A 970 " --> pdb=" O ASN A 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 731 Processing helix chain 'B' and resid 732 through 752 removed outlier: 3.801A pdb=" N THR B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 737 " --> pdb=" O SER B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 787 removed outlier: 4.000A pdb=" N ILE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 786 " --> pdb=" O LEU B 782 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS B 787 " --> pdb=" O ARG B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 813 Processing helix chain 'B' and resid 821 through 828 removed outlier: 4.045A pdb=" N PHE B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 836 removed outlier: 3.673A pdb=" N THR B 835 " --> pdb=" O PHE B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 849 removed outlier: 3.504A pdb=" N SER B 849 " --> pdb=" O SER B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 877 removed outlier: 3.828A pdb=" N ILE B 858 " --> pdb=" O MET B 854 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 875 " --> pdb=" O MET B 871 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 876 " --> pdb=" O ALA B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 899 removed outlier: 5.046A pdb=" N TYR B 892 " --> pdb=" O GLY B 888 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 899 " --> pdb=" O PHE B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 965 removed outlier: 3.694A pdb=" N PHE B 922 " --> pdb=" O ALA B 918 " (cutoff:3.500A) Proline residue: B 924 - end of helix removed outlier: 3.673A pdb=" N THR B 930 " --> pdb=" O ILE B 926 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE B 931 " --> pdb=" O PHE B 927 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 940 " --> pdb=" O LEU B 936 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN B 954 " --> pdb=" O GLN B 950 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE B 956 " --> pdb=" O GLU B 952 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 957 " --> pdb=" O GLU B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 978 removed outlier: 3.852A pdb=" N GLU B 970 " --> pdb=" O ASN B 966 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 977 " --> pdb=" O LYS B 973 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 730 Processing helix chain 'C' and resid 732 through 752 removed outlier: 3.772A pdb=" N THR C 736 " --> pdb=" O SER C 732 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N MET C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 785 removed outlier: 3.541A pdb=" N VAL C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 793 removed outlier: 3.636A pdb=" N PHE C 792 " --> pdb=" O ILE C 789 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 793 " --> pdb=" O SER C 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 789 through 793' Processing helix chain 'C' and resid 795 through 813 removed outlier: 3.799A pdb=" N LEU C 811 " --> pdb=" O SER C 807 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE C 812 " --> pdb=" O LEU C 808 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 813 " --> pdb=" O VAL C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 826 removed outlier: 3.927A pdb=" N LEU C 822 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 834 removed outlier: 3.621A pdb=" N VAL C 830 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG C 832 " --> pdb=" O ARG C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 849 Processing helix chain 'C' and resid 850 through 853 Processing helix chain 'C' and resid 854 through 876 removed outlier: 3.784A pdb=" N ILE C 858 " --> pdb=" O MET C 854 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN C 874 " --> pdb=" O ILE C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 885 removed outlier: 3.627A pdb=" N PHE C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 899 removed outlier: 3.647A pdb=" N THR C 899 " --> pdb=" O PHE C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 912 removed outlier: 3.594A pdb=" N LEU C 911 " --> pdb=" O ILE C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 945 Proline residue: C 924 - end of helix removed outlier: 3.503A pdb=" N PHE C 927 " --> pdb=" O ILE C 923 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR C 930 " --> pdb=" O ILE C 926 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE C 940 " --> pdb=" O LEU C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 977 removed outlier: 3.763A pdb=" N GLU C 959 " --> pdb=" O HIS C 955 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE C 967 " --> pdb=" O HIS C 963 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN C 968 " --> pdb=" O GLU C 964 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN C 969 " --> pdb=" O ASP C 965 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU C 970 " --> pdb=" O ASN C 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 731 Processing helix chain 'D' and resid 732 through 752 removed outlier: 3.860A pdb=" N THR D 736 " --> pdb=" O SER D 732 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 787 removed outlier: 4.004A pdb=" N ILE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL D 786 " --> pdb=" O LEU D 782 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS D 787 " --> pdb=" O ARG D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 813 Processing helix chain 'D' and resid 823 through 828 removed outlier: 3.743A pdb=" N LEU D 827 " --> pdb=" O ARG D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 836 removed outlier: 3.651A pdb=" N THR D 835 " --> pdb=" O PHE D 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 849 Processing helix chain 'D' and resid 854 through 877 removed outlier: 3.817A pdb=" N ILE D 858 " --> pdb=" O MET D 854 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 874 " --> pdb=" O ILE D 870 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU D 875 " --> pdb=" O MET D 871 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE D 876 " --> pdb=" O ALA D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 899 removed outlier: 5.083A pdb=" N TYR D 892 " --> pdb=" O GLY D 888 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR D 899 " --> pdb=" O PHE D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 978 removed outlier: 3.672A pdb=" N PHE D 922 " --> pdb=" O ALA D 918 " (cutoff:3.500A) Proline residue: D 924 - end of helix removed outlier: 3.677A pdb=" N THR D 930 " --> pdb=" O ILE D 926 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE D 931 " --> pdb=" O PHE D 927 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 940 " --> pdb=" O LEU D 936 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN D 954 " --> pdb=" O GLN D 950 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS D 955 " --> pdb=" O LYS D 951 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE D 956 " --> pdb=" O GLU D 952 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE D 957 " --> pdb=" O GLU D 953 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN D 966 " --> pdb=" O SER D 962 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE D 967 " --> pdb=" O HIS D 963 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN D 969 " --> pdb=" O ASP D 965 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 970 " --> pdb=" O ASN D 966 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 973 " --> pdb=" O ASN D 969 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 977 " --> pdb=" O LYS D 973 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE D 978 " --> pdb=" O LEU D 974 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.673A pdb=" N LEU I 126 " --> pdb=" O SER I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 removed outlier: 3.669A pdb=" N GLU I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.914A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 65 removed outlier: 3.725A pdb=" N VAL J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS J 65 " --> pdb=" O ASP J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 65' Processing helix chain 'J' and resid 138 through 142 removed outlier: 3.561A pdb=" N THR J 141 " --> pdb=" O GLY J 138 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY J 142 " --> pdb=" O ASP J 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 138 through 142' Processing helix chain 'K' and resid 122 through 128 removed outlier: 3.672A pdb=" N LEU K 126 " --> pdb=" O SER K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 189 removed outlier: 3.669A pdb=" N GLU K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.914A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 removed outlier: 3.724A pdb=" N VAL L 64 " --> pdb=" O PRO L 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS L 65 " --> pdb=" O ASP L 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 61 through 65' Processing helix chain 'L' and resid 138 through 142 removed outlier: 3.560A pdb=" N THR L 141 " --> pdb=" O GLY L 138 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY L 142 " --> pdb=" O ASP L 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 138 through 142' Processing sheet with id=AA1, first strand: chain 'E' and resid 20 through 21 removed outlier: 3.590A pdb=" N LYS E 26 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 20 through 21 removed outlier: 3.590A pdb=" N LYS F 26 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 20 through 21 removed outlier: 3.590A pdb=" N LYS G 26 " --> pdb=" O VAL G 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.590A pdb=" N LYS H 26 " --> pdb=" O VAL H 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.575A pdb=" N SER I 7 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU I 74 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR I 72 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.504A pdb=" N MET I 11 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU I 106 " --> pdb=" O MET I 11 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N TYR I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP I 36 " --> pdb=" O TRP I 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.504A pdb=" N MET I 11 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU I 106 " --> pdb=" O MET I 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 115 through 119 removed outlier: 3.573A pdb=" N THR I 115 " --> pdb=" O ASN I 138 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR I 174 " --> pdb=" O ASN I 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 154 through 155 removed outlier: 3.686A pdb=" N LYS I 148 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR I 193 " --> pdb=" O PHE I 210 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE I 210 " --> pdb=" O TYR I 193 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS I 195 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS I 208 " --> pdb=" O CYS I 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA I 197 " --> pdb=" O ILE I 206 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE I 206 " --> pdb=" O ALA I 197 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS I 199 " --> pdb=" O SER I 204 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER I 204 " --> pdb=" O HIS I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.849A pdb=" N SER J 7 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER J 21 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU J 18 " --> pdb=" O MET J 83 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU J 81 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP J 73 " --> pdb=" O SER J 78 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR J 80 " --> pdb=" O SER J 71 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.078A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 116 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N MET J 34 " --> pdb=" O THR J 50 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG J 44 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR J 50 " --> pdb=" O TYR J 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.078A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 116 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR J 111 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.904A pdb=" N GLY J 148 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR J 184 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER J 189 " --> pdb=" O HIS J 173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.904A pdb=" N GLY J 148 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR J 184 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 160 through 163 Processing sheet with id=AB7, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.575A pdb=" N SER K 7 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU K 74 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR K 72 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.505A pdb=" N MET K 11 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU K 106 " --> pdb=" O MET K 11 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP K 36 " --> pdb=" O TRP K 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.505A pdb=" N MET K 11 " --> pdb=" O LYS K 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU K 106 " --> pdb=" O MET K 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 115 through 119 removed outlier: 3.574A pdb=" N THR K 115 " --> pdb=" O ASN K 138 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR K 174 " --> pdb=" O ASN K 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 154 through 155 removed outlier: 3.687A pdb=" N LYS K 148 " --> pdb=" O GLU K 196 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR K 193 " --> pdb=" O PHE K 210 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE K 210 " --> pdb=" O TYR K 193 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS K 195 " --> pdb=" O LYS K 208 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS K 208 " --> pdb=" O CYS K 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA K 197 " --> pdb=" O ILE K 206 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE K 206 " --> pdb=" O ALA K 197 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS K 199 " --> pdb=" O SER K 204 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER K 204 " --> pdb=" O HIS K 199 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 3 through 7 removed outlier: 3.849A pdb=" N SER L 7 " --> pdb=" O SER L 21 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER L 21 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU L 18 " --> pdb=" O MET L 83 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU L 81 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER L 78 " --> pdb=" O ASP L 73 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP L 73 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR L 80 " --> pdb=" O SER L 71 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER L 71 " --> pdb=" O TYR L 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.078A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 116 " --> pdb=" O TYR L 94 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N MET L 34 " --> pdb=" O THR L 50 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG L 44 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR L 50 " --> pdb=" O TYR L 59 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.078A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 116 " --> pdb=" O TYR L 94 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR L 111 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.904A pdb=" N GLY L 148 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR L 184 " --> pdb=" O GLY L 153 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER L 189 " --> pdb=" O HIS L 173 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.904A pdb=" N GLY L 148 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR L 184 " --> pdb=" O GLY L 153 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 160 through 163 792 hydrogen bonds defined for protein. 