Starting phenix.real_space_refine on Mon May 4 10:37:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ld2_63000/05_2026/9ld2_63000.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ld2_63000/05_2026/9ld2_63000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ld2_63000/05_2026/9ld2_63000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ld2_63000/05_2026/9ld2_63000.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ld2_63000/05_2026/9ld2_63000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ld2_63000/05_2026/9ld2_63000.map" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.025 sd= 0.313 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 87 5.16 5 C 12483 2.51 5 N 3318 2.21 5 O 3912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19800 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3352 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 16, 'TRANS': 420} Chain: "G" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "H" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1574 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3352 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 16, 'TRANS': 420} Chain: "I" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "J" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1574 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "C" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3352 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 16, 'TRANS': 420} Chain: "K" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1590 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "L" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1574 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 15, 'TRANS': 195} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.31, per 1000 atoms: 0.27 Number of scatterers: 19800 At special positions: 0 Unit cell: (156.576, 154.712, 262.824, 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 87 16.00 O 3912 8.00 N 3318 7.00 C 12483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 138 " - pdb=" SG CYS H 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 148 " - pdb=" SG CYS I 204 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS J 138 " - pdb=" SG CYS J 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 148 " - pdb=" SG CYS K 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B1134 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 717 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C 709 " Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.0 seconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 50 sheets defined 27.1% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 768 removed outlier: 3.529A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.717A pdb=" N PHE A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 842 removed outlier: 4.024A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 removed outlier: 3.562A pdb=" N ASP A 848 " --> pdb=" O ALA A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 886 Processing helix chain 'A' and resid 895 through 1033 removed outlier: 3.711A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 195 through 200 removed outlier: 4.124A pdb=" N THR G 199 " --> pdb=" O SER G 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 131 Processing helix chain 'H' and resid 185 through 190 removed outlier: 3.986A pdb=" N LYS H 190 " --> pdb=" O PRO H 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 768 Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.725A pdb=" N PHE B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 842 removed outlier: 4.023A pdb=" N GLY B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 removed outlier: 3.556A pdb=" N ASP B 848 " --> pdb=" O ALA B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 886 Processing helix chain 'B' and resid 895 through 1033 removed outlier: 3.730A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B1023 " --> pdb=" O ARG B1019 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 195 through 200 removed outlier: 4.133A pdb=" N THR I 199 " --> pdb=" O SER I 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 131 Processing helix chain 'J' and resid 185 through 190 removed outlier: 3.999A pdb=" N LYS J 190 " --> pdb=" O PRO J 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 768 removed outlier: 3.534A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.714A pdb=" N PHE C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 842 removed outlier: 4.021A pdb=" N GLY C 842 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 848 removed outlier: 3.562A pdb=" N ASP C 848 " --> pdb=" O ALA C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 886 Processing helix chain 'C' and resid 895 through 1033 removed outlier: 3.714A pdb=" N SER C1003 " --> pdb=" O GLY C 999 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN C1023 " --> pdb=" O ARG C1019 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 76 No H-bonds generated for 'chain 'K' and resid 74 through 76' Processing helix chain 'K' and resid 195 through 200 removed outlier: 4.135A pdb=" N THR K 199 " --> pdb=" O SER K 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 190 removed outlier: 3.994A pdb=" N LYS L 190 " --> pdb=" O PRO L 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.184A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.184A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER A1097 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1088 through 1089 removed outlier: 4.131A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.664A pdb=" N VAL G 5 " --> pdb=" O GLU G 23 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 71 " --> pdb=" O PHE G 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'G' and resid 35 through 38 removed outlier: 6.530A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 93 through 95 removed outlier: 6.111A pdb=" N TYR G 94 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.725A pdb=" N GLY G 147 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 143 through 144 removed outlier: 3.545A pdb=" N ALA G 144 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL G 192 " --> pdb=" O ALA G 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 171 through 173 Processing sheet with id=AB2, first strand: chain 'G' and resid 177 through 178 Processing sheet with id=AB3, first strand: chain 'G' and resid 206 through 208 removed outlier: 4.033A pdb=" N VAL G 206 " --> pdb=" O VAL G 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AB5, first strand: chain 'H' and resid 36 through 39 removed outlier: 3.702A pdb=" N ILE H 100 " --> pdb=" O SER H 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 120 through 122 removed outlier: 3.748A pdb=" N LEU H 136 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU H 182 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE H 140 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR H 176 " --> pdb=" O ASP H 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 195 through 196 removed outlier: 3.725A pdb=" N TYR H 195 " --> pdb=" O VAL H 210 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 199 through 201 removed outlier: 3.722A pdb=" N VAL H 199 " --> pdb=" O VAL H 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.166A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.166A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B1097 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1088 through 1089 removed outlier: 4.125A pdb=" N PHE B1121 " --> pdb=" O PHE B1089 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 5 through 7 removed outlier: 3.673A pdb=" N VAL I 5 " --> pdb=" O GLU I 23 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER I 71 " --> pdb=" O PHE I 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AC5, first strand: chain 'I' and resid 46 through 50 removed outlier: 6.529A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA I 97 " --> pdb=" O HIS I 35 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE I 37 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR I 95 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR I 94 " --> pdb=" O GLY I 114 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 128 through 132 removed outlier: 3.741A pdb=" N GLY I 147 " --> pdb=" O LEU I 132 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 143 through 144 removed outlier: 3.535A pdb=" N ALA I 144 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL I 192 " --> pdb=" O ALA I 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 171 through 