Starting phenix.real_space_refine on Sat Mar 16 19:18:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/03_2024/6n4r_0342_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/03_2024/6n4r_0342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/03_2024/6n4r_0342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/03_2024/6n4r_0342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/03_2024/6n4r_0342_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/03_2024/6n4r_0342_neut.pdb" } resolution = 4.2 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= 0.003 sd= 0.469 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 118 5.16 5 C 10074 2.51 5 N 2468 2.21 5 O 2784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 788": "NH1" <-> "NH2" Residue "C ARG 783": "NH1" <-> "NH2" Residue "D ARG 788": "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" Residue "A ARG 783": "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: 15444 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 8, 'TRANS': 216} Chain: "C" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1984 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1841 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 8, 'TRANS': 216} 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: "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: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 213} 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: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 213} Chain: "A" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1984 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 234} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 7.49, per 1000 atoms: 0.48 Number of scatterers: 15444 At special positions: 0 Unit cell: (142.8, 147.6, 172.8, 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 118 16.00 O 2784 8.00 N 2468 7.00 C 10074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS C 941 " - pdb=" SG CYS A 941 " distance=2.04 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.03 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=2.03 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=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS I 135 " - pdb=" SG CYS I 195 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.04 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: 4.64 Conformation dependent library (CDL) restraints added in 3.0 seconds 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 24 sheets defined 43.1% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.591A pdb=" N LEU B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 752 removed outlier: 3.690A pdb=" N THR B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N MET B 750 " --> pdb=" O ASN B 746 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.810A pdb=" N VAL B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 786 No H-bonds generated for 'chain 'B' and resid 784 through 786' Processing helix chain 'B' and resid 789 through 794 removed outlier: 3.924A pdb=" N ASP B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 809 Processing helix chain 'B' and resid 810 through 813 removed outlier: 3.979A pdb=" N LEU B 813 " --> pdb=" O GLU B 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 813' Processing helix chain 'B' and resid 819 through 828 removed outlier: 3.598A pdb=" N LEU B 822 " --> pdb=" O LEU B 819 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER B 824 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG B 826 " --> pdb=" O ARG B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 837 removed outlier: 3.868A pdb=" N LEU B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 849 removed outlier: 4.036A pdb=" N VAL B 844 " --> pdb=" O MET B 840 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 845 " --> pdb=" O ARG B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 877 removed outlier: 3.652A pdb=" N MET B 854 " --> pdb=" O VAL B 850 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 857 " --> pdb=" O GLY B 853 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE B 870 " --> pdb=" O TYR B 866 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET B 871 " --> pdb=" O ILE B 867 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 875 " --> pdb=" O MET B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 885 Processing helix chain 'B' and resid 886 through 899 removed outlier: 4.889A pdb=" N TYR B 892 " --> pdb=" O GLY B 888 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B 899 " --> pdb=" O PHE B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 907 Processing helix chain 'B' and resid 918 through 930 Proline residue: B 924 - end of helix Processing helix chain 'B' and resid 932 through 944 removed outlier: 3.569A pdb=" N VAL B 937 " --> pdb=" O MET B 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 731 Processing helix chain 'C' and resid 732 through 751 Processing helix chain 'C' and resid 759 through 786 removed outlier: 3.759A pdb=" N ASN C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 767 " --> pdb=" O ASN C 763 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 786 " --> pdb=" O LEU C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 813 removed outlier: 3.804A pdb=" N LEU C 798 " --> pdb=" O ASP C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 828 removed outlier: 3.680A pdb=" N ARG C 823 " --> pdb=" O SER C 820 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER C 824 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 825 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG C 826 " --> pdb=" O ARG C 823 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU C 827 " --> pdb=" O SER C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 834 removed outlier: 3.938A pdb=" N LEU C 833 " --> pdb=" O ARG C 829 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 834 " --> pdb=" O VAL C 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 829 through 834' Processing helix chain 'C' and resid 837 through 849 removed outlier: 3.866A pdb=" N ARG C 841 " --> pdb=" O VAL C 837 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS C 842 " --> pdb=" O PRO C 838 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE C 843 " --> pdb=" O GLN C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 876 removed outlier: 3.833A pdb=" N MET C 854 " --> pdb=" O VAL C 850 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 859 " --> pdb=" O LEU C 855 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE C 870 " --> pdb=" O TYR C 866 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET C 871 " --> pdb=" O ILE C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 880 through 885 removed outlier: 3.832A pdb=" N PHE C 884 " --> pdb=" O PHE C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 899 removed outlier: 4.911A pdb=" N TYR C 892 " --> pdb=" O GLY C 888 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 899 " --> pdb=" O PHE C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 912 Processing helix chain 'C' and resid 