2217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 6.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4844 1.34 - 1.46: 4358 1.46 - 1.58: 7378 1.58 - 1.71: 0 1.71 - 1.83: 192 Bond restraints: 16772 Sorted by residual: bond pdb=" CA SER C 849 " pdb=" C SER C 849 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.34e-02 5.57e+03 4.49e+00 bond pdb=" CG LEU B 833 " pdb=" CD2 LEU B 833 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.79e+00 bond pdb=" CG LEU D 833 " pdb=" CD2 LEU D 833 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.68e+00 bond pdb=" CG LEU A 887 " pdb=" CD2 LEU A 887 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.48e+00 bond pdb=" CG LEU C 887 " pdb=" CD2 LEU C 887 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.45e+00 ... (remaining 16767 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.90: 310 104.90 - 112.32: 8429 112.32 - 119.74: 5973 119.74 - 127.15: 7839 127.15 - 134.57: 229 Bond angle restraints: 22780 Sorted by residual: angle pdb=" C GLY I 51 " pdb=" N THR I 52 " pdb=" CA THR I 52 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C GLY K 51 " pdb=" N THR K 52 " pdb=" CA THR K 52 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C PRO B 756 " pdb=" N MET B 757 " pdb=" CA MET B 757 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C PRO D 756 " pdb=" N MET D 757 " pdb=" CA MET D 757 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C THR J 140 " pdb=" N THR J 141 " pdb=" CA THR J 141 " ideal model delta sigma weight residual 122.82 128.79 -5.97 1.42e+00 4.96e-01 1.77e+01 ... (remaining 22775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 9349 15.02 - 30.04: 445 30.04 - 45.07: 122 45.07 - 60.09: 6 60.09 - 75.11: 16 Dihedral angle restraints: 9938 sinusoidal: 3922 harmonic: 6016 Sorted by residual: dihedral pdb=" CA PHE A 792 " pdb=" C PHE A 792 " pdb=" N LYS A 793 " pdb=" CA LYS A 793 " ideal model delta harmonic sigma weight residual 180.00 148.43 31.57 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA PHE C 792 " pdb=" C PHE C 792 " pdb=" N LYS C 793 " pdb=" CA LYS C 793 " ideal model delta harmonic sigma weight residual 180.00 148.84 31.16 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA GLU B 753 " pdb=" C GLU B 753 " pdb=" N HIS B 754 " pdb=" CA HIS B 754 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 9935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2332 0.087 - 0.173: 259 0.173 - 0.260: 19 0.260 - 0.347: 0 0.347 - 0.433: 2 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CB ILE B 851 " pdb=" CA ILE B 851 " pdb=" CG1 ILE B 851 " pdb=" CG2 ILE B 851 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CB ILE D 851 " pdb=" CA ILE D 851 " pdb=" CG1 ILE D 851 " pdb=" CG2 ILE D 851 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA HIS D 755 " pdb=" N HIS D 755 " pdb=" C HIS D 755 " pdb=" CB HIS D 755 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2609 not shown) Planarity restraints: 2802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 909 " -0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO A 910 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 910 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 910 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 909 " 0.058 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO B 910 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 910 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 910 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 909 " -0.055 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO D 910 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 910 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 910 " -0.046 5.00e-02 4.00e+02 ... (remaining 2799 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4466 2.81 - 3.33: 14652 3.33 - 3.86: 25536 3.86 - 4.38: 27144 4.38 - 4.90: 47800 Nonbonded interactions: 119598 Sorted by model distance: nonbonded pdb=" O SER K 7 " pdb=" OG1 THR K 22 " model vdw 2.288 2.440 nonbonded pdb=" O SER I 7 " pdb=" OG1 THR I 22 " model vdw 2.289 2.440 nonbonded pdb=" OE2 GLU B 760 " pdb=" ND2 ASN B 763 " model vdw 2.294 2.520 nonbonded pdb=" O TYR A 723 " pdb=" OG1 THR A 727 " model vdw 2.306 2.440 nonbonded pdb=" OG SER I 7 " pdb=" OG1 THR I 22 " model vdw 2.313 2.440 ... (remaining 119593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 720 through 724 or (resid 725 and (name N or name CA or na \ me C or name O or name CB )) or resid 726 through 980)) selection = chain 'C' selection = (chain 'D' and (resid 720 through 724 or (resid 725 and (name N or name CA or na \ me C or name O or name CB )) or resid 726 through 980)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.940 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: 0.000 Extract box with map and model: 9.700 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 41.060 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 16772 Z= 0.482 Angle : 1.033 9.580 22780 Z= 0.559 Chirality : 0.055 0.433 2612 Planarity : 0.009 0.088 2802 Dihedral : 10.165 75.110 5978 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.11 % Allowed : 1.57 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.41 (0.16), residues: 2028 helix: -1.73 (0.15), residues: 786 sheet: -1.58 (0.25), residues: 376 loop : -3.04 (0.17), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP L 36 HIS 0.012 0.003 HIS C 955 PHE 0.040 0.004 PHE B 865 TYR 0.027 0.003 TYR C 741 ARG 0.013 0.001 ARG D 832 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 538 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 ASP cc_start: 0.8682 (t0) cc_final: 0.8423 (t0) REVERT: A 840 MET cc_start: 0.8748 (mmt) cc_final: 0.8523 (mmp) REVERT: A 866 TYR cc_start: 0.8442 (t80) cc_final: 0.8169 (t80) REVERT: A 889 GLU cc_start: 0.5694 (mm-30) cc_final: 0.4731 (mm-30) REVERT: A 933 MET cc_start: 0.8346 (mmm) cc_final: 0.7778 (ttp) REVERT: A 945 MET cc_start: 0.8632 (mtp) cc_final: 0.8366 (mtp) REVERT: A 947 ILE cc_start: 0.7342 (mt) cc_final: 0.7091 (pt) REVERT: B 825 PHE cc_start: 0.8790 (m-80) cc_final: 0.8278 (m-80) REVERT: B 873 THR cc_start: 0.8829 (m) cc_final: 0.8574 (m) REVERT: B 945 MET cc_start: 0.7649 (mmt) cc_final: 0.7346 (mmt) REVERT: E 24 TRP cc_start: 0.7703 (p90) cc_final: 0.7347 (p90) REVERT: F 6 MET cc_start: 0.7193 (mmp) cc_final: 0.6467 (mmp) REVERT: F 10 ASP cc_start: 0.6937 (p0) cc_final: 0.6512 (p0) REVERT: F 24 TRP cc_start: 0.7632 (p90) cc_final: 0.7174 (p-90) REVERT: C 763 ASN cc_start: 0.8564 (m110) cc_final: 0.7893 (t0) REVERT: C 784 ILE cc_start: 0.8563 (tt) cc_final: 0.8324 (tp) REVERT: C 861 MET cc_start: 0.7193 (ttp) cc_final: 0.6805 (ttp) REVERT: C 889 GLU cc_start: 0.5171 (mm-30) cc_final: 0.4649 (mm-30) REVERT: C 901 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8596 (tm-30) REVERT: C 917 TYR cc_start: 0.8857 (m-80) cc_final: 0.8613 (m-80) REVERT: C 947 