Starting phenix.real_space_refine on Tue Aug 6 09:10:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcr_43139/08_2024/8vcr_43139.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcr_43139/08_2024/8vcr_43139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcr_43139/08_2024/8vcr_43139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcr_43139/08_2024/8vcr_43139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcr_43139/08_2024/8vcr_43139.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vcr_43139/08_2024/8vcr_43139.cif" } resolution = 3.0 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= 0.000 sd= 0.012 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 78 5.16 5 C 10110 2.51 5 N 2667 2.21 5 O 3132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 847": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D ARG 94": "NH1" <-> "NH2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "G ARG 18": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G ARG 45": "NH1" <-> "NH2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ARG 43": "NH1" <-> "NH2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 847": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 847": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C ARG 1107": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15987 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3411 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 24, 'TRANS': 420} Chain: "D" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1009 Classifications: {'peptide': 128} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1009 Classifications: {'peptide': 128} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1009 Classifications: {'peptide': 128} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "B" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3411 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 24, 'TRANS': 420} Chain: "C" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3411 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 24, 'TRANS': 420} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.78, per 1000 atoms: 0.67 Number of scatterers: 15987 At special positions: 0 Unit cell: (111.86, 111.86, 172.96, 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 78 16.00 O 3132 8.00 N 2667 7.00 C 10110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS B 790 " distance=2.07 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 790 " - pdb=" SG CYS C 704 " distance=2.02 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 100 " - pdb=" SG CYS D 100E" distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 100E" distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 704 " - pdb=" SG CYS C 790 " distance=2.01 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A 717 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A1134 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B 717 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C 717 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C1134 " " NAG D 301 " - " ASN D 31 " " NAG E 301 " - " ASN E 31 " " NAG H 301 " - " ASN H 31 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN C 801 " Time building additional restraints: 5.75 Conformation dependent library (CDL) restraints added in 2.6 seconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3774 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 30 sheets defined 37.1% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.868A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.944A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.851A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 842 removed outlier: 3.861A pdb=" N GLY A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 839 " --> pdb=" O LYS A 835 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A 840 " --> pdb=" O GLN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'A' and resid 847 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.703A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.281A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.847A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.420A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.223A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.555A pdb=" N ASN D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N SER D 65 " --> pdb=" O SER D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 65' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.524A pdb=" N THR D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.554A pdb=" N ASN E 64 " --> pdb=" O PRO E 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER E 65 " --> pdb=" O SER E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 65' Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.524A pdb=" N THR E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.503A pdb=" N ASP F 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.502A pdb=" N ASP G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE G 83 " --> pdb=" O SER G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.554A pdb=" N ASN H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER H 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.523A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.503A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.868A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.946A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.851A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 