918 through 959 removed outlier: 3.723A pdb=" N ILE C 923 " --> pdb=" O TRP C 919 " (cutoff:3.500A) Proline residue: C 924 - end of helix removed outlier: 3.868A pdb=" N PHE C 927 " --> pdb=" O ILE C 923 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET C 945 " --> pdb=" O CYS C 941 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 948 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN C 949 " --> pdb=" O MET C 945 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 950 " --> pdb=" O ALA C 946 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C 954 " --> pdb=" O GLN C 950 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N HIS C 955 " --> pdb=" O LYS C 951 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 731 Processing helix chain 'D' and resid 732 through 752 removed outlier: 3.690A pdb=" N THR D 736 " --> pdb=" O SER D 732 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N MET D 750 " --> pdb=" O ASN D 746 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 783 removed outlier: 3.809A pdb=" N VAL D 764 " --> pdb=" O GLU D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 786 No H-bonds generated for 'chain 'D' and resid 784 through 786' Processing helix chain 'D' and resid 789 through 794 removed outlier: 3.924A pdb=" N ASP D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 809 Processing helix chain 'D' and resid 810 through 813 removed outlier: 3.979A pdb=" N LEU D 813 " --> pdb=" O GLU D 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 810 through 813' Processing helix chain 'D' and resid 819 through 828 removed outlier: 3.597A pdb=" N LEU D 822 " --> pdb=" O LEU D 819 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER D 824 " --> pdb=" O VAL D 821 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG D 826 " --> pdb=" O ARG D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 837 removed outlier: 3.868A pdb=" N LEU D 833 " --> pdb=" O ARG D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 849 removed outlier: 4.035A pdb=" N VAL D 844 " --> pdb=" O MET D 840 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER D 845 " --> pdb=" O ARG D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 877 removed outlier: 3.653A pdb=" N MET D 854 " --> pdb=" O VAL D 850 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL D 857 " --> pdb=" O GLY D 853 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE D 870 " --> pdb=" O TYR D 866 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET D 871 " --> pdb=" O ILE D 867 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN D 874 " --> pdb=" O ILE D 870 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 875 " --> pdb=" O MET D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 885 Processing helix chain 'D' and resid 886 through 899 removed outlier: 4.889A pdb=" N TYR D 892 " --> pdb=" O GLY D 888 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR D 899 " --> pdb=" O PHE D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 907 Processing helix chain 'D' and resid 918 through 930 Proline residue: D 924 - end of helix Processing helix chain 'D' and resid 932 through 944 removed outlier: 3.569A pdb=" N VAL D 937 " --> pdb=" O MET D 933 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 129 Processing helix chain 'I' and resid 184 through 188 Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.852A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.786A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'K' and resid 122 through 129 Processing helix chain 'K' and resid 184 through 188 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.852A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 76 No H-bonds generated for 'chain 'L' and resid 74 through 76' Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.787A pdb=" N ASP L 90 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR L 91 " --> pdb=" O SER L 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 87 through 91' Processing helix chain 'A' and resid 721 through 731 Processing helix chain 'A' and resid 732 through 751 Processing helix chain 'A' and resid 759 through 786 removed outlier: 3.759A pdb=" N ASN A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 767 " --> pdb=" O ASN A 763 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 813 removed outlier: 3.803A pdb=" N LEU A 798 " --> pdb=" O ASP A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 828 removed outlier: 3.680A pdb=" N ARG A 823 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER A 824 " --> pdb=" O VAL A 821 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 825 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 826 " --> pdb=" O ARG A 823 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A 827 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 834 removed outlier: 3.938A pdb=" N LEU A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 829 through 834' Processing helix chain 'A' and resid 837 through 849 removed outlier: 3.866A pdb=" N ARG A 841 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A 842 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 876 removed outlier: 3.833A pdb=" N MET A 854 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET A 871 " --> pdb=" O ILE A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 885 removed outlier: 3.832A pdb=" N PHE A 884 " --> pdb=" O PHE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 899 removed outlier: 4.911A pdb=" N TYR A 892 " --> pdb=" O GLY A 888 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 899 " --> pdb=" O PHE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 918 through 959 removed outlier: 3.723A pdb=" N ILE A 923 " --> pdb=" O TRP A 919 " (cutoff:3.500A) Proline residue: A 924 - end of helix removed outlier: 3.868A pdb=" N PHE A 927 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET A 945 " --> pdb=" O CYS A 941 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 949 " --> pdb=" O MET A 945 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 954 " --> pdb=" O GLN A 950 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N HIS A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain 'F' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'G' and resid 19 through 21 Processing sheet with id=AA4, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 7 removed outlier: 4.118A pdb=" N SER I 7 " --> pdb=" O THR I 22 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER I 64 " --> pdb=" O THR I 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 13 removed outlier: 7.264A pdb=" N LEU I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP I 36 " --> pdb=" O TRP I 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 115 through 119 removed outlier: 5.569A pdb=" N TYR I 174 " --> pdb=" O ASN I 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 146 through 150 removed outlier: 4.005A pdb=" N ASN I 146 " --> pdb=" O THR I 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.869A pdb=" N LEU J 18 " --> pdb=" O MET J 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR J 40 " --> pdb=" O LEU J 45 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU J 45 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR J 50 " --> pdb=" O TYR J 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR J 59 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR J 111 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.861A pdb=" N GLY J 148 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR J 146 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL J 192 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLY J 148 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL J 190 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU J 150 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER J 188 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS J 152 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU J 186 " --> pdb=" O LYS J 152 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR J 154 " --> pdb=" O TYR J 184 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER J 189 " --> pdb=" O HIS J 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.861A pdb=" N GLY J 148 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR J 146 " --> pdb=" O VAL J 192 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL J 192 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLY J 148 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL J 190 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU J 150 " --> pdb=" O SER J 188 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER J 188 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS J 152 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU J 186 " --> pdb=" O LYS J 152 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR J 154 " --> pdb=" O TYR J 184 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 160 through 163 Processing sheet with id=AB6, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.119A pdb=" N SER K 7 " --> pdb=" O THR K 22 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER K 64 " --> pdb=" O THR K 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 13 removed outlier: 7.263A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP K 36 " --> pdb=" O TRP K 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 115 through 119 removed outlier: 5.568A pdb=" N TYR K 174 " --> pdb=" O ASN K 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 146 through 150 removed outlier: 4.005A pdb=" N ASN K 146 " --> pdb=" O THR K 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 3 through 6 removed outlier: 3.870A pdb=" N LEU L 18 " --> pdb=" O MET L 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR L 40 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU L 45 " --> pdb=" O THR L 40 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR L 50 " --> pdb=" O TYR L 59 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR L 59 " --> pdb=" O THR L 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.319A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR L 111 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.861A pdb=" N GLY L 148 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR L 146 " --> pdb=" O VAL L 192 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL L 192 " --> pdb=" O THR L 146 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLY L 148 " --> pdb=" O VAL L 190 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL L 190 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU L 150 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER L 188 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS L 152 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU L 186 " --> pdb=" O LYS L 152 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR L 154 " --> pdb=" O TYR L 184 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER L 189 " --> pdb=" O HIS L 173 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.861A pdb=" N GLY L 148 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR L 146 " --> pdb=" O VAL L 192 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL L 192 " --> pdb=" O THR L 146 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLY L 148 " --> pdb=" O VAL L 190 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL L 190 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU L 150 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER L 188 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS L 152 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU L 186 " --> pdb=" O LYS L 152 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR L 154 " --> pdb=" O TYR L 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 160 through 163 712 hydrogen bonds defined for protein. 1962 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: 4.81 Time building geometry restraints manager: 5.16 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: 4563 1.34 - 1.46: 4159 1.46 - 1.58: 6942 1.58 - 1.71: 0 1.71 - 1.83: 188 Bond restraints: 15852 Sorted by residual: bond pdb=" CB VAL B 932 " pdb=" CG2 VAL B 932 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.11e+00 bond pdb=" CB VAL D 932 " pdb=" CG2 VAL D 932 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.00e+00 bond pdb=" CG LEU A 887 " pdb=" CD2 LEU A 887 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.99e+00 bond pdb=" CG LEU C 887 " pdb=" CD2 LEU C 887 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.95e+00 bond pdb=" CA ILE B 851 " pdb=" C ILE B 851 " ideal model delta sigma weight residual 1.524 1.545 -0.021 1.11e-02 8.12e+03 3.49e+00 ... (remaining 15847 not shown) Histogram of bond angle deviations from ideal: 98.66 - 106.13: 397 106.13 - 113.61: 8827 113.61 - 121.08: 7910 121.08 - 128.56: 4228 128.56 - 136.04: 178 Bond angle restraints: 21540 Sorted by residual: angle pdb=" C THR B 758 " pdb=" N GLU B 759 " pdb=" CA GLU B 759 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C THR D 758 " pdb=" N GLU D 759 " pdb=" CA GLU D 759 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" N ILE C 851 " pdb=" CA ILE C 851 " pdb=" C ILE C 851 " ideal model delta sigma weight residual 108.88 118.01 -9.13 2.16e+00 2.14e-01 1.79e+01 angle pdb=" N ILE A 851 " pdb=" CA ILE A 851 " pdb=" C ILE A 851 " ideal model delta sigma weight residual 108.88 117.97 -9.09 2.16e+00 2.14e-01 1.77e+01 angle pdb=" C GLY I 51 " pdb=" N THR I 52 " pdb=" CA THR I 52 " ideal model delta sigma weight residual 122.61 129.04 -6.43 1.56e+00 4.11e-01 1.70e+01 ... (remaining 21535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 8730 15.00 - 29.99: 470 29.99 - 44.99: 136 44.99 - 59.99: 5 59.99 - 74.99: 12 Dihedral angle restraints: 9353 sinusoidal: 3667 harmonic: 5686 Sorted by residual: dihedral pdb=" CB CYS C 941 " pdb=" SG CYS C 941 " pdb=" SG CYS A 941 " pdb=" CB CYS A 941 " ideal model delta sinusoidal sigma weight residual -86.00 -142.20 56.20 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CA PHE D 931 " pdb=" C PHE D 931 " pdb=" N VAL D 932 " pdb=" CA VAL D 932 " ideal model delta harmonic sigma weight