173 Processing sheet with id=AC9, first strand: chain 'I' and resid 177 through 178 Processing sheet with id=AD1, first strand: chain 'I' and resid 206 through 208 removed outlier: 4.027A pdb=" N VAL I 206 " --> pdb=" O VAL I 215 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AD3, first strand: chain 'J' and resid 36 through 39 removed outlier: 3.683A pdb=" N ILE J 100 " --> pdb=" O SER J 92 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 120 through 122 removed outlier: 3.734A pdb=" N LEU J 136 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU J 182 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE J 140 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR J 176 " --> pdb=" O ASP J 142 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 195 through 196 removed outlier: 3.722A pdb=" N TYR J 195 " --> pdb=" O VAL J 210 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 199 through 201 removed outlier: 3.733A pdb=" N VAL J 199 " --> pdb=" O VAL J 206 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.173A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.173A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER C1097 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1088 through 1089 removed outlier: 4.128A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.668A pdb=" N VAL K 5 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER K 71 " --> pdb=" O PHE K 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AE3, first strand: chain 'K' and resid 35 through 38 removed outlier: 6.514A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 93 through 95 removed outlier: 6.118A pdb=" N TYR K 94 " --> pdb=" O GLY K 114 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 128 through 132 removed outlier: 3.741A pdb=" N GLY K 147 " --> pdb=" O LEU K 132 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 143 through 144 removed outlier: 3.564A pdb=" N ALA K 144 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL K 192 " --> pdb=" O ALA K 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'K' and resid 171 through 173 Processing sheet with id=AE8, first strand: chain 'K' and resid 177 through 178 Processing sheet with id=AE9, first strand: chain 'K' and resid 206 through 208 removed outlier: 4.037A pdb=" N VAL K 206 " --> pdb=" O VAL K 215 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AF2, first strand: chain 'L' and resid 36 through 39 removed outlier: 3.713A pdb=" N ILE L 100 " --> pdb=" O SER L 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 120 through 122 removed outlier: 3.735A pdb=" N LEU L 136 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU L 182 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE L 140 " --> pdb=" O ALA L 178 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 195 through 196 removed outlier: 3.730A pdb=" N TYR L 195 " --> pdb=" O VAL L 210 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 199 through 201 removed outlier: 3.749A pdb=" N VAL L 199 " --> pdb=" O VAL L 206 " (cutoff:3.500A) 734 hydrogen bonds defined for protein. 2082 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: 3.35 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6408 1.34 - 1.46: 4487 1.46 - 1.58: 9196 1.58 - 1.70: 0 1.70 - 1.81: 117 Bond restraints: 20208 Sorted by residual: bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.66e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.54e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.54e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 20203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 26676 1.06 - 2.11: 586 2.11 - 3.17: 182 3.17 - 4.23: 30 4.23 - 5.29: 15 Bond angle restraints: 27489 Sorted by residual: angle pdb=" C ASP K 54 " pdb=" N THR K 55 " pdb=" CA THR K 55 " ideal model delta sigma weight residual 121.54 125.72 -4.18 1.91e+00 2.74e-01 4.80e+00 angle pdb=" C ASP I 54 " pdb=" N THR I 55 " pdb=" CA THR I 55 " ideal model delta sigma weight residual 121.54 125.72 -4.18 1.91e+00 2.74e-01 4.79e+00 angle pdb=" C ASP G 54 " pdb=" N THR G 55 " pdb=" CA THR G 55 " ideal model delta sigma weight residual 121.54 125.69 -4.15 1.91e+00 2.74e-01 4.73e+00 angle pdb=" N SER J 58 " pdb=" CA SER J 58 " pdb=" C SER J 58 " ideal model delta sigma weight residual 108.07 111.15 -3.08 1.59e+00 3.96e-01 3.75e+00 angle pdb=" N SER L 58 " pdb=" CA SER L 58 " pdb=" C SER L 58 " ideal model delta sigma weight residual 108.07 111.08 -3.01 1.59e+00 3.96e-01 3.58e+00 ... (remaining 27484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 11840 16.37 - 32.74: 398 32.74 - 49.11: 89 49.11 - 65.48: 15 65.48 - 81.86: 3 Dihedral angle restraints: 12345 sinusoidal: 4923 harmonic: 7422 Sorted by residual: dihedral pdb=" CA GLU H 52 " pdb=" C GLU H 52 " pdb=" N VAL H 53 " pdb=" CA VAL H 53 " ideal model delta harmonic sigma weight residual -180.00 -164.25 -15.75 0 5.00e+00 4.00e-02 9.92e+00 dihedral pdb=" CA GLU J 52 " pdb=" C GLU J 52 " pdb=" N VAL J 53 " pdb=" CA VAL J 53 " ideal model delta harmonic sigma weight residual 180.00 -164.42 -15.58 0 5.00e+00 4.00e-02 9.71e+00 dihedral pdb=" N LYS A1028 " pdb=" CA LYS A1028 " pdb=" CB LYS A1028 " pdb=" CG LYS A1028 " ideal model delta sinusoidal sigma weight residual -60.00 -119.92 59.92 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 12342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2783 0.055 - 0.110: 419 0.110 - 0.165: 20 0.165 - 0.220: 0 0.220 - 0.275: 3 Chirality restraints: 3225 Sorted by residual: chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 801 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 3222 not shown) Planarity restraints: 3537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 60 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.32e+00 pdb=" N PRO H 61 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 60 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO L 61 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 60 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO J 61 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO J 61 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 61 " -0.021 5.00e-02 4.00e+02 ... (remaining 3534 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3535 2.78 - 3.31: 19019 3.31 - 3.84: 32786 3.84 - 4.37: 34495 4.37 - 4.90: 61586 Nonbonded interactions: 151421 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.247 3.040 nonbonded pdb=" O PRO G 131 " pdb=" OG SER H 125 " model vdw 2.253 3.040 nonbonded pdb=" O PRO I 131 " pdb=" OG SER J 125 " model vdw 2.255 3.040 ... (remaining 151416 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.570 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.002 0.038 20253 Z= 0.114 Angle : 0.446 8.491 27597 Z= 0.228 Chirality : 0.039 0.275 3225 Planarity : 0.003 0.038 3519 Dihedral : 8.564 81.856 7506 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.12 % Allowed : 6.58 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.16), residues: 2559 helix: 1.93 (0.19), residues: 666 sheet: -2.05 (0.20), residues: 600 loop : -3.25 (0.14), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 815 TYR 0.003 0.000 TYR K 95 PHE 0.005 0.001 PHE J 143 TRP 0.005 0.000 TRP I 111 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00215 (20208) covalent geometry : angle 0.43556 (27489) SS BOND : bond 0.00070 ( 27) SS BOND : angle 0.29141 ( 54) hydrogen bonds : bond 0.16895 ( 719) hydrogen bonds : angle 6.96553 ( 2082) link_NAG-ASN : bond 0.00606 ( 18) link_NAG-ASN : angle 2.20806 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 553 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 718 PHE cc_start: 0.8235 (m-80) cc_final: 0.7632 (m-10) REVERT: A 825 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8455 (mmmm) REVERT: A 1029 MET cc_start: 0.8366 (tpp) cc_final: 0.8114 (tpp) REVERT: A 1089 PHE cc_start: 0.7366 (p90) cc_final: 0.7134 (p90) REVERT: A 1103 PHE cc_start: 0.8106 (m-80) cc_final: 0.7737 (m-80) REVERT: A 1104 VAL cc_start: 0.8371 (t) cc_final: 0.7528 (m) REVERT: A 1109 PHE cc_start: 0.8070 (t80) cc_final: 0.7463 (t80) REVERT: G 30 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7877 (ttpp) REVERT: G 31 ASP cc_start: 0.7585 (p0) cc_final: 0.6649 (p0) REVERT: G 60 TYR cc_start: 0.7759 (m-80) cc_final: 0.7501 (m-80) REVERT: G 118 THR cc_start: 0.8486 (m) cc_final: 0.8181 (p) REVERT: H 87 ASP cc_start: 0.7678 (m-30) cc_final: 0.7466 (m-30) REVERT: H 89 TYR cc_start: 0.7073 (m-80) cc_final: 0.6781 (m-80) REVERT: H 91 CYS cc_start: 0.8176 (t) cc_final: 0.7904 (t) REVERT: B 718 PHE cc_start: 