Starting phenix.real_space_refine on Tue Jan 21 19:28:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rt5_19479/01_2025/8rt5_19479.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rt5_19479/01_2025/8rt5_19479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rt5_19479/01_2025/8rt5_19479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rt5_19479/01_2025/8rt5_19479.map" model { file = "/net/cci-nas-00/data/ceres_data/8rt5_19479/01_2025/8rt5_19479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rt5_19479/01_2025/8rt5_19479.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.021 sd= 0.060 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 64 5.16 5 C 10928 2.51 5 N 3232 2.21 5 O 3232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17456 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "E" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "G" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "H" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "J" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "K" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "M" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "N" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "P" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "Q" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "S" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "T" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "u" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "v" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "V" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "W" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "Y" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "Z" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "b" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "c" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "e" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "f" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "h" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "i" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "k" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "l" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "n" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "o" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "y" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "z" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Time building chain proxies: 9.51, per 1000 atoms: 0.54 Number of scatterers: 17456 At special positions: 0 Unit cell: (167.519, 167.519, 67.221, 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 64 16.00 O 3232 8.00 N 3232 7.00 C 10928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.98 Conformation dependent library (CDL) restraints added in 2.4 seconds 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4064 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 32 sheets defined 18.7% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 127 through 135 removed outlier: 3.573A pdb=" N GLN E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 148 Processing helix chain 'H' and resid 71 through 73 No H-bonds generated for 'chain 'H' and resid 71 through 73' Processing helix chain 'H' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN H 131 " --> pdb=" O TYR H 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 148 Processing helix chain 'K' and resid 71 through 73 No H-bonds generated for 'chain 'K' and resid 71 through 73' Processing helix chain 'K' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN K 131 " --> pdb=" O TYR K 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 148 Processing helix chain 'N' and resid 71 through 73 No H-bonds generated for 'chain 'N' and resid 71 through 73' Processing helix chain 'N' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN N 131 " --> pdb=" O TYR N 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 148 Processing helix chain 'Q' and resid 71 through 73 No H-bonds generated for 'chain 'Q' and resid 71 through 73' Processing helix chain 'Q' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN Q 131 " --> pdb=" O TYR Q 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 148 Processing helix chain 'T' and resid 71 through 73 No H-bonds generated for 'chain 'T' and resid 71 through 73' Processing helix chain 'T' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN T 131 " --> pdb=" O TYR T 127 " (cutoff:3.500A) Processing helix chain 'u' and resid 136 through 148 Processing helix chain 'v' and resid 71 through 73 No H-bonds generated for 'chain 'v' and resid 71 through 73' Processing helix chain 'v' and resid 127 through 135 removed outlier: 3.573A pdb=" N GLN v 131 " --> pdb=" O TYR v 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 148 Processing helix chain 'W' and resid 71 through 73 No H-bonds generated for 'chain 'W' and resid 71 through 73' Processing helix chain 'W' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN W 131 " --> pdb=" O TYR W 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 136 through 148 Processing helix chain 'Z' and resid 71 through 73 No H-bonds generated for 'chain 'Z' and resid 71 through 73' Processing helix chain 'Z' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN Z 131 " --> pdb=" O TYR Z 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 136 through 148 Processing helix chain 'c' and resid 71 through 73 No H-bonds generated for 'chain 'c' and resid 71 through 73' Processing helix chain 'c' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN c 131 " --> pdb=" O TYR c 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 136 through 148 Processing helix chain 'f' and resid 71 through 73 No H-bonds generated for 'chain 'f' and resid 71 through 73' Processing helix chain 'f' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN f 131 " --> pdb=" O TYR f 127 " (cutoff:3.500A) Processing helix chain 'h' and resid 136 through 148 Processing helix chain 'i' and resid 71 through 73 No H-bonds generated for 'chain 'i' and resid 71 through 73' Processing helix chain 'i' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN i 131 " --> pdb=" O TYR i 127 " (cutoff:3.500A) Processing helix chain 'k' and resid 136 through 148 Processing helix chain 'l' and resid 71 through 73 No H-bonds generated for 'chain 'l' and resid 71 through 73' Processing helix chain 'l' and resid 127 through 135 removed outlier: 3.573A pdb=" N GLN l 131 " --> pdb=" O TYR l 127 " (cutoff:3.500A) Processing helix chain 'n' and resid 136 through 148 Processing helix chain 'o' and resid 71 through 73 No H-bonds generated for 'chain 'o' and resid 71 through 73' Processing helix chain 'o' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN o 131 " --> pdb=" O TYR o 127 " (cutoff:3.500A) Processing helix chain 'y' and resid 136 through 148 Processing helix chain 'z' and resid 71 through 73 No H-bonds generated for 'chain 'z' and resid 71 through 73' Processing helix chain 'z' and resid 127 through 135 removed outlier: 3.573A pdb=" N GLN z 131 " --> pdb=" O TYR z 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG B 34 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG B 126 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 36 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS B 55 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE B 125 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET B 57 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 48 Processing sheet with id=AA3, first strand: chain 'E' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG E 34 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG E 126 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL E 36 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS E 55 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE E 125 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET E 57 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 44 through 48 Processing sheet with id=AA5, first strand: chain 