Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 17:28:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/04_2023/6n4r_0342_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/04_2023/6n4r_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_0342/04_2023/6n4r_0342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/04_2023/6n4r_0342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/04_2023/6n4r_0342_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n4r_0342/04_2023/6n4r_0342_neut.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-1.21rc1-4938/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: 8.05, per 1000 atoms: 0.52 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: 5.87 Conformation dependent library (CDL) restraints added in 2.3 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: 0.84 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: 4.37 Time building geometry restraints manager: 6.37 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: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 10.580 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 38.320 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.760 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.846 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 outliers start: 4 outliers final: 0 residues processed: 571 average time/residue: 0.2958 time to fit residues: 240.5106 Evaluate side-chains 387 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6547 ------------------------------------------------------------------------------- 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: 0.0670 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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: 0.7535 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 15852 Z= 0.227 Angle : 0.682 7.530 21540 Z= 0.354 Chirality : 0.043 0.169 2466 Planarity : 0.005 0.053 2634 Dihedral : 5.469 23.502 2086 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.23 % 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: -2.00 (0.18), residues: 1918 helix: -0.60 (0.19), residues: 714 sheet: -0.52 (0.26), residues: 410 loop : -2.41 (0.20), residues: 794 *********************** 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 483 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 479 time to evaluate : 1.900 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 outliers start: 4 outliers final: 0 residues processed: 479 average time/residue: 0.3040 time to fit residues: 206.5093 Evaluate side-chains 360 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4989 ------------------------------------------------------------------------------- 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: 0.0040 chunk 53 optimal weight: 0.5980 chunk 143 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 172 optimal weight: 0.0570 chunk 186 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.4110 ------------------------------------------------------------------------------- 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 A 935 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 15852 Z= 0.186 Angle : 0.646 10.457 21540 Z= 0.330 Chirality : 0.042 0.151 2466 Planarity : 0.005 0.055 2634 Dihedral : 5.127 26.024 2086 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 0.00 % 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: -1.50 (0.19), residues: 1918 helix: -0.07 (0.19), residues: 718 sheet: -0.22 (0.27), residues: 410 loop : -2.30 (0.20), residues: 790 *********************** 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 465 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 1.790 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 outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.3003 time to fit residues: 203.4001 Evaluate side-chains 353 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3473 ------------------------------------------------------------------------------- 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: 2.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 ASN D 896 GLN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS A 769 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 15852 Z= 0.352 Angle : 0.719 10.068 21540 Z= 0.371 Chirality : 0.045 0.183 2466 Planarity : 0.005 0.047 2634 Dihedral : 5.246 27.182 2086 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 0.06 % 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: -1.44 (0.19), residues: 1918 helix: -0.02 (0.19), residues: 718 sheet: -0.05 (0.27), residues: 402 loop : -2.34 (0.20), residues: 798 *********************** 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 439 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 438 time to evaluate : 1.775 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 outliers start: 1 outliers final: 0 residues processed: 438 average time/residue: 0.2932 time to fit residues: 184.3473 Evaluate side-chains 346 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5198 ------------------------------------------------------------------------------- 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: 0.1980 chunk 104 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 ASN ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 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: 0.7568 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 15852 Z= 0.230 Angle : 0.657 9.738 21540 Z= 0.336 Chirality : 0.043 0.163 2466 Planarity : 0.005 0.050 2634 Dihedral : 5.004 28.807 2086 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 0.12 % 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: -1.19 (0.19), residues: 1918 helix: 0.27 (0.20), residues: 718 sheet: -0.10 (0.27), residues: 410 loop : -2.18 (0.21), residues: 790 *********************** 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 441 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 439 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 440 average time/residue: 0.2918 time to fit residues: 187.4016 Evaluate side-chains 341 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4741 ------------------------------------------------------------------------------- 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: 0.9980 chunk 165 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 183 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 ASN ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN J 31 ASN J 77 ASN K 91 GLN A 896 GLN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4046 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= 0.209 Angle : 0.633 10.188 21540 Z= 0.323 Chirality : 0.042 0.206 2466 Planarity : 0.004 0.037 2634 Dihedral : 4.858 32.513 2086 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.12 % 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: -0.98 (0.19), residues: 1918 helix: 0.51 (0.20), residues: 716 sheet: -0.02 (0.27), residues: 408 loop : -2.11 (0.21), residues: 794 *********************** 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 431 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 429 time to evaluate : 1.926 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 outliers start: 2 outliers final: 0 residues processed: 429 average time/residue: 0.2992 time to fit residues: 185.6059 Evaluate side-chains 339 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.833 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5707 ------------------------------------------------------------------------------- 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: 0.3980 chunk 20 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 183 optimal weight: 0.3980 chunk 114 optimal weight: 50.0000 chunk 111 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 113 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 15852 Z= 0.202 Angle : 0.634 8.650 21540 Z= 0.322 Chirality : 0.043 0.188 2466 Planarity : 0.004 0.036 2634 Dihedral : 4.774 32.286 2086 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 0.00 % 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: -0.93 (0.19), residues: 1918 helix: 0.53 (0.20), residues: 728 sheet: 0.01 (0.26), residues: 408 loop : -2.09 (0.21), residues: 782 *********************** 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 426 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.2854 time to fit residues: 176.9023 Evaluate side-chains 340 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 1.721 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5240 ------------------------------------------------------------------------------- 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: 4.9990 chunk 109 optimal weight: 0.0970 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 0.0060 chunk 116 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 17 optimal weight: 0.0870 chunk 143 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 overall best weight: 0.3972 ------------------------------------------------------------------------------- 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 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN J 77 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 15852 Z= 0.181 Angle : 0.640 7.542 21540 Z= 0.323 Chirality : 0.042 0.171 2466 Planarity : 0.004 0.052 2634 Dihedral : 4.704 32.327 2086 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.17 % 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: -0.79 (0.19), residues: 1918 helix: 0.70 (0.20), residues: 732 sheet: 0.00 (0.26), residues: 408 loop : -2.04 (0.22), residues: 778 *********************** 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 431 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 428 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 429 average time/residue: 0.2955 time to fit residues: 183.5292 Evaluate side-chains 342 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1360 time to fit residues: 2.8600 ------------------------------------------------------------------------------- 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: 0.2980 chunk 170 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 102 optimal weight: 0.0020 chunk 74 optimal weight: 0.5980 chunk 134 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 896 GLN ** 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 91 GLN J 77 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 15852 Z= 0.179 Angle : 0.640 8.621 21540 Z= 0.320 Chirality : 0.042 0.161 2466 Planarity : 0.004 0.040 2634 Dihedral : 4.631 32.575 2086 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.12 % 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: 0.81 (0.20), residues: 732 sheet: -0.02 (0.25), residues: 420 loop : -1.99 (0.22), residues: 766 *********************** 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 430 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 428 time to evaluate : 1.849 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 outliers start: 2 outliers final: 0 residues processed: 428 average time/residue: 0.2991 time to fit residues: 185.3813 Evaluate side-chains 335 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7656 ------------------------------------------------------------------------------- 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: 2.9990 chunk 85 optimal weight: 0.9990 chunk 125 optimal weight: 0.0070 chunk 189 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 160 optimal weight: 0.4980 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 769 ASN C 961 GLN D 769 ASN ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN I 95 HIS K 95 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 15852 Z= 0.211 Angle : 0.674 8.981 21540 Z= 0.339 Chirality : 0.043 0.207 2466 Planarity : 0.004 0.040 2634 Dihedral : 4.710 32.249 2086 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer Outliers : 0.12 % 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: -0.68 (0.19), residues: 1918 helix: 0.83 (0.20), residues: 730 sheet: 0.06 (0.25), residues: 414 loop : -2.02 (0.22), residues: 774 ********************** 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 412 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 410 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: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 410 average time/residue: 0.2911 time to fit residues: 174.5372 Evaluate side-chains 331 residues out of total 1738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3136 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.1980 chunk 150 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 769 ASN ** D 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN I 95 HIS ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.193749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.143517 restraints weight = 25480.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134687 restraints weight = 22377.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.137142 restraints weight = 20382.132| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 15852 Z= 0.196 Angle : 0.666 9.248 21540 Z= 0.334 Chirality : 0.043 0.272 2466 Planarity : 0.004 0.048 2634 Dihedral : 4.713 32.614 2086 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.12 % 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: -0.61 (0.20), residues: 1918 helix: 0.92 (0.20), residues: 730 sheet: 0.07 (0.25), residues: 414 loop : -2.00 (0.22), residues: 774 =============================================================================== Job complete usr+sys time: 3821.37 seconds wall clock time: 69 minutes 57.05 seconds (4197.05 seconds total)