0.8071 (m-80) cc_final: 0.7434 (m-10) REVERT: B 1029 MET cc_start: 0.8594 (tpp) cc_final: 0.8005 (tpp) REVERT: B 1031 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6838 (mt-10) REVERT: B 1089 PHE cc_start: 0.6668 (p90) cc_final: 0.6399 (p90) REVERT: B 1104 VAL cc_start: 0.7777 (t) cc_final: 0.7169 (m) REVERT: B 1109 PHE cc_start: 0.7909 (t80) cc_final: 0.7670 (t80) REVERT: I 31 ASP cc_start: 0.7681 (p0) cc_final: 0.7075 (p0) REVERT: I 34 MET cc_start: 0.7851 (mmm) cc_final: 0.7373 (mmm) REVERT: I 118 THR cc_start: 0.8535 (m) cc_final: 0.8184 (p) REVERT: J 112 GLN cc_start: 0.1411 (OUTLIER) cc_final: 0.0928 (pm20) REVERT: J 182 LEU cc_start: 0.7953 (tp) cc_final: 0.7705 (tp) REVERT: C 718 PHE cc_start: 0.8295 (m-80) cc_final: 0.7748 (m-10) REVERT: C 743 CYS cc_start: 0.5328 (m) cc_final: 0.4900 (m) REVERT: C 1031 GLU cc_start: 0.7498 (mt-10) cc_final: 0.6911 (mt-10) REVERT: C 1103 PHE cc_start: 0.7489 (m-80) cc_final: 0.6932 (m-80) REVERT: C 1109 PHE cc_start: 0.8037 (t80) cc_final: 0.7535 (t80) REVERT: K 54 ASP cc_start: 0.7738 (p0) cc_final: 0.7445 (p0) REVERT: K 108 PHE cc_start: 0.7921 (t80) cc_final: 0.7543 (t80) REVERT: K 118 THR cc_start: 0.8641 (m) cc_final: 0.8177 (p) REVERT: L 87 ASP cc_start: 0.7433 (m-30) cc_final: 0.6969 (m-30) REVERT: L 89 TYR cc_start: 0.7430 (m-80) cc_final: 0.6956 (m-80) REVERT: L 91 CYS cc_start: 0.8213 (t) cc_final: 0.7961 (t) REVERT: L 176 TYR cc_start: 0.6408 (m-80) cc_final: 0.6207 (m-10) outliers start: 90 outliers final: 15 residues processed: 614 average time/residue: 0.1584 time to fit residues: 145.6234 Evaluate side-chains 405 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 387 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 ASN A 762 GLN A 784 GLN A 872 GLN A 949 GLN A 954 GLN A 955 ASN A 969 ASN A 992 GLN A1005 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN G 13 GLN G 39 GLN G 82 GLN G 84 ASN H 16 GLN H 40 GLN H 130 GLN H 171 GLN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 762 GLN B 784 GLN B 872 GLN B 954 GLN B 955 ASN B 969 ASN B 992 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN I 13 GLN I 39 GLN I 82 GLN I 84 ASN J 16 GLN J 40 GLN J 112 GLN J 130 GLN J 171 GLN ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN C 762 GLN C 784 GLN C 853 GLN C 872 GLN C 954 GLN C 955 ASN C 969 ASN C 992 GLN C1064 HIS C1071 GLN C1101 HIS K 13 GLN K 39 GLN K 82 GLN L 40 GLN L 130 GLN L 171 GLN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.113895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.083622 restraints weight = 93380.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.083695 restraints weight = 70275.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.082768 restraints weight = 63592.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.082988 restraints weight = 67189.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.083007 restraints weight = 58954.495| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20253 Z= 0.189 Angle : 0.678 9.829 27597 Z= 0.339 Chirality : 0.044 0.319 3225 Planarity : 0.005 0.051 3519 Dihedral : 5.920 58.644 3165 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.02 % Allowed : 12.57 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.16), residues: 2559 helix: 2.45 (0.20), residues: 687 sheet: -1.99 (0.20), residues: 600 loop : -2.96 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1000 TYR 0.022 0.002 TYR C 837 PHE 0.030 0.002 PHE I 108 TRP 0.029 0.002 TRP L 189 HIS 0.007 0.002 HIS H 192 Details of bonding type rmsd covalent geometry : bond 0.00405 (20208) covalent geometry : angle 0.66327 (27489) SS BOND : bond 0.01037 ( 27) SS BOND : angle 2.20402 ( 54) hydrogen bonds : bond 0.05130 ( 719) hydrogen bonds : angle 5.14497 ( 2082) link_NAG-ASN : bond 0.00649 ( 18) link_NAG-ASN : angle 2.41773 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 408 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 718 PHE cc_start: 0.8543 (m-80) cc_final: 0.7919 (m-80) REVERT: A 825 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8572 (mttm) REVERT: A 837 TYR cc_start: 0.8600 (t80) cc_final: 0.7984 (t80) REVERT: A 869 MET cc_start: 0.9168 (mmm) cc_final: 0.8960 (mmm) REVERT: A 902 MET cc_start: 0.8688 (mmm) cc_final: 0.8304 (mmm) REVERT: A 906 PHE cc_start: 0.9483 (m-80) cc_final: 0.8886 (t80) REVERT: A 1029 MET cc_start: 0.8314 (tpp) cc_final: 0.8023 (tpp) REVERT: A 1033 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7749 (p) REVERT: A 1050 MET cc_start: 0.6998 (ttm) cc_final: 0.6781 (ttm) REVERT: A 1067 TYR cc_start: 0.7774 (p90) cc_final: 0.7572 (p90) REVERT: A 1101 HIS cc_start: 0.8779 (m170) cc_final: 0.8428 (m90) REVERT: G 23 GLU cc_start: 0.7977 (tp30) cc_final: 0.7594 (tm-30) REVERT: G 31 ASP cc_start: 0.7526 (p0) cc_final: 0.6549 (p0) REVERT: G 118 THR cc_start: 0.8774 (m) cc_final: 0.8316 (p) REVERT: H 28 ASP cc_start: 0.8445 (m-30) cc_final: 0.8144 (p0) REVERT: H 198 GLN cc_start: 0.5893 (mp10) cc_final: 0.5214 (mp10) REVERT: B 709 ASN cc_start: 0.6801 (p0) cc_final: 0.6562 (p0) REVERT: B 718 PHE cc_start: 0.8550 (m-80) cc_final: 0.7164 (m-10) REVERT: B 776 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5395 (mmmt) REVERT: B 833 PHE cc_start: 0.8281 (m-80) cc_final: 0.7848 (m-80) REVERT: B 1067 TYR cc_start: 0.7686 (p90) cc_final: 0.6931 (p90) REVERT: B 1089 PHE cc_start: 0.7285 (p90) cc_final: 0.6943 (p90) REVERT: B 1103 PHE cc_start: 0.8691 (m-80) cc_final: 0.7999 (m-80) REVERT: B 1109 PHE cc_start: 0.8080 (t80) cc_final: 0.7680 (t80) REVERT: I 31 ASP cc_start: 0.7694 (p0) cc_final: 0.7131 (p0) REVERT: I 118 THR cc_start: 0.8832 (m) cc_final: 0.8428 (p) REVERT: I 179 GLN cc_start: 0.9084 (mt0) cc_final: 0.8794 (mp10) REVERT: J 87 ASP cc_start: 0.7076 (m-30) cc_final: 0.6594 (m-30) REVERT: C 718 PHE cc_start: 0.8545 (m-80) cc_final: 0.7948 (m-10) REVERT: C 836 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: C 906 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8862 (t80) REVERT: C 1029 MET cc_start: 0.8604 (tpp) cc_final: 0.8332 (tpp) REVERT: C 1109 PHE cc_start: 0.7976 (t80) cc_final: 0.7726 (t80) REVERT: C 1111 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8383 (mt-10) REVERT: K 86 LEU cc_start: 0.8596 (mm) cc_final: 0.8032 (mm) REVERT: K 118 THR cc_start: 0.8888 (m) cc_final: 0.8453 (p) REVERT: L 87 ASP cc_start: 0.7205 (m-30) cc_final: 0.6779 (m-30) REVERT: L 89 TYR cc_start: 0.6933 (m-80) cc_final: 0.6694 (m-80) REVERT: L 153 LYS cc_start: 0.8772 (tptp) cc_final: 0.8528 (tptp) REVERT: L 176 TYR cc_start: 0.7312 (m-80) cc_final: 0.6994 (m-80) REVERT: L 182 LEU cc_start: 0.8273 (tp) cc_final: 0.7980 (tt) outliers start: 88 outliers final: 45 residues processed: 472 average time/residue: 0.1454 time to fit residues: 104.5021 Evaluate side-chains 412 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 362 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 710 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 836 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 836 GLN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 148 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 41 optimal weight: 0.3980 chunk 224 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 222 optimal weight: 0.8980 chunk 177 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 ASN ** K 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.113081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.081985 restraints weight = 93431.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.081363 restraints weight = 76041.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.081326 restraints weight = 58322.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.081448 restraints weight = 53128.