ILE cc_start: 0.7205 (mt) cc_final: 0.6991 (pt) REVERT: C 966 ASN cc_start: 0.8706 (m-40) cc_final: 0.8454 (m110) REVERT: D 742 LEU cc_start: 0.9222 (tp) cc_final: 0.9000 (tp) REVERT: D 750 MET cc_start: 0.7436 (ttp) cc_final: 0.7100 (ttp) REVERT: D 772 PHE cc_start: 0.8455 (m-80) cc_final: 0.8244 (m-80) REVERT: D 804 VAL cc_start: 0.8771 (t) cc_final: 0.8525 (p) REVERT: D 825 PHE cc_start: 0.8831 (m-80) cc_final: 0.8290 (m-80) REVERT: D 840 MET cc_start: 0.8803 (mmt) cc_final: 0.8574 (mmp) REVERT: D 874 GLN cc_start: 0.8761 (mt0) cc_final: 0.8512 (mt0) REVERT: D 917 TYR cc_start: 0.8779 (m-80) cc_final: 0.8486 (m-80) REVERT: G 24 TRP cc_start: 0.7646 (p90) cc_final: 0.7232 (p90) REVERT: H 6 MET cc_start: 0.8168 (mmp) cc_final: 0.7457 (ptt) REVERT: I 11 MET cc_start: 0.4870 (ttp) cc_final: 0.4553 (ttm) REVERT: I 29 ILE cc_start: 0.5889 (mt) cc_final: 0.5444 (pt) REVERT: I 91 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7713 (tm-30) REVERT: I 98 THR cc_start: 0.8371 (m) cc_final: 0.7819 (p) REVERT: I 164 TRP cc_start: 0.7593 (m-90) cc_final: 0.7104 (m-90) REVERT: I 176 MET cc_start: 0.5371 (tmm) cc_final: 0.4853 (tmm) REVERT: J 13 LYS cc_start: 0.6015 (mttp) cc_final: 0.5795 (mmtt) REVERT: J 74 ASN cc_start: 0.7783 (m-40) cc_final: 0.7497 (m-40) REVERT: J 76 LYS cc_start: 0.8217 (mttp) cc_final: 0.7836 (tttt) REVERT: J 95 TYR cc_start: 0.6375 (m-80) cc_final: 0.4729 (m-80) REVERT: J 114 GLN cc_start: 0.7364 (pt0) cc_final: 0.7140 (pm20) REVERT: J 154 TYR cc_start: 0.7788 (p90) cc_final: 0.7282 (p90) REVERT: K 11 MET cc_start: 0.5450 (ttp) cc_final: 0.4834 (ttp) REVERT: K 29 ILE cc_start: 0.6240 (mt) cc_final: 0.5797 (pt) REVERT: K 91 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7619 (tm-30) REVERT: K 98 THR cc_start: 0.8591 (m) cc_final: 0.8006 (p) REVERT: K 164 TRP cc_start: 0.7754 (m-90) cc_final: 0.7338 (m-90) REVERT: K 176 MET cc_start: 0.5840 (tmm) cc_final: 0.5423 (tmm) REVERT: L 95 TYR cc_start: 0.6146 (m-80) cc_final: 0.5208 (m-80) REVERT: L 111 TYR cc_start: 0.7291 (t80) cc_final: 0.6556 (t80) REVERT: L 114 GLN cc_start: 0.7010 (pt0) cc_final: 0.6780 (pm20) REVERT: L 154 TYR cc_start: 0.6967 (p90) cc_final: 0.6432 (p90) outliers start: 2 outliers final: 0 residues processed: 540 average time/residue: 0.2897 time to fit residues: 225.2210 Evaluate side-chains 374 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 158 optimal weight: 30.0000 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 117 optimal weight: 0.2980 chunk 183 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN ** A 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN B 746 ASN B 874 GLN ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 746 ASN C 754 HIS ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 ASN ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 966 ASN D 746 ASN D 896 GLN I 39 GLN I 95 HIS ** I 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 ASN J 99 HIS J 164 ASN K 39 GLN K 95 HIS K 167 GLN K 213 ASN L 99 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16772 Z= 0.235 Angle : 0.675 8.486 22780 Z= 0.357 Chirality : 0.043 0.176 2612 Planarity : 0.005 0.065 2802 Dihedral : 5.468 28.000 2198 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.26 % Allowed : 9.39 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.01 (0.18), residues: 2028 helix: -0.01 (0.18), residues: 796 sheet: -1.26 (0.27), residues: 376 loop : -2.68 (0.18), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 24 HIS 0.004 0.001 HIS B 755 PHE 0.025 0.002 PHE C 761 TYR 0.015 0.001 TYR L 95 ARG 0.005 0.000 ARG C 829 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 420 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 866 TYR cc_start: 0.8376 (t80) cc_final: 0.8137 (t80) REVERT: A 945 MET cc_start: 0.8200 (mtp) cc_final: 0.7753 (mtp) REVERT: B 757 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6580 (tmm) REVERT: B 873 THR cc_start: 0.8628 (m) cc_final: 0.8375 (m) REVERT: B 945 MET cc_start: 0.7981 (mmt) cc_final: 0.7513 (mmt) REVERT: B 950 GLN cc_start: 0.8151 (mm110) cc_final: 0.7703 (pp30) REVERT: F 6 MET cc_start: 0.7167 (mmp) cc_final: 0.6611 (mmp) REVERT: F 10 ASP cc_start: 0.7019 (p0) cc_final: 0.6759 (p0) REVERT: F 23 LEU cc_start: 0.6419 (tp) cc_final: 0.6075 (tt) REVERT: F 24 TRP cc_start: 0.7698 (p90) cc_final: 0.7357 (p-90) REVERT: F 26 LYS cc_start: 0.7211 (mttt) cc_final: 0.6953 (mttt) REVERT: C 791 PHE cc_start: 0.7422 (t80) cc_final: 0.6956 (t80) REVERT: C 819 LEU cc_start: 0.3983 (OUTLIER) cc_final: 0.3590 (pp) REVERT: C 861 MET cc_start: 0.7063 (ttp) cc_final: 0.6732 (ttp) REVERT: C 889 GLU cc_start: 0.4926 (mm-30) cc_final: 0.4418 (mm-30) REVERT: C 917 TYR cc_start: 0.8840 (m-80) cc_final: 0.8513 (m-80) REVERT: C 966 ASN cc_start: 0.8587 (m110) cc_final: 0.8287 (m110) REVERT: D 742 LEU cc_start: 0.9265 (tp) cc_final: 0.8921 (tp) REVERT: D 825 PHE cc_start: 0.8813 (m-80) cc_final: 0.8268 (m-80) REVERT: D 832 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8078 (ttt-90) REVERT: D 845 SER cc_start: 0.8932 (t) cc_final: 0.8683 (p) REVERT: D 861 MET cc_start: 0.8479 (tpp) cc_final: 0.7329 (ttp) REVERT: D 917 TYR cc_start: 0.8724 (m-80) cc_final: 0.8440 (m-80) REVERT: H 19 MET cc_start: 0.5415 (mtm) cc_final: 0.5156 (mmt) REVERT: H 24 TRP cc_start: 0.6890 (p90) cc_final: 0.6368 (p-90) REVERT: I 29 ILE cc_start: 0.6250 (mt) cc_final: 0.5716 (pt) REVERT: I 91 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7524 (tm-30) REVERT: I 164 TRP cc_start: 0.7417 (m-90) cc_final: 0.6924 (m-90) REVERT: I 176 MET cc_start: 0.4739 (tmm) cc_final: 0.4345 (tmm) REVERT: J 93 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7204 (ptm) REVERT: J 95 TYR cc_start: 0.6062 (m-80) cc_final: 0.5368 (m-80) REVERT: J 114 GLN cc_start: 0.7482 (pt0) cc_final: 0.7177 (pm20) REVERT: K 29 ILE cc_start: 0.6471 (mt) cc_final: 0.5996 (pt) REVERT: K 91 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7506 (tm-30) REVERT: K 98 THR cc_start: 0.7901 (m) cc_final: 0.7361 (p) REVERT: K 164 TRP cc_start: 0.7592 (m-90) cc_final: 0.7261 (m-90) REVERT: L 182 ASP cc_start: 0.8325 (m-30) cc_final: 0.7949 (t0) outliers start: 60 outliers final: 37 residues processed: 444 average time/residue: 0.2901 time to fit residues: 194.4461 Evaluate side-chains 405 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 364 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 826 ARG Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 966 ASN Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 826 ARG Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 739 ILE Chi-restraints excluded: chain D residue 744 VAL Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 182 ASP Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN A 968 ASN B 874 GLN ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 ASN D 874 GLN I 39 GLN I 191 ASN J 39 GLN J 205 ASN K 39 GLN L 39 GLN L 82 GLN L 205 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16772 Z= 0.369 Angle : 0.715 9.271 22780 Z= 0.372 Chirality : 0.045 0.202 2612 Planarity : 0.005 0.064 2802 Dihedral : 5.446 39.320 2198 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.64 % Allowed : 11.24 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.67 (0.18), residues: 2028 helix: 0.32 (0.18), residues: 834 sheet: -1.08 (0.27), residues: 380 loop : -2.67 (0.19), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 24 HIS 0.010 0.002 HIS D 955 PHE 0.023 0.002 PHE C 761 TYR 0.018 0.001 TYR K 50 ARG 0.006 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 370 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 866 TYR cc_start: 0.8430 (t80) cc_final: 0.8225 (t80) REVERT: A 889 GLU cc_start: 0.5464 (mm-30) cc_final: 0.4539 (mm-30) REVERT: A 945 MET cc_start: 0.8224 (mtp) cc_final: 0.7997 (ttm) REVERT: B 757 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.5902 (tmm) REVERT: B 761 PHE cc_start: 0.7105 (m-10) cc_final: 0.6901 (m-10) REVERT: B 775 ILE cc_start: 0.8792 (mt) cc_final: 0.8566 (pt) REVERT: B 791 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.6350 (t80) REVERT: B 873 THR cc_start: 0.8762 (m) cc_final: 0.8539 (m) REVERT: B 889 GLU cc_start: 0.5716 (mm-30) cc_final: 0.5491 (mm-30) REVERT: B 945 MET cc_start: 0.7921 (mmt) cc_final: 0.7233 (mmm) REVERT: B 950 GLN cc_start: 0.8088 (mm110) cc_final: 0.7671 (tm-30) REVERT: F 23 LEU cc_start: 0.6755 (tp) cc_final: 0.6423 (tt) REVERT: C 819 LEU cc_start: 0.3916 (OUTLIER) cc_final: 0.3637 (pp) REVERT: C 861 MET cc_start: 0.7120 (ttp) cc_final: 0.6802 (ttp) REVERT: C 889 GLU cc_start: 0.4612 (mm-30) cc_final: 0.4067 (mm-30) REVERT: C 917 TYR cc_start: 0.8918 (m-80) cc_final: 0.8598 (m-80) REVERT: D 825 PHE cc_start: 0.8866 (m-80) cc_final: 0.8288 (m-80) REVERT: D 832 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8195 (ttt-90) REVERT: D 845 SER cc_start: 0.9060 (t) cc_final: 0.8811 (p) REVERT: D 861 MET cc_start: 0.8574 (tpp) cc_final: 0.7854 (ttp) REVERT: D 952 GLU cc_start: 0.8898 (tp30) cc_final: 0.8532 (tp30) REVERT: G 23 LEU cc_start: 0.8245 (mm) cc_final: 0.7725 (tt) REVERT: H 6 MET cc_start: 0.8066 (mmp) cc_final: 0.7459 (ptp) REVERT: I 29 ILE cc_start: 0.6483 (mt) cc_final: 0.5885 (pt) REVERT: I 91 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7520 (tm-30) REVERT: I 164 TRP cc_start: 0.7447 (m-90) cc_final: 0.7013 (m-90) REVERT: I 176 MET cc_start: 0.4668 (tmm) cc_final: 0.4256 (tmm) REVERT: J 89 GLU cc_start: 0.7221 (tp30) cc_final: 0.6815 (tp30) REVERT: J 95 TYR cc_start: 0.6260 (m-80) cc_final: 0.5915 (m-80) REVERT: J 114 GLN cc_start: 0.7487 (pt0) cc_final: 0.7160 (mm110) REVERT: K 11 MET cc_start: 0.4675 (ttp) cc_final: 0.4302 (ttm) REVERT: K 29 ILE cc_start: 0.6431 (mt) cc_final: 0.5904 (pt) REVERT: K 91 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7890 (tm-30) REVERT: K 98 THR cc_start: 0.7965 (m) cc_final: 0.7302 (p) REVERT: K 164 TRP cc_start: 0.7395 (m-90) cc_final: 0.7079 (m-90) REVERT: K 176 MET cc_start: 0.4693 (tmm) cc_final: 0.4381 (tmm) outliers start: 67 outliers final: 49 residues processed: 410 average time/residue: 0.2676 time to fit residues: 165.6408 Evaluate side-chains 399 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 346 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 963 HIS Chi-restraints excluded: chain F residue 7 TRP Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 191 ASN Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 182 ASP Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 95 optimal weight: 0.0770 chunk 20 optimal weight: 0.4980 chunk 87 optimal weight: 0.0870 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 174 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN B 874 GLN ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16772 Z= 0.188 Angle : 0.630 13.287 22780 Z= 0.322 Chirality : 0.042 0.198 2612 Planarity : 0.004 0.043 2802 Dihedral : 5.037 32.155 2198 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.09 % Allowed : 13.46 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.09 (0.19), residues: 2028 helix: 1.00 (0.19), residues: 818 sheet: -0.86 (0.27), residues: 380 loop : -2.49 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 5 HIS 0.008 0.001 HIS C 963 PHE 0.017 0.001 PHE C 761 TYR 0.015 0.001 TYR A 723 ARG 0.002 0.000 ARG A 826 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 370 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 806 LEU cc_start: 0.8503 (mp) cc_final: 0.8253 (mp) REVERT: A 840 MET cc_start: 0.8708 (mmp) cc_final: 0.8078 (mmp) REVERT: B 757 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5795 (tmm) REVERT: B 761 PHE cc_start: 0.7086 (m-10) cc_final: 0.6862 (m-10) REVERT: B 791 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.6441 (t80) REVERT: B 799 PHE cc_start: 0.7351 (t80) cc_final: 0.7094 (t80) REVERT: B 873 THR cc_start: 0.8551 (m) cc_final: 0.8328 (m) REVERT: B 950 GLN cc_start: 0.7986 (mm110) cc_final: 0.7691 (tm-30) REVERT: C 819 LEU cc_start: 0.3184 (OUTLIER) cc_final: 0.2947 (pp) REVERT: C 861 MET cc_start: 0.7056 (ttp) cc_final: 0.6620 (ttp) REVERT: C 917 TYR cc_start: 0.8823 (m-80) cc_final: 0.8545 (m-80) REVERT: C 965 ASP cc_start: 0.9442 (p0) cc_final: 0.9188 (p0) REVERT: D 735 PHE cc_start: 0.8328 (t80) cc_final: 0.7972 (t80) REVERT: D 761 PHE cc_start: 0.6137 (m-10) cc_final: 0.5922 (m-10) REVERT: D 825 PHE cc_start: 0.8816 (m-80) cc_final: 0.8279 (m-80) REVERT: D 832 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8152 (ttt-90) REVERT: D 845 SER cc_start: 0.9056 (t) cc_final: 0.8803 (p) REVERT: D 861 MET cc_start: 0.8439 (tpp) cc_final: 0.7636 (ttp) REVERT: D 952 GLU cc_start: 0.8816 (tp30) cc_final: 0.8511 (tm-30) REVERT: G 23 LEU cc_start: 0.8380 (mm) cc_final: 0.7951 (tt) REVERT: H 6 MET cc_start: 0.8047 (mmp) cc_final: 0.7351 (mtm) REVERT: I 29 ILE cc_start: 0.6424 (mt) cc_final: 0.5882 (pt) REVERT: I 91 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7341 (tm-30) REVERT: I 164 TRP cc_start: 0.7300 (m-90) cc_final: 0.6897 (m-90) REVERT: I 176 MET cc_start: 0.4796 (tmm) cc_final: 0.4434 (tmm) REVERT: J 89 GLU cc_start: 0.7234 (tp30) cc_final: 0.6740 (tp30) REVERT: J 95 TYR cc_start: 0.6206 (m-80) cc_final: 0.5927 (m-80) REVERT: J 114 GLN cc_start: 0.7288 (pt0) cc_final: 0.6773 (pm20) REVERT: J 154 TYR cc_start: 0.7057 (p90) cc_final: 0.6355 (p90) REVERT: K 11 MET cc_start: 0.4933 (ttp) cc_final: 0.4601 (ttm) REVERT: K 29 ILE cc_start: 0.6467 (mt) cc_final: 0.5998 (pt) REVERT: K 98 THR cc_start: 0.7747 (m) cc_final: 0.7263 (p) REVERT: K 164 TRP cc_start: 0.7286 (m-90) cc_final: 0.6681 (m-90) REVERT: K 176 MET cc_start: 0.4774 (tmm) cc_final: 0.3628 (ptm) REVERT: L 34 MET cc_start: 0.8322 (mmp) cc_final: 0.7935 (mmm) REVERT: L 154 TYR cc_start: 0.6357 (p90) cc_final: 0.5710 (p90) outliers start: 57 outliers final: 42 residues processed: 402 average time/residue: 0.2562 time to fit residues: 155.9095 Evaluate side-chains 394 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 348 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 963 HIS Chi-restraints excluded: chain F residue 7 TRP Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 826 ARG Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 182 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 134 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 968 ASN B 874 GLN B 954 GLN ** B 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 ASN K 39 GLN L 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16772 Z= 0.262 Angle : 0.649 13.931 22780 Z= 0.328 Chirality : 0.043 0.201 2612 Planarity : 0.004 0.059 2802 Dihedral : 4.988 27.256 2198 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.75 % Allowed : 15.80 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.91 (0.19), residues: 2028 helix: 1.08 (0.18), residues: 830 sheet: -0.66 (0.28), residues: 380 loop : -2.43 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 24 HIS 0.007 0.001 HIS I 190 PHE 0.019 0.002 PHE C 761 TYR 0.013 0.001 TYR K 50 ARG 0.003 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 354 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LYS cc_start: 0.7500 (ttpp) cc_final: 0.7286 (ttmm) REVERT: A 966 ASN cc_start: 0.8788 (m110) cc_final: 0.8490 (m110) REVERT: B 757 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.5587 (tmm) REVERT: B 761 PHE cc_start: 0.7065 (m-10) cc_final: 0.6705 (m-10) REVERT: B 775 ILE cc_start: 0.8857 (mt) cc_final: 0.8656 (pt) REVERT: B 791 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.6546 (t80) REVERT: B 873 THR cc_start: 0.8598 (m) cc_final: 0.8371 (m) REVERT: B 889 GLU cc_start: 0.5562 (mm-30) cc_final: 0.5343 (mm-30) REVERT: B 945 MET cc_start: 0.8024 (mmt) cc_final: 0.7539 (mmm) REVERT: B 950 GLN cc_start: 0.8009 (mm110) cc_final: 0.7689 (tm-30) REVERT: F 24 TRP cc_start: 0.6654 (p-90) cc_final: 0.6323 (p-90) REVERT: C 819 LEU cc_start: 0.3261 (OUTLIER) cc_final: 0.3003 (pp) REVERT: C 861 MET cc_start: 0.7106 (ttp) cc_final: 0.6685 (ttp) REVERT: C 889 GLU cc_start: 0.4706 (mm-30) cc_final: 0.4046 (mm-30) REVERT: C 965 ASP cc_start: 0.9496 (p0) cc_final: 0.9252 (p0) REVERT: D 735 PHE cc_start: 0.8432 (t80) cc_final: 0.8023 (t80) REVERT: D 757 MET cc_start: 0.4920 (tpp) cc_final: 0.4458 (tmm) REVERT: D 825 PHE cc_start: 0.8824 (m-80) cc_final: 0.8295 (m-80) REVERT: D 832 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8178 (ttt-90) REVERT: D 845 SER cc_start: 0.9063 (t) cc_final: 0.8796 (p) REVERT: D 861 MET cc_start: 0.8518 (tpp) cc_final: 0.7796 (ttp) REVERT: G 23 LEU cc_start: 0.8358 (mm) cc_final: 0.7910 (tt) REVERT: H 6 MET cc_start: 0.7982 (mmp) cc_final: 0.7316 (mtm) REVERT: H 19 MET cc_start: 0.4674 (mtm) cc_final: 0.4353 (ptm) REVERT: I 29 ILE cc_start: 0.6471 (mt) cc_final: 0.6065 (pt) REVERT: I 98 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7227 (p) REVERT: I 164 TRP cc_start: 0.7326 (m-90) cc_final: 0.6937 (m-90) REVERT: I 169 SER cc_start: 0.8168 (t) cc_final: 0.7775 (p) REVERT: I 176 MET cc_start: 0.4749 (tmm) cc_final: 0.3949 (tpt) REVERT: I 190 HIS cc_start: 0.4621 (OUTLIER) cc_final: 0.4285 (t-90) REVERT: J 89 GLU cc_start: 0.7208 (tp30) cc_final: 0.6666 (tp30) REVERT: J 95 TYR cc_start: 0.6257 (m-80) cc_final: 0.5859 (m-80) REVERT: J 114 GLN cc_start: 0.7351 (pt0) cc_final: 0.7029 (tp40) REVERT: K 11 MET cc_start: 0.5133 (ttp) cc_final: 0.4808 (ttm) REVERT: K 29 ILE cc_start: 0.6446 (mt) cc_final: 0.5951 (pt) REVERT: K 98 THR cc_start: 0.7811 (m) cc_final: 0.7315 (p) REVERT: K 164 TRP cc_start: 0.7322 (m-90) cc_final: 0.7084 (m-90) REVERT: K 176 MET cc_start: 0.4759 (tmm) cc_final: 0.4551 (tmm) REVERT: L 34 MET cc_start: 0.8278 (mmp) cc_final: 0.8003 (mmm) outliers start: 69 outliers final: 49 residues processed: 392 average time/residue: 0.2541 time to fit residues: 150.5218 Evaluate side-chains 393 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 338 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 7 TRP Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 851 ILE Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 98 THR Chi-restraints excluded: chain I residue 190 HIS Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 182 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 114 optimal weight: 0.0870 chunk 48 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16772 Z= 0.198 Angle : 0.624 10.719 22780 Z= 0.315 Chirality : 0.042 0.194 2612 Planarity : 0.004 0.059 2802 Dihedral : 4.776 25.440 2198 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.20 % Allowed : 16.72 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.64 (0.19), residues: 2028 helix: 1.28 (0.19), residues: 824 sheet: -0.29 (0.29), residues: 366 loop : -2.33 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 24 HIS 0.006 0.001 HIS D 963 PHE 0.020 0.001 PHE C 761 TYR 0.018 0.001 TYR A 866 ARG 0.004 0.000 ARG C 783 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 353 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LYS cc_start: 0.7453 (ttpp) cc_final: 0.7182 (ttmm) REVERT: A 783 ARG cc_start: 0.8843 (tpp80) cc_final: 0.8503 (mtp180) REVERT: A 796 TRP cc_start: 0.7458 (m100) cc_final: 0.7096 (m100) REVERT: B 757 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5299 (tmm) REVERT: B 761 PHE cc_start: 0.7134 (m-10) cc_final: 0.6888 (m-10) REVERT: B 775 ILE cc_start: 0.8917 (mt) cc_final: 0.8690 (pt) REVERT: B 873 THR cc_start: 0.8513 (m) cc_final: 0.8280 (m) REVERT: B 889 GLU cc_start: 0.5456 (mm-30) cc_final: 0.5240 (mm-30) REVERT: B 950 GLN cc_start: 0.7729 (mm110) cc_final: 0.7402 (tm-30) REVERT: F 24 TRP cc_start: 0.6692 (p-90) cc_final: 0.6466 (p-90) REVERT: C 819 LEU cc_start: 0.3069 (OUTLIER) cc_final: 0.2800 (pp) REVERT: C 861 MET cc_start: 0.7143 (ttp) cc_final: 0.6777 (ttp) REVERT: C 889 GLU cc_start: 0.4974 (mm-30) cc_final: 0.4342 (mm-30) REVERT: C 917 TYR cc_start: 0.8839 (m-80) cc_final: 0.8553 (m-80) REVERT: C 965 ASP cc_start: 0.9500 (p0) cc_final: 0.9276 (p0) REVERT: D 735 PHE cc_start: 0.8415 (t80) cc_final: 0.7986 (t80) REVERT: D 757 MET cc_start: 0.5147 (tpp) cc_final: 0.4744 (tmm) REVERT: D 825 PHE cc_start: 0.8846 (m-80) cc_final: 0.8261 (m-80) REVERT: D 832 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8111 (ttt-90) REVERT: D 845 SER cc_start: 0.9049 (t) cc_final: 0.8798 (p) REVERT: D 861 MET cc_start: 0.8468 (tpp) cc_final: 0.7703 (ttp) REVERT: D 945 MET cc_start: 0.7283 (mmt) cc_final: 0.6504 (mmt) REVERT: G 23 LEU cc_start: 0.8472 (mm) cc_final: 0.8191 (tt) REVERT: H 6 MET cc_start: 0.8005 (mmp) cc_final: 0.7416 (mtm) REVERT: H 19 MET cc_start: 0.4514 (mtm) cc_final: 0.4248 (ptp) REVERT: I 29 ILE cc_start: 0.6609 (mt) cc_final: 0.6216 (pt) REVERT: I 98 THR cc_start: 0.7669 (m) cc_final: 0.7215 (p) REVERT: I 164 TRP cc_start: 0.7292 (m-90) cc_final: 0.6934 (m-90) REVERT: I 176 MET cc_start: 0.4743 (tmm) cc_final: 0.3980 (tpt) REVERT: I 190 HIS cc_start: 0.4828 (OUTLIER) cc_final: 0.4536 (t-90) REVERT: J 89 GLU cc_start: 0.7233 (tp30) cc_final: 0.6807 (mt-10) REVERT: J 95 TYR cc_start: 0.6460 (m-80) cc_final: 0.6119 (m-80) REVERT: J 114 GLN cc_start: 0.7244 (pt0) cc_final: 0.7039 (tp40) REVERT: K 11 MET cc_start: 0.4987 (ttp) cc_final: 0.4654 (ttm) REVERT: K 98 THR cc_start: 0.7747 (m) cc_final: 0.7270 (p) REVERT: K 164 TRP cc_start: 0.7184 (m-90) cc_final: 0.6967 (m-90) REVERT: K 176 MET cc_start: 0.4772 (tmm) cc_final: 0.4567 (tmm) REVERT: L 34 MET cc_start: 0.8368 (mmp) cc_final: 0.8148 (mmm) REVERT: L 93 MET cc_start: 0.8019 (ptp) cc_final: 0.7715 (ptm) REVERT: L 154 TYR cc_start: 0.6364 (p90) cc_final: 0.5749 (p90) outliers start: 59 outliers final: 47 residues processed: 385 average time/residue: 0.2701 time to fit residues: 156.8046 Evaluate side-chains 393 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 342 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 7 TRP Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 190 HIS Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 182 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 142 optimal weight: 0.0050 chunk 110 optimal weight: 4.9990 chunk 164 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 194 optimal weight: 40.0000 chunk 121 optimal weight: 0.0040 chunk 118 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 961 GLN K 39 GLN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16772 Z= 0.181 Angle : 0.625 11.608 22780 Z= 0.315 Chirality : 0.042 0.209 2612 Planarity : 0.004 0.052 2802 Dihedral : 4.697 24.209 2198 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.37 % Allowed : 17.37 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.53 (0.19), residues: 2028 helix: 1.35 (0.19), residues: 824 sheet: -0.18 (0.29), residues: 366 loop : -2.26 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 5 HIS 0.006 0.001 HIS A 963 PHE 0.019 0.001 PHE A 791 TYR 0.015 0.001 TYR A 723 ARG 0.004 0.000 ARG C 783 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 352 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LYS