residual 180.00 149.28 30.72 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA PHE B 931 " pdb=" C PHE B 931 " pdb=" N VAL B 932 " pdb=" CA VAL B 932 " ideal model delta harmonic sigma weight residual 180.00 149.28 30.72 0 5.00e+00 4.00e-02 3.77e+01 ... (remaining 9350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1750 0.055 - 0.110: 546 0.110 - 0.165: 146 0.165 - 0.220: 19 0.220 - 0.275: 5 Chirality restraints: 2466 Sorted by residual: chirality pdb=" CB VAL D 850 " pdb=" CA VAL D 850 " pdb=" CG1 VAL D 850 " pdb=" CG2 VAL D 850 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB VAL B 850 " pdb=" CA VAL B 850 " pdb=" CG1 VAL B 850 " pdb=" CG2 VAL B 850 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE L 70 " pdb=" CA ILE L 70 " pdb=" CG1 ILE L 70 " pdb=" CG2 ILE L 70 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2463 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 931 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.31e+01 pdb=" C PHE C 931 " -0.063 2.00e-02 2.50e+03 pdb=" O PHE C 931 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL C 932 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 931 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C PHE A 931 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE A 931 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 932 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 930 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C THR A 930 " 0.056 2.00e-02 2.50e+03 pdb=" O THR A 930 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE A 931 " -0.019 2.00e-02 2.50e+03 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2363 2.76 - 3.29: 14506 3.29 - 3.83: 24476 3.83 - 4.36: 26874 4.36 - 4.90: 45793 Nonbonded interactions: 114012 Sorted by model distance: nonbonded pdb=" NZ LYS L 218 " pdb=" OE2 GLU L 220 " model vdw 2.222 2.520 nonbonded pdb=" NZ LYS J 218 " pdb=" OE2 GLU J 220 " model vdw 2.222 2.520 nonbonded pdb=" OE2 GLU D 779 " pdb=" NH2 ARG D 783 " model vdw 2.270 2.520 nonbonded pdb=" OE2 GLU B 779 " pdb=" NH2 ARG B 783 " model vdw 2.270 2.520 nonbonded pdb=" O LEU B 802 " pdb=" OG1 THR B 805 " model vdw 2.297 2.440 ... (remaining 114007 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' and resid 720 through 944) selection = (chain 'B' and (resid 720 through 736 or (resid 737 and (name N or name CA or na \ me C or name O or name CB )) or resid 738 through 944)) selection = (chain 'C' and resid 720 through 944) selection = (chain 'D' and (resid 720 through 736 or (resid 737 and (name N or name CA or na \ me C or name O or name CB )) or resid 738 through 944)) } 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: 2.630 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: 10.010 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 38.930 Find NCS groups from input model: 1.070 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 0.077 15852 Z= 0.511 Angle : 1.074 12.449 21540 Z= 0.571 Chirality : 0.057 0.275 2466 Planarity : 0.008 0.073 2634 Dihedral : 10.265 74.986 5610 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.23 % Allowed : 3.11 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.27 (0.16), residues: 1918 helix: -2.08 (0.16), residues: 676 sheet: -0.92 (0.25), residues: 402 loop : -2.83 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 883 HIS 0.008 0.002 HIS B 721 PHE 0.031 0.004 PHE A 927 TYR 0.026 0.003 TYR C 741 ARG 0.011 0.001 ARG A 879 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 571 time to evaluate : 1.945 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: B 765 LEU cc_start: 0.9072 (mt) cc_final: 0.8842 (mt) REVERT: B 840 MET cc_start: 0.8458 (mmt) cc_final: 0.8150 (mmt) REVERT: B 854 MET cc_start: 0.8390 (mmm) cc_final: 0.8043 (mmm) REVERT: B 874 GLN cc_start: 0.8546 (mt0) cc_final: 0.8313 (mt0) REVERT: B 889 GLU cc_start: 0.7733 (mt-10) cc_final: 0.6804 (mm-30) REVERT: B 917 TYR cc_start: 0.8965 (m-10) cc_final: 0.8608 (m-10) REVERT: C 729 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8496 (tp) REVERT: C 784 ILE cc_start: 0.8710 (pp) cc_final: 0.8370 (tt) REVERT: D 780 ILE cc_start: 0.8616 (tp) cc_final: 0.8404 (tp) REVERT: D 797 SER cc_start: 0.9035 (m) cc_final: 0.8791 (p) REVERT: D 854 MET cc_start: 0.8413 (mmm) cc_final: 0.8078 (mmm) REVERT: D 874 GLN cc_start: 0.8545 (mt0) cc_final: 0.8309 (mt0) REVERT: D 889 GLU cc_start: 0.7727 (mt-10) cc_final: 0.6776 (mm-30) REVERT: D 917 TYR cc_start: 0.8971 (m-10) cc_final: 0.8601 (m-10) REVERT: G 19 MET cc_start: 0.5686 (mtm) cc_final: 0.5373 (mtm) REVERT: I 27 LEU cc_start: 0.8977 (tp) cc_final: 0.8472 (mp) REVERT: I 28 SER cc_start: 0.7962 (t) cc_final: 0.7589 (t) REVERT: I 31 SER cc_start: 0.9351 (m) cc_final: 0.9053 (t) REVERT: I 37 TYR cc_start: 0.8714 (m-80) cc_final: 0.8340 (m-10) REVERT: I 63 PHE cc_start: 0.7958 (m-10) cc_final: 0.7739 (m-10) REVERT: I 73 SER cc_start: 0.8975 (p) cc_final: 0.8774 (t) REVERT: J 13 LYS cc_start: 0.8971 (mttp) cc_final: 0.8539 (tppt) REVERT: J 86 LEU cc_start: 0.8876 (mt) cc_final: 0.8598 (mp) REVERT: J 163 TRP cc_start: 0.3711 (m100) cc_final: 0.3277 (m100) REVERT: K 73 SER cc_start: 0.9041 (p) cc_final: 0.8749 (t) REVERT: K 91 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8473 (tm-30) REVERT: L 3 GLN cc_start: 0.7578 (mm110) cc_final: 0.7365 (mm-40) REVERT: L 13 LYS cc_start: 0.8982 (mttp) cc_final: 0.8671 (tppt) REVERT: L 86 LEU cc_start: 0.8868 (mt) cc_final: 0.8538 (mp) REVERT: L 90 ASP cc_start: 0.9029 (m-30) cc_final: 0.8817 (m-30) REVERT: L 183 LEU cc_start: 0.7650 (mt) cc_final: 0.7079 (pp) REVERT: A 729 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8450 (tp) REVERT: A 779 GLU cc_start: 0.7939 (tt0) cc_final: 0.7437 (tt0) REVERT: A 784 ILE cc_start: 0.8627 (pp) cc_final: 0.8272 (tt) REVERT: A 831 PHE cc_start: 0.8005 (m-10) cc_final: 0.7688 (t80) REVERT: A 933 MET cc_start: 0.8480 (mmt) cc_final: 0.8177 (mmm) outliers start: 4 outliers final: 0 residues processed: 571 average time/residue: 0.2924 time to fit residues: 239.4190 Evaluate side-chains 397 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 395 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.7980 chunk 144 optimal weight: 0.0270 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 ASN ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 ASN J 39 GLN J 77 ASN L 39 GLN A 754 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15852 Z= 0.217 Angle : 0.670 7.636 21540 Z= 0.348 Chirality : 0.042 0.175 2466 Planarity : 0.005 0.053 2634 Dihedral : 5.392 22.426 2086 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.23 % Allowed : 3.74 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.18), residues: 1918 helix: -0.63 (0.19), residues: 720 sheet: -0.49 (0.26), residues: 410 loop : -2.43 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 883 HIS 0.007 0.001 HIS C 787 PHE 0.027 0.002 PHE D 749 TYR 0.010 0.001 TYR D 866 ARG 0.007 0.001 ARG B 832 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 487 time to evaluate : 1.743 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: B 765 LEU cc_start: 0.9054 (mt) cc_final: 0.8782 (mt) REVERT: B 780 ILE cc_start: 0.8480 (tp) cc_final: 0.8175 (tp) REVERT: B 840 MET cc_start: 0.8450 (mmt) cc_final: 0.8136 (mmt) REVERT: B 874 GLN cc_start: 0.8500 (mt0) cc_final: 0.8091 (mt0) REVERT: B 889 GLU cc_start: 0.7495 (mt-10) cc_final: 0.6838 (mm-30) REVERT: C 722 MET cc_start: 0.8385 (pmm) cc_final: 0.7419 (pmm) REVERT: C 773 THR cc_start: 0.9463 (p) cc_final: 0.9234 (p) REVERT: C 775 ILE cc_start: 0.9329 (mt) cc_final: 0.9128 (mm) REVERT: C 831 PHE cc_start: 0.7879 (m-10) cc_final: 0.7397 (t80) REVERT: D 780 ILE cc_start: 0.8641 (tp) cc_final: 0.8429 (tp) REVERT: D 797 SER cc_start: 0.9008 (m) cc_final: 0.8803 (p) REVERT: D 874 GLN cc_start: 0.8481 (mt0) cc_final: 0.8140 (mt0) REVERT: D 889 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6755 (mm-30) REVERT: I 31 SER cc_start: 0.9466 (m) cc_final: 0.9118 (t) REVERT: I 37 TYR cc_start: 0.8806 (m-80) cc_final: 0.8486 (m-10) REVERT: I 59 VAL cc_start: 0.8797 (t) cc_final: 0.8409 (p) REVERT: I 91 GLN cc_start: 0.9399 (pp30) cc_final: 0.9182 (pp30) REVERT: I 176 MET cc_start: 0.6345 (ttp) cc_final: 0.5260 (ptp) REVERT: J 13 LYS cc_start: 0.8915 (mttp) cc_final: 0.8654 (tppt) REVERT: J 83 MET cc_start: 0.8009 (mtm) cc_final: 0.7591 (mtm) REVERT: K 31 SER cc_start: 0.9521 (m) cc_final: 0.9152 (t) REVERT: K 91 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8393 (tm-30) REVERT: K 214 GLU cc_start: 0.7136 (pp20) cc_final: 0.6497 (pp20) REVERT: L 13 LYS cc_start: 0.8941 (mttp) cc_final: 0.8718 (tppt) REVERT: L 183 LEU cc_start: 0.7718 (mt) cc_final: 0.7002 (pp) REVERT: A 722 MET cc_start: 0.8416 (pmm) cc_final: 0.7362 (pmm) REVERT: A 773 THR cc_start: 0.9497 (p) cc_final: 0.9258 (p) REVERT: A 831 PHE cc_start: 0.7932 (m-10) cc_final: 0.7535 (t80) outliers start: 4 outliers final: 0 residues processed: 487 average time/residue: 0.2847 time to fit residues: 196.6033 Evaluate side-chains 375 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.6980 chunk 53 optimal weight: 0.0870 chunk 143 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 186 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 ASN D 769 ASN ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS J 77 ASN L 77 ASN A 935 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15852 Z= 0.220 Angle : 0.655 10.699 21540 Z= 0.335 Chirality : 0.042 0.148 2466 Planarity : 0.005 0.053 2634 Dihedral : 5.136 21.932 2086 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.19), residues: 1918 helix: -0.10 (0.19), residues: 716 sheet: -0.25 (0.27), residues: 410 loop : -2.29 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 883 HIS 0.006 0.001 HIS B 755 PHE 0.019 0.001 PHE D 749 TYR 0.010 0.001 TYR K 193 ARG 0.011 0.001 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 1.720 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: B 780 ILE cc_start: 0.8619 (tp) cc_final: 0.8413 (tp) REVERT: B 840 MET cc_start: 0.8459 (mmt) cc_final: 0.8160 (mmt) REVERT: B 854 MET cc_start: 0.8248 (mmm) cc_final: 0.7992 (mmm) REVERT: B 889 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6874 (mm-30) REVERT: C 874 GLN cc_start: 0.8319 (tp40) cc_final: 0.8094 (tp40) REVERT: D 840 MET cc_start: 0.8473 (mmt) cc_final: 0.8133 (mmt) REVERT: D 841 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7933 (mmm160) REVERT: D 854 MET cc_start: 0.8265 (mmm) cc_final: 0.8019 (mmm) REVERT: D 889 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6906 (mm-30) REVERT: E 19 MET cc_start: 0.6503 (tpp) cc_final: 0.6052 (mmm) REVERT: I 27 LEU cc_start: 0.8994 (tp) cc_final: 0.8477 (mp) REVERT: I 28 SER cc_start: 0.8111 (t) cc_final: 0.7710 (t) REVERT: I 31 SER cc_start: 0.9504 (m) cc_final: 0.9200 (t) REVERT: I 37 TYR cc_start: 0.8816 (m-80) cc_final: 0.8576 (m-10) REVERT: I 59 VAL cc_start: 0.8886 (t) cc_final: 0.8463 (p) REVERT: I 91 GLN cc_start: 0.9268 (pp30) cc_final: 0.9044 (pp30) REVERT: I 176 MET cc_start: 0.6354 (ttp) cc_final: 0.5549 (ptp) REVERT: J 13 LYS cc_start: 0.8904 (mttp) cc_final: 0.8618 (tppt) REVERT: J 76 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8191 (tmtt) REVERT: J 86 LEU cc_start: 0.8600 (mp) cc_final: 0.8376 (mt) REVERT: J 183 LEU cc_start: 0.8431 (mt) cc_final: 0.7728 (pp) REVERT: K 31 SER cc_start: 0.9577 (m) cc_final: 0.9253 (t) REVERT: L 13 LYS cc_start: 0.8941 (mttp) cc_final: 0.8657 (tppt) REVERT: L 183 LEU cc_start: 0.7787 (mt) cc_final: 0.7067 (pp) REVERT: A 831 PHE cc_start: 0.7959 (m-10) cc_final: 0.7476 (t80) REVERT: A 874 GLN cc_start: 0.8422 (tt0) cc_final: 0.8203 (tm-30) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.2666 time to fit residues: 177.7641 Evaluate side-chains 355 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 19 optimal weight: 0.2980 chunk 82 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 173 optimal weight: 0.0270 chunk 183 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 164 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN B 896 GLN C 896 GLN C 935 ASN D 769 ASN D 896 GLN J 77 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN A 769 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15852 Z= 0.180 Angle : 0.618 8.713 21540 Z= 0.315 Chirality : 0.042 0.175 2466 Planarity : 0.004 0.051 2634 Dihedral : 4.911 26.891 2086 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1918 helix: 0.24 (0.20), residues: 718 sheet: -0.09 (0.27), residues: 410 loop : -2.19 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 883 HIS 0.006 0.001 HIS B 755 PHE 0.027 0.001 PHE B 749 TYR 0.013 0.001 TYR L 95 ARG 0.009 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 458 time to evaluate : 1.624 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: B 840 MET cc_start: 0.8530 (mmt) cc_final: 0.8223 (mmt) REVERT: B 889 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6818 (mm-30) REVERT: C 831 PHE cc_start: 0.7916 (m-10) cc_final: 0.7304 (t80) REVERT: C 841 ARG cc_start: 0.8026 (mtt180) cc_final: 0.7811 (mpt180) REVERT: C 874 GLN cc_start: 0.8406 (tp40) cc_final: 0.8121 (tp40) REVERT: D 780 ILE cc_start: 0.8545 (tp) cc_final: 0.8304 (tp) REVERT: D 840 MET cc_start: 0.8484 (mmt) cc_final: 0.8124 (mmt) REVERT: D 874 GLN cc_start: 0.8230 (mt0) cc_final: 0.7759 (mt0) REVERT: D 889 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6758 (mm-30) REVERT: E 19 MET cc_start: 0.6366 (tpp) cc_final: 0.6027 (mmm) REVERT: G 24 TRP cc_start: 0.8365 (p90) cc_final: 0.8067 (p90) REVERT: H 6 MET cc_start: 0.7397 (mtp) cc_final: 0.6947 (mpp) REVERT: I 31 SER cc_start: 0.9500 (m) cc_final: 0.9208 (t) REVERT: I 37 TYR cc_start: 0.8884 (m-80) cc_final: 0.8573 (m-10) REVERT: I 59 VAL cc_start: 0.8914 (t) cc_final: 0.8568 (p) REVERT: I 91 GLN cc_start: 0.9283 (pp30) cc_final: 0.8991 (pp30) REVERT: I 176 MET cc_start: 0.6396 (ttp) cc_final: 0.5450 (ptm) REVERT: J 86 LEU cc_start: 0.8575 (mp) cc_final: 0.8370 (mt) REVERT: J 182 ASP cc_start: 0.8134 (m-30) cc_final: 0.7789 (t0) REVERT: J 183 LEU cc_start: 0.8445 (mt) cc_final: 0.7640 (pp) REVERT: K 31 SER cc_start: 0.9580 (m) cc_final: 0.9233 (t) REVERT: L 