Starting phenix.real_space_refine (version: dev) on Wed Feb 22 02:30:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4q_0341/02_2023/6n4q_0341_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4q_0341/02_2023/6n4q_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_0341/02_2023/6n4q_0341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4q_0341/02_2023/6n4q_0341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4q_0341/02_2023/6n4q_0341_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4q_0341/02_2023/6n4q_0341_neut.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 9.18, per 1000 atoms: 0.56 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: 6.16 Conformation dependent library (CDL) restraints added in 2.3 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: 0.97 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: 5.21 Time building geometry restraints manager: 6.86 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.750 Check model and map are aligned: 0.240 Process input model: 42.140 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 % 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 *********************** 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 : 2.007 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 outliers start: 2 outliers final: 0 residues processed: 540 average time/residue: 0.2993 time to fit residues: 232.8077 Evaluate side-chains 364 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 1.835 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4838 ------------------------------------------------------------------------------- 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: 0.7980 chunk 81 optimal weight: 0.9980 chunk 158 optimal weight: 30.0000 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 117 optimal weight: 0.0030 chunk 183 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 763 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 ASN ** C 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 746 ASN D 874 GLN D 896 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 HIS I 191 ASN I 213 ASN J 99 HIS J 205 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: 0.7295 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 16772 Z= 0.248 Angle : 0.691 9.060 22780 Z= 0.366 Chirality : 0.044 0.185 2612 Planarity : 0.005 0.065 2802 Dihedral : 5.533 28.428 2198 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 3.20 % 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: -1.95 (0.18), residues: 2028 helix: 0.03 (0.18), residues: 786 sheet: -1.18 (0.27), residues: 376 loop : -2.63 (0.19), residues: 866 *********************** 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 474 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 415 time to evaluate : 1.776 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 outliers start: 59 outliers final: 38 residues processed: 439 average time/residue: 0.2758 time to fit residues: 180.5841 Evaluate side-chains 397 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 359 time to evaluate : 1.937 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1753 time to fit residues: 14.2199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 0.4980 chunk 56 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 124 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 968 ASN B 874 GLN ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 ASN K 39 GLN L 39 GLN L 205 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 16772 Z= 0.295 Angle : 0.691 11.768 22780 Z= 0.358 Chirality : 0.043 0.211 2612 Planarity : 0.005 0.058 2802 Dihedral : 5.331 34.228 2198 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 1.52 % 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: -1.54 (0.18), residues: 2028 helix: 0.46 (0.18), residues: 824 sheet: -0.98 (0.27), residues: 380 loop : -2.62 (0.19), residues: 824 *********************** 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 405 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 377 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 395 average time/residue: 0.2677 time to fit residues: 159.6585 Evaluate side-chains 360 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 344 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1610 time to fit residues: 7.1028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 95 optimal weight: 0.0770 chunk 20 optimal weight: 0.5980 chunk 87 optimal weight: 0.0050 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 174 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 overall best weight: 0.7154 ------------------------------------------------------------------------------- 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** K 39 GLN L 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 16772 Z= 0.237 Angle : 0.659 15.065 22780 Z= 0.335 Chirality : 0.043 0.265 2612 Planarity : 0.004 0.064 2802 Dihedral : 5.106 26.397 2198 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 1.95 % 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: -1.07 (0.19), residues: 2028 helix: 1.05 (0.19), residues: 800 sheet: -0.89 (0.26), residues: 400 loop : -2.44 (0.19), residues: 828 *********************** 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 405 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 369 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 386 average time/residue: 0.2695 time to fit residues: 157.0887 Evaluate side-chains 369 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 347 time to evaluate : 1.902 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1477 time to fit residues: 8.8747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 874 GLN ** C 896 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: 0.7325 moved from start: 0.3910 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= 0.256 Angle : 0.657 10.739 22780 Z= 0.333 Chirality : 0.043 0.195 2612 Planarity : 0.004 0.064 2802 Dihedral : 5.016 26.387 2198 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer Outliers : 1.03 % 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: 1.11 (0.19), residues: 822 sheet: -0.57 (0.27), residues: 386 loop : -2.47 (0.20), residues: 820 *********************** 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 379 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 360 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 371 average time/residue: 0.2694 time to fit residues: 151.6049 Evaluate side-chains 352 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 344 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1423 time to fit residues: 4.7354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 