842 removed outlier: 3.862A pdb=" N GLY B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 839 " --> pdb=" O LYS B 835 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS B 840 " --> pdb=" O GLN B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 846 No H-bonds generated for 'chain 'B' and resid 844 through 846' Processing helix chain 'B' and resid 847 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.703A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.280A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.848A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.421A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.222A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.868A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.946A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.852A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 842 removed outlier: 3.862A pdb=" N GLY C 838 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 846 No H-bonds generated for 'chain 'C' and resid 844 through 846' Processing helix chain 'C' and resid 847 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.703A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.280A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.847A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.419A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.222A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.265A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.366A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.967A pdb=" N CYS D 92 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG D 94 " --> pdb=" O LEU D 100J" (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU D 100J" --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE D 96 " --> pdb=" O ASN D 100H" (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE D 100F" --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS D 100 " --> pdb=" O SER D 100D" (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER D 100D" --> pdb=" O CYS D 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.366A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.966A pdb=" N CYS E 92 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG E 94 " --> pdb=" O LEU E 100J" (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU E 100J" --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE E 96 " --> pdb=" O ASN E 100H" (cutoff:3.500A) removed outlier: 5.027A pdb=" N PHE E 100F" --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS E 100 " --> pdb=" O SER E 100D" (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER E 100D" --> pdb=" O CYS E 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.874A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.582A pdb=" N LEU F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N HIS F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.621A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.875A pdb=" N GLU G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.583A pdb=" N LEU G 33 " --> pdb=" O HIS G 49 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N HIS G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.621A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.365A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.967A pdb=" N CYS H 92 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG H 94 " --> pdb=" O LEU H 100J" (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU H 100J" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE H 96 " --> pdb=" O ASN H 100H" (cutoff:3.500A) removed outlier: 5.028A pdb=" N PHE H 100F" --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS H 100 " --> pdb=" O SER H 100D" (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER H 100D" --> pdb=" O CYS H 100 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.874A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.582A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.621A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.265A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.408A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.265A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 852 hydrogen bonds defined for protein. 2394 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4881 1.33 - 1.46: 3105 1.46 - 1.58: 8250 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 16338 Sorted by residual: bond pdb=" CA ASN H 31 " pdb=" C ASN H 31 " ideal model delta sigma weight residual 1.524 1.472 0.051 1.33e-02 5.65e+03 1.49e+01 bond pdb=" CA ASN E 31 " pdb=" C ASN E 31 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.33e-02 5.65e+03 1.36e+01 bond pdb=" C ASN E 31 " pdb=" N SER E 32 " ideal model delta sigma weight residual 1.334 1.302 0.033 1.38e-02 5.25e+03 5.57e+00 bond pdb=" C ASN H 31 " pdb=" N SER H 32 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.38e-02 5.25e+03 5.12e+00 bond pdb=" CA ASN D 31 " pdb=" C ASN D 31 " ideal model delta sigma weight residual 1.524 1.496 0.028 1.33e-02 5.65e+03 4.39e+00 ... (remaining 16333 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.61: 460 106.61 - 113.48: 9200 113.48 - 120.35: 5838 120.35 - 127.21: 6576 127.21 - 134.08: 171 Bond angle restraints: 22245 Sorted by residual: angle pdb=" CA CYS C 840 " pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " ideal model delta sigma weight residual 114.40 123.02 -8.62 2.30e+00 1.89e-01 1.41e+01 angle pdb=" CA CYS A 840 " pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " ideal model delta sigma weight residual 114.40 123.02 -8.62 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA CYS B 840 " pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " ideal model delta sigma weight residual 114.40 123.00 -8.60 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA CYS A 851 " pdb=" CB CYS A 851 " pdb=" SG CYS A 851 " ideal model delta sigma weight residual 114.40 121.64 -7.24 2.30e+00 1.89e-01 9.91e+00 angle pdb=" CA CYS C 851 " pdb=" CB CYS C 851 " pdb=" SG CYS C 851 " ideal model delta sigma weight residual 114.40 121.63 -7.23 2.30e+00 1.89e-01 9.89e+00 ... (remaining 22240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9271 17.91 - 35.83: 590 35.83 - 53.74: 108 53.74 - 71.65: 39 71.65 - 89.57: 30 Dihedral angle restraints: 10038 sinusoidal: 4149 harmonic: 5889 Sorted by residual: dihedral pdb=" CA ARG A1039 " pdb=" C ARG A1039 " pdb=" N VAL A1040 " pdb=" CA VAL A1040 " ideal model delta harmonic sigma weight residual 180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG C1039 " pdb=" C ARG C1039 " pdb=" N VAL C1040 " pdb=" CA VAL C1040 " ideal model delta harmonic sigma weight residual -180.00 -154.62 -25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG B1039 " pdb=" C ARG B1039 " pdb=" N VAL B1040 " pdb=" CA VAL B1040 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 10035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2093 0.066 - 0.133: 479 0.133 - 0.199: 23 0.199 - 0.265: 1 0.265 - 0.332: 2 Chirality restraints: 2598 Sorted by residual: chirality pdb=" C1 NAG H 301 " pdb=" ND2 ASN H 31 " pdb=" C2 NAG H 301 " pdb=" O5 NAG H 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG E 301 " pdb=" ND2 ASN E 31 " pdb=" C2 NAG E 301 " pdb=" O5 NAG E 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG D 301 " pdb=" ND2 ASN D 31 " pdb=" C2 NAG D 301 " pdb=" O5 NAG D 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2595 not shown) Planarity restraints: 2859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 301 " 0.143 2.00e-02 2.50e+03 1.18e-01 1.73e+02 pdb=" C7 NAG H 301 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG H 301 " 0.106 2.00e-02 2.50e+03 pdb=" N2 NAG H 301 " -0.189 2.00e-02 2.50e+03 pdb=" O7 NAG H 301 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 301 " 0.122 2.00e-02 2.50e+03 1.01e-01 1.28e+02 pdb=" C7 NAG D 301 " -0.034 2.00e-02 2.50e+03 pdb=" C8 NAG D 301 " 0.092 2.00e-02 2.50e+03 pdb=" N2 NAG D 301 " -0.162 2.00e-02 2.50e+03 pdb=" O7 NAG D 301 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 301 " -0.115 2.00e-02 2.50e+03 9.53e-02 1.13e+02 pdb=" C7 NAG E 301 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG E 301 " -0.087 2.00e-02 2.50e+03 pdb=" N2 NAG E 301 " 0.152 2.00e-02 2.50e+03 pdb=" O7 NAG E 301 " 0.018 2.00e-02 2.50e+03 ... (remaining 2856 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 308 2.69 - 3.24: 15452 3.24 - 3.80: 24591 3.80 - 4.35: 33733 4.35 - 4.90: 57526 Nonbonded interactions: 131610 Sorted by model distance: nonbonded pdb=" NZ LYS G 39 " pdb=" O GLU G 81 " model vdw 2.139 3.120 nonbonded pdb=" NZ LYS F 39 " pdb=" O GLU F 81 " model vdw 2.140 3.120 nonbonded pdb=" NZ LYS L 39 " pdb=" O GLU L 81 " model vdw 2.140 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.215 3.120 nonbonded pdb=" NZ LYS C 811 " pdb=" OD2 ASP C 820 " model vdw 2.215 3.120 ... (remaining 131605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 44.970 Find NCS groups from input model: 0.530 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 0.053 16338 Z= 0.548 Angle : 0.766 9.611 22245 Z= 0.402 Chirality : 0.052 0.332 2598 Planarity : 0.006 0.118 2841 Dihedral : 13.519 89.567 6183 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.18), residues: 2022 helix: 0.58 (0.20), residues: 588 sheet: 0.54 (0.23), residues: 483 loop : -0.48 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP H 103 HIS 0.010 0.003 HIS E 77 PHE 0.019 0.002 PHE C1121 TYR 0.027 0.003 TYR E 52 ARG 0.012 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 THR cc_start: 0.8219 (p) cc_final: 0.8014 (m) REVERT: A 772 VAL cc_start: 0.8513 (t) cc_final: 0.8217 (p) REVERT: A 780 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6930 (mm-30) REVERT: A 833 PHE cc_start: 0.7173 (m-10) cc_final: 0.6148 (t80) REVERT: A 837 TYR cc_start: 0.7946 (t80) cc_final: 0.7557 (t80) REVERT: A 854 LYS cc_start: 0.8148 (tttt) cc_final: 0.7762 (tttt) REVERT: A 855 PHE cc_start: 0.8145 (m-80) cc_final: 0.7830 (m-80) REVERT: A 858 LEU cc_start: 0.8169 (mt) cc_final: 0.7901 (mm) REVERT: A 952 VAL cc_start: 0.8354 (t) cc_final: 0.7938 (p) REVERT: A 994 ASP cc_start: 0.7305 (m-30) cc_final: 0.7002 (m-30) REVERT: A 1010 GLN cc_start: 0.7710 (tp40) cc_final: 0.7462 (tp40) REVERT: A 1122 VAL cc_start: 0.8075 (t) cc_final: 0.7803 (p) REVERT: L 5 THR cc_start: 0.8181 (m) cc_final: 0.7948 (p) REVERT: L 28 SER cc_start: 0.8211 (t) cc_final: 0.7958 (p) REVERT: B 723 THR cc_start: 0.8165 (p) cc_final: 0.7951 (p) REVERT: B 752 LEU cc_start: 0.8376 (mt) cc_final: 0.8141 (mt) REVERT: B 772 VAL cc_start: 0.8544 (t) cc_final: 0.8317 (t) REVERT: B 833 PHE cc_start: 0.7321 (m-10) cc_final: 0.6367 (t80) REVERT: B 866 THR cc_start: 0.8488 (p) cc_final: 0.8077 (t) REVERT: B 905 ARG cc_start: 0.8381 (mmt90) cc_final: 0.8163 (mmm-85) REVERT: B 927 PHE cc_start: 0.8057 (t80) cc_final: 0.7854 (t80) REVERT: B 1098 ASN cc_start: 0.7525 (p0) cc_final: 0.7322 (p0) REVERT: C 735 SER cc_start: 0.7922 (t) cc_final: 0.7719 (p) REVERT: C 780 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6974 (mm-30) REVERT: C 837 TYR cc_start: 0.8026 (t80) cc_final: 0.7660 (t80) REVERT: C 854 LYS cc_start: 0.8105 (tttt) cc_final: 0.7897 (tttt) REVERT: C 957 GLU cc_start: 0.7260 (tp30) cc_final: 0.6833 (tp30) REVERT: C 964 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7728 (ttmm) REVERT: C 994 ASP cc_start: 0.7385 (m-30) cc_final: 0.7146 (m-30) REVERT: C 995 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7413 (mmm-85) REVERT: C 1122 VAL cc_start: 0.8329 (t) cc_final: 0.8117 (p) outliers start: 0 outliers final: 1 residues processed: 390 average time/residue: 1.1283 time to fit residues: 492.5884 Evaluate side-chains 353 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 352 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.6980 chunk 150 optimal weight: 0.4980 chunk 83 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 94 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 179 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 804 GLN A 824 ASN A1108 ASN B 751 ASN B 804 GLN B 824 ASN B1010 GLN C 804 GLN C 824 ASN C 872 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16338 Z= 0.298 Angle : 0.637 10.690 22245 Z= 0.325 Chirality : 0.044 0.170 2598 Planarity : 0.005 0.052 2841 Dihedral : 6.085 58.037 2627 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.83 % Allowed : 8.35 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.63 (0.18), residues: 2022 helix: 1.43 (0.21), residues: 612 sheet: 0.78 (0.24), residues: 453 loop : -0.38 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 103 HIS 0.004 0.001 HIS H 77 PHE 0.028 0.002 PHE C 927 TYR 0.023 0.002 TYR B1067 ARG 0.005 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 367 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 833 PHE cc_start: 0.7319 (m-10) cc_final: 0.6342 (t80) REVERT: A 837 TYR cc_start: 0.7705 (t80) cc_final: 0.7390 (t80) REVERT: A 855 PHE cc_start: 0.7769 (m-80) cc_final: 0.7432 (m-80) REVERT: A 873 TYR cc_start: 0.7892 (m-10) cc_final: 0.7664 (m-10) REVERT: A 952 VAL cc_start: 0.8273 (t) cc_final: 0.7866 (p) REVERT: A 994 ASP cc_start: 0.7099 (m-30) cc_final: 0.6659 (m-30) REVERT: A 1010 GLN cc_start: 0.7608 (tp40) cc_final: 0.7407 (tp40) REVERT: A 1138 TYR cc_start: 0.6764 (t80) cc_final: 0.6554 (t80) REVERT: D 90 TYR cc_start: 0.8833 (m-80) cc_final: 0.8521 (m-80) REVERT: G 37 GLN cc_start: 0.8502 (tt0) cc_final: 0.8293 (tt0) REVERT: H 89 LEU cc_start: 0.8661 (tp) cc_final: 0.8444 (tt) REVERT: B 823 PHE cc_start: 0.5827 (m-80) cc_final: 0.5625 (m-80) REVERT: B 833 PHE cc_start: 0.7429 (m-10) cc_final: 0.6530 (t80) REVERT: B 866 THR cc_start: 0.8533 (p) cc_final: 0.8215 (t) REVERT: B 905 ARG cc_start: 0.8441 (mmt90) cc_final: 0.8223 (mmt-90) REVERT: C 855 PHE cc_start: 0.7764 (m-80) cc_final: 0.7419 (m-80) REVERT: C 860 VAL cc_start: 0.8917 (m) cc_final: 0.8638 (t) REVERT: C 957 GLU cc_start: 0.7080 (tp30) cc_final: 0.6655 (tp30) REVERT: C 994 ASP cc_start: 0.7234 (m-30) cc_final: 0.6964 (m-30) REVERT: C 1018 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8021 (mp) REVERT: C 1031 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7805 (mt-10) outliers start: 32 outliers final: 8 residues processed: 372 average time/residue: 1.0394 time to fit residues: 435.0469 Evaluate side-chains 353 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 343 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 0.2980 chunk 55 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 180 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 144 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A1108 ASN L 38 GLN B 824 ASN B 949 GLN C 804 GLN C 824 ASN C 872 GLN C 969 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16338 Z= 0.284 Angle : 0.588 9.988 22245 Z= 0.300 Chirality : 0.044 0.178 2598 Planarity : 0.005 0.055 2841 Dihedral : 5.581 53.991 2627 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.72 % Allowed : 10.81 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.76 (0.18), residues: 2022 helix: 1.77 (0.21), residues: 615 sheet: 0.71 (0.23), residues: 483 loop : -0.45 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 103 HIS 0.005 0.001 HIS G 49 PHE 0.019 0.002 PHE B1121 TYR 0.019 0.002 TYR B1067 ARG 0.006 0.000 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 355 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 833 PHE cc_start: 0.7305 (m-10) cc_final: 0.6328 (t80) REVERT: A 837 TYR cc_start: 0.7633 (t80) cc_final: 0.7279 (t80) REVERT: A 855 PHE cc_start: 0.7804 (m-80) cc_final: 0.7374 (m-80) REVERT: A 873 TYR cc_start: 0.7982 (m-10) cc_final: 0.7617 (m-10) REVERT: A 952 VAL cc_start: 0.8282 (t) cc_final: 0.7873 (p) REVERT: A 994 ASP cc_start: 0.7004 (m-30) cc_final: 0.6650 (m-30) REVERT: A 1139 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: G 37 GLN cc_start: 0.8520 (tt0) cc_final: 0.8313 (tt0) REVERT: H 89 LEU cc_start: 0.8651 (tp) cc_final: 0.8444 (tt) REVERT: B 739 THR cc_start: 0.8503 (m) cc_final: 0.8282 (t) REVERT: B 773 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6608 (tm-30) REVERT: B 823 PHE cc_start: 0.5749 (m-80) cc_final: 0.5519 (m-80) REVERT: B 866 THR cc_start: 0.8557 (p) cc_final: 0.8230 (t) REVERT: B 873 TYR cc_start: 0.7822 (m-10) cc_final: 0.7616 (m-10) REVERT: B 905 ARG cc_start: 0.8460 (mmt90) cc_final: 0.8090 (mmt180) REVERT: B 994 ASP cc_start: 0.7004 (m-30) cc_final: 0.6752 (m-30) REVERT: B 1031 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: C 957 GLU cc_start: 0.7097 (tp30) cc_final: 0.6673 (tp30) REVERT: C 994 ASP cc_start: 0.7083 (m-30) cc_final: 0.6810 (m-30) REVERT: C 1031 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7705 (mt-10) outliers start: 30 outliers final: 15 residues processed: 360 average time/residue: 1.0780 time to fit residues: 435.1271 Evaluate side-chains 370 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 352 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1031 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 120 optimal weight: 0.1980 chunk 180 optimal weight: 0.7980 chunk 191 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN B 824 ASN B 954 GLN B1010 GLN C 804 GLN C 824 ASN C 872 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16338 Z= 0.393 Angle : 0.627 9.972 22245 Z= 0.318 Chirality : 0.046 0.184 2598 Planarity : 0.005 0.064 2841 Dihedral : 5.462 47.231 2627 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.92 % Allowed : 11.78 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.68 (0.18), residues: 2022 helix: 1.69 (0.20), residues: 618 sheet: 0.73 (0.23), residues: 483 loop : -0.53 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 103 HIS 0.007 0.002 HIS H 77 PHE 0.023 0.002 PHE B1121 TYR 0.019 0.002 TYR B1067 ARG 0.006 0.000 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 363 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 833 PHE cc_start: 0.7296 (m-10) cc_final: 0.6350 (t80) REVERT: A 837 TYR cc_start: 0.7717 (t80) cc_final: 0.7425 (t80) REVERT: A 855 PHE cc_start: 0.7810 (m-80) cc_final: 0.7388 (m-80) REVERT: A 866 THR cc_start: 0.8420 (p) cc_final: 0.8128 (t) REVERT: A 952 VAL cc_start: 0.8315 (t) cc_final: 0.7917 (p) REVERT: A 994 ASP cc_start: 0.7008 (m-30) cc_final: 0.6650 (m-30) REVERT: A 1010 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7107 (mp10) REVERT: A 1031 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: A 1138 TYR cc_start: 0.6756 (t80) cc_final: 0.6474 (t80) REVERT: A 1139 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: H 89 LEU cc_start: 0.8654 (tp) cc_final: 0.8434 (tt) REVERT: B 773 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6693 (tm-30) REVERT: B 866 THR cc_start: 0.8500 (p) cc_final: 0.8223 (t) REVERT: B 873 TYR cc_start: 0.7874 (m-10) cc_final: 0.7668 (m-10) REVERT: B 905 ARG cc_start: 0.8463 (mmt90) cc_final: 0.8260 (mmt180) REVERT: B 1010 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7326 (mm-40) REVERT: B 1031 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7777 (mt-10) REVERT: C 854 LYS cc_start: 0.8305 (tptt) cc_final: 0.8092 (tptt) REVERT: C 855 PHE cc_start: 0.7806 (m-80) cc_final: 0.7589 (m-80) REVERT: C 957 GLU cc_start: 0.7103 (tp30) cc_final: 0.6688 (tp30) REVERT: C 994 ASP cc_start: 0.7083 (m-30) cc_final: 0.6793 (m-30) REVERT: C 1031 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: C 1139 ASP cc_start: 0.7133 (t0) cc_final: 0.6894 (t0) outliers start: 51 outliers final: 22 residues processed: 383 average time/residue: 1.0749 time to fit residues: 463.9371 Evaluate side-chains 378 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 350 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 2 optimal weight: 0.0870 chunk 142 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 824 ASN B 824 ASN B 954 GLN C 804 GLN C 824 ASN C 872 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16338 Z= 0.344 Angle : 0.604 10.545 22245 Z= 0.307 Chirality : 0.044 0.175 2598 Planarity : 0.005 0.062 2841 Dihedral : 5.204 39.199 2625 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.97 % Allowed : 13.04 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.71 (0.18), residues: 2022 helix: 1.76 (0.20), residues: 618 sheet: 0.76 (0.23), residues: 483 loop : -0.56 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 103 HIS 0.006 0.002 HIS H 77 PHE 0.020 0.002 PHE B1121 TYR 0.019 0.002 TYR B1067 ARG 0.004 0.000 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 354 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6625 (tm-30) REVERT: A 837 TYR cc_start: 0.7715 (t80) cc_final: 0.7273 (t80) REVERT: A 952 VAL cc_start: 0.8315 (t) cc_final: 0.7916 (p) REVERT: A 994 ASP cc_start: 0.6971 (m-30) cc_final: 0.6619 (m-30) REVERT: A 1010 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7248 (mm110) REVERT: A 1031 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: A 1139 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6956 (m-30) REVERT: D 11 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8045 (mt) REVERT: G 4 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7854 (mtm) REVERT: H 89 LEU cc_start: 0.8649 (tp) cc_final: 0.8426 (tt) REVERT: B 773 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6693 (tm-30) REVERT: B 866 THR cc_start: 0.8427 (p) cc_final: 0.8124 (t) REVERT: B 873 TYR cc_start: 0.7893 (m-10) cc_final: 0.7635 (m-10) REVERT: B 1010 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6917 (mp10) REVERT: B 1031 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: C 773 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6785 (tm-30) REVERT: C 855 PHE cc_start: 0.7828 (m-80) cc_final: 0.7482 (m-80) REVERT: C 957 GLU cc_start: 0.7100 (tp30) cc_final: 0.6689 (tp30) REVERT: C 994 ASP cc_start: 0.7064 (m-30) cc_final: 0.6789 (m-30) REVERT: C 1031 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: C 1073 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7604 (mtmm) REVERT: C 1139 ASP cc_start: 0.7126 (t0) cc_final: 0.6897 (t0) outliers start: 52 outliers final: 31 residues processed: 374 average time/residue: 1.0812 time to fit residues: 453.3527 Evaluate side-chains 394 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 354 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 0.1980 chunk 47 optimal weight: 0.4980 chunk 191 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 100 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A1108 ASN B 824 ASN B 935 GLN B 954 GLN B1002 GLN C 804 GLN C 824 ASN C 872 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16338 Z= 0.303 Angle : 0.584 11.181 22245 Z= 0.296 Chirality : 0.044 0.168 2598 Planarity : 0.005 0.059 2841 Dihedral : 4.886 39.110 2625 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.60 % Allowed : 12.92 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.75 (0.18), residues: 2022 helix: 1.79 (0.20), residues: 621 sheet: 0.80 (0.23), residues: 483 loop : -0.55 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 103 HIS 0.006 0.002 HIS H 77 PHE 0.018 0.002 PHE B1121 TYR 0.020 0.002 TYR B1067 ARG 0.005 0.000 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 355 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6619 (tm-30) REVERT: A 833 PHE cc_start: 0.7304 (m-10) cc_final: 0.6269 (t80) REVERT: A 837 TYR cc_start: 0.7690 (t80) cc_final: 0.7306 (t80) REVERT: A 855 PHE cc_start: 0.7779 (m-80) cc_final: 0.7366 (m-80) REVERT: A 866 THR cc_start: 0.8467 (p) cc_final: 0.8186 (t) REVERT: A 952 VAL cc_start: 0.8309 (t) cc_final: 0.7904 (p) REVERT: A 994 ASP cc_start: 0.6947 (m-30) cc_final: 0.6613 (m-30) REVERT: A 1010 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7277 (mm110) REVERT: A 1031 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: A 1139 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: G 4 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7839 (mtm) REVERT: H 89 LEU cc_start: 0.8635 (tp) cc_final: 0.8423 (tt) REVERT: B 773 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6406 (tm-30) REVERT: B 866 THR cc_start: 0.8550 (p) cc_final: 0.8222 (t) REVERT: B 873 TYR cc_start: 0.7900 (m-10) cc_final: 0.7674 (m-10) REVERT: B 905 ARG cc_start: 0.8411 (mmt180) cc_final: 0.8090 (mmt180) REVERT: B 1031 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: B 1098 ASN cc_start: 0.7508 (p0) cc_final: 0.7266 (p0) REVERT: C 773 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6791 (tm-30) REVERT: C 855 PHE cc_start: 0.7746 (m-80) cc_final: 0.7464 (m-80) REVERT: C 957 GLU cc_start: 0.7090 (tp30) cc_final: 0.6690 (tp30) REVERT: C 994 ASP cc_start: 0.7042 (m-30) cc_final: 0.6761 (m-30) REVERT: C 1031 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: C 1073 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7634 (mtmm) REVERT: C 1139 ASP cc_start: 0.7109 (t0) cc_final: 0.6861 (t0) outliers start: 63 outliers final: 38 residues processed: 381 average time/residue: 1.0655 time to fit residues: 457.4574 Evaluate side-chains 396 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 351 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 109 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 119 optimal weight: 0.0170 chunk 116 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 824 ASN A1108 ASN B 824 ASN B 935 GLN B 954 GLN B1010 GLN B1135 ASN C 804 GLN C 824 ASN C 872 GLN C 969 ASN C1135 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16338 Z= 0.380 Angle : 0.620 10.773 22245 Z= 0.313 Chirality : 0.046 0.198 2598 Planarity : 0.005 0.063 2841 Dihedral : 4.873 40.114 2625 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.37 % Allowed : 13.55 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2022 helix: 1.67 (0.20), residues: 618 sheet: 0.76 (0.23), residues: 483 loop : -0.59 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 103 HIS 0.007 0.002 HIS H 77 PHE 0.022 0.002 PHE B1121 TYR 0.020 0.002 TYR B1067 ARG 0.003 0.000 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 358 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6652 (tm-30) REVERT: A 833 PHE cc_start: 0.7279 (m-10) cc_final: 0.6277 (t80) REVERT: A 837 TYR cc_start: 0.7746 (t80) cc_final: 0.7411 (t80) REVERT: A 855 PHE cc_start: 0.7874 (m-80) cc_final: 0.7371 (m-80) REVERT: A 866 THR cc_start: 0.8468 (p) cc_final: 0.8210 (t) REVERT: A 952 VAL cc_start: 0.8328 (t) cc_final: 0.7941 (p) REVERT: A 994 ASP cc_start: 0.7051 (m-30) cc_final: 0.6705 (m-30) REVERT: A 1010 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7272 (mm110) REVERT: A 1031 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: A 1139 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: D 11 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8034 (mt) REVERT: G 4 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7876 (mtm) REVERT: H 89 LEU cc_start: 0.8670 (tp) cc_final: 0.8432 (tt) REVERT: B 773 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6673 (tm-30) REVERT: B 866 THR cc_start: 0.8571 (p) cc_final: 0.8277 (t) REVERT: B 1010 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7385 (mm-40) REVERT: B 1031 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: B 1098 ASN cc_start: 0.7523 (p0) cc_final: 0.7285 (p0) REVERT: C 773 GLU cc_start: 0.7037 (mm-30) cc_final: 0.6824 (tm-30) REVERT: C 804 GLN cc_start: 0.7871 (mm110) cc_final: 0.7468 (mp-120) REVERT: C 854 LYS cc_start: 0.8376 (tptt) cc_final: 0.8149 (tppt) REVERT: C 855 PHE cc_start: 0.7776 (m-80) cc_final: 0.7467 (m-80) REVERT: C 945 LEU cc_start: 0.7916 (mm) cc_final: 0.7670 (mt) REVERT: C 957 GLU cc_start: 0.7090 (tp30) cc_final: 0.6694 (tp30) REVERT: C 994 ASP cc_start: 0.7067 (m-30) cc_final: 0.6807 (m-30) REVERT: C 1031 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: C 1073 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7666 (mtmm) outliers start: 59 outliers final: 34 residues processed: 380 average time/residue: 1.0932 time to fit residues: 469.6916 Evaluate side-chains 395 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 352 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.0870 chunk 76 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 121 optimal weight: 0.0980 chunk 130 optimal weight: 0.6980 chunk 94 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 150 optimal weight: 0.1980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A1108 ASN F 32 ASN B 824 ASN B 949 GLN B1010 GLN C 824 ASN C 872 GLN C 954 GLN C 969 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16338 Z= 0.193 Angle : 0.551 11.153 22245 Z= 0.280 Chirality : 0.042 0.165 2598 Planarity : 0.005 0.055 2841 Dihedral : 4.556 37.791 2625 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.03 % Allowed : 14.69 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.89 (0.18), residues: 2022 helix: 1.95 (0.21), residues: 621 sheet: 0.92 (0.24), residues: 453 loop : -0.48 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 35A HIS 0.004 0.001 HIS H 77 PHE 0.015 0.001 PHE C 927 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 346 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7730 (ttp-170) REVERT: A 837 TYR cc_start: 0.7663 (t80) cc_final: 0.7161 (t80) REVERT: A 866 THR cc_start: 0.8429 (p) cc_final: 0.8167 (t) REVERT: A 952 VAL cc_start: 0.8286 (t) cc_final: 0.7884 (p) REVERT: A 994 ASP cc_start: 0.6973 (m-30) cc_final: 0.6652 (m-30) REVERT: A 1010 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7261 (mm110) REVERT: A 1031 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: A 1139 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: D 111 VAL cc_start: 0.8160 (t) cc_final: 0.7927 (m) REVERT: G 4 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7818 (mtm) REVERT: H 89 LEU cc_start: 0.8645 (tp) cc_final: 0.8422 (tt) REVERT: B 773 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6348 (tm-30) REVERT: B 866 THR cc_start: 0.8545 (p) cc_final: 0.8244 (t) REVERT: B 873 TYR cc_start: 0.7885 (m-10) cc_final: 0.7617 (m-10) REVERT: B 953 ASN cc_start: 0.7951 (m-40) cc_final: 0.7714 (m-40) REVERT: B 1031 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: B 1098 ASN cc_start: 0.7469 (p0) cc_final: 0.7222 (p0) REVERT: C 773 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6730 (tm-30) REVERT: C 804 GLN cc_start: 0.7795 (mm110) cc_final: 0.7404 (mp-120) REVERT: C 854 LYS cc_start: 0.8363 (tptt) cc_final: 0.8124 (tppt) REVERT: C 855 PHE cc_start: 0.7672 (m-80) cc_final: 0.7415 (m-80) REVERT: C 945 LEU cc_start: 0.7905 (mm) cc_final: 0.7674 (mt) REVERT: C 957 GLU cc_start: 0.7086 (tp30) cc_final: 0.6694 (tp30) REVERT: C 994 ASP cc_start: 0.7018 (m-30) cc_final: 0.6735 (m-30) REVERT: C 1073 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7657 (mtmm) outliers start: 53 outliers final: 32 residues processed: 368 average time/residue: 1.0729 time to fit residues: 445.2609 Evaluate side-chains 382 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 344 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 935 GLN A1108 ASN F 32 ASN B 824 ASN B 954 GLN B1010 GLN C 751 ASN C 824 ASN C 872 GLN C 954 GLN C 969 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 16338 Z= 0.565 Angle : 0.693 10.648 22245 Z= 0.353 Chirality : 0.050 0.189 2598 Planarity : 0.005 0.069 2841 Dihedral : 5.019 41.234 2625 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.20 % Allowed : 14.92 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2022 helix: 1.53 (0.20), residues: 618 sheet: 0.88 (0.24), residues: 468 loop : -0.76 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 103 HIS 0.010 0.003 HIS H 77 PHE 0.030 0.003 PHE B1121 TYR 0.026 0.003 TYR D 34 ARG 0.004 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 358 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 773 GLU cc_start: 0.6627 (tm-30) cc_final: 0.5537 (tm-30) REVERT: A 833 PHE cc_start: 0.7369 (m-10) cc_final: 0.6329 (t80) REVERT: A 837 TYR cc_start: 0.7827 (t80) cc_final: 0.7383 (t80) REVERT: A 855 PHE cc_start: 0.7960 (m-80) cc_final: 0.7458 (m-80) REVERT: A 866 THR cc_start: 0.8488 (p) cc_final: 0.8233 (t) REVERT: A 952 VAL cc_start: 0.8340 (t) cc_final: 0.7951 (p) REVERT: A 994 ASP cc_start: 0.7014 (m-30) cc_final: 0.6618 (m-30) REVERT: A 1028 LYS cc_start: 0.8443 (mtpp) cc_final: 0.8223 (mttt) REVERT: A 1031 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: A 1040 VAL cc_start: 0.7086 (OUTLIER) cc_final: 0.6800 (t) REVERT: A 1122 VAL cc_start: 0.8172 (t) cc_final: 0.7948 (p) REVERT: A 1139 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: G 4 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7993 (mtm) REVERT: B 773 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6699 (tm-30) REVERT: B 866 THR cc_start: 0.8575 (p) cc_final: 0.8265 (t) REVERT: B 873 TYR cc_start: 0.7918 (m-10) cc_final: 0.7659 (m-10) REVERT: B 1010 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7375 (mm-40) REVERT: B 1031 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: B 1098 ASN cc_start: 0.7531 (p0) cc_final: 0.7307 (p0) REVERT: C 773 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6765 (tm-30) REVERT: C 804 GLN cc_start: 0.7838 (mm110) cc_final: 0.7418 (mp-120) REVERT: C 854 LYS cc_start: 0.8387 (tptt) cc_final: 0.8105 (tppt) REVERT: C 855 PHE cc_start: 0.7857 (m-80) cc_final: 0.7546 (m-80) REVERT: C 907 ASN cc_start: 0.8136 (t0) cc_final: 0.7859 (t0) REVERT: C 945 LEU cc_start: 0.7950 (mm) cc_final: 0.7713 (mt) REVERT: C 952 VAL cc_start: 0.8230 (t) cc_final: 0.7811 (p) REVERT: C 957 GLU cc_start: 0.7090 (tp30) cc_final: 0.6696 (tp30) REVERT: C 994 ASP cc_start: 0.7089 (m-30) cc_final: 0.6842 (m-30) REVERT: C 1019 ARG cc_start: 0.7039 (ttp-170) cc_final: 0.6826 (ttp80) REVERT: C 1031 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7752 (mt-10) REVERT: C 1073 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7663 (mtmm) outliers start: 56 outliers final: 33 residues processed: 383 average time/residue: 1.0896 time to fit residues: 467.8625 Evaluate side-chains 394 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 353 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 4 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 130 optimal weight: 0.1980 chunk 197 optimal weight: 0.0170 chunk 181 optimal weight: 0.5980 chunk 157 optimal weight: 0.2980 chunk 16 optimal weight: 0.0170 chunk 121 optimal weight: 0.0170 chunk 96 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 overall best weight: 0.1094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 935 GLN A1108 ASN F 32 ASN B 824 ASN B 872 GLN B 935 GLN B1010 GLN C 824 ASN C 872 GLN C 954 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16338 Z= 0.151 Angle : 0.548 11.163 22245 Z= 0.278 Chirality : 0.042 0.164 2598 Planarity : 0.005 0.055 2841 Dihedral : 4.492 36.917 2625 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.43 % Allowed : 17.10 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.88 (0.18), residues: 2022 helix: 1.95 (0.21), residues: 621 sheet: 1.17 (0.25), residues: 423 loop : -0.58 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.004 0.001 HIS C1048 PHE 0.025 0.001 PHE D 78 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG C 815 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 347 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 815 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7743 (ttp-170) REVERT: A 837 TYR cc_start: 0.7569 (t80) cc_final: 0.7125 (t80) REVERT: A 855 PHE cc_start: 0.7798 (m-80) cc_final: 0.7339 (m-80) REVERT: A 866 THR cc_start: 0.8406 (p) cc_final: 0.8148 (t) REVERT: A 952 VAL cc_start: 0.8273 (t) cc_final: 0.7869 (p) REVERT: A 994 ASP cc_start: 0.6956 (m-30) cc_final: 0.6639 (m-30) REVERT: A 1010 GLN cc_start: 0.7538 (tp40) cc_final: 0.7267 (mm110) REVERT: A 1028 LYS cc_start: 0.8292 (mtpp) cc_final: 0.8033 (mttt) REVERT: A 1031 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7662 (mt-10) REVERT: A 1139 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6996 (m-30) REVERT: D 111 VAL cc_start: 0.8123 (t) cc_final: 0.7913 (m) REVERT: H 89 LEU cc_start: 0.8656 (tp) cc_final: 0.8445 (tt) REVERT: B 773 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6305 (tm-30) REVERT: B 815 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7394 (ttp-170) REVERT: B 866 THR cc_start: 0.8518 (p) cc_final: 0.8226 (t) REVERT: B 873 TYR cc_start: 0.7856 (m-10) cc_final: 0.7605 (m-10) REVERT: B 953 ASN cc_start: 0.7925 (m-40) cc_final: 0.7684 (m-40) REVERT: B 1010 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7309 (mm-40) REVERT: B 1031 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: B 1098 ASN cc_start: 0.7462 (p0) cc_final: 0.7226 (p0) REVERT: C 804 GLN cc_start: 0.7751 (mm110) cc_final: 0.7399 (mp-120) REVERT: C 854 LYS cc_start: 0.8355 (tptt) cc_final: 0.8077 (tppt) REVERT: C 855 PHE cc_start: 0.7590 (m-80) cc_final: 0.7358 (m-80) REVERT: C 945 LEU cc_start: 0.7745 (mm) cc_final: 0.7524 (mt) REVERT: C 957 GLU cc_start: 0.7088 (tp30) cc_final: 0.6857 (tp30) REVERT: C 994 ASP cc_start: 0.6995 (m-30) cc_final: 0.6742 (m-30) REVERT: C 1031 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: C 1071 GLN cc_start: 0.8406 (mt0) cc_final: 0.7935 (mt0) REVERT: C 1073 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7627 (mtmm) outliers start: 25 outliers final: 16 residues processed: 358 average time/residue: 1.1015 time to fit residues: 446.4848 Evaluate side-chains 364 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 342 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1139 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 157 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 935 GLN A1108 ASN F 32 ASN B 824 ASN B 935 GLN B 954 GLN B1010 GLN C 751 ASN C 824 ASN C 872 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.098485 restraints weight = 22614.101| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.04 r_work: 0.3085 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 16338 Z= 0.492 Angle : 0.663 10.679 22245 Z= 0.337 Chirality : 0.048 0.180 2598 Planarity : 0.005 0.065 2841 Dihedral : 4.829 40.152 2625 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.23 % Allowed : 16.47 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2022 helix: 1.64 (0.20), residues: 618 sheet: 1.02 (0.25), residues: 438 loop : -0.66 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 103 HIS 0.009 0.002 HIS H 77 PHE 0.027 0.002 PHE B1121 TYR 0.025 0.003 TYR D 50 ARG 0.005 0.000 ARG B 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7256.08 seconds wall clock time: 127 minutes 50.36 seconds (7670.36 seconds total)