3 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7693 (mm-40) REVERT: L 183 LEU cc_start: 0.7759 (mt) cc_final: 0.7042 (pp) REVERT: A 791 PHE cc_start: 0.8232 (t80) cc_final: 0.7992 (t80) REVERT: A 831 PHE cc_start: 0.7869 (m-10) cc_final: 0.7453 (t80) REVERT: A 874 GLN cc_start: 0.8395 (tt0) cc_final: 0.8131 (tm-30) outliers start: 1 outliers final: 0 residues processed: 458 average time/residue: 0.2909 time to fit residues: 191.2661 Evaluate side-chains 363 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 126 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN D 769 ASN J 77 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS A 769 ASN A 896 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15852 Z= 0.243 Angle : 0.636 10.082 21540 Z= 0.325 Chirality : 0.042 0.163 2466 Planarity : 0.004 0.048 2634 Dihedral : 4.853 27.545 2086 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1918 helix: 0.32 (0.19), residues: 720 sheet: -0.08 (0.26), residues: 422 loop : -2.17 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 883 HIS 0.006 0.001 HIS B 755 PHE 0.030 0.002 PHE B 749 TYR 0.010 0.001 TYR L 184 ARG 0.006 0.001 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 443 time to evaluate : 1.647 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: B 780 ILE cc_start: 0.8631 (tp) cc_final: 0.8393 (tp) REVERT: B 840 MET cc_start: 0.8606 (mmt) cc_final: 0.8246 (mmt) REVERT: B 889 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7062 (mm-30) REVERT: C 874 GLN cc_start: 0.8419 (tp40) cc_final: 0.8119 (tp40) REVERT: C 931 PHE cc_start: 0.8583 (t80) cc_final: 0.8273 (t80) REVERT: D 840 MET cc_start: 0.8594 (mmt) cc_final: 0.8246 (mmt) REVERT: D 841 ARG cc_start: 0.8247 (mmm160) cc_final: 0.7726 (mmm160) REVERT: D 854 MET cc_start: 0.8141 (mmm) cc_final: 0.7817 (mmm) REVERT: D 889 GLU cc_start: 0.7664 (mt-10) cc_final: 0.6967 (mm-30) REVERT: E 19 MET cc_start: 0.6244 (tpp) cc_final: 0.5667 (mmm) REVERT: G 24 TRP cc_start: 0.8454 (p90) cc_final: 0.8074 (p90) REVERT: H 6 MET cc_start: 0.7427 (mtp) cc_final: 0.7007 (mpp) REVERT: I 27 LEU cc_start: 0.8956 (tp) cc_final: 0.8474 (mt) REVERT: I 28 SER cc_start: 0.7939 (t) cc_final: 0.7392 (t) REVERT: I 31 SER cc_start: 0.9534 (m) cc_final: 0.9245 (t) REVERT: I 37 TYR cc_start: 0.8785 (m-80) cc_final: 0.8446 (m-10) REVERT: I 90 GLN cc_start: 0.8440 (tt0) cc_final: 0.8206 (tm-30) REVERT: I 91 GLN cc_start: 0.9223 (pp30) cc_final: 0.8997 (pp30) REVERT: J 182 ASP cc_start: 0.8030 (m-30) cc_final: 0.7631 (t0) REVERT: K 31 SER cc_start: 0.9580 (m) cc_final: 0.9266 (t) REVERT: K 63 PHE cc_start: 0.7971 (m-10) cc_final: 0.7517 (m-80) REVERT: K 214 GLU cc_start: 0.7042 (pp20) cc_final: 0.6555 (pp20) REVERT: L 3 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7675 (mm-40) REVERT: A 831 PHE cc_start: 0.7881 (m-10) cc_final: 0.7562 (t80) REVERT: A 952 GLU cc_start: 0.8794 (pp20) cc_final: 0.8385 (pp20) outliers start: 1 outliers final: 0 residues processed: 443 average time/residue: 0.2886 time to fit residues: 184.0721 Evaluate side-chains 350 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 0.0170 chunk 45 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 152 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 60 optimal weight: 0.3980 chunk 96 optimal weight: 7.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 ASN D 769 ASN ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15852 Z= 0.173 Angle : 0.609 8.743 21540 Z= 0.309 Chirality : 0.041 0.202 2466 Planarity : 0.004 0.052 2634 Dihedral : 4.705 31.099 2086 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % 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: -0.92 (0.19), residues: 1918 helix: 0.59 (0.20), residues: 716 sheet: -0.11 (0.26), residues: 428 loop : -2.07 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 883 HIS 0.006 0.001 HIS B 755 PHE 0.029 0.001 PHE D 749 TYR 0.008 0.001 TYR J 184 ARG 0.024 0.001 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 1.799 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: B 780 ILE cc_start: 0.8642 (tp) cc_final: 0.8420 (tp) REVERT: B 840 MET cc_start: 0.8641 (mmt) cc_final: 0.8295 (mmt) REVERT: B 841 ARG cc_start: 0.8413 (mmm160) cc_final: 0.7401 (mmm-85) REVERT: B 854 MET cc_start: 0.8062 (mmm) cc_final: 0.7843 (mmm) REVERT: B 889 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6884 (mm-30) REVERT: C 783 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7638 (ttp80) REVERT: C 831 PHE cc_start: 0.8030 (m-10) cc_final: 0.7290 (t80) REVERT: C 874 GLN cc_start: 0.8442 (tp40) cc_final: 0.8164 (tp40) REVERT: D 780 ILE cc_start: 0.8661 (tp) cc_final: 0.8424 (tp) REVERT: D 840 MET cc_start: 0.8610 (mmt) cc_final: 0.8238 (mmt) REVERT: D 841 ARG cc_start: 0.8298 (mmm160) cc_final: 0.7824 (mmm160) REVERT: D 889 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6858 (mm-30) REVERT: E 19 MET cc_start: 0.6207 (tpp) cc_final: 0.5563 (mmm) REVERT: E 26 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7466 (mmtp) REVERT: G 24 TRP cc_start: 0.8385 (p90) cc_final: 0.7982 (p90) REVERT: H 6 MET cc_start: 0.7345 (mtp) cc_final: 0.6935 (mpp) REVERT: I 27 LEU cc_start: 0.8930 (tp) cc_final: 0.8473 (mp) REVERT: I 28 SER cc_start: 0.7914 (t) cc_final: 0.7486 (t) REVERT: I 31 SER cc_start: 0.9523 (m) cc_final: 0.9246 (t) REVERT: I 37 TYR cc_start: 0.8785 (m-80) cc_final: 0.8581 (m-10) REVERT: I 59 VAL cc_start: 0.9137 (t) cc_final: 0.8790 (p) REVERT: I 63 PHE cc_start: 0.8068 (m-10) cc_final: 0.7581 (m-80) REVERT: I 91 GLN cc_start: 0.9184 (pp30) cc_final: 0.8916 (pp30) REVERT: I 104 LYS cc_start: 0.8468 (mmmt) cc_final: 0.8216 (mmmt) REVERT: J 114 GLN cc_start: 0.7765 (tp40) cc_final: 0.7537 (tp40) REVERT: J 182 ASP cc_start: 0.7966 (m-30) cc_final: 0.7634 (t0) REVERT: J 217 LYS cc_start: 0.6624 (mmmm) cc_final: 0.5895 (mmmm) REVERT: K 31 SER cc_start: 0.9561 (m) cc_final: 0.9239 (t) REVERT: K 63 PHE cc_start: 0.7986 (m-10) cc_final: 0.7642 (m-80) REVERT: L 3 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7804 (mm-40) REVERT: L 13 LYS cc_start: 0.8944 (mttp) cc_final: 0.8720 (tppt) REVERT: A 831 PHE cc_start: 0.7936 (m-10) cc_final: 0.7477 (t80) REVERT: A 950 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7640 (tp-100) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2790 time to fit residues: 181.3605 Evaluate side-chains 361 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.0170 chunk 20 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 102 optimal weight: 0.0770 chunk 183 optimal weight: 0.2980 chunk 114 optimal weight: 0.0040 chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 113 optimal weight: 6.9990 overall best weight: 0.