cc_start: 0.7475 (ttpp) cc_final: 0.7238 (ttmm) REVERT: A 796 TRP cc_start: 0.7466 (m100) cc_final: 0.7088 (m100) REVERT: A 933 MET cc_start: 0.8250 (mmm) cc_final: 0.7774 (mtp) REVERT: B 757 MET cc_start: 0.6125 (OUTLIER) cc_final: 0.5268 (tmm) REVERT: B 761 PHE cc_start: 0.7080 (m-10) cc_final: 0.6832 (m-10) REVERT: B 775 ILE cc_start: 0.8929 (mt) cc_final: 0.8691 (pt) REVERT: B 873 THR cc_start: 0.8459 (m) cc_final: 0.8238 (m) REVERT: F 24 TRP cc_start: 0.6643 (p-90) cc_final: 0.6411 (p-90) REVERT: C 819 LEU cc_start: 0.3057 (OUTLIER) cc_final: 0.2794 (pp) REVERT: C 861 MET cc_start: 0.7133 (ttp) cc_final: 0.6775 (ttp) REVERT: C 965 ASP cc_start: 0.9506 (p0) cc_final: 0.9287 (p0) REVERT: D 735 PHE cc_start: 0.8391 (t80) cc_final: 0.7967 (t80) REVERT: D 757 MET cc_start: 0.5020 (tpp) cc_final: 0.4712 (tmm) REVERT: D 825 PHE cc_start: 0.8742 (m-80) cc_final: 0.8192 (m-80) REVERT: D 832 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8082 (ttt-90) REVERT: D 845 SER cc_start: 0.9046 (t) cc_final: 0.8799 (p) REVERT: D 861 MET cc_start: 0.8458 (tpp) cc_final: 0.7691 (ttp) REVERT: G 23 LEU cc_start: 0.8332 (mm) cc_final: 0.7959 (tt) REVERT: H 6 MET cc_start: 0.7987 (mmp) cc_final: 0.7401 (mtm) REVERT: H 19 MET cc_start: 0.4577 (mtm) cc_final: 0.4208 (ptp) REVERT: I 29 ILE cc_start: 0.6596 (mt) cc_final: 0.6179 (pt) REVERT: I 98 THR cc_start: 0.7646 (m) cc_final: 0.7196 (p) REVERT: I 164 TRP cc_start: 0.7402 (m-90) cc_final: 0.7049 (m-90) REVERT: I 176 MET cc_start: 0.4746 (tmm) cc_final: 0.4010 (tpt) REVERT: I 190 HIS cc_start: 0.4833 (OUTLIER) cc_final: 0.4500 (t-90) REVERT: J 89 GLU cc_start: 0.7196 (tp30) cc_final: 0.6754 (mt-10) REVERT: J 95 TYR cc_start: 0.6557 (m-80) cc_final: 0.6217 (m-80) REVERT: J 154 TYR cc_start: 0.7060 (p90) cc_final: 0.6408 (p90) REVERT: K 11 MET cc_start: 0.5000 (ttp) cc_final: 0.4676 (ttm) REVERT: K 98 THR cc_start: 0.7710 (m) cc_final: 0.7182 (p) REVERT: K 164 TRP cc_start: 0.7183 (m-90) cc_final: 0.6680 (m-90) REVERT: K 176 MET cc_start: 0.4561 (tmm) cc_final: 0.3950 (ptm) REVERT: L 34 MET cc_start: 0.8305 (mmp) cc_final: 0.8008 (mmm) REVERT: L 154 TYR cc_start: 0.6477 (p90) cc_final: 0.5864 (p90) outliers start: 62 outliers final: 52 residues processed: 384 average time/residue: 0.2684 time to fit residues: 155.0616 Evaluate side-chains 393 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 337 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain F residue 7 TRP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 739 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 190 HIS Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 182 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 153 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16772 Z= 0.240 Angle : 0.668 14.023 22780 Z= 0.333 Chirality : 0.043 0.215 2612 Planarity : 0.004 0.050 2802 Dihedral : 4.716 24.767 2198 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.42 % Allowed : 17.43 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.60 (0.19), residues: 2028 helix: 1.21 (0.19), residues: 834 sheet: -0.17 (0.28), residues: 366 loop : -2.26 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 5 HIS 0.005 0.001 HIS D 963 PHE 0.021 0.001 PHE D 761 TYR 0.014 0.001 TYR J 95 ARG 0.007 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 339 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LYS cc_start: 0.7414 (ttpp) cc_final: 0.7161 (ttmm) REVERT: A 796 TRP cc_start: 0.7435 (m100) cc_final: 0.7038 (m100) REVERT: A 889 GLU cc_start: 0.5252 (mm-30) cc_final: 0.4330 (mt-10) REVERT: A 945 MET cc_start: 0.8697 (ttm) cc_final: 0.8481 (ttp) REVERT: B 757 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.5264 (tmm) REVERT: B 761 PHE cc_start: 0.7068 (m-10) cc_final: 0.6822 (m-10) REVERT: B 775 ILE cc_start: 0.8930 (mt) cc_final: 0.8681 (pt) REVERT: B 873 THR cc_start: 0.8516 (m) cc_final: 0.8292 (m) REVERT: F 24 TRP cc_start: 0.6548 (p-90) cc_final: 0.6336 (p-90) REVERT: C 819 LEU cc_start: 0.3094 (OUTLIER) cc_final: 0.2818 (pp) REVERT: C 861 MET cc_start: 0.7159 (ttp) cc_final: 0.6804 (ttp) REVERT: C 889 GLU cc_start: 0.4941 (mm-30) cc_final: 0.4326 (mm-30) REVERT: C 965 ASP cc_start: 0.9497 (p0) cc_final: 0.9279 (p0) REVERT: D 735 PHE cc_start: 0.8440 (t80) cc_final: 0.7981 (t80) REVERT: D 757 MET cc_start: 0.5070 (tpp) cc_final: 0.4708 (tmm) REVERT: D 825 PHE cc_start: 0.8759 (m-80) cc_final: 0.8243 (m-80) REVERT: D 832 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8218 (ttt-90) REVERT: D 845 SER cc_start: 0.9052 (t) cc_final: 0.8804 (p) REVERT: D 861 MET cc_start: 0.8511 (tpp) cc_final: 0.7744 (ttp) REVERT: G 23 LEU cc_start: 0.8361 (mm) cc_final: 0.8054 (tt) REVERT: H 6 MET cc_start: 0.7999 (mmp) cc_final: 0.7664 (mtm) REVERT: H 19 MET cc_start: 0.4608 (mtm) cc_final: 0.4273 (ptp) REVERT: H 24 TRP cc_start: 0.7787 (p90) cc_final: 0.7365 (p-90) REVERT: I 29 ILE cc_start: 0.6616 (mt) cc_final: 0.6180 (pt) REVERT: I 98 THR cc_start: 0.7685 (m) cc_final: 0.7238 (p) REVERT: I 164 TRP cc_start: 0.7406 (m-90) cc_final: 0.7144 (m-90) REVERT: I 176 MET cc_start: 0.4768 (tmm) cc_final: 0.4481 (tmm) REVERT: I 190 HIS cc_start: 0.4818 (OUTLIER) cc_final: 0.4505 (t-90) REVERT: J 89 GLU cc_start: 0.7295 (tp30) cc_final: 0.6634 (mt-10) REVERT: J 95 TYR cc_start: 0.6588 (m-80) cc_final: 0.6151 (m-80) REVERT: J 114 GLN cc_start: 0.6991 (tp40) cc_final: 0.5340 (pm20) REVERT: K 11 MET cc_start: 0.5055 (ttp) cc_final: 0.4666 (ttp) REVERT: K 98 THR cc_start: 0.7755 (m) cc_final: 0.7220 (p) REVERT: L 34 MET cc_start: 0.8330 (mmp) cc_final: 0.8039 (mmm) REVERT: L 93 MET cc_start: 0.7988 (ptp) cc_final: 0.7658 (ptm) REVERT: L 154 TYR cc_start: 0.6523 (p90) cc_final: 0.5838 (p90) outliers start: 63 outliers final: 57 residues processed: 373 average time/residue: 0.2556 time to fit residues: 143.2327 Evaluate side-chains 394 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 333 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 739 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 805 THR Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 190 HIS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 182 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.7980 chunk 186 optimal weight: 0.4980 chunk 170 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16772 Z= 0.230 Angle : 0.663 12.958 22780 Z= 0.332 Chirality : 0.043 0.223 2612 Planarity : 0.004 0.046 2802 Dihedral : 4.723 24.862 2198 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.64 % Allowed : 17.81 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.19), residues: 2028 helix: 1.21 (0.19), residues: 834 sheet: -0.12 (0.28), residues: 366 loop : -2.23 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 24 HIS 0.006 0.001 HIS D 963 PHE 0.022 0.001 PHE D 761 TYR 0.017 0.001 TYR A 723 ARG 0.006 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 340 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LYS cc_start: 0.7425 (ttpp) cc_final: 0.7145 (ttmm) REVERT: A 796 TRP cc_start: 0.7409 (m100) cc_final: 0.6993 (m100) REVERT: A 889 GLU cc_start: 0.5240 (mm-30) cc_final: 0.4331 (mt-10) REVERT: B 757 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.5261 (tmm) REVERT: B 761 PHE cc_start: 0.7041 (m-10) cc_final: 0.6681 (m-10) REVERT: B 765 LEU cc_start: 0.7783 (mm) cc_final: 0.7577 (mm) REVERT: B 775 ILE cc_start: 0.8860 (mt) cc_final: 0.8628 (pt) REVERT: B 873 THR cc_start: 0.8526 (m) cc_final: 0.8303 (m) REVERT: C 819 LEU cc_start: 0.3122 (OUTLIER) cc_final: 0.2839 (pp) REVERT: C 861 MET cc_start: 0.7163 (ttp) cc_final: 0.6803 (ttp) REVERT: C 889 GLU cc_start: 0.4927 (mm-30) cc_final: 0.4317 (mm-30) REVERT: C 965 ASP cc_start: 0.9496 (p0) cc_final: 0.9282 (p0) REVERT: D 735 PHE cc_start: 0.8440 (t80) cc_final: 0.7963 (t80) REVERT: D 757 MET cc_start: 0.5096 (tpp) cc_final: 0.4708 (tmm) REVERT: D 825 PHE cc_start: 0.8734 (m-80) cc_final: 0.8180 (m-80) REVERT: D 832 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8217 (ttt-90) REVERT: D 845 SER cc_start: 0.9054 (t) cc_final: 0.8810 (p) REVERT: D 861 MET cc_start: 0.8507 (tpp) cc_final: 0.7739 (ttp) REVERT: G 23 LEU cc_start: 0.8311 (mm) cc_final: 0.8076 (tt) REVERT: H 6 MET cc_start: 0.8075 (mmp) cc_final: 0.7703 (mtm) REVERT: H 19 MET cc_start: 0.4910 (mtm) cc_final: 0.3916 (ptp) REVERT: H 24 TRP cc_start: 0.7766 (p90) cc_final: 0.7341 (p-90) REVERT: I 29 ILE cc_start: 0.6739 (mt) cc_final: 0.6277 (pt) REVERT: I 98 THR cc_start: 0.7688 (m) cc_final: 0.7242 (p) REVERT: I 164 TRP cc_start: 0.7402 (m-90) cc_final: 0.7149 (m-90) REVERT: I 176 MET cc_start: 0.4779 (tmm) cc_final: 0.4489 (tmm) REVERT: I 190 HIS cc_start: 0.4857 (OUTLIER) cc_final: 0.4551 (t-90) REVERT: J 89 GLU cc_start: 0.7242 (tp30) cc_final: 0.6641 (mt-10) REVERT: J 95 TYR cc_start: 0.6680 (m-80) cc_final: 0.6313 (m-80) REVERT: J 114 GLN cc_start: 0.7015 (tp40) cc_final: 0.5465 (pm20) REVERT: K 11 MET cc_start: 0.5318 (ttp) cc_final: 0.4937 (ttp) REVERT: L 34 MET cc_start: 0.8326 (mmp) cc_final: 0.8056 (mmm) REVERT: L 93 MET cc_start: 0.7961 (ptp) cc_final: 0.7745 (ptm) outliers start: 67 outliers final: 55 residues processed: 378 average time/residue: 0.2632 time to fit residues: 149.3561 Evaluate side-chains 397 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 338 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain E residue 25 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 739 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 824 SER Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 742 LEU Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 190 HIS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 182 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 1.9990 chunk 191 optimal weight: 0.4980 chunk 117 optimal weight: 0.0000 chunk 91 optimal weight: 0.7980 chunk 133 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16772 Z= 0.200 Angle : 0.676 14.495 22780 Z= 0.336 Chirality : 0.043 0.229 2612 Planarity : 0.004 0.055 2802 Dihedral : 4.705 24.002 2198 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.04 % Allowed : 18.30 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.46 (0.19), residues: 2028 helix: 1.32 (0.19), residues: 822 sheet: -0.12 (0.28), residues: 366 loop : -2.13 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP F 24 HIS 0.006 0.001 HIS D 963 PHE 0.024 0.001 PHE A 791 TYR 0.013 0.001 TYR A 866 ARG 0.013 0.000 ARG E 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4056 Ramachandran restraints generated. 2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 351 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 LYS cc_start: 0.7429 (ttpp) cc_final: 0.7095 (ttmm) REVERT: A 783 ARG cc_start: 0.8135 (mtp180) cc_final: 0.7731 (mtp180) REVERT: A 796 TRP cc_start: 0.7368 (m100) cc_final: 0.6987 (m100) REVERT: A 889 GLU cc_start: 0.5182 (mm-30) cc_final: 0.4277 (mt-10) REVERT: A 945 MET cc_start: 0.8743 (ttp) cc_final: 0.8486 (ttp) REVERT: B 757 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.5076 (tmm) REVERT: B 761 PHE cc_start: 0.7043 (m-10) cc_final: 0.6708 (m-10) REVERT: B 775 ILE cc_start: 0.8858 (mt) cc_final: 0.8627 (pt) REVERT: B 873 THR cc_start: 0.8477 (m) cc_final: 0.8254 (m) REVERT: C 819 LEU cc_start: 0.3121 (OUTLIER) cc_final: 0.2849 (pp) REVERT: C 861 MET cc_start: 0.7154 (ttp) cc_final: 0.6793 (ttp) REVERT: C 889 GLU cc_start: 0.4868 (mm-30) cc_final: 0.4276 (mm-30) REVERT: C 959 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8031 (mm-30) REVERT: C 965 ASP cc_start: 0.9488 (p0) cc_final: 0.9267 (p0) REVERT: D 735 PHE cc_start: 0.8438 (t80) cc_final: 0.7942 (t80) REVERT: D 757 MET cc_start: 0.5083 (tpp) cc_final: 0.4711 (tmm) REVERT: D 825 PHE cc_start: 0.8646 (m-80) cc_final: 0.8130 (m-80) REVERT: D 832 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8216 (ttt-90) REVERT: D 845 SER cc_start: 0.9054 (t) cc_final: 0.8810 (p) REVERT: D 861 MET cc_start: 0.8460 (tpp) cc_final: 0.7670 (ttp) REVERT: G 19 MET cc_start: 0.6296 (tpt) cc_final: 0.5666 (tpt) REVERT: G 23 LEU cc_start: 0.8490 (mm) cc_final: 0.8199 (tt) REVERT: H 6 MET cc_start: 0.8085 (mmp) cc_final: 0.7720 (mtm) REVERT: H 19 MET cc_start: 0.4656 (mtm) cc_final: 0.3945 (ptp) REVERT: H 24 TRP cc_start: 0.7760 (p90) cc_final: 0.7337 (p-90) REVERT: I 29 ILE cc_start: 0.6735 (mt) cc_final: 0.6265 (pt) REVERT: I 98 THR cc_start: 0.7668 (m) cc_final: 0.7221 (p) REVERT: I 164 TRP cc_start: 0.7394 (m-90) cc_final: 0.7147 (m-90) REVERT: I 176 MET cc_start: 0.4773 (tmm) cc_final: 0.4492 (tmm) REVERT: I 190 HIS cc_start: 0.4886 (OUTLIER) cc_final: 0.4582 (t-90) REVERT: J 95 TYR cc_start: 0.6685 (m-80) cc_final: 0.6359 (m-80) REVERT: J 114 GLN cc_start: 0.6988 (tp40) cc_final: 0.5401 (pm20) REVERT: K 11 MET cc_start: 0.5243 (ttp) cc_final: 0.4784 (ttp) REVERT: K 98 THR cc_start: 0.7651 (m) cc_final: 0.7054 (p) REVERT: L 34 MET cc_start: 0.8299 (mmp) cc_final: 0.8046 (mmm) REVERT: L 93 MET cc_start: 0.7960 (ptp) cc_final: 0.7654 (ptm) REVERT: L 154 TYR cc_start: 0.6469 (p90) cc_final: 0.5904 (p90) outliers start: 56 outliers final: 50 residues processed: 380 average time/residue: 0.2611 time to fit residues: 148.8569 Evaluate side-chains 398 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 344 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 721 HIS Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 847 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 942 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 938 VAL Chi-restraints excluded: chain D residue 721 HIS Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 824 SER Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 832 ARG Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 851 ILE Chi-restraints excluded: chain D residue 882 GLU Chi-restraints excluded: chain D residue 942 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 16 CYS Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 190 HIS Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 25 VAL Chi-restraints excluded: chain K residue 107 ILE Chi-restraints excluded: chain K residue 109 ARG Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 182 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN B 954 GLN ** B 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.218885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136292 restraints weight = 25771.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132967 restraints weight = 13992.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135146 restraints weight = 8654.854| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16772 Z= 0.240 Angle : 0.693 13.132 22780 Z= 0.344 Chirality : 0.044 0.231 2612 Planarity : 0.004 0.057 2802 Dihedral : 4.783 24.600 2198 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.42 % Allowed : 18.40 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.53 (0.19), residues: 2028 helix: 1.19 (0.19), residues: 834 sheet: -0.12 (0.28), residues: 366 loop : -2.14 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP F 24 HIS 0.006 0.001 HIS D 963 PHE 0.023 0.001 PHE A 791 TYR 0.017 0.001 TYR A 723 ARG 0.011 0.000 ARG E 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3869.39 seconds wall clock time: 70 minutes 12.38 seconds (4212.38 seconds total)