195 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 102 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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** J 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16772 Z= 0.186 Angle : 0.644 9.271 22780 Z= 0.322 Chirality : 0.042 0.203 2612 Planarity : 0.004 0.054 2802 Dihedral : 4.812 24.381 2198 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer Outliers : 1.52 % 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: -0.73 (0.19), residues: 2028 helix: 1.25 (0.19), residues: 826 sheet: -0.41 (0.28), residues: 386 loop : -2.42 (0.20), residues: 816 *********************** 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 395 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 367 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 378 average time/residue: 0.2715 time to fit residues: 154.1130 Evaluate side-chains 361 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 345 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2174 time to fit residues: 8.2790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 chunk 142 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 194 optimal weight: 9.9990 chunk 121 optimal weight: 0.0570 chunk 118 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 90 GLN L 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4293 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= 0.202 Angle : 0.663 11.108 22780 Z= 0.332 Chirality : 0.043 0.210 2612 Planarity : 0.004 0.047 2802 Dihedral : 4.796 24.219 2198 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 0.92 % 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: 1.23 (0.19), residues: 826 sheet: -0.30 (0.28), residues: 386 loop : -2.30 (0.20), residues: 816 *********************** 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 367 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 350 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 358 average time/residue: 0.2701 time to fit residues: 146.7562 Evaluate side-chains 345 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 337 time to evaluate : 3.061 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1788 time to fit residues: 5.6245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.0020 chunk 123 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 153 optimal weight: 9.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 ASN ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 GLN ** B 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4434 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= 0.208 Angle : 0.683 11.101 22780 Z= 0.339 Chirality : 0.043 0.218 2612 Planarity : 0.004 0.044 2802 Dihedral : 4.793 22.793 2198 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 1.25 % 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: -0.61 (0.19), residues: 2028 helix: 1.24 (0.19), residues: 826 sheet: -0.22 (0.27), residues: 386 loop : -2.31 (0.20), residues: 816 *********************** 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 371 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 348 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 357 average time/residue: 0.2697 time to fit residues: 144.8309 Evaluate side-chains 353 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 338 time to evaluate : 1.934 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1534 time to fit residues: 6.9649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.6980 chunk 186 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 961 GLN B 954 GLN ** B 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 ASN I 167 GLN ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 16772 Z= 0.254 Angle : 0.707 15.521 22780 Z= 0.349 Chirality : 0.043 0.231 2612 Planarity : 0.004 0.041 2802 Dihedral : 4.831 23.963 2198 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 0.65 % 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: -0.65 (0.19), residues: 2028 helix: 1.17 (0.19), residues: 832 sheet: -0.23 (0.27), residues: 386 loop : -2.32 (0.20), residues: 810 *********************** 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 352 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 340 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 345 average time/residue: 0.2697 time to fit residues: 140.5950 Evaluate side-chains 345 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 336 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1513 time to fit residues: 5.1021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 91 optimal weight: 0.5980 chunk 133 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 185 optimal weight: 0.0870 chunk 160 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 16772 Z= 0.192 Angle : 0.691 12.456 22780 Z= 0.341 Chirality : 0.043 0.277 2612 Planarity : 0.004 0.048 2802 Dihedral : 4.819 25.506 2198 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 0.33 % 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: -0.51 (0.19), residues: 2028 helix: 1.34 (0.19), residues: 820 sheet: -0.16 (0.27), residues: 386 loop : -2.25 (0.21), residues: 822 ********************** 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 356 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 350 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 351 average time/residue: 0.2734 time to fit residues: 146.7618 Evaluate side-chains 342 residues out of total 1846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 338 time to evaluate : 1.842 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1440 time to fit residues: 3.7121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 164 optimal weight: 0.0980 chunk 20 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 966 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.220575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136389 restraints weight = 25729.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135526 restraints weight = 14212.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136230 restraints weight = 8942.963| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 16772 Z= 0.225 Angle : 0.712 14.443 22780 Z= 0.350 Chirality : 0.043 0.222 2612 Planarity : 0.004 0.054 2802 Dihedral : 4.831 27.565 2198 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 0.38 % 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: -0.55 (0.19), residues: 2028 helix: 1.26 (0.19), residues: 832 sheet: -0.14 (0.27), residues: 386 loop : -2.29 (0.21), residues: 810 =============================================================================== Job complete usr+sys time: 3689.27 seconds wall clock time: 67 minutes 14.57 seconds (4034.57 seconds total)