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 GLN D 769 ASN ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN K 190 HIS A 769 ASN A 935 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15852 Z= 0.151 Angle : 0.602 8.912 21540 Z= 0.302 Chirality : 0.041 0.176 2466 Planarity : 0.004 0.055 2634 Dihedral : 4.503 30.645 2086 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.06 % Allowed : 1.56 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % 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: -0.69 (0.20), residues: 1918 helix: 0.83 (0.20), residues: 716 sheet: 0.08 (0.26), residues: 432 loop : -2.05 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 5 HIS 0.006 0.001 HIS B 755 PHE 0.027 0.001 PHE D 749 TYR 0.013 0.001 TYR I 88 ARG 0.008 0.001 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 456 time to evaluate : 1.722 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: B 780 ILE cc_start: 0.8605 (tp) cc_final: 0.8357 (tp) REVERT: B 840 MET cc_start: 0.8560 (mmt) cc_final: 0.8213 (mmt) REVERT: B 866 TYR cc_start: 0.9020 (t80) cc_final: 0.8723 (t80) REVERT: B 889 GLU cc_start: 0.7470 (mt-10) cc_final: 0.6871 (mm-30) REVERT: C 874 GLN cc_start: 0.8429 (tp40) cc_final: 0.8159 (tp40) REVERT: D 780 ILE cc_start: 0.8610 (tp) cc_final: 0.8341 (tt) REVERT: D 840 MET cc_start: 0.8602 (mmt) cc_final: 0.8277 (mmt) REVERT: D 841 ARG cc_start: 0.8328 (mmm160) cc_final: 0.7920 (mmm160) REVERT: D 866 TYR cc_start: 0.8979 (t80) cc_final: 0.8732 (t80) REVERT: D 883 TRP cc_start: 0.8525 (p90) cc_final: 0.7341 (p90) REVERT: D 889 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6893 (mm-30) REVERT: E 19 MET cc_start: 0.5657 (tpp) cc_final: 0.5224 (mmm) REVERT: E 26 LYS cc_start: 0.7997 (ttmm) cc_final: 0.7559 (ttmm) REVERT: G 24 TRP cc_start: 0.8384 (p90) cc_final: 0.8046 (p90) REVERT: H 6 MET cc_start: 0.7411 (mtp) cc_final: 0.6965 (mpp) REVERT: I 27 LEU cc_start: 0.8937 (tp) cc_final: 0.8518 (mp) REVERT: I 28 SER cc_start: 0.7896 (t) cc_final: 0.7557 (t) REVERT: I 31 SER cc_start: 0.9521 (m) cc_final: 0.9260 (t) REVERT: I 37 TYR cc_start: 0.8846 (m-80) cc_final: 0.8569 (m-10) REVERT: I 59 VAL cc_start: 0.9109 (t) cc_final: 0.8789 (p) REVERT: J 46 GLU cc_start: 0.8420 (tt0) cc_final: 0.8178 (mt-10) REVERT: J 182 ASP cc_start: 0.7822 (m-30) cc_final: 0.7505 (t0) REVERT: J 217 LYS cc_start: 0.6624 (mmmm) cc_final: 0.5916 (mmmm) REVERT: K 17 GLU cc_start: 0.8260 (tt0) cc_final: 0.7892 (tt0) REVERT: K 27 LEU cc_start: 0.9056 (tp) cc_final: 0.8560 (mp) REVERT: K 28 SER cc_start: 0.7947 (p) cc_final: 0.7570 (p) REVERT: K 31 SER cc_start: 0.9502 (m) cc_final: 0.9216 (t) REVERT: K 63 PHE cc_start: 0.7877 (m-10) cc_final: 0.7596 (m-80) REVERT: K 91 GLN cc_start: 0.9011 (pp30) cc_final: 0.8797 (pp30) REVERT: K 214 GLU cc_start: 0.7268 (pp20) cc_final: 0.6942 (pp20) REVERT: L 163 TRP cc_start: 0.3627 (m100) cc_final: 0.3363 (m100) REVERT: A 739 ILE cc_start: 0.8596 (mm) cc_final: 0.8054 (tp) REVERT: A 831 PHE cc_start: 0.7905 (m-10) cc_final: 0.7432 (t80) outliers start: 1 outliers final: 0 residues processed: 456 average time/residue: 0.2758 time to fit residues: 182.0982 Evaluate side-chains 363 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 124 optimal weight: 0.0010 chunk 90 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 HIS D 769 ASN ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN J 77 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.003 0.052 15852 Z= 0.187 Angle : 0.626 7.833 21540 Z= 0.317 Chirality : 0.042 0.171 2466 Planarity : 0.004 0.051 2634 Dihedral : 4.516 30.123 2086 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % 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: -0.71 (0.19), residues: 1918 helix: 0.70 (0.20), residues: 740 sheet: 0.07 (0.26), residues: 432 loop : -2.02 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 883 HIS 0.006 0.001 HIS C 721 PHE 0.029 0.001 PHE C 792 TYR 0.007 0.001 TYR J 184 ARG 0.017 0.001 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 1.822 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: B 780 ILE cc_start: 0.8759 (tp) cc_final: 0.8494 (tt) REVERT: B 824 SER cc_start: 0.9204 (t) cc_final: 0.8971 (t) REVERT: B 840 MET cc_start: 0.8740 (mmt) cc_final: 0.8405 (mmt) REVERT: B 874 GLN cc_start: 0.8287 (mt0) cc_final: 0.8062 (mt0) REVERT: B 889 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7048 (mm-30) REVERT: C 759 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8171 (tm-30) REVERT: C 783 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7621 (ttp80) REVERT: C 831 PHE cc_start: 0.8021 (m-10) cc_final: 0.7269 (t80) REVERT: C 874 GLN cc_start: 0.8448 (tp40) cc_final: 0.8193 (tp40) REVERT: D 722 MET cc_start: 0.8568 (pmm) cc_final: 0.8344 (pmm) REVERT: D 780 ILE cc_start: 0.8679 (tp) cc_final: 0.8420 (tt) REVERT: D 840 MET cc_start: 0.8748 (mmt) cc_final: 0.8475 (mmt) REVERT: D 841 ARG cc_start: 0.8337 (mmm160) cc_final: 0.7937 (mmm160) REVERT: D 883 TRP cc_start: 0.8572 (p90) cc_final: 0.7381 (p90) REVERT: D 889 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6902 (mm-30) REVERT: E 19 MET cc_start: 0.5860 (tpp) cc_final: 0.5462 (mmm) REVERT: G 24 TRP cc_start: 0.8432 (p90) cc_final: 0.8076 (p90) REVERT: H 6 MET cc_start: 0.7374 (mtp) cc_final: 0.6957 (mpp) REVERT: I 27 LEU cc_start: 0.8946 (tp) cc_final: 0.8461 (mp) REVERT: I 28 SER cc_start: 0.7946 (t) cc_final: 0.7524 (p) REVERT: I 31 SER cc_start: 0.9530 (m) cc_final: 0.9273 (t) REVERT: I 37 TYR cc_start: 0.8873 (m-80) cc_final: 0.8612 (m-10) REVERT: I 59 VAL cc_start: 0.9158 (t) cc_final: 0.8829 (p) REVERT: I 63 PHE cc_start: 0.8146 (m-10) cc_final: 0.7737 (m-10) REVERT: I 91 GLN cc_start: 0.9200 (pp30) cc_final: 0.8867 (pp30) REVERT: J 13 LYS cc_start: 0.8946 (mttp) cc_final: 0.8602 (tppt) REVERT: J 46 GLU cc_start: 0.8438 (tt0) cc_final: 0.8210 (mt-10) REVERT: J 182 ASP cc_start: 0.7807 (m-30) cc_final: 0.7500 (t0) REVERT: J 217 LYS cc_start: 0.6691 (mmmm) cc_final: 0.5981 (mmmm) REVERT: K 27 LEU cc_start: 0.9052 (tp) cc_final: 0.8470 (mp) REVERT: K 28 SER cc_start: 0.7929 (p) cc_final: 0.7622 (p) REVERT: K 31 SER cc_start: 0.9505 (m) cc_final: 0.9235 (t) REVERT: K 63 PHE cc_start: 0.8126 (m-10) cc_final: 0.7576 (m-80) REVERT: K 83 ASP cc_start: 0.8908 (m-30) cc_final: 0.8702 (m-30) REVERT: K 91 GLN cc_start: 0.9028 (pp30) cc_final: 0.8792 (pp30) REVERT: A 831 PHE cc_start: 0.7747 (m-10) cc_final: 0.7397 (t80) REVERT: A 945 MET cc_start: 0.7757 (tpp) cc_final: 0.7536 (tpp) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.2845 time to fit residues: 177.8717 Evaluate side-chains 354 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 52 optimal weight: 0.4980 chunk 154 optimal weight: 0.1980 chunk 161 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 GLN C 961 GLN ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15852 Z= 0.185 Angle : 0.635 7.373 21540 Z= 0.322 Chirality : 0.042 0.174 2466 Planarity : 0.004 0.056 2634 Dihedral : 4.541 29.928 2086 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.06 % Allowed : 0.75 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1918 helix: 0.71 (0.19), residues: 742 sheet: 0.04 (0.25), residues: 432 loop : -1.97 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 163 HIS 0.006 0.001 HIS B 755 PHE 0.027 0.001 PHE C 891 TYR 0.007 0.001 TYR A 892 ARG 0.012 0.001 ARG A 725 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 432 time to evaluate : 1.830 