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.081596 restraints weight = 49578.419| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 20253 Z= 0.166 Angle : 0.673 10.193 27597 Z= 0.338 Chirality : 0.045 0.311 3225 Planarity : 0.004 0.047 3519 Dihedral : 5.691 55.814 3142 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.62 % Allowed : 13.03 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.16), residues: 2559 helix: 2.48 (0.20), residues: 693 sheet: -1.77 (0.21), residues: 597 loop : -2.87 (0.15), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1039 TYR 0.027 0.002 TYR A 789 PHE 0.033 0.002 PHE L 143 TRP 0.015 0.001 TRP J 189 HIS 0.008 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00369 (20208) covalent geometry : angle 0.65869 (27489) SS BOND : bond 0.00370 ( 27) SS BOND : angle 2.22546 ( 54) hydrogen bonds : bond 0.05024 ( 719) hydrogen bonds : angle 4.82024 ( 2082) link_NAG-ASN : bond 0.00841 ( 18) link_NAG-ASN : angle 2.36387 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 397 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.6022 (p0) cc_final: 0.5793 (p0) REVERT: A 718 PHE cc_start: 0.8502 (m-80) cc_final: 0.7826 (m-80) REVERT: A 740 MET cc_start: 0.7890 (mmm) cc_final: 0.7245 (mmm) REVERT: A 819 GLU cc_start: 0.7522 (tt0) cc_final: 0.7188 (tt0) REVERT: A 825 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8548 (mttm) REVERT: A 837 TYR cc_start: 0.8607 (t80) cc_final: 0.7958 (t80) REVERT: A 869 MET cc_start: 0.9262 (mmm) cc_final: 0.8981 (mmm) REVERT: A 902 MET cc_start: 0.8818 (mmm) cc_final: 0.8438 (mmm) REVERT: A 906 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8949 (t80) REVERT: A 1029 MET cc_start: 0.8545 (tpp) cc_final: 0.8112 (tpp) REVERT: A 1033 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.7936 (p) REVERT: A 1063 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7367 (tm) REVERT: A 1106 GLN cc_start: 0.7708 (pm20) cc_final: 0.6585 (pm20) REVERT: A 1109 PHE cc_start: 0.8071 (t80) cc_final: 0.7279 (t80) REVERT: G 23 GLU cc_start: 0.8268 (tp30) cc_final: 0.7663 (tm-30) REVERT: G 31 ASP cc_start: 0.7905 (p0) cc_final: 0.6716 (p0) REVERT: G 32 TYR cc_start: 0.7861 (m-10) cc_final: 0.7373 (m-10) REVERT: G 118 THR cc_start: 0.8822 (m) cc_final: 0.8380 (p) REVERT: G 174 PHE cc_start: 0.6904 (m-80) cc_final: 0.6556 (m-80) REVERT: G 189 VAL cc_start: 0.7812 (p) cc_final: 0.7516 (m) REVERT: H 28 ASP cc_start: 0.8781 (m-30) cc_final: 0.8341 (p0) REVERT: H 89 TYR cc_start: 0.7055 (m-80) cc_final: 0.6807 (m-80) REVERT: H 138 CYS cc_start: 0.6175 (t) cc_final: 0.5716 (t) REVERT: H 198 GLN cc_start: 0.5411 (mp10) cc_final: 0.4561 (mp10) REVERT: B 718 PHE cc_start: 0.8632 (m-80) cc_final: 0.7116 (m-10) REVERT: B 780 GLU cc_start: 0.7385 (mp0) cc_final: 0.7167 (mp0) REVERT: B 833 PHE cc_start: 0.8242 (m-80) cc_final: 0.7931 (m-80) REVERT: B 837 TYR cc_start: 0.7371 (t80) cc_final: 0.7004 (m-80) REVERT: B 866 THR cc_start: 0.9663 (p) cc_final: 0.9351 (p) REVERT: B 902 MET cc_start: 0.8951 (mmm) cc_final: 0.8586 (mmm) REVERT: B 1029 MET cc_start: 0.8998 (tpp) cc_final: 0.8345 (tpp) REVERT: B 1067 TYR cc_start: 0.7931 (p90) cc_final: 0.6994 (p90) REVERT: B 1089 PHE cc_start: 0.7463 (p90) cc_final: 0.7158 (p90) REVERT: B 1109 PHE cc_start: 0.8200 (t80) cc_final: 0.7667 (t80) REVERT: I 31 ASP cc_start: 0.8007 (p0) cc_final: 0.7289 (p0) REVERT: I 38 ARG cc_start: 0.7258 (ttm-80) cc_final: 0.6527 (mtt180) REVERT: I 118 THR cc_start: 0.8790 (m) cc_final: 0.8350 (p) REVERT: I 174 PHE cc_start: 0.7164 (m-80) cc_final: 0.6747 (m-80) REVERT: I 189 VAL cc_start: 0.7703 (p) cc_final: 0.7397 (m) REVERT: J 89 TYR cc_start: 0.6831 (m-80) cc_final: 0.6576 (m-80) REVERT: J 153 LYS cc_start: 0.8302 (tptp) cc_final: 0.7890 (tptp) REVERT: J 198 GLN cc_start: 0.5322 (mp10) cc_final: 0.4404 (mp10) REVERT: C 718 PHE cc_start: 0.8632 (m-80) cc_final: 0.7938 (m-10) REVERT: C 837 TYR cc_start: 0.7005 (t80) cc_final: 0.6779 (m-80) REVERT: C 906 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.8858 (t80) REVERT: C 1109 PHE cc_start: 0.8089 (t80) cc_final: 0.7805 (t80) REVERT: C 1111 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8615 (pp20) REVERT: K 38 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7170 (mtp180) REVERT: K 68 PHE cc_start: 0.7759 (m-80) cc_final: 0.7375 (m-80) REVERT: K 118 THR cc_start: 0.8870 (m) cc_final: 0.8374 (p) REVERT: K 174 PHE cc_start: 0.7279 (m-80) cc_final: 0.6951 (m-80) REVERT: K 189 VAL cc_start: 0.7581 (p) cc_final: 0.7334 (m) REVERT: L 87 ASP cc_start: 0.7481 (m-30) cc_final: 0.6858 (m-30) REVERT: L 89 TYR cc_start: 0.7293 (m-80) cc_final: 0.6892 (m-80) REVERT: L 153 LYS cc_start: 0.8783 (tptp) cc_final: 0.8419 (tptp) REVERT: L 176 TYR cc_start: 0.7342 (m-80) cc_final: 0.7078 (m-80) REVERT: L 182 LEU cc_start: 0.8165 (tp) cc_final: 0.7778 (tt) outliers start: 101 outliers final: 54 residues processed: 463 average time/residue: 0.1466 time to fit residues: 102.7535 Evaluate side-chains 415 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 356 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 184 TYR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1088 HIS Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 177 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 150 optimal weight: 0.0570 chunk 121 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 95 optimal weight: 0.0060 chunk 33 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 0.4914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L 71 ASN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.113364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.079136 restraints weight = 93625.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.080858 restraints weight = 56245.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.081436 restraints weight = 43094.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.081934 restraints weight = 38396.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.081934 restraints weight = 35576.821| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 20253 Z= 0.135 Angle : 0.651 12.908 27597 Z= 0.323 Chirality : 0.044 0.305 3225 Planarity : 0.004 0.047 3519 Dihedral : 5.513 56.553 3140 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.75 % Allowed : 14.72 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.17), residues: 2559 helix: 2.68 (0.20), residues: 693 sheet: -1.65 (0.21), residues: 603 loop : -2.76 (0.15), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1039 TYR 0.029 0.001 TYR I 32 PHE 0.028 0.002 PHE I 108 TRP 0.012 0.001 TRP L 152 HIS 0.005 0.001 HIS H 192 Details of bonding type rmsd covalent geometry : bond 0.00300 (20208) covalent geometry : angle 0.63914 (27489) SS BOND : bond 0.00309 ( 27) SS BOND : angle 1.88926 ( 54) hydrogen bonds : bond 0.04674 ( 719) hydrogen bonds : angle 4.56201 ( 2082) link_NAG-ASN : bond 0.00611 ( 18) link_NAG-ASN : angle 2.31758 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 380 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.5389 (p0) cc_final: 0.5142 (p0) REVERT: A 718 PHE cc_start: 0.7987 (m-80) cc_final: 0.7200 (m-80) REVERT: A 740 MET cc_start: 0.7192 (mmm) cc_final: 0.6891 (mmm) REVERT: A 767 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8609 (tt) REVERT: A 819 GLU cc_start: 0.7442 (tt0) cc_final: 0.7123 (tt0) REVERT: A 825 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8598 (mttm) REVERT: A 837 TYR cc_start: 0.8557 (t80) cc_final: 0.7887 (t80) REVERT: A 869 MET cc_start: 0.9343 (mmm) cc_final: 0.9079 (mmm) REVERT: A 902 MET cc_start: 0.8964 (mmm) cc_final: 0.8530 (mmm) REVERT: A 906 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.8967 (t80) REVERT: A 1029 MET cc_start: 0.8372 (tpp) cc_final: 0.8050 (tpp) REVERT: A 1033 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7795 (p) REVERT: A 1063 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7091 (tm) REVERT: A 1067 TYR cc_start: 0.7709 (p90) cc_final: 0.7051 (p90) REVERT: A 1101 HIS cc_start: 0.8088 (p-80) cc_final: 0.7727 (p-80) REVERT: G 23 GLU cc_start: 0.7925 (tp30) cc_final: 0.7589 (tm-30) REVERT: G 30 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7866 (ttpp) REVERT: G 31 ASP cc_start: 0.7632 (p0) cc_final: 0.7161 (p0) REVERT: G 118 THR cc_start: 0.8661 (m) cc_final: 0.8266 (p) REVERT: G 174 PHE cc_start: 0.6871 (m-80) cc_final: 0.6572 (m-80) REVERT: G 189 VAL cc_start: 0.7791 (p) cc_final: 0.7556 (m) REVERT: H 138 CYS cc_start: 0.6870 (t) cc_final: 0.6277 (t) REVERT: B 718 PHE cc_start: 0.8055 (m-80) cc_final: 0.6882 (m-10) REVERT: B 833 PHE cc_start: 0.8192 (m-80) cc_final: 0.7864 (m-80) REVERT: B 837 TYR cc_start: 0.7398 (t80) cc_final: 0.6989 (m-80) REVERT: B 864 LEU cc_start: 0.9494 (pt) cc_final: 0.9281 (tp) REVERT: B 866 THR cc_start: 0.9538 (p) cc_final: 0.9337 (p) REVERT: B 869 MET cc_start: 0.9499 (mmm) cc_final: 0.9151 (mmm) REVERT: B 902 MET cc_start: 0.9117 (mmm) cc_final: 0.8745 (mmm) REVERT: B 1029 MET cc_start: 0.8862 (tpp) cc_final: 0.8149 (tpp) REVERT: B 1067 TYR cc_start: 0.7542 (p90) cc_final: 0.6961 (p90) REVERT: B 1089 PHE cc_start: 0.7020 (p90) cc_final: 0.6779 (p90) REVERT: B 1109 PHE cc_start: 0.7948 (t80) cc_final: 0.7666 (t80) REVERT: I 30 LYS cc_start: 0.8349 (ttpp) cc_final: 0.8134 (ttpp) REVERT: I 31 ASP cc_start: 0.7363 (p0) cc_final: 0.6832 (p0) REVERT: I 38 ARG cc_start: 0.7100 (ttm-80) cc_final: 0.6515 (ttm-80) REVERT: I 118 THR cc_start: 0.8689 (m) cc_final: 