'H' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG H 34 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG H 126 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL H 36 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS H 55 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE H 125 " --> pdb=" O HIS H 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET H 57 " --> pdb=" O PHE H 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 44 through 48 Processing sheet with id=AA7, first strand: chain 'K' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG K 34 " --> pdb=" O ALA K 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG K 126 " --> pdb=" O ARG K 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL K 36 " --> pdb=" O ARG K 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS K 55 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE K 125 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N MET K 57 " --> pdb=" O PHE K 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 44 through 48 Processing sheet with id=AA9, first strand: chain 'N' and resid 25 through 26 removed outlier: 6.794A pdb=" N ARG N 34 " --> pdb=" O ALA N 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG N 126 " --> pdb=" O ARG N 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL N 36 " --> pdb=" O ARG N 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS N 55 " --> pdb=" O LEU N 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE N 125 " --> pdb=" O HIS N 55 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N MET N 57 " --> pdb=" O PHE N 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 44 through 48 Processing sheet with id=AB2, first strand: chain 'Q' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG Q 34 " --> pdb=" O ALA Q 124 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG Q 126 " --> pdb=" O ARG Q 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL Q 36 " --> pdb=" O ARG Q 126 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS Q 55 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE Q 125 " --> pdb=" O HIS Q 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET Q 57 " --> pdb=" O PHE Q 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 44 through 48 Processing sheet with id=AB4, first strand: chain 'T' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG T 34 " --> pdb=" O ALA T 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG T 126 " --> pdb=" O ARG T 34 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL T 36 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS T 55 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE T 125 " --> pdb=" O HIS T 55 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N MET T 57 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 44 through 48 Processing sheet with id=AB6, first strand: chain 'v' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG v 34 " --> pdb=" O ALA v 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG v 126 " --> pdb=" O ARG v 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL v 36 " --> pdb=" O ARG v 126 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS v 55 " --> pdb=" O LEU v 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE v 125 " --> pdb=" O HIS v 55 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N MET v 57 " --> pdb=" O PHE v 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'v' and resid 44 through 48 Processing sheet with id=AB8, first strand: chain 'W' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG W 34 " --> pdb=" O ALA W 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG W 126 " --> pdb=" O ARG W 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL W 36 " --> pdb=" O ARG W 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS W 55 " --> pdb=" O LEU W 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE W 125 " --> pdb=" O HIS W 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET W 57 " --> pdb=" O PHE W 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 44 through 48 Processing sheet with id=AC1, first strand: chain 'Z' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG Z 34 " --> pdb=" O ALA Z 124 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG Z 126 " --> pdb=" O ARG Z 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL Z 36 " --> pdb=" O ARG Z 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS Z 55 " --> pdb=" O LEU Z 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE Z 125 " --> pdb=" O HIS Z 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET Z 57 " --> pdb=" O PHE Z 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Z' and resid 44 through 48 Processing sheet with id=AC3, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG c 34 " --> pdb=" O ALA c 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG c 126 " --> pdb=" O ARG c 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL c 36 " --> pdb=" O ARG c 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS c 55 " --> pdb=" O LEU c 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE c 125 " --> pdb=" O HIS c 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET c 57 " --> pdb=" O PHE c 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 44 through 48 Processing sheet with id=AC5, first strand: chain 'f' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG f 34 " --> pdb=" O ALA f 124 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG f 126 " --> pdb=" O ARG f 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL f 36 " --> pdb=" O ARG f 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS f 55 " --> pdb=" O LEU f 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE f 125 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET f 57 " --> pdb=" O PHE f 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 44 through 48 Processing sheet with id=AC7, first strand: chain 'i' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG i 34 " --> pdb=" O ALA i 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG i 126 " --> pdb=" O ARG i 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL i 36 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS i 55 " --> pdb=" O LEU i 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE i 125 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET i 57 " --> pdb=" O PHE i 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'i' and resid 44 through 48 Processing sheet with id=AC9, first strand: chain 'l' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG l 34 " --> pdb=" O ALA l 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG l 126 " --> pdb=" O ARG l 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL l 36 " --> pdb=" O ARG l 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS l 55 " --> pdb=" O LEU l 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE l 125 " --> pdb=" O HIS l 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET l 57 " --> pdb=" O PHE l 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'l' and resid 44 through 48 Processing sheet with id=AD2, first strand: chain 'o' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG o 34 " --> pdb=" O ALA o 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG o 126 " --> pdb=" O ARG o 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL o 36 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS o 55 " --> pdb=" O LEU o 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE o 125 " --> pdb=" O HIS o 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET o 57 " --> pdb=" O PHE o 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'o' and resid 44 through 48 Processing sheet with id=AD4, first strand: chain 'z' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG z 34 " --> pdb=" O ALA z 124 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG z 126 " --> pdb=" O ARG z 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL z 36 " --> pdb=" O ARG z 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS z 55 " --> pdb=" O LEU z 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE z 125 " --> pdb=" O HIS z 55 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N MET z 57 " --> pdb=" O PHE z 125 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'z' and resid 44 through 48 640 hydrogen bonds defined for protein. 