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: B 780 ILE cc_start: 0.8830 (tp) cc_final: 0.8543 (tt) REVERT: B 829 ARG cc_start: 0.8302 (mmt180) cc_final: 0.7823 (mmt-90) REVERT: B 840 MET cc_start: 0.8762 (mmt) cc_final: 0.8383 (mmt) REVERT: B 889 GLU cc_start: 0.7646 (mt-10) cc_final: 0.6941 (mm-30) REVERT: C 831 PHE cc_start: 0.7911 (m-10) cc_final: 0.7235 (t80) REVERT: C 874 GLN cc_start: 0.8395 (tp40) cc_final: 0.8162 (tp40) REVERT: D 722 MET cc_start: 0.8578 (pmm) cc_final: 0.8329 (pmm) REVERT: D 780 ILE cc_start: 0.8635 (tp) cc_final: 0.8375 (tt) REVERT: D 840 MET cc_start: 0.8765 (mmt) cc_final: 0.8503 (mmt) REVERT: D 841 ARG cc_start: 0.8334 (mmm160) cc_final: 0.7944 (mmm160) REVERT: D 883 TRP cc_start: 0.8536 (p90) cc_final: 0.7301 (p90) REVERT: D 889 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6913 (mm-30) REVERT: E 19 MET cc_start: 0.5709 (tpp) cc_final: 0.5368 (mmm) REVERT: G 24 TRP cc_start: 0.8582 (p90) cc_final: 0.8250 (p90) REVERT: H 6 MET cc_start: 0.7379 (mtp) cc_final: 0.6957 (mpp) REVERT: I 27 LEU cc_start: 0.8927 (tp) cc_final: 0.8472 (mp) REVERT: I 28 SER cc_start: 0.8045 (t) cc_final: 0.7650 (p) REVERT: I 31 SER cc_start: 0.9526 (m) cc_final: 0.9263 (t) REVERT: I 37 TYR cc_start: 0.8836 (m-80) cc_final: 0.8515 (m-10) REVERT: I 59 VAL cc_start: 0.9017 (t) cc_final: 0.8681 (p) REVERT: I 91 GLN cc_start: 0.9163 (pp30) cc_final: 0.8851 (pp30) REVERT: I 104 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8220 (mmmm) REVERT: J 46 GLU cc_start: 0.8442 (tt0) cc_final: 0.8209 (mt-10) REVERT: J 87 ARG cc_start: 0.7749 (mmt180) cc_final: 0.7543 (mmp80) REVERT: J 182 ASP cc_start: 0.7763 (m-30) cc_final: 0.7468 (t0) REVERT: J 217 LYS cc_start: 0.6517 (mmmm) cc_final: 0.5837 (mmmm) REVERT: K 31 SER cc_start: 0.9526 (m) cc_final: 0.9219 (t) REVERT: K 63 PHE cc_start: 0.8123 (m-10) cc_final: 0.7608 (m-80) REVERT: K 91 GLN cc_start: 0.9024 (pp30) cc_final: 0.8761 (pp30) REVERT: L 163 TRP cc_start: 0.3588 (m100) cc_final: 0.3379 (m100) REVERT: A 831 PHE cc_start: 0.7741 (m-10) cc_final: 0.7400 (t80) REVERT: A 945 MET cc_start: 0.7783 (tpp) cc_final: 0.7564 (tpp) outliers start: 1 outliers final: 0 residues processed: 433 average time/residue: 0.2844 time to fit residues: 178.9253 Evaluate side-chains 354 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 125 optimal weight: 0.0770 chunk 189 optimal weight: 0.9990 chunk 174 optimal weight: 0.4980 chunk 150 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 769 ASN ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 ASN ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15852 Z= 0.190 Angle : 0.641 7.327 21540 Z= 0.324 Chirality : 0.042 0.172 2466 Planarity : 0.004 0.055 2634 Dihedral : 4.529 29.595 2086 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.12 % Allowed : 0.46 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1918 helix: 0.69 (0.19), residues: 746 sheet: 0.03 (0.26), residues: 432 loop : -1.95 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 24 HIS 0.009 0.001 HIS D 755 PHE 0.028 0.001 PHE C 792 TYR 0.007 0.001 TYR C 892 ARG 0.011 0.001 ARG A 725 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 430 time to evaluate : 1.673 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: B 780 ILE cc_start: 0.8839 (tp) cc_final: 0.8571 (tt) REVERT: B 829 ARG cc_start: 0.8242 (mmt180) cc_final: 0.7640 (mmt-90) REVERT: B 840 MET cc_start: 0.8770 (mmt) cc_final: 0.8432 (mmt) REVERT: B 889 GLU cc_start: 0.7669 (mt-10) cc_final: 0.6976 (mm-30) REVERT: C 874 GLN cc_start: 0.8390 (tp40) cc_final: 0.8154 (tp40) REVERT: C 905 MET cc_start: 0.8845 (tpp) cc_final: 0.8588 (tpp) REVERT: D 722 MET cc_start: 0.8634 (pmm) cc_final: 0.8343 (pmm) REVERT: D 780 ILE cc_start: 0.8808 (tp) cc_final: 0.8606 (tt) REVERT: D 840 MET cc_start: 0.8796 (mmt) cc_final: 0.8523 (mmt) REVERT: D 841 ARG cc_start: 0.8355 (mmm160) cc_final: 0.7967 (mmm160) REVERT: D 883 TRP cc_start: 0.8538 (p90) cc_final: 0.7326 (p90) REVERT: D 889 GLU cc_start: 0.7654 (mt-10) cc_final: 0.6932 (mm-30) REVERT: E 19 MET cc_start: 0.5800 (tpp) cc_final: 0.5455 (mmm) REVERT: G 24 TRP cc_start: 0.8597 (p90) cc_final: 0.8200 (p90) REVERT: H 6 MET cc_start: 0.7466 (mtp) cc_final: 0.7035 (mpp) REVERT: I 10 LEU cc_start: 0.8931 (mt) cc_final: 0.8691 (mt) REVERT: I 27 LEU cc_start: 0.8966 (tp) cc_final: 0.8539 (mp) REVERT: I 28 SER cc_start: 0.8020 (t) cc_final: 0.7657 (p) REVERT: I 31 SER cc_start: 0.9532 (m) cc_final: 0.9291 (t) REVERT: I 37 TYR cc_start: 0.8871 (m-80) cc_final: 0.8629 (m-10) REVERT: I 59 VAL cc_start: 0.9027 (t) cc_final: 0.8686 (p) REVERT: I 63 PHE cc_start: 0.8315 (m-10) cc_final: 0.7878 (m-80) REVERT: J 13 LYS cc_start: 0.8946 (mttp) cc_final: 0.8528 (tppt) REVERT: J 46 GLU cc_start: 0.8449 (tt0) cc_final: 0.8189 (mt-10) REVERT: J 87 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7545 (mmp80) REVERT: J 182 ASP cc_start: 0.7719 (m-30) cc_final: 0.7486 (t0) REVERT: J 217 LYS cc_start: 0.6508 (mmmm) cc_final: 0.5826 (mmmm) REVERT: K 31 SER cc_start: 0.9518 (m) cc_final: 0.9230 (t) REVERT: K 63 PHE cc_start: 0.8063 (m-10) cc_final: 0.7507 (m-80) REVERT: K 91 GLN cc_start: 0.9022 (pp30) cc_final: 0.8736 (pp30) REVERT: K 92 TRP cc_start: 0.8571 (t-100) cc_final: 0.8049 (t-100) REVERT: K 214 GLU cc_start: 0.7394 (pp20) cc_final: 0.6626 (pp20) REVERT: L 163 TRP cc_start: 0.3644 (m100) cc_final: 0.3416 (m100) REVERT: A 739 ILE cc_start: 0.8571 (mm) cc_final: 0.8094 (tp) REVERT: A 779 GLU cc_start: 0.8258 (tt0) cc_final: 0.7877 (tt0) REVERT: A 783 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.7871 (ttp80) REVERT: A 831 PHE cc_start: 0.7752 (m-10) cc_final: 0.7413 (t80) REVERT: A 945 MET cc_start: 0.7856 (tpp) cc_final: 0.7562 (tpp) outliers start: 2 outliers final: 1 residues processed: 431 average time/residue: 0.2759 time to fit residues: 172.8306 Evaluate side-chains 356 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 0.0020 chunk 63 optimal weight: 0.2980 chunk 155 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 GLN D 769 ASN ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 125 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 = 0.4168 r_free = 0.4168 target = 0.195573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.145644 restraints weight = 25289.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139205 restraints weight = 26752.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.141271 restraints weight = 22901.261| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15852 Z= 0.171 Angle : 0.637 8.611 21540 Z= 0.320 Chirality : 0.042 0.154 2466 Planarity : 0.004 0.041 2634 Dihedral : 4.513 29.864 2086 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1918 helix: 0.81 (0.19), residues: 744 sheet: 0.06 (0.26), residues: 432 loop : -1.97 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP K 164 HIS 0.010 0.001 HIS B 755 PHE 0.024 0.001 PHE A 891 TYR 0.009 0.001 TYR K 87 ARG 0.010 0.001 ARG A 725 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3890.92 seconds wall clock time: 70 minutes 23.37 seconds (4223.37 seconds total)