0.8295 (p) REVERT: I 174 PHE cc_start: 0.7114 (m-80) cc_final: 0.6711 (m-80) REVERT: I 179 GLN cc_start: 0.9187 (pt0) cc_final: 0.8892 (mp10) REVERT: I 189 VAL cc_start: 0.7703 (p) cc_final: 0.7412 (m) REVERT: J 153 LYS cc_start: 0.8333 (tptp) cc_final: 0.7939 (tptp) REVERT: C 718 PHE cc_start: 0.8101 (m-80) cc_final: 0.7632 (m-10) REVERT: C 906 PHE cc_start: 0.9467 (m-80) cc_final: 0.8924 (t80) REVERT: C 1029 MET cc_start: 0.8798 (tpp) cc_final: 0.8560 (tpp) REVERT: K 118 THR cc_start: 0.8853 (m) cc_final: 0.8404 (p) REVERT: K 174 PHE cc_start: 0.7227 (m-80) cc_final: 0.6865 (m-80) REVERT: K 189 VAL cc_start: 0.7648 (p) cc_final: 0.7448 (m) REVERT: L 87 ASP cc_start: 0.6922 (m-30) cc_final: 0.6439 (m-30) REVERT: L 132 ASN cc_start: 0.9176 (t0) cc_final: 0.8976 (p0) REVERT: L 153 LYS cc_start: 0.8652 (tptp) cc_final: 0.8355 (tptp) REVERT: L 176 TYR cc_start: 0.7297 (m-80) cc_final: 0.6892 (m-80) outliers start: 82 outliers final: 56 residues processed: 438 average time/residue: 0.1518 time to fit residues: 100.2778 Evaluate side-chains 414 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 352 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 91 CYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 195 TYR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 CYS Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1088 HIS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 190 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 GLN L 192 HIS ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.109776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.077850 restraints weight = 92221.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.077894 restraints weight = 70586.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.077657 restraints weight = 56112.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.077822 restraints weight = 55123.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077880 restraints weight = 49174.005| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 20253 Z= 0.243 Angle : 0.736 11.953 27597 Z= 0.372 Chirality : 0.046 0.309 3225 Planarity : 0.005 0.062 3519 Dihedral : 5.600 52.392 3140 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.39 % Allowed : 15.27 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2559 helix: 2.36 (0.19), residues: 693 sheet: -1.70 (0.21), residues: 609 loop : -2.68 (0.15), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 38 TYR 0.028 0.002 TYR A 789 PHE 0.031 0.002 PHE H 143 TRP 0.034 0.002 TRP J 189 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00540 (20208) covalent geometry : angle 0.71554 (27489) SS BOND : bond 0.00537 ( 27) SS BOND : angle 2.60623 ( 54) hydrogen bonds : bond 0.05573 ( 719) hydrogen bonds : angle 4.80973 ( 2082) link_NAG-ASN : bond 0.01211 ( 18) link_NAG-ASN : angle 3.07561 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 372 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 718 PHE cc_start: 0.8443 (m-80) cc_final: 0.7806 (m-80) REVERT: A 740 MET cc_start: 0.7682 (mmm) cc_final: 0.7143 (mmm) REVERT: A 776 LYS cc_start: 0.6410 (mmtp) cc_final: 0.5966 (tppt) REVERT: A 819 GLU cc_start: 0.7527 (tt0) cc_final: 0.7173 (tt0) REVERT: A 837 TYR cc_start: 0.8522 (t80) cc_final: 0.7898 (t80) REVERT: A 869 MET cc_start: 0.9268 (mmm) cc_final: 0.8979 (mmm) REVERT: A 894 LEU cc_start: -0.1277 (OUTLIER) cc_final: -0.1480 (tp) REVERT: A 902 MET cc_start: 0.8860 (mmm) cc_final: 0.8426 (mmm) REVERT: A 906 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8866 (t80) REVERT: A 1029 MET cc_start: 0.8580 (tpp) cc_final: 0.8086 (tpp) REVERT: A 1101 HIS cc_start: 0.8893 (p-80) cc_final: 0.8470 (p-80) REVERT: G 23 GLU cc_start: 0.8362 (tp30) cc_final: 0.7878 (tm-30) REVERT: G 174 PHE cc_start: 0.7223 (m-80) cc_final: 0.6993 (m-80) REVERT: G 189 VAL cc_start: 0.8028 (p) cc_final: 0.7780 (m) REVERT: B 718 PHE cc_start: 0.8548 (m-80) cc_final: 0.7716 (m-10) REVERT: B 814 LYS cc_start: 0.8748 (mptt) cc_final: 0.8387 (mptt) REVERT: B 837 TYR cc_start: 0.7580 (t80) cc_final: 0.7069 (m-80) REVERT: B 864 LEU cc_start: 0.9458 (pt) cc_final: 0.9189 (tp) REVERT: B 869 MET cc_start: 0.9315 (mmm) cc_final: 0.9023 (mmm) REVERT: B 906 PHE cc_start: 0.9471 (OUTLIER) cc_final: 0.8914 (t80) REVERT: B 1067 TYR cc_start: 0.7968 (p90) cc_final: 0.7646 (p90) REVERT: B 1089 PHE cc_start: 0.7629 (p90) cc_final: 0.7316 (p90) REVERT: B 1109 PHE cc_start: 0.8176 (t80) cc_final: 0.7542 (t80) REVERT: B 1111 GLU cc_start: 0.7968 (pm20) cc_final: 0.7070 (pm20) REVERT: I 38 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.6978 (ttm-80) REVERT: I 118 THR cc_start: 0.8899 (m) cc_final: 0.8517 (p) REVERT: I 174 PHE cc_start: 0.7312 (m-80) cc_final: 0.7010 (m-80) REVERT: I 189 VAL cc_start: 0.7808 (p) cc_final: 0.7540 (m) REVERT: J 153 LYS cc_start: 0.8434 (tptp) cc_final: 0.7893 (tptp) REVERT: C 718 PHE cc_start: 0.8482 (m-80) cc_final: 0.7893 (m-10) REVERT: C 740 MET cc_start: 0.8021 (mmm) cc_final: 0.7317 (tmm) REVERT: C 814 LYS cc_start: 0.8584 (mptt) cc_final: 0.8314 (mptt) REVERT: C 906 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8673 (t80) REVERT: C 1014 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8566 (mmm-85) REVERT: K 118 THR cc_start: 0.9005 (m) cc_final: 0.8600 (p) REVERT: K 174 PHE cc_start: 0.7468 (m-80) cc_final: 0.7228 (m-80) REVERT: K 189 VAL cc_start: 0.7762 (p) cc_final: 0.7530 (m) REVERT: L 75 LEU cc_start: 0.7773 (tp) cc_final: 0.7571 (tp) REVERT: L 83 GLU cc_start: 0.4925 (pp20) cc_final: 0.4658 (pp20) REVERT: L 132 ASN cc_start: 0.8949 (t0) cc_final: 0.8714 (p0) outliers start: 96 outliers final: 54 residues processed: 440 average time/residue: 0.1447 time to fit residues: 96.2306 Evaluate side-chains 398 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 340 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 154 PHE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1088 HIS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 209 optimal weight: 0.4980 chunk 125 optimal weight: 6.9990 chunk 226 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 148 optimal weight: 20.0000 chunk 134 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.110704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.078603 restraints weight = 92293.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078769 restraints weight = 72275.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.078512 restraints weight = 59028.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.078807 restraints weight = 53594.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.078835 restraints weight = 48536.604| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 20253 Z= 0.165 Angle : 0.717 12.267 27597 Z= 0.354 Chirality : 0.045 0.292 3225 Planarity : 0.004 0.061 3519 Dihedral : 5.347 53.408 3132 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.80 % Allowed : 17.15 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.17), residues: 2559 helix: 2.65 (0.20), residues: 690 sheet: -1.77 (0.20), residues: 624 loop : -2.59 (0.15), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1014 TYR 0.030 0.002 TYR A 789 PHE 0.026 0.002 PHE K 68 TRP 0.013 0.001 TRP K 47 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00374 (20208) covalent geometry : angle 0.69805 (27489) SS BOND : bond 0.00269 ( 27) SS BOND : angle 2.30277 ( 54) hydrogen bonds : bond 0.05029 ( 719) hydrogen bonds : angle 4.62960 ( 2082) link_NAG-ASN : bond 0.00989 ( 18) link_NAG-ASN : angle 3.02421 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 352 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.6546 (p0) cc_final: 0.6339 (p0) REVERT: A 718 PHE cc_start: 0.8466 (m-80) cc_final: 0.7854 (m-80) REVERT: A 740 MET cc_start: 0.7719 (mmm) cc_final: 0.7326 (tpp) REVERT: A 767 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8563 (tt) REVERT: A 819 GLU cc_start: 0.7581 (tt0) cc_final: 0.7269 (tt0) REVERT: A 837 TYR cc_start: 0.8501 (t80) cc_final: 0.7920 (t80) REVERT: A 869 MET cc_start: 0.9273 (mmm) cc_final: 0.8985 (mmm) REVERT: A 894 LEU cc_start: -0.1196 (OUTLIER) cc_final: -0.1407 (tp) REVERT: A 902 MET cc_start: 0.8993 (mmm) cc_final: 0.8402 (mmm) REVERT: A 906 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8814 (t80) REVERT: A 1029 MET cc_start: 0.8573 (tpp) cc_final: 0.8157 (tpp) REVERT: A 1101 HIS cc_start: 0.8898 (p-80) cc_final: 0.8421 (p-80) REVERT: G 23 GLU cc_start: 0.8206 (tp30) cc_final: 0.7757 (tm-30) REVERT: G 118 THR cc_start: 0.8791 (m) cc_final: 0.8369 (p) REVERT: G 174 PHE cc_start: 0.7187 (m-80) cc_final: 0.6970 (m-80) REVERT: G 189 VAL cc_start: 0.7938 (p) cc_final: 0.7693 (m) REVERT: H 188 GLN cc_start: 0.8450 (pp30) cc_final: 0.7455 (pp30) REVERT: B 718 PHE cc_start: 0.8560 (m-80) cc_final: 0.7470 (m-80) REVERT: B 740 MET cc_start: 0.7193 (mmm) cc_final: 0.6904 (mmm) REVERT: B 780 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7286 (mp0) REVERT: B 814 LYS cc_start: 0.8668 (mptt) cc_final: 0.8404 (mptt) REVERT: B 833 PHE cc_start: 0.8303 (m-80) cc_final: 0.7838 (m-80) REVERT: B 837 TYR cc_start: 0.7636 (t80) cc_final: 0.7133 (m-80) REVERT: B 864 LEU cc_start: 0.9492 (pt) cc_final: 0.9247 (tp) REVERT: B 869 MET cc_start: 0.9336 (mmm) cc_final: 0.9059 (mmm) REVERT: B 902 MET cc_start: 0.9423 (tpp) cc_final: 0.8836 (mmm) REVERT: B 906 PHE cc_start: 0.9520 (OUTLIER) cc_final: 0.8761 (t80) REVERT: B 1029 MET cc_start: 0.9012 (tpp) cc_final: 0.8790 (tpp) REVERT: B 1067 TYR cc_start: 0.7963 (p90) cc_final: 0.7151 (p90) REVERT: B 1089 PHE cc_start: 0.7663 (p90) cc_final: 0.7319 (p90) REVERT: B 1109 PHE cc_start: 0.8256 (t80) cc_final: 0.7541 (t80) REVERT: B 1111 GLU cc_start: 0.8049 (pm20) cc_final: 0.7745 (pm20) REVERT: I 38 ARG cc_start: 0.7201 (ttm-80) cc_final: 0.6849 (ttm-80) REVERT: I 174 PHE cc_start: 0.7183 (m-80) cc_final: 0.6936 (m-80) REVERT: I 179 GLN cc_start: 0.9090 (pt0) cc_final: 0.8738 (mp10) REVERT: I 189 VAL cc_start: 0.7764 (p) cc_final: 0.7496 (m) REVERT: J 83 GLU cc_start: 0.5685 (pp20) cc_final: 0.5284 (pp20) REVERT: J 153 LYS cc_start: 0.8292 (tptp) cc_final: 0.7912 (tptp) REVERT: J 198 GLN cc_start: 0.5595 (pm20) cc_final: 0.4825 (mp-120) REVERT: C 718 PHE cc_start: 0.8501 (m-80) cc_final: 0.7837 (m-10) REVERT: C 740 MET cc_start: 0.8009 (mmm) cc_final: 0.7460 (mmm) REVERT: C 814 LYS cc_start: 0.8550 (mptt) cc_final: 0.8314 (mptt) REVERT: C 819 GLU cc_start: 0.7810 (tt0) cc_final: 0.7562 (tt0) REVERT: C 906 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8594 (t80) REVERT: C 1067 TYR cc_start: 0.7457 (p90) cc_final: 0.7211 (p90) REVERT: C 1110 TYR cc_start: 0.8849 (t80) cc_final: 0.8589 (t80) REVERT: K 31 ASP cc_start: 0.8164 (p0) cc_final: 0.7873 (p0) REVERT: K 108 PHE cc_start: 0.8277 (t80) cc_final: 0.7952 (t80) REVERT: K 118 THR cc_start: 0.8837 (m) cc_final: 0.8369 (p) REVERT: K 174 PHE cc_start: 0.7475 (m-80) cc_final: 0.7229 (m-80) REVERT: K 189 VAL cc_start: 0.7663 (p) cc_final: 0.7450 (m) REVERT: L 132 ASN cc_start: 0.9021 (t0) cc_final: 0.8803 (p0) REVERT: L 176 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.7032 (m-10) outliers start: 83 outliers final: 55 residues processed: 410 average time/residue: 0.1512 time to fit residues: 94.2828 Evaluate side-chains 389 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 328 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 153 LYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 836 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 154 PHE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1088 HIS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 176 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 5 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 179 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 198 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.111192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.078767 restraints weight = 92725.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.079297 restraints weight = 67214.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.078976 restraints weight = 53418.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.079114 restraints weight = 52602.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.079321 restraints weight = 47160.294| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 20253 Z= 0.152 Angle : 0.707 10.724 27597 Z= 0.348 Chirality : 0.045 0.292 3225 Planarity : 0.005 0.073 3519 Dihedral : 5.174 53.400 3132 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.43 % Allowed : 17.83 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.17), residues: 2559 helix: 2.80 (0.20), residues: 690 sheet: -1.73 (0.20), residues: 636 loop : -2.62 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1014 TYR 0.042 0.002 TYR C 837 PHE 0.033 0.002 PHE H 143 TRP 0.011 0.001 TRP K 47 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00348 (20208) covalent geometry : angle 0.69061 (27489) SS BOND : bond 0.00244 ( 27) SS BOND : angle 2.11119 ( 54) hydrogen bonds : bond 0.04820 ( 719) hydrogen bonds : angle 4.50668 ( 2082) link_NAG-ASN : bond 0.00818 ( 18) link_NAG-ASN : angle 2.91289 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 350 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.6500 (p0) cc_final: 0.6261 (p0) REVERT: A 718 PHE cc_start: 0.8482 (m-80) cc_final: 0.7165 (m-80) REVERT: A 740 MET cc_start: 0.7714 (mmm) cc_final: 0.7156 (mmm) REVERT: A 767 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8585 (tt) REVERT: A 819 GLU cc_start: 0.7586 (tt0) cc_final: 0.7267 (tt0) REVERT: A 837 TYR cc_start: 0.8557 (t80) cc_final: 0.7971 (t80) REVERT: A 869 MET cc_start: 0.9284 (mmm) cc_final: 0.8883 (mmm) REVERT: A 894 LEU cc_start: -0.1291 (OUTLIER) cc_final: -0.1495 (tp) REVERT: A 902 MET cc_start: 0.9004 (mmm) cc_final: 0.8474 (mmm) REVERT: A 906 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8842 (t80) REVERT: A 1029 MET cc_start: 0.8565 (tpp) cc_final: 0.8245 (tpp) REVERT: A 1067 TYR cc_start: 0.7889 (p90) cc_final: 0.7011 (p90) REVERT: A 1101 HIS cc_start: 0.8960 (p-80) cc_final: 0.8511 (p-80) REVERT: G 23 GLU cc_start: 0.8178 (tp30) cc_final: 0.7753 (tm-30) REVERT: G 32 TYR cc_start: 0.7978 (m-10) cc_final: 0.7443 (m-80) REVERT: G 118 THR cc_start: 0.8789 (m) cc_final: 0.8399 (p) REVERT: G 174 PHE cc_start: 0.7202 (m-80) cc_final: 0.6983 (m-80) REVERT: G 189 VAL cc_start: 0.7891 (p) cc_final: 0.7647 (m) REVERT: H 176 TYR cc_start: 0.7105 (m-10) cc_final: 0.6866 (m-10) REVERT: B 718 PHE cc_start: 0.8601 (m-80) cc_final: 0.7600 (m-80) REVERT: B 740 MET cc_start: 0.7190 (mmm) cc_final: 0.6851 (mmm) REVERT: B 780 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7272 (mp0) REVERT: B 814 LYS cc_start: 0.8646 (mptt) cc_final: 0.8390 (mptt) REVERT: B 837 TYR cc_start: 0.7703 (t80) cc_final: 0.7208 (m-80) REVERT: B 864 LEU cc_start: 0.9502 (pt) cc_final: 0.9254 (tp) REVERT: B 869 MET cc_start: 0.9349 (mmm) cc_final: 0.9106 (mmm) REVERT: B 902 MET cc_start: 0.9424 (tpp) cc_final: 0.8852 (mmm) REVERT: B 906 PHE cc_start: 0.9544 (OUTLIER) cc_final: 0.8803 (t80) REVERT: B 1029 MET cc_start: 0.8975 (tpp) cc_final: 0.8740 (tpp) REVERT: B 1067 TYR cc_start: 0.7947 (p90) cc_final: 0.7155 (p90) REVERT: B 1089 PHE cc_start: 0.7710 (p90) cc_final: 0.7306 (p90) REVERT: B 1109 PHE cc_start: 0.8237 (t80) cc_final: 0.7590 (t80) REVERT: I 38 ARG cc_start: 0.7212 (ttm-80) cc_final: 0.6852 (ttm-80) REVERT: I 174 PHE cc_start: 0.7241 (m-80) cc_final: 0.6975 (m-80) REVERT: I 179 GLN cc_start: 0.9069 (pt0) cc_final: 0.8714 (mp10) REVERT: I 189 VAL cc_start: 0.7731 (p) cc_final: 0.7481 (m) REVERT: J 153 LYS cc_start: 0.8182 (tptp) cc_final: 0.7865 (tptp) REVERT: J 198 GLN cc_start: 0.5545 (pm20) cc_final: 0.4749 (mp-120) REVERT: C 718 PHE cc_start: 0.8499 (m-80) cc_final: 0.7838 (m-10) REVERT: C 740 MET cc_start: 0.7960 (mmm) cc_final: 0.7471 (mmm) REVERT: C 814 LYS cc_start: 0.8550 (mptt) cc_final: 0.8322 (mptt) REVERT: C 906 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8586 (t80) REVERT: C 1052 PHE cc_start: 0.8688 (m-80) cc_final: 0.8450 (m-10) REVERT: C 1067 TYR cc_start: 0.7492 (p90) cc_final: 0.7237 (p90) REVERT: C 1110 TYR cc_start: 0.8904 (t80) cc_final: 0.8616 (t80) REVERT: K 31 ASP cc_start: 0.8084 (p0) cc_final: 0.7776 (p0) REVERT: K 118 THR cc_start: 0.8879 (m) cc_final: 0.8482 (p) REVERT: K 174 PHE cc_start: 0.7511 (m-80) cc_final: 0.7260 (m-80) REVERT: K 189 VAL cc_start: 0.7621 (p) cc_final: 0.7393 (m) REVERT: L 83 GLU cc_start: 0.5176 (OUTLIER) cc_final: 0.4863 (pp20) REVERT: L 176 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6907 (m-10) outliers start: 75 outliers final: 56 residues processed: 401 average time/residue: 0.1417 time to fit residues: 86.3630 Evaluate side-chains 402 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 339 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 153 LYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 154 PHE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1088 HIS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain L residue 176 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 1.9990 chunk 235 optimal weight: 0.3980 chunk 213 optimal weight: 0.0670 chunk 199 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 189 optimal weight: 9.9990 chunk 172 optimal weight: 0.3980 chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 GLN A 969 ASN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 ASN ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.111845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.080259 restraints weight = 92776.