1680 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: 6.63 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5962 1.34 - 1.45: 2802 1.45 - 1.57: 8884 1.57 - 1.68: 16 1.68 - 1.80: 128 Bond restraints: 17792 Sorted by residual: bond pdb=" CG PRO M 137 " pdb=" CD PRO M 137 " ideal model delta sigma weight residual 1.503 1.439 0.064 3.40e-02 8.65e+02 3.49e+00 bond pdb=" CG PRO S 137 " pdb=" CD PRO S 137 " ideal model delta sigma weight residual 1.503 1.440 0.063 3.40e-02 8.65e+02 3.46e+00 bond pdb=" CG PRO u 137 " pdb=" CD PRO u 137 " ideal model delta sigma weight residual 1.503 1.440 0.063 3.40e-02 8.65e+02 3.45e+00 bond pdb=" CG PRO Y 137 " pdb=" CD PRO Y 137 " ideal model delta sigma weight residual 1.503 1.440 0.063 3.40e-02 8.65e+02 3.45e+00 bond pdb=" CG PRO V 137 " pdb=" CD PRO V 137 " ideal model delta sigma weight residual 1.503 1.440 0.063 3.40e-02 8.65e+02 3.45e+00 ... (remaining 17787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 22736 1.50 - 2.99: 1077 2.99 - 4.49: 123 4.49 - 5.98: 32 5.98 - 7.48: 48 Bond angle restraints: 24016 Sorted by residual: angle pdb=" CA PRO J 137 " pdb=" N PRO J 137 " pdb=" CD PRO J 137 " ideal model delta sigma weight residual 112.00 105.72 6.28 1.40e+00 5.10e-01 2.01e+01 angle pdb=" CA PRO e 137 " pdb=" N PRO e 137 " pdb=" CD PRO e 137 " ideal model delta sigma weight residual 112.00 105.73 6.27 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PRO n 137 " pdb=" N PRO n 137 " pdb=" CD PRO n 137 " ideal model delta sigma weight residual 112.00 105.74 6.26 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PRO b 137 " pdb=" N PRO b 137 " pdb=" CD PRO b 137 " ideal model delta sigma weight residual 112.00 105.75 6.25 1.40e+00 5.10e-01 1.99e+01 angle pdb=" CA PRO P 137 " pdb=" N PRO P 137 " pdb=" CD PRO P 137 " ideal model delta sigma weight residual 112.00 105.75 6.25 1.40e+00 5.10e-01 1.99e+01 ... (remaining 24011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 9744 15.06 - 30.12: 816 30.12 - 45.17: 144 45.17 - 60.23: 64 60.23 - 75.29: 16 Dihedral angle restraints: 10784 sinusoidal: 4464 harmonic: 6320 Sorted by residual: dihedral pdb=" CG ARG N 34 " pdb=" CD ARG N 34 " pdb=" NE ARG N 34 " pdb=" CZ ARG N 34 " ideal model delta sinusoidal sigma weight residual 90.00 130.80 -40.80 2 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" CG ARG o 34 " pdb=" CD ARG o 34 " pdb=" NE ARG o 34 " pdb=" CZ ARG o 34 " ideal model delta sinusoidal sigma weight residual 90.00 130.80 -40.80 2 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" CG ARG Z 34 " pdb=" CD ARG Z 34 " pdb=" NE ARG Z 34 " pdb=" CZ ARG Z 34 " ideal model delta sinusoidal sigma weight residual 90.00 130.79 -40.79 2 1.50e+01 4.44e-03 9.11e+00 ... (remaining 10781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1383 0.033 - 0.066: 757 0.066 - 0.098: 271 0.098 - 0.131: 165 0.131 - 0.164: 16 Chirality restraints: 2592 Sorted by residual: chirality pdb=" CA PRO e 137 " pdb=" N PRO e 137 " pdb=" C PRO e 137 " pdb=" CB PRO e 137 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA PRO A 137 " pdb=" N PRO A 137 " pdb=" C PRO A 137 " pdb=" CB PRO A 137 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA PRO Y 137 " pdb=" N PRO Y 137 " pdb=" C PRO Y 137 " pdb=" CB PRO Y 137 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 2589 not shown) Planarity restraints: 3152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 136 " -0.070 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO S 137 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO S 137 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO S 137 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR k 136 " 0.070 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO k 137 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO k 137 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO k 137 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 136 " 0.070 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO G 137 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO G 137 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO G 137 " 0.056 5.00e-02 4.00e+02 ... (remaining 3149 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 150 2.57 - 3.15: 13482 3.15 - 3.74: 27234 3.74 - 4.32: 40468 4.32 - 4.90: 67458 Nonbonded interactions: 148792 Sorted by model distance: nonbonded pdb=" NZ LYS i 87 " pdb=" O MET k 145 " model vdw 1.988 3.120 nonbonded pdb=" NZ LYS l 87 " pdb=" O MET n 145 " model vdw 2.112 3.120 nonbonded pdb=" NZ LYS T 87 " pdb=" O MET u 145 " model vdw 2.115 3.120 nonbonded pdb=" NH1 ARG n 144 " pdb=" OD2 ASP o 71 " model vdw 2.120 3.120 nonbonded pdb=" NZ LYS Q 87 " pdb=" O MET S 145 " model vdw 2.166 3.120 ... (remaining 148787 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'b' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'n' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'l' selection = chain 'o' selection = chain 'v' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.680 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.380 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: 0.020 Load rotamer database and sin/cos tables:13.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 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 : 0.007 0.079 17792 Z= 0.465 Angle : 0.789 7.478 24016 Z= 0.466 Chirality : 0.050 0.164 2592 Planarity : 0.008 0.102 3152 Dihedral : 12.352 75.289 6720 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2080 helix: 2.22 (0.26), residues: 320 sheet: 0.52 (0.16), residues: 880 loop : -0.75 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS Q 83 PHE 0.009 0.002 PHE f 77 TYR 0.014 0.002 TYR l 127 ARG 0.009 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 776 time to evaluate : 2.018 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: A 136 THR cc_start: 0.7681 (t) cc_final: 0.7428 (t) REVERT: h 136 THR cc_start: 0.7747 (t) cc_final: 0.7356 (t) REVERT: l 129 ASP cc_start: 0.6701 (p0) cc_final: 0.6495 (p0) REVERT: n 136 THR cc_start: 0.6566 (t) cc_final: 0.6033 (t) outliers start: 0 outliers final: 3 residues processed: 776 average time/residue: 1.2958 time to fit residues: 1121.6565 Evaluate side-chains 608 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 605 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain W residue 114 ASN Chi-restraints excluded: chain c residue 114 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN E 89 GLN E 94 ASN H 94 ASN N 94 ASN Q 89 GLN Q 94 ASN T 94 ASN v 94 ASN W 45 GLN W 89 GLN Z 89 GLN Z 94 ASN c 94 ASN f 94 ASN i 94 ASN l 89 GLN l 94 ASN o 94 ASN z 94 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.058038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.044210 restraints weight = 59002.050| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.94 r_work: 0.2539 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17792 Z= 0.284 Angle : 0.670 7.422 24016 Z= 0.349 Chirality : 0.048 0.182 2592 Planarity : 0.005 0.044 3152 Dihedral : 4.348 15.311 2502 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 4.50 % Allowed : 16.34 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2080 helix: 2.62 (0.26), residues: 320 sheet: 0.68 (0.16), residues: 864 loop : -0.69 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 83 PHE 0.010 0.001 PHE v 77 TYR 0.017 0.001 TYR S 138 ARG 0.008 0.001 ARG c 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 650 time to evaluate : 1.873 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: A 140 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9456 (mm) REVERT: B 22 ASP cc_start: 0.9154 (t0) cc_final: 0.8748 (p0) REVERT: B 30 ASP cc_start: 0.8688 (t0) cc_final: 0.8439 (t0) REVERT: B 42 ASP cc_start: 0.9241 (t0) cc_final: 0.8872 (t0) REVERT: B 63 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8864 (tp-100) REVERT: D 136 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.8633 (t) REVERT: D 139 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8623 (pp20) REVERT: D 140 LEU cc_start: 0.9648 (mp) cc_final: 0.9085 (mp) REVERT: E 30 ASP cc_start: 0.8660 (t0) cc_final: 0.8448 (t0) REVERT: E 63 GLN cc_start: 0.9359 (mm-40) cc_final: 0.8973 (tp-100) REVERT: E 111 GLN cc_start: 0.8558 (tt0) cc_final: 0.8306 (tt0) REVERT: G 135 LYS cc_start: 0.8634 (ttmm) cc_final: 0.8225 (tppp) REVERT: G 136 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9050 (t) REVERT: G 139 GLU cc_start: 0.9389 (mt-10) cc_final: 0.9156 (mp0) REVERT: H 111 GLN cc_start: 0.8378 (tt0) cc_final: 0.8076 (tt0) REVERT: K 30 ASP cc_start: 0.8754 (t0) cc_final: 0.8475 (t0) REVERT: K 63 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8238 (tm-30) REVERT: M 135 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8552 (ttpt) REVERT: M 139 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8797 (tm-30) REVERT: N 30 ASP cc_start: 0.8826 (t0) cc_final: 0.8588 (t0) REVERT: P 143 GLU cc_start: 0.9193 (tp30) cc_final: 0.8991 (tp30) REVERT: Q 30 ASP cc_start: 0.8783 (t0) cc_final: 0.8552 (t0) REVERT: Q 59 GLU cc_start: 0.9295 (tt0) cc_final: 0.8743 (tt0) REVERT: Q 63 GLN cc_start: 0.9097 (tp-100) cc_final: 0.8875 (tp-100) REVERT: Q 86 ILE cc_start: 0.9770 (pt) cc_final: 0.9492 (pp) REVERT: Q 89 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8754 (mm-40) REVERT: Q 111 GLN cc_start: 0.8404 (tt0) cc_final: 0.8122 (mt0) REVERT: S 146 LEU cc_start: 0.9194 (mt) cc_final: 0.8943 (mm) REVERT: T 63 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8948 (tp-100) REVERT: u 139 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8800 (tm-30) REVERT: v 30 ASP cc_start: 0.8809 (t0) cc_final: 0.8581 (t0) REVERT: v 111 GLN cc_start: 0.8463 (tt0) cc_final: 0.8258 (tt0) REVERT: V 136 THR cc_start: 0.9561 (t) cc_final: 0.9217 (t) REVERT: V 143 GLU cc_start: 0.9294 (tp30) cc_final: 0.9080 (tp30) REVERT: W 30 ASP cc_start: 0.8748 (t0) cc_final: 0.8519 (t0) REVERT: W 111 GLN cc_start: 0.8562 (tt0) cc_final: 0.8145 (tt0) REVERT: Y 139 GLU cc_start: 0.9470 (mt-10) cc_final: 0.9234 (pm20) REVERT: Z 30 ASP cc_start: 0.8778 (t0) cc_final: 0.8524 (t0) REVERT: Z 59 GLU cc_start: 0.9239 (tt0) cc_final: 0.8704 (tt0) REVERT: Z 63 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8888 (tp-100) REVERT: Z 111 GLN cc_start: 0.8554 (tt0) cc_final: 0.8124 (tt0) REVERT: b 136 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9129 (t) REVERT: c 63 GLN cc_start: 0.9106 (tp-100) cc_final: 0.8886 (tp-100) REVERT: c 91 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9013 (mm-30) REVERT: e 135 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8274 (ttpt) REVERT: e 136 THR cc_start: 0.9477 (OUTLIER) cc_final: 0.9214 (t) REVERT: f 30 ASP cc_start: 0.8788 (t0) cc_final: 0.8514 (t0) REVERT: f 91 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8934 (mm-30) REVERT: h 138 TYR cc_start: 0.9163 (t80) cc_final: 0.8859 (t80) REVERT: i 22 ASP cc_start: 0.9118 (t0) cc_final: 0.8745 (p0) REVERT: i 30 ASP cc_start: 0.8745 (t0) cc_final: 0.8465 (t0) REVERT: i 42 ASP cc_start: 0.9270 (t0) cc_final: 0.8889 (t0) REVERT: k 142 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8784 (ptm-80) REVERT: l 30 ASP cc_start: 0.8621 (t0) cc_final: 0.8382 (t0) REVERT: l 111 GLN cc_start: 0.8597 (tt0) cc_final: 0.8139 (tt0) REVERT: o 63 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8804 (tp-100) REVERT: y 136 THR cc_start: 0.9540 (OUTLIER) cc_final: 0.9189 (t) REVERT: z 30 ASP cc_start: 0.8826 (t0) cc_final: 0.8550 (t0) REVERT: z 92 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9496 (mm) outliers start: 82 outliers final: 18 residues processed: 677 average time/residue: 1.1241 time to fit residues: 860.3225 Evaluate side-chains 614 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 587 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 114 ASN Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain e residue 151 THR Chi-restraints excluded: chain i residue 71 ASP Chi-restraints excluded: chain i residue 130 THR Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain l residue 122 GLU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 117 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 17 optimal weight: 0.1980 chunk 140 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 94 ASN Q 89 GLN W 89 GLN Z 89 GLN ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.056717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.042907 restraints weight = 59506.184| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.95 r_work: 0.2519 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17792 Z= 0.320 Angle : 0.640 6.937 24016 Z= 0.335 Chirality : 0.048 0.234 2592 Planarity : 0.003 0.034 3152 Dihedral : 4.214 27.297 2498 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 4.55 % Allowed : 17.71 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2080 helix: 2.94 (0.26), residues: 320 sheet: 0.68 (0.16), residues: 864 loop : -0.58 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS i 55 PHE 0.011 0.002 PHE f 77 TYR 0.012 0.001 TYR o 29 ARG 0.004 0.001 ARG z 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 618 time to evaluate : 2.039 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: A 140 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9004 (mp) REVERT: B 22 ASP cc_start: 0.9164 (t0) cc_final: 0.8738 (p0) REVERT: B 30 ASP cc_start: 0.8766 (t0) cc_final: 0.8466 (t0) REVERT: B 42 ASP cc_start: 0.9294 (t0) cc_final: 0.8885 (t0) REVERT: D 139 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8531 (pp20) REVERT: D 140 LEU cc_start: 0.9639 (mp) cc_final: 0.9077 (mp) REVERT: E 30 ASP cc_start: 0.8925 (t0) cc_final: 0.8656 (t0) REVERT: E 59 GLU cc_start: 0.9226 (tt0) cc_final: 0.8633 (tt0) REVERT: E 63 GLN cc_start: 0.9328 (mm-40) cc_final: 0.9079 (tm-30) REVERT: E 111 GLN cc_start: 0.8637 (tt0) cc_final: 0.8421 (tt0) REVERT: E 122 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8917 (tp30) REVERT: G 135 LYS cc_start: 0.8624 (ttmm) cc_final: 0.8212 (tppp) REVERT: H 63 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8929 (tp-100) REVERT: H 111 GLN cc_start: 0.8379 (tt0) cc_final: 0.8052 (tt0) REVERT: H 122 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8716 (mm-30) REVERT: K 30 ASP cc_start: 0.8836 (t0) cc_final: 0.8548 (t0) REVERT: K 50 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9319 (tm) REVERT: K 63 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8167 (tm-30) REVERT: K 122 GLU cc_start: 0.9381 (tp30) cc_final: 0.9100 (tp30) REVERT: N 22 ASP cc_start: 0.9090 (t0) cc_final: 0.8812 (p0) REVERT: N 30 ASP cc_start: 0.8726 (t0) cc_final: 0.8451 (t0) REVERT: N 42 ASP cc_start: 0.9197 (t0) cc_final: 0.8912 (t0) REVERT: N 63 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8903 (tp-100) REVERT: P 143 GLU cc_start: 0.9228 (tp30) cc_final: 0.8989 (tp30) REVERT: Q 30 ASP cc_start: 0.8832 (t0) cc_final: 0.8520 (t0) REVERT: Q 59 GLU cc_start: 0.9210 (tt0) cc_final: 0.8666 (tt0) REVERT: Q 86 ILE cc_start: 0.9798 (pt) cc_final: 0.9593 (pp) REVERT: Q 111 GLN cc_start: 0.8472 (tt0) cc_final: 0.8177 (mt0) REVERT: S 139 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8719 (tm-30) REVERT: T 63 GLN cc_start: 0.9123 (tp-100) cc_final: 0.8891 (tp-100) REVERT: T 122 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8902 (tp30) REVERT: v 30 ASP cc_start: 0.8863 (t0) cc_final: 0.8609 (t0) REVERT: v 111 GLN cc_start: 0.8469 (tt0) cc_final: 0.8193 (tt0) REVERT: V 143 GLU cc_start: 0.9260 (tp30) cc_final: 0.8993 (tp30) REVERT: W 22 ASP cc_start: 0.9174 (t0) cc_final: 0.8802 (p0) REVERT: W 30 ASP cc_start: 0.8692 (t0) cc_final: 0.8433 (t0) REVERT: W 42 ASP cc_start: 0.9209 (t0) cc_final: 0.8960 (t0) REVERT: W 63 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8902 (tp-100) REVERT: W 111 GLN cc_start: 0.8514 (tt0) cc_final: 0.8074 (tt0) REVERT: Y 136 THR cc_start: 0.9426 (OUTLIER) cc_final: 0.9092 (t) REVERT: Z 30 ASP cc_start: 0.8888 (t0) cc_final: 0.8573 (t0) REVERT: Z 59 GLU cc_start: 0.9232 (tt0) cc_final: 0.8570 (tt0) REVERT: Z 111 GLN cc_start: 0.8464 (tt0) cc_final: 0.8018 (tt0) REVERT: b 138 TYR cc_start: 0.9206 (t80) cc_final: 0.8986 (t80) REVERT: c 63 GLN cc_start: 0.9209 (tp-100) cc_final: 0.8987 (tp-100) REVERT: c 91 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8974 (mm-30) REVERT: f 30 ASP cc_start: 0.8836 (t0) cc_final: 0.8555 (t0) REVERT: f 63 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8241 (tm-30) REVERT: f 91 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8865 (mm-30) REVERT: f 92 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9466 (mm) REVERT: f 122 GLU cc_start: 0.9346 (tp30) cc_final: 0.9069 (tp30) REVERT: i 22 ASP cc_start: 0.9158 (t0) cc_final: 0.8761 (p0) REVERT: i 42 ASP cc_start: 0.9298 (t0) cc_final: 0.8928 (t0) REVERT: i 63 GLN cc_start: 0.9099 (tp-100) cc_final: 0.8870 (tp-100) REVERT: i 122 GLU cc_start: 0.9221 (tt0) cc_final: 0.8978 (tp30) REVERT: k 135 LYS cc_start: 0.8662 (mttt) cc_final: 0.8130 (ttpt) REVERT: k 143 GLU cc_start: 0.9300 (tp30) cc_final: 0.9045 (tp30) REVERT: l 30 ASP cc_start: 0.8745 (t0) cc_final: 0.8388 (t0) REVERT: l 59 GLU cc_start: 0.9116 (tt0) cc_final: 0.8374 (tt0) REVERT: l 111 GLN cc_start: 0.8473 (tt0) cc_final: 0.8006 (tt0) REVERT: n 143 GLU cc_start: 0.9280 (tp30) cc_final: 0.9080 (tp30) REVERT: o 63 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8892 (tp-100) REVERT: y 142 ARG cc_start: 0.9325 (ttm-80) cc_final: 0.9102 (ttm-80) REVERT: z 30 ASP cc_start: 0.8818 (t0) cc_final: 0.8518 (t0) REVERT: z 63 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8326 (tm-30) REVERT: z 92 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9473 (mm) REVERT: z 122 GLU cc_start: 0.9371 (tp30) cc_final: 0.8948 (tp30) outliers start: 83 outliers final: 24 residues processed: 639 average time/residue: 1.2111 time to fit residues: 871.0604 Evaluate side-chains 597 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 565 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain N residue 63 GLN Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 122 GLU Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain c residue 114 ASN Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 151 THR Chi-restraints excluded: chain f residue 57 MET Chi-restraints excluded: chain f residue 92 LEU Chi-restraints excluded: chain h residue 151 THR Chi-restraints excluded: chain i residue 130 THR Chi-restraints excluded: chain l residue 114 ASN Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 71 ASP Chi-restraints excluded: chain z residue 92 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 94 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN Q 89 GLN v 89 GLN W 89 GLN l 89 GLN o 45 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.055797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.042239 restraints weight = 59477.975| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 3.91 r_work: 0.2505 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17792 Z= 0.342 Angle : 0.646 7.874 24016 Z= 0.337 Chirality : 0.049 0.238 2592 Planarity : 0.003 0.030 3152 Dihedral : 4.212 26.206 2498 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 4.28 % Allowed : 20.12 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2080 helix: 2.92 (0.26), residues: 320 sheet: 0.67 (0.17), residues: 864 loop : -0.60 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS i 55 PHE 0.012 0.002 PHE f 77 TYR 0.016 0.001 TYR A 138 ARG 0.004 0.000 ARG Z 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 592 time to evaluate : 2.126 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: A 140 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9309 (mm) REVERT: B 22 ASP cc_start: 0.9183 (t0) cc_final: 0.8772 (p0) REVERT: B 30 ASP cc_start: 0.8805 (t0) cc_final: 0.8510 (t0) REVERT: B 42 ASP cc_start: 0.9320 (t0) cc_final: 0.8973 (t0) REVERT: B 63 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8888 (tp-100) REVERT: D 139 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8515 (pp20) REVERT: D 140 LEU cc_start: 0.9674 (mp) cc_final: 0.9111 (mp) REVERT: E 30 ASP cc_start: 0.8931 (t0) cc_final: 0.8639 (t0) REVERT: E 59 GLU cc_start: 0.9175 (tt0) cc_final: 0.8614 (tt0) REVERT: E 63 GLN cc_start: 0.9323 (mm-40) cc_final: 0.9056 (tm-30) REVERT: E 111 GLN cc_start: 0.8554 (tt0) cc_final: 0.8183 (tt0) REVERT: E 122 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8993 (tp30) REVERT: G 135 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8107 (tppp) REVERT: H 63 GLN cc_start: 0.9145 (tp-100) cc_final: 0.8852 (tp-100) REVERT: H 111 GLN cc_start: 0.8396 (tt0) cc_final: 0.8046 (tt0) REVERT: K 30 ASP cc_start: 0.8893 (t0) cc_final: 0.8594 (t0) REVERT: K 57 MET cc_start: 0.8904 (ttp) cc_final: 0.8701 (ttp) REVERT: K 63 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8242 (tm-30) REVERT: K 122 GLU cc_start: 0.9352 (tp30) cc_final: 0.9094 (tp30) REVERT: N 22 ASP cc_start: 0.9104 (t0) cc_final: 0.8787 (p0) REVERT: N 30 ASP cc_start: 0.8807 (t0) cc_final: 0.8502 (t0) REVERT: N 42 ASP cc_start: 0.9254 (t0) cc_final: 0.8954 (t0) REVERT: N 47 ASP cc_start: 0.9142 (m-30) cc_final: 0.8931 (m-30) REVERT: N 59 GLU cc_start: 0.9328 (tt0) cc_final: 0.8674 (mt-10) REVERT: N 63 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8861 (tp-100) REVERT: P 143 GLU cc_start: 0.9265 (tp30) cc_final: 0.9006 (tp30) REVERT: Q 30 ASP cc_start: 0.8906 (t0) cc_final: 0.8574 (t0) REVERT: Q 59 GLU cc_start: 0.9184 (tt0) cc_final: 0.8570 (tt0) REVERT: Q 63 GLN cc_start: 0.9082 (tp-100) cc_final: 0.8872 (tp-100) REVERT: Q 86 ILE cc_start: 0.9804 (pt) cc_final: 0.9588 (pp) REVERT: Q 111 GLN cc_start: 0.8446 (tt0) cc_final: 0.8118 (tt0) REVERT: S 139 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8708 (pp20) REVERT: T 63 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8934 (tp-100) REVERT: u 143 GLU cc_start: 0.9351 (tp30) cc_final: 0.9142 (tp30) REVERT: v 30 ASP cc_start: 0.8881 (t0) cc_final: 0.8617 (t0) REVERT: v 92 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9498 (mm) REVERT: v 111 GLN cc_start: 0.8503 (tt0) cc_final: 0.8202 (tt0) REVERT: v 112 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.9128 (ttp) REVERT: V 143 GLU cc_start: 0.9280 (tp30) cc_final: 0.8991 (tp30) REVERT: W 22 ASP cc_start: 0.9186 (t0) cc_final: 0.8785 (p0) REVERT: W 30 ASP cc_start: 0.8766 (t0) cc_final: 0.8479 (t0) REVERT: W 42 ASP cc_start: 0.9249 (t0) cc_final: 0.8972 (t0) REVERT: W 59 GLU cc_start: 0.9317 (tt0) cc_final: 0.8963 (tt0) REVERT: W 63 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8903 (tp-100) REVERT: W 111 GLN cc_start: 0.8570 (tt0) cc_final: 0.8068 (tt0) REVERT: W 122 GLU cc_start: 0.9286 (tp30) cc_final: 0.8942 (tp30) REVERT: Z 30 ASP cc_start: 0.8944 (t0) cc_final: 0.8603 (t0) REVERT: Z 59 GLU cc_start: 0.9178 (tt0) cc_final: 0.8498 (tt0) REVERT: Z 63 GLN cc_start: 0.9087 (tp-100) cc_final: 0.8880 (tp-100) REVERT: Z 111 GLN cc_start: 0.8518 (tt0) cc_final: 0.8049 (tt0) REVERT: c 86 ILE cc_start: 0.9671 (pt) cc_final: 0.9439 (pp) REVERT: c 91 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8978 (mm-30) REVERT: e 139 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9026 (pt0) REVERT: f 30 ASP cc_start: 0.8878 (t0) cc_final: 0.8576 (t0) REVERT: f 57 MET cc_start: 0.8929 (ttp) cc_final: 0.8724 (ttp) REVERT: f 63 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8397 (tm-30) REVERT: f 91 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8902 (mm-30) REVERT: f 92 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9492 (mm) REVERT: f 112 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.9067 (ttp) REVERT: f 122 GLU cc_start: 0.9364 (tp30) cc_final: 0.9094 (tp30) REVERT: h 139 GLU cc_start: 0.9120 (tt0) cc_final: 0.8772 (pt0) REVERT: i 22 ASP cc_start: 0.9162 (t0) cc_final: 0.8792 (p0) REVERT: i 42 ASP cc_start: 0.9307 (t0) cc_final: 0.8929 (t0) REVERT: i 63 GLN cc_start: 0.9121 (tp-100) cc_final: 0.8861 (tp-100) REVERT: i 65 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9362 (mp) REVERT: k 147 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8954 (ttp80) REVERT: l 30 ASP cc_start: 0.8859 (t0) cc_final: 0.8480 (t0) REVERT: l 59 GLU cc_start: 0.9157 (tt0) cc_final: 0.8371 (tt0) REVERT: l 111 GLN cc_start: 0.8573 (tt0) cc_final: 0.8278 (tt0) REVERT: o 63 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8903 (tp-100) REVERT: z 22 ASP cc_start: 0.9046 (t0) cc_final: 0.8844 (p0) REVERT: z 30 ASP cc_start: 0.8896 (t0) cc_final: 0.8585 (t0) REVERT: z 63 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8458 (tm-30) REVERT: z 92 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9492 (mm) REVERT: z 112 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.9114 (ttp) REVERT: z 122 GLU cc_start: 0.9306 (tp30) cc_final: 0.8834 (tp30) outliers start: 78 outliers final: 29 residues processed: 616 average time/residue: 1.1740 time to fit residues: 814.0239 Evaluate side-chains 584 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 545 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain N residue 63 GLN Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 114 ASN Chi-restraints excluded: chain c residue 114 ASN Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 143 GLU Chi-restraints excluded: chain e residue 151 THR Chi-restraints excluded: chain f residue 92 LEU Chi-restraints excluded: chain f residue 112 MET Chi-restraints excluded: chain h residue 151 THR Chi-restraints excluded: chain i residue 57 MET Chi-restraints excluded: chain i residue 65 LEU Chi-restraints excluded: chain i residue 114 ASN Chi-restraints excluded: chain i residue 130 THR Chi-restraints excluded: chain k residue 147 ARG Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain z residue 92 LEU Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 65 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN Q 89 GLN v 89 GLN W 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.055696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.041985 restraints weight = 58399.862| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 3.83 r_work: 0.2497 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17792 Z= 0.334 Angle : 0.664 8.386 24016 Z= 0.348 Chirality : 0.049 0.199 2592 Planarity : 0.003 0.032 3152 Dihedral : 4.252 27.146 2498 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 4.00 % Allowed : 21.16 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2080 helix: 2.65 (0.26), residues: 320 sheet: 0.62 (0.17), residues: 864 loop : -0.63 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS z 55 PHE 0.012 0.002 PHE f 77 TYR 0.021 0.001 TYR S 138 ARG 0.005 0.000 ARG l 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 597 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASP cc_start: 0.9170 (t0) cc_final: 0.8774 (p0) REVERT: B 30 ASP cc_start: 0.8792 (t0) cc_final: 0.8518 (t0) REVERT: B 42 ASP cc_start: 0.9328 (t0) cc_final: 0.9031 (t0) REVERT: B 63 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8857 (tp-100) REVERT: B 111 GLN cc_start: 0.8324 (tt0) cc_final: 0.8068 (tt0) REVERT: D 139 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8460 (pp20) REVERT: D 140 LEU cc_start: 0.9683 (mp) cc_final: 0.9122 (mp) REVERT: D 146 LEU cc_start: 0.9006 (mm) cc_final: 0.8744 (mm) REVERT: E 22 ASP cc_start: 0.9245 (t0) cc_final: 0.8759 (p0) REVERT: E 30 ASP cc_start: 0.8918 (t0) cc_final: 0.8615 (t0) REVERT: E 42 ASP cc_start: 0.9308 (t0) cc_final: 0.8858 (t0) REVERT: E 59 GLU cc_start: 0.9111 (tt0) cc_final: 0.8481 (tt0) REVERT: E 63 GLN cc_start: 0.9335 (mm-40) cc_final: 0.9055 (tm-30) REVERT: E 71 ASP cc_start: 0.8836 (t0) cc_final: 0.8551 (t0) REVERT: E 111 GLN cc_start: 0.8611 (tt0) cc_final: 0.8251 (tt0) REVERT: E 122 GLU cc_start: 0.9237 (mt-10) cc_final: 0.9000 (tp30) REVERT: H 63 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8904 (tp-100) REVERT: H 111 GLN cc_start: 0.8403 (tt0) cc_final: 0.8010 (tt0) REVERT: K 30 ASP cc_start: 0.8882 (t0) cc_final: 0.8598 (t0) REVERT: K 63 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8356 (tm-30) REVERT: K 112 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.9115 (ttp) REVERT: K 122 GLU cc_start: 0.9294 (tp30) cc_final: 0.8842 (tp30) REVERT: M 143 GLU cc_start: 0.9426 (tp30) cc_final: 0.9191 (tp30) REVERT: M 150 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8678 (mm) REVERT: N 22 ASP cc_start: 0.9174 (t0) cc_final: 0.8785 (p0) REVERT: N 30 ASP cc_start: 0.8829 (t0) cc_final: 0.8546 (t0) REVERT: N 42 ASP cc_start: 0.9268 (t0) cc_final: 0.8980 (t0) REVERT: N 47 ASP cc_start: 0.9145 (m-30) cc_final: 0.8910 (m-30) REVERT: N 63 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8848 (tp-100) REVERT: N 111 GLN cc_start: 0.8318 (tt0) cc_final: 0.8074 (tt0) REVERT: P 143 GLU cc_start: 0.9305 (tp30) cc_final: 0.9065 (tp30) REVERT: P 146 LEU cc_start: 0.9020 (mm) cc_final: 0.8758 (mm) REVERT: Q 22 ASP cc_start: 0.9223 (t0) cc_final: 0.8728 (p0) REVERT: Q 30 ASP cc_start: 0.8959 (t0) cc_final: 0.8627 (t0) REVERT: Q 42 ASP cc_start: 0.9294 (t0) cc_final: 0.8863 (t0) REVERT: Q 59 GLU cc_start: 0.9154 (tt0) cc_final: 0.8495 (tt0) REVERT: Q 63 GLN cc_start: 0.9125 (tp-100) cc_final: 0.8906 (tp-100) REVERT: Q 86 ILE cc_start: 0.9801 (pt) cc_final: 0.9577 (pp) REVERT: Q 111 GLN cc_start: 0.8422 (tt0) cc_final: 0.8040 (tt0) REVERT: S 139 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8654 (pp20) REVERT: T 22 ASP cc_start: 0.9096 (t0) cc_final: 0.8695 (p0) REVERT: T 63 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8940 (tp-100) REVERT: u 143 GLU cc_start: 0.9394 (tp30) cc_final: 0.9193 (tp30) REVERT: v 30 ASP cc_start: 0.8850 (t0) cc_final: 0.8621 (t0) REVERT: v 63 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8847 (tp-100) REVERT: v 92 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9507 (mm) REVERT: v 111 GLN cc_start: 0.8521 (tt0) cc_final: 0.8212 (tt0) REVERT: v 112 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.9152 (ttp) REVERT: V 143 GLU cc_start: 0.9312 (tp30) cc_final: 0.9015 (tp30) REVERT: W 22 ASP cc_start: 0.9194 (t0) cc_final: 0.8782 (p0) REVERT: W 30 ASP cc_start: 0.8798 (t0) cc_final: 0.8543 (t0) REVERT: W 42 ASP cc_start: 0.9273 (t0) cc_final: 0.9004 (t0) REVERT: W 59 GLU cc_start: 0.9307 (tt0) cc_final: 0.8961 (tt0) REVERT: W 63 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8889 (tp-100) REVERT: W 111 GLN cc_start: 0.8587 (tt0) cc_final: 0.8049 (tt0) REVERT: Z 22 ASP cc_start: 0.9227 (t0) cc_final: 0.8757 (p0) REVERT: Z 30 ASP cc_start: 0.8987 (t0) cc_final: 0.8644 (t0) REVERT: Z 42 ASP cc_start: 0.9290 (t0) cc_final: 0.8857 (t0) REVERT: Z 59 GLU cc_start: 0.9132 (tt0) cc_final: 0.8370 (tt0) REVERT: Z 63 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8889 (tp-100) REVERT: Z 111 GLN cc_start: 0.8577 (tt0) cc_final: 0.8127 (tt0) REVERT: c 22 ASP cc_start: 0.9076 (t0) cc_final: 0.8734 (p0) REVERT: c 86 ILE cc_start: 0.9670 (pt) cc_final: 0.9430 (pp) REVERT: c 91 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8946 (mm-30) REVERT: c 111 GLN cc_start: 0.8323 (tt0) cc_final: 0.8108 (tt0) REVERT: e 135 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7727 (tppp) REVERT: e 143 GLU cc_start: 0.9273 (tp30) cc_final: 0.8998 (tp30) REVERT: f 30 ASP cc_start: 0.8857 (t0) cc_final: 0.8588 (t0) REVERT: f 63 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8444 (tm-30) REVERT: f 91 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8842 (mm-30) REVERT: f 112 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.9091 (ttp) REVERT: f 122 GLU cc_start: 0.9305 (tp30) cc_final: 0.9068 (tp30) REVERT: i 22 ASP cc_start: 0.9190 (t0) cc_final: 0.8805 (p0) REVERT: i 42 ASP cc_start: 0.9309 (t0) cc_final: 0.9014 (t0) REVERT: i 47 ASP cc_start: 0.9167 (m-30) cc_final: 0.8949 (m-30) REVERT: i 63 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8870 (tp-100) REVERT: i 86 ILE cc_start: 0.9745 (pt) cc_final: 0.9530 (pp) REVERT: i 111 GLN cc_start: 0.8364 (tt0) cc_final: 0.8105 (tt0) REVERT: i 122 GLU cc_start: 0.9265 (tp30) cc_final: 0.8931 (tp30) REVERT: k 135 LYS cc_start: 0.8947 (mttp) cc_final: 0.8606 (ttmt) REVERT: k 146 LEU cc_start: 0.9020 (mm) cc_final: 0.8765 (mm) REVERT: k 147 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.8999 (ttp80) REVERT: l 30 ASP cc_start: 0.8922 (t0) cc_final: 0.8552 (t0) REVERT: l 59 GLU cc_start: 0.9121 (tt0) cc_final: 0.8305 (tt0) REVERT: l 63 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8801 (tp-100) REVERT: l 111 GLN cc_start: 0.8556 (tt0) cc_final: 0.7539 (tm-30) REVERT: o 63 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8906 (tp-100) REVERT: z 22 ASP cc_start: 0.9087 (t0) cc_final: 0.8763 (p0) REVERT: z 30 ASP cc_start: 0.8878 (t0) cc_final: 0.8591 (t0) REVERT: z 42 ASP cc_start: 0.9346 (t0) cc_final: 0.9078 (t0) REVERT: z 63 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8462 (tm-30) REVERT: z 92 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9496 (mm) REVERT: z 112 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9128 (ttp) REVERT: z 122 GLU cc_start: 0.9171 (tp30) cc_final: 0.8879 (tp30) outliers start: 73 outliers final: 35 residues processed: 618 average time/residue: 1.1983 time to fit residues: 832.3025 Evaluate side-chains 595 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 551 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain N residue 63 GLN Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 114 ASN Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 151 THR Chi-restraints excluded: chain f residue 57 MET Chi-restraints excluded: chain f residue 92 LEU Chi-restraints excluded: chain f residue 112 MET Chi-restraints excluded: chain h residue 151 THR Chi-restraints excluded: chain i residue 57 MET Chi-restraints excluded: chain i residue 130 THR Chi-restraints excluded: chain k residue 147 ARG Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 92 LEU Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 58 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 89 GLN T 89 GLN v 89 GLN ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 89 GLN f 131 GLN o 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.055282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.041503 restraints weight = 60291.066| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 3.96 r_work: 0.2499 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 17792 Z= 0.373 Angle : 0.701 9.592 24016 Z= 0.365 Chirality : 0.049 0.209 2592 Planarity : 0.003 0.030 3152 Dihedral : 4.355 27.225 2498 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 4.06 % Allowed : 22.20 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2080 helix: 2.41 (0.26), residues: 320 sheet: 0.55 (0.17), residues: 864 loop : -0.65 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS Z 55 PHE 0.013 0.002 PHE v 77 TYR 0.020 0.001 TYR k 138 ARG 0.006 0.000 ARG H 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 566 time to evaluate : 2.094 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: A 143 GLU cc_start: 0.9387 (tp30) cc_final: 0.9160 (tp30) REVERT: B 22 ASP cc_start: 0.9231 (t0) cc_final: 0.8776 (p0) REVERT: B 30 ASP cc_start: 0.8850 (t0) cc_final: 0.8584 (t0) REVERT: B 42 ASP cc_start: 0.9328 (t0) cc_final: 0.8984 (t0) REVERT: B 47 ASP cc_start: 0.9166 (m-30) cc_final: 0.8957 (m-30) REVERT: B 59 GLU cc_start: 0.9337 (tt0) cc_final: 0.8985 (tt0) REVERT: B 63 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8920 (tp-100) REVERT: B 111 GLN cc_start: 0.8365 (tt0) cc_final: 0.8110 (tt0) REVERT: D 139 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8422 (pp20) REVERT: D 140 LEU cc_start: 0.9698 (mp) cc_final: 0.9089 (mp) REVERT: E 22 ASP cc_start: 0.9246 (t0) cc_final: 0.8762 (p0) REVERT: E 30 ASP cc_start: 0.8932 (t0) cc_final: 0.8639 (t0) REVERT: E 42 ASP cc_start: 0.9343 (t0) cc_final: 0.8953 (t0) REVERT: E 59 GLU cc_start: 0.9057 (tt0) cc_final: 0.8356 (tt0) REVERT: E 63 GLN cc_start: 0.9324 (mm-40) cc_final: 0.8967 (tp-100) REVERT: E 111 GLN cc_start: 0.8626 (tt0) cc_final: 0.8241 (tt0) REVERT: G 142 ARG cc_start: 0.9297 (ttm-80) cc_final: 0.9059 (ttm-80) REVERT: H 22 ASP cc_start: 0.9104 (t0) cc_final: 0.8726 (p0) REVERT: H 63 GLN cc_start: 0.9186 (tp-100) cc_final: 0.8898 (tp-100) REVERT: H 111 GLN cc_start: 0.8405 (tt0) cc_final: 0.8003 (tt0) REVERT: K 22 ASP cc_start: 0.9127 (t0) cc_final: 0.8804 (p0) REVERT: K 30 ASP cc_start: 0.8836 (t0) cc_final: 0.8553 (t0) REVERT: K 63 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8355 (tm-30) REVERT: K 112 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.9076 (ttp) REVERT: K 122 GLU cc_start: 0.9270 (tp30) cc_final: 0.9018 (tp30) REVERT: M 139 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8369 (pp20) REVERT: M 142 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.9086 (ttm-80) REVERT: M 143 GLU cc_start: 0.9406 (tp30) cc_final: 0.9189 (tp30) REVERT: N 22 ASP cc_start: 0.9194 (t0) cc_final: 0.8810 (p0) REVERT: N 30 ASP cc_start: 0.8891 (t0) cc_final: 0.8627 (t0) REVERT: N 42 ASP cc_start: 0.9283 (t0) cc_final: 0.9015 (t0) REVERT: N 47 ASP cc_start: 0.9141 (m-30) cc_final: 0.8923 (m-30) REVERT: N 63 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8916 (tp-100) REVERT: N 86 ILE cc_start: 0.9742 (pt) cc_final: 0.9539 (pp) REVERT: N 111 GLN cc_start: 0.8382 (tt0) cc_final: 0.8141 (tt0) REVERT: P 143 GLU cc_start: 0.9323 (tp30) cc_final: 0.9048 (tp30) REVERT: Q 22 ASP cc_start: 0.9239 (t0) cc_final: 0.8775 (p0) REVERT: Q 30 ASP cc_start: 0.8933 (t0) cc_final: 0.8596 (t0) REVERT: Q 42 ASP cc_start: 0.9357 (t0) cc_final: 0.9009 (t0) REVERT: Q 59 GLU cc_start: 0.9138 (tt0) cc_final: 0.8429 (tt0) REVERT: Q 111 GLN cc_start: 0.8457 (tt0) cc_final: 0.8094 (tt0) REVERT: S 139 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8665 (pp20) REVERT: T 22 ASP cc_start: 0.9114 (t0) cc_final: 0.8703 (p0) REVERT: T 63 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8951 (tp-100) REVERT: u 143 GLU cc_start: 0.9368 (tp30) cc_final: 0.9162 (tp30) REVERT: v 22 ASP cc_start: 0.9122 (t0) cc_final: 0.8808 (p0) REVERT: v 30 ASP cc_start: 0.8875 (t0) cc_final: 0.8655 (t0) REVERT: v 42 ASP cc_start: 0.9385 (t0) cc_final: 0.9125 (t0) REVERT: v 63 GLN cc_start: 0.9142 (tp-100) cc_final: 0.8904 (tp-100) REVERT: v 111 GLN cc_start: 0.8552 (tt0) cc_final: 0.8233 (tt0) REVERT: v 112 MET cc_start: 0.9445 (OUTLIER) cc_final: 0.9195 (ttp) REVERT: V 143 GLU cc_start: 0.9292 (tp30) cc_final: 0.8988 (tp30) REVERT: W 22 ASP cc_start: 0.9210 (t0) cc_final: 0.8812 (p0) REVERT: W 30 ASP cc_start: 0.8844 (t0) cc_final: 0.8605 (t0) REVERT: W 42 ASP cc_start: 0.9291 (t0) cc_final: 0.9028 (t0) REVERT: W 63 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8926 (tp-100) REVERT: W 111 GLN cc_start: 0.8625 (tt0) cc_final: 0.8111 (tt0) REVERT: Z 22 ASP cc_start: 0.9237 (t0) cc_final: 0.8770 (p0) REVERT: Z 30 ASP cc_start: 0.8948 (t0) cc_final: 0.8650 (t0) REVERT: Z 42 ASP cc_start: 0.9327 (t0) cc_final: 0.8981 (t0) REVERT: Z 59 GLU cc_start: 0.9098 (tt0) cc_final: 0.8330 (tt0) REVERT: Z 63 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8894 (tp-100) REVERT: Z 111 GLN cc_start: 0.8614 (tt0) cc_final: 0.7693 (tm-30) REVERT: c 22 ASP cc_start: 0.9121 (t0) cc_final: 0.8732 (p0) REVERT: c 50 LEU cc_start: 0.9357 (tm) cc_final: 0.9118 (tm) REVERT: c 86 ILE cc_start: 0.9676 (pt) cc_final: 0.9449 (pp) REVERT: c 91 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8959 (mm-30) REVERT: c 111 GLN cc_start: 0.8357 (tt0) cc_final: 0.8126 (tt0) REVERT: f 30 ASP cc_start: 0.8841 (t0) cc_final: 0.8585 (t0) REVERT: f 63 GLN cc_start: 0.9107 (tm-30) cc_final: 0.8466 (tm-30) REVERT: f 91 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8906 (mm-30) REVERT: f 112 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.9111 (ttp) REVERT: f 122 GLU cc_start: 0.9275 (tp30) cc_final: 0.8982 (tp30) REVERT: i 22 ASP cc_start: 0.9246 (t0) cc_final: 0.8848 (p0) REVERT: i 42 ASP cc_start: 0.9325 (t0) cc_final: 0.9087 (t0) REVERT: i 47 ASP cc_start: 0.9170 (m-30) cc_final: 0.8962 (m-30) REVERT: i 59 GLU cc_start: 0.9310 (tt0) cc_final: 0.8802 (tt0) REVERT: i 86 ILE cc_start: 0.9738 (pt) cc_final: 0.9518 (pp) REVERT: i 111 GLN cc_start: 0.8401 (tt0) cc_final: 0.8133 (tt0) REVERT: k 139 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8465 (tm-30) REVERT: k 146 LEU cc_start: 0.9069 (mm) cc_final: 0.8792 (mm) REVERT: k 147 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8941 (ttp80) REVERT: l 30 ASP cc_start: 0.8978 (t0) cc_final: 0.8619 (t0) REVERT: l 59 GLU cc_start: 0.9084 (tt0) cc_final: 0.8257 (tt0) REVERT: l 63 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8887 (tp-100) REVERT: l 111 GLN cc_start: 0.8630 (tt0) cc_final: 0.7689 (tm-30) REVERT: o 63 GLN cc_start: 0.9188 (tp-100) cc_final: 0.8895 (tp-100) REVERT: o 112 MET cc_start: 0.9356 (tpp) cc_final: 0.9086 (ttp) REVERT: z 22 ASP cc_start: 0.9098 (t0) cc_final: 0.8790 (p0) REVERT: z 30 ASP cc_start: 0.8817 (t0) cc_final: 0.8594 (t0) REVERT: z 63 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8497 (tm-30) REVERT: z 92 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9498 (mm) REVERT: z 112 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.9152 (ttp) outliers start: 74 outliers final: 39 residues processed: 597 average time/residue: 1.1621 time to fit residues: 780.2043 Evaluate side-chains 587 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 540 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain M residue 142 ARG Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain N residue 63 GLN Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 114 ASN Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain e residue 151 THR Chi-restraints excluded: chain f residue 92 LEU Chi-restraints excluded: chain f residue 112 MET Chi-restraints excluded: chain h residue 151 THR Chi-restraints excluded: chain i residue 130 THR Chi-restraints excluded: chain k residue 147 ARG Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 114 ASN Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 92 LEU Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 101 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 0.0020 chunk 142 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 89 GLN K 131 GLN Q 89 GLN v 131 GLN f 89 GLN l 45 GLN z 131 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.056914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.043376 restraints weight = 57657.537| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 3.83 r_work: 0.2546 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17792 Z= 0.248 Angle : 0.706 9.797 24016 Z= 0.366 Chirality : 0.050 0.239 2592 Planarity : 0.003 0.022 3152 Dihedral : 4.283 15.455 2496 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 2.58 % Allowed : 26.15 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.18), residues: 2080 helix: 2.39 (0.27), residues: 320 sheet: 0.35 (0.16), residues: 944 loop : -0.52 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS Z 55 PHE 0.010 0.001 PHE E 77 TYR 0.016 0.001 TYR G 138 ARG 0.004 0.000 ARG l 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 596 time to evaluate : 1.941 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: B 22 ASP cc_start: 0.9237 (t0) cc_final: 0.8793 (p0) REVERT: B 30 ASP cc_start: 0.8856 (t0) cc_final: 0.8585 (t0) REVERT: B 42 ASP cc_start: 0.9316 (t0) cc_final: 0.9050 (t0) REVERT: B 45 GLN cc_start: 0.8925 (tp40) cc_final: 0.8032 (tm-30) REVERT: B 47 ASP cc_start: 0.9103 (m-30) cc_final: 0.8549 (m-30) REVERT: B 59 GLU cc_start: 0.9348 (tt0) cc_final: 0.8701 (mt-10) REVERT: B 60 GLU cc_start: 0.8928 (mp0) cc_final: 0.8583 (mm-30) REVERT: B 63 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8884 (tm-30) REVERT: B 111 GLN cc_start: 0.8292 (tt0) cc_final: 0.8063 (tt0) REVERT: D 139 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8461 (pp20) REVERT: D 140 LEU cc_start: 0.9698 (mp) cc_final: 0.9171 (mp) REVERT: D 146 LEU cc_start: 0.8915 (mm) cc_final: 0.8594 (mm) REVERT: E 22 ASP cc_start: 0.9228 (t0) cc_final: 0.8766 (p0) REVERT: E 30 ASP cc_start: 0.8943 (t0) cc_final: 0.8656 (t0) REVERT: E 42 ASP cc_start: 0.9330 (t0) cc_final: 0.8946 (t0) REVERT: E 59 GLU cc_start: 0.8952 (tt0) cc_final: 0.8271 (tt0) REVERT: E 63 GLN cc_start: 0.9338 (mm-40) cc_final: 0.9019 (tp-100) REVERT: E 111 GLN cc_start: 0.8599 (tt0) cc_final: 0.8235 (tt0) REVERT: G 142 ARG cc_start: 0.9310 (ttm-80) cc_final: 0.9082 (ttm-80) REVERT: H 22 ASP cc_start: 0.9061 (t0) cc_final: 0.8744 (p0) REVERT: H 59 GLU cc_start: 0.9363 (tt0) cc_final: 0.8740 (tt0) REVERT: H 63 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8899 (tp-100) REVERT: H 111 GLN cc_start: 0.8401 (tt0) cc_final: 0.8017 (tt0) REVERT: K 30 ASP cc_start: 0.8807 (t0) cc_final: 0.8573 (t0) REVERT: K 42 ASP cc_start: 0.9321 (t0) cc_final: 0.9063 (t0) REVERT: K 63 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8330 (tm-30) REVERT: K 112 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.9009 (ttp) REVERT: M 139 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8320 (pp20) REVERT: M 143 GLU cc_start: 0.9402 (tp30) cc_final: 0.9149 (tp30) REVERT: N 22 ASP cc_start: 0.9198 (t0) cc_final: 0.8800 (p0) REVERT: N 30 ASP cc_start: 0.8872 (t0) cc_final: 0.8613 (t0) REVERT: N 42 ASP cc_start: 0.9262 (t0) cc_final: 0.8997 (t0) REVERT: N 45 GLN cc_start: 0.8899 (tp40) cc_final: 0.7939 (tm-30) REVERT: N 47 ASP cc_start: 0.9097 (m-30) cc_final: 0.8390 (m-30) REVERT: N 63 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8844 (tm-30) REVERT: N 86 ILE cc_start: 0.9759 (pt) cc_final: 0.9538 (pp) REVERT: N 111 GLN cc_start: 0.8312 (tt0) cc_final: 0.8067 (tt0) REVERT: P 143 GLU cc_start: 0.9325 (tp30) cc_final: 0.9065 (tp30) REVERT: Q 22 ASP cc_start: 0.9213 (t0) cc_final: 0.8793 (p0) REVERT: Q 30 ASP cc_start: 0.8944 (t0) cc_final: 0.8597 (t0) REVERT: Q 42 ASP cc_start: 0.9328 (t0) cc_final: 0.8976 (t0) REVERT: Q 59 GLU cc_start: 0.8963 (tt0) cc_final: 0.8128 (tt0) REVERT: Q 60 GLU cc_start: 0.9031 (mp0) cc_final: 0.8730 (mm-30) REVERT: Q 63 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8802 (tp-100) REVERT: Q 86 ILE cc_start: 0.9764 (pt) cc_final: 0.9554 (pp) REVERT: Q 111 GLN cc_start: 0.8451 (tt0) cc_final: 0.8083 (tt0) REVERT: S 139 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8628 (pp20) REVERT: T 22 ASP cc_start: 0.9084 (t0) cc_final: 0.8681 (p0) REVERT: T 45 GLN cc_start: 0.8897 (tp40) cc_final: 0.8043 (tm-30) REVERT: T 47 ASP cc_start: 0.8976 (m-30) cc_final: 0.8378 (m-30) REVERT: T 63 GLN cc_start: 0.9138 (tp-100) cc_final: 0.8899 (tp-100) REVERT: u 143 GLU cc_start: 0.9406 (tp30) cc_final: 0.9175 (tp30) REVERT: v 22 ASP cc_start: 0.9113 (t0) cc_final: 0.8817 (p0) REVERT: v 30 ASP cc_start: 0.8742 (t0) cc_final: 0.8503 (t0) REVERT: v 42 ASP cc_start: 0.9354 (t0) cc_final: 0.9080 (t0) REVERT: v 63 GLN cc_start: 0.9094 (tp-100) cc_final: 0.8867 (tp-100) REVERT: v 111 GLN cc_start: 0.8550 (tt0) cc_final: 0.8234 (tt0) REVERT: v 112 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9094 (ttp) REVERT: V 143 GLU cc_start: 0.9280 (tp30) cc_final: 0.8964 (tp30) REVERT: W 22 ASP cc_start: 0.9221 (t0) cc_final: 0.8810 (p0) REVERT: W 30 ASP cc_start: 0.8851 (t0) cc_final: 0.8606 (t0) REVERT: W 42 ASP cc_start: 0.9280 (t0) cc_final: 0.9054 (t0) REVERT: W 63 GLN cc_start: 0.9156 (tp-100) cc_final: 0.8840 (tp-100) REVERT: W 111 GLN cc_start: 0.8607 (tt0) cc_final: 0.8094 (tt0) REVERT: Z 22 ASP cc_start: 0.9209 (t0) cc_final: 0.8768 (p0) REVERT: Z 30 ASP cc_start: 0.8948 (t0) cc_final: 0.8639 (t0) REVERT: Z 42 ASP cc_start: 0.9332 (t0) cc_final: 0.8963 (t0) REVERT: Z 59 GLU cc_start: 0.9042 (tt0) cc_final: 0.8283 (tt0) REVERT: Z 111 GLN cc_start: 0.8573 (tt0) cc_final: 0.8162 (tt0) REVERT: c 22 ASP cc_start: 0.9085 (t0) cc_final: 0.8749 (p0) REVERT: c 45 GLN cc_start: 0.8871 (tp40) cc_final: 0.8172 (tm-30) REVERT: c 47 ASP cc_start: 0.8980 (m-30) cc_final: 0.8293 (m-30) REVERT: c 50 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8861 (tm) REVERT: c 86 ILE cc_start: 0.9681 (pt) cc_