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.079990 restraints weight = 68212.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.080071 restraints weight = 56475.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080441 restraints weight = 49970.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.080473 restraints weight = 45724.610| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20253 Z= 0.142 Angle : 0.708 9.464 27597 Z= 0.350 Chirality : 0.044 0.294 3225 Planarity : 0.004 0.072 3519 Dihedral : 5.041 53.514 3132 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.29 % Allowed : 18.38 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.17), residues: 2559 helix: 2.91 (0.20), residues: 690 sheet: -1.55 (0.20), residues: 633 loop : -2.58 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 63 TYR 0.034 0.002 TYR C 789 PHE 0.036 0.002 PHE K 108 TRP 0.011 0.001 TRP L 152 HIS 0.006 0.001 HIS J 82 Details of bonding type rmsd covalent geometry : bond 0.00323 (20208) covalent geometry : angle 0.69260 (27489) SS BOND : bond 0.00259 ( 27) SS BOND : angle 1.90630 ( 54) hydrogen bonds : bond 0.04628 ( 719) hydrogen bonds : angle 4.35506 ( 2082) link_NAG-ASN : bond 0.00763 ( 18) link_NAG-ASN : angle 2.82624 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 362 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.6016 (p0) cc_final: 0.5761 (p0) REVERT: A 718 PHE cc_start: 0.8375 (m-80) cc_final: 0.7139 (m-80) REVERT: A 740 MET cc_start: 0.7612 (mmm) cc_final: 0.7126 (mmm) REVERT: A 767 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8643 (tt) REVERT: A 819 GLU cc_start: 0.7545 (tt0) cc_final: 0.7289 (tt0) REVERT: A 837 TYR cc_start: 0.8499 (t80) cc_final: 0.7914 (t80) REVERT: A 866 THR cc_start: 0.9510 (p) cc_final: 0.9124 (p) REVERT: A 869 MET cc_start: 0.9238 (mmm) cc_final: 0.8819 (mmm) REVERT: A 894 LEU cc_start: -0.1523 (OUTLIER) cc_final: -0.1725 (tp) REVERT: A 902 MET cc_start: 0.8970 (mmm) cc_final: 0.8463 (mmm) REVERT: A 906 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8814 (t80) REVERT: A 1029 MET cc_start: 0.8531 (tpp) cc_final: 0.8229 (tpp) REVERT: A 1067 TYR cc_start: 0.7843 (p90) cc_final: 0.6976 (p90) REVERT: A 1101 HIS cc_start: 0.8795 (p-80) cc_final: 0.8327 (p-80) REVERT: A 1110 TYR cc_start: 0.8603 (t80) cc_final: 0.8347 (t80) REVERT: G 23 GLU cc_start: 0.8039 (tp30) cc_final: 0.7626 (tm-30) REVERT: G 118 THR cc_start: 0.8737 (m) cc_final: 0.8353 (p) REVERT: G 174 PHE cc_start: 0.7186 (m-80) cc_final: 0.6940 (m-80) REVERT: G 189 VAL cc_start: 0.7921 (p) cc_final: 0.7673 (m) REVERT: H 83 GLU cc_start: 0.6482 (pt0) cc_final: 0.6070 (pm20) REVERT: B 718 PHE cc_start: 0.8505 (m-80) cc_final: 0.7850 (m-80) REVERT: B 740 MET cc_start: 0.7041 (mmm) cc_final: 0.6774 (mmm) REVERT: B 814 LYS cc_start: 0.8585 (mptt) cc_final: 0.8340 (mptt) REVERT: B 833 PHE cc_start: 0.8075 (m-80) cc_final: 0.7607 (m-80) REVERT: B 837 TYR cc_start: 0.7690 (t80) cc_final: 0.7218 (m-80) REVERT: B 864 LEU cc_start: 0.9484 (pt) cc_final: 0.9226 (tp) REVERT: B 869 MET cc_start: 0.9302 (mmm) cc_final: 0.9061 (mmm) REVERT: B 902 MET cc_start: 0.9374 (tpp) cc_final: 0.8825 (mmm) REVERT: B 906 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8783 (t80) REVERT: B 1029 MET cc_start: 0.8937 (tpp) cc_final: 0.8690 (tpp) REVERT: B 1067 TYR cc_start: 0.7866 (p90) cc_final: 0.7171 (p90) REVERT: B 1089 PHE cc_start: 0.7578 (p90) cc_final: 0.7174 (p90) REVERT: I 38 ARG cc_start: 0.7157 (ttm-80) cc_final: 0.6798 (ttm-80) REVERT: I 90 ASP cc_start: 0.7768 (p0) cc_final: 0.7559 (p0) REVERT: I 174 PHE cc_start: 0.7215 (m-80) cc_final: 0.6982 (m-80) REVERT: I 179 GLN cc_start: 0.9017 (pt0) cc_final: 0.8665 (mp10) REVERT: I 189 VAL cc_start: 0.7691 (p) cc_final: 0.7435 (m) REVERT: J 52 GLU cc_start: 0.7533 (tp30) cc_final: 0.7015 (tp30) REVERT: J 153 LYS cc_start: 0.8150 (tptp) cc_final: 0.7824 (tptp) REVERT: J 198 GLN cc_start: 0.5483 (pm20) cc_final: 0.4860 (mp-120) REVERT: C 718 PHE cc_start: 0.8393 (m-80) cc_final: 0.7878 (m-10) REVERT: C 814 LYS cc_start: 0.8486 (mptt) cc_final: 0.8270 (mptt) REVERT: C 819 GLU cc_start: 0.7794 (tt0) cc_final: 0.7539 (tt0) REVERT: C 906 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8548 (t80) REVERT: C 1110 TYR cc_start: 0.8824 (t80) cc_final: 0.8544 (t80) REVERT: K 31 ASP cc_start: 0.7938 (p0) cc_final: 0.7397 (p0) REVERT: K 118 THR cc_start: 0.8794 (m) cc_final: 0.8431 (p) REVERT: K 174 PHE cc_start: 0.7600 (m-80) cc_final: 0.7344 (m-80) REVERT: K 189 VAL cc_start: 0.7553 (p) cc_final: 0.7323 (m) REVERT: L 83 GLU cc_start: 0.4874 (OUTLIER) cc_final: 0.4628 (pp20) REVERT: L 132 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8433 (p0) REVERT: L 153 LYS cc_start: 0.8526 (tptp) cc_final: 0.8249 (tptp) REVERT: L 176 TYR cc_start: 0.6938 (m-10) cc_final: 0.6537 (m-10) outliers start: 72 outliers final: 56 residues processed: 406 average time/residue: 0.1474 time to fit residues: 91.1576 Evaluate side-chains 398 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 335 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 153 LYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 154 PHE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1088 HIS Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 132 ASN Chi-restraints excluded: chain L residue 148 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 184 optimal weight: 10.0000 chunk 203 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.109303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.076885 restraints weight = 91908.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077317 restraints weight = 67030.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.077102 restraints weight = 51368.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077257 restraints weight = 54695.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.077270 restraints weight = 48493.352| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 20253 Z= 0.211 Angle : 0.765 12.652 27597 Z= 0.385 Chirality : 0.046 0.298 3225 Planarity : 0.005 0.070 3519 Dihedral : 5.242 52.091 3132 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.06 % Allowed : 19.57 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.17), residues: 2559 helix: 2.45 (0.20), residues: 708 sheet: -1.70 (0.20), residues: 648 loop : -2.61 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1014 TYR 0.031 0.002 TYR A 789 PHE 0.038 0.002 PHE K 108 TRP 0.048 0.002 TRP J 189 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00482 (20208) covalent geometry : angle 0.74996 (27489) SS BOND : bond 0.00315 ( 27) SS BOND : angle 2.23375 ( 54) hydrogen bonds : bond 0.05349 ( 719) hydrogen bonds : angle 4.60010 ( 2082) link_NAG-ASN : bond 0.00681 ( 18) link_NAG-ASN : angle 2.77474 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 364 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.6409 (p0) cc_final: 0.6163 (p0) REVERT: A 718 PHE cc_start: 0.8508 (m-80) cc_final: 0.7888 (m-80) REVERT: A 723 THR cc_start: 0.8557 (m) cc_final: 0.8283 (p) REVERT: A 740 MET cc_start: 0.7664 (mmm) cc_final: 0.7140 (mmm) REVERT: A 767 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8700 (tt) REVERT: A 819 GLU cc_start: 0.7535 (tt0) cc_final: 0.7269 (tt0) REVERT: A 837 TYR cc_start: 0.8673 (t80) cc_final: 0.8123 (t80) REVERT: A 869 MET cc_start: 0.9282 (mmm) cc_final: 0.8918 (mmm) REVERT: A 894 LEU cc_start: -0.1176 (OUTLIER) cc_final: -0.1385 (tp) REVERT: A 906 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8890 (t80) REVERT: A 984 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8554 (tt) REVERT: A 1101 HIS cc_start: 0.9013 (p-80) cc_final: 0.8554 (p-80) REVERT: A 1110 TYR cc_start: 0.8768 (t80) cc_final: 0.8521 (t80) REVERT: G 23 GLU cc_start: 0.8113 (tp30) cc_final: 0.7721 (tm-30) REVERT: G 118 THR cc_start: 0.8797 (m) cc_final: 0.8441 (p) REVERT: G 174 PHE cc_start: 0.7364 (m-80) cc_final: 0.7114 (m-80) REVERT: G 189 VAL cc_start: 0.7930 (p) cc_final: 0.7685 (m) REVERT: H 83 GLU cc_start: 0.6921 (pt0) cc_final: 0.6335 (pm20) REVERT: B 718 PHE cc_start: 0.8597 (m-80) cc_final: 0.7632 (m-80) REVERT: B 740 MET cc_start: 0.7138 (mmm) cc_final: 0.6931 (mmm) REVERT: B 814 LYS cc_start: 0.8624 (mptt) cc_final: 0.8386 (mptt) REVERT: B 837 TYR cc_start: 0.7829 (t80) cc_final: 0.7287 (m-80) REVERT: B 864 LEU cc_start: 0.9531 (pt) cc_final: 0.9266 (tp) REVERT: B 869 MET cc_start: 0.9406 (mmm) cc_final: 0.9154 (mmm) REVERT: B 902 MET cc_start: 0.9442 (tpp) cc_final: 0.8852 (mmm) REVERT: B 906 PHE cc_start: 0.9481 (OUTLIER) cc_final: 0.8827 (t80) REVERT: B 1067 TYR cc_start: 0.7945 (p90) cc_final: 0.7183 (p90) REVERT: B 1089 PHE cc_start: 0.7865 (p90) cc_final: 0.7458 (p90) REVERT: B 1109 PHE cc_start: 0.8299 (t80) cc_final: 0.7496 (t80) REVERT: I 174 PHE cc_start: 0.7369 (m-80) cc_final: 0.7117 (m-10) REVERT: I 189 VAL cc_start: 0.7653 (p) cc_final: 0.7449 (m) REVERT: J 198 GLN cc_start: 0.5505 (pm20) cc_final: 0.4857 (mp10) REVERT: C 718 PHE cc_start: 0.8523 (m-80) cc_final: 0.7895 (m-10) REVERT: C 814 LYS cc_start: 0.8508 (mptt) cc_final: 0.8287 (mptt) REVERT: C 906 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8687 (t80) REVERT: K 31 ASP cc_start: 0.8081 (p0) cc_final: 0.7553 (p0) REVERT: K 83 MET cc_start: 0.7394 (tpt) cc_final: 0.6974 (mpp) REVERT: K 118 THR cc_start: 0.8851 (m) cc_final: 0.8471 (p) REVERT: K 174 PHE cc_start: 0.7732 (m-80) cc_final: 0.7450 (m-80) REVERT: K 189 VAL cc_start: 0.7585 (p) cc_final: 0.7363 (m) REVERT: L 83 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.5272 (pp20) REVERT: L 176 TYR cc_start: 0.6937 (m-10) cc_final: 0.6676 (m-10) outliers start: 67 outliers final: 51 residues processed: 407 average time/residue: 0.1494 time to fit residues: 92.4821 Evaluate side-chains 407 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 349 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 153 LYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1088 HIS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 81 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 188 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 201 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.107948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075210 restraints weight = 92313.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.075690 restraints weight = 63903.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.076735 restraints weight = 51485.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.076687 restraints weight = 42284.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.076612 restraints weight = 36593.568| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 20253 Z= 0.247 Angle : 0.804 11.104 27597 Z= 0.408 Chirality : 0.047 0.301 3225 Planarity : 0.005 0.072 3519 Dihedral : 5.484 52.214 3132 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.20 % Allowed : 19.48 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.17), residues: 2559 helix: 2.44 (0.20), residues: 690 sheet: -1.73 (0.19), residues: 660 loop : -2.69 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 19 TYR 0.032 0.002 TYR A 789 PHE 0.039 0.002 PHE K 108 TRP 0.033 0.002 TRP J 189 HIS 0.009 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00560 (20208) covalent geometry : angle 0.78908 (27489) SS BOND : bond 0.00362 ( 27) SS BOND : angle 2.26605 ( 54) hydrogen bonds : bond 0.05569 ( 719) hydrogen bonds : angle 4.77903 ( 2082) link_NAG-ASN : bond 0.00645 ( 18) link_NAG-ASN : angle 2.81943 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 374 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 709 ASN cc_start: 0.6083 (p0) cc_final: 0.5801 (p0) REVERT: A 718 PHE cc_start: 0.8331 (m-80) cc_final: 0.7826 (m-80) REVERT: A 723 THR cc_start: 0.8518 (m) cc_final: 0.8278 (p) REVERT: A 740 MET cc_start: 0.7521 (mmm) cc_final: 0.7174 (mmm) REVERT: A 767 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8661 (tt) REVERT: A 819 GLU cc_start: 0.7449 (tt0) cc_final: 0.7155 (tt0) REVERT: A 837 TYR cc_start: 0.8559 (t80) cc_final: 0.8051 (t80) REVERT: A 869 MET cc_start: 0.9308 (mmm) cc_final: 0.8976 (mmm) REVERT: A 894 LEU cc_start: -0.0888 (OUTLIER) cc_final: -0.1105 (tp) REVERT: A 906 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8854 (t80) REVERT: A 1101 HIS cc_start: 0.8777 (p-80) cc_final: 0.8274 (p-80) REVERT: A 1110 TYR cc_start: 0.8658 (t80) cc_final: 0.8453 (t80) REVERT: G 11 VAL cc_start: 0.8480 (m) cc_final: 0.8260 (p) REVERT: G 23 GLU cc_start: 0.8071 (tp30) cc_final: 0.7738 (tm-30) REVERT: G 118 THR cc_start: 0.8625 (m) cc_final: 0.8360 (p) REVERT: G 174 PHE cc_start: 0.7524 (m-80) cc_final: 0.7221 (m-80) REVERT: G 189 VAL cc_start: 0.8020 (p) cc_final: 0.7773 (m) REVERT: H 138 CYS cc_start: 0.6873 (t) cc_final: 0.6185 (t) REVERT: B 718 PHE cc_start: 0.8409 (m-80) cc_final: 0.7533 (m-80) REVERT: B 740 MET cc_start: 0.6995 (mmm) cc_final: 0.6219 (mmm) REVERT: B 814 LYS cc_start: 0.8629 (mptt) cc_final: 0.8402 (mptt) REVERT: B 837 TYR cc_start: 0.7733 (t80) cc_final: 0.7257 (m-80) REVERT: B 869 MET cc_start: 0.9431 (mmm) cc_final: 0.9194 (mmm) REVERT: B 902 MET cc_start: 0.9415 (tpp) cc_final: 0.8825 (mmm) REVERT: B 906 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.8793 (t80) REVERT: B 1067 TYR cc_start: 0.7970 (p90) cc_final: 0.7292 (p90) REVERT: B 1089 PHE cc_start: 0.7974 (p90) cc_final: 0.7536 (p90) REVERT: B 1109 PHE cc_start: 0.8281 (t80) cc_final: 0.7448 (t80) REVERT: I 174 PHE cc_start: 0.7533 (m-80) cc_final: 0.7267 (m-80) REVERT: I 189 VAL cc_start: 0.7686 (p) cc_final: 0.7449 (m) REVERT: J 52 GLU cc_start: 0.7496 (tp30) cc_final: 0.7098 (tp30) REVERT: J 198 GLN cc_start: 0.5319 (pm20) cc_final: 0.4651 (mp10) REVERT: C 718 PHE cc_start: 0.8321 (m-80) cc_final: 0.7745 (m-10) REVERT: C 819 GLU cc_start: 0.7737 (tt0) cc_final: 0.7491 (tt0) REVERT: C 833 PHE cc_start: 0.8582 (m-80) cc_final: 0.8089 (m-80) REVERT: C 906 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8691 (t80) REVERT: K 31 ASP cc_start: 0.8063 (p0) cc_final: 0.7586 (p0) REVERT: K 118 THR cc_start: 0.8697 (m) cc_final: 0.8389 (p) REVERT: K 174 PHE cc_start: 0.7916 (m-80) cc_final: 0.7603 (m-80) REVERT: K 189 VAL cc_start: 0.7615 (p) cc_final: 0.7400 (m) REVERT: L 52 GLU cc_start: 0.7720 (tp30) cc_final: 0.7506 (tp30) REVERT: L 176 TYR cc_start: 0.6882 (m-10) cc_final: 0.6656 (m-10) outliers start: 70 outliers final: 58 residues processed: 417 average time/residue: 0.1487 time to fit residues: 92.9295 Evaluate side-chains 407 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 344 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 153 LYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 836 GLN Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 154 PHE Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 182 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1088 HIS Chi-restraints excluded: chain K residue 6 GLU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 121 SER Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 178 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 227 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 187 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 149 optimal weight: 0.0010 chunk 119 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.109779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.077623 restraints weight = 92757.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.078041 restraints weight = 68634.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077765 restraints weight = 52768.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.077910 restraints weight = 52835.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.078012 restraints weight = 47580.917| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20253 Z= 0.161 Angle : 0.803 16.286 27597 Z= 0.402 Chirality : 0.046 0.289 3225 Planarity : 0.005 0.081 3519 Dihedral : 5.502 52.972 3132 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.88 % Allowed : 20.07 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.17), residues: 2559 helix: 2.70 (0.20), residues: 690 sheet: -1.56 (0.21), residues: 597 loop : -2.60 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1014 TYR 0.040 0.002 TYR B1007 PHE 0.037 0.002 PHE K 108 TRP 0.036 0.002 TRP J 189 HIS 0.008 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00367 (20208) covalent geometry : angle 0.79101 (27489) SS BOND : bond 0.00276 ( 27) SS BOND : angle 1.81201 ( 54) hydrogen bonds : bond 0.04956 ( 719) hydrogen bonds : angle 4.58945 ( 2082) link_NAG-ASN : bond 0.00715 ( 18) link_NAG-ASN : angle 2.81685 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4495.36 seconds wall clock time: 78 minutes 25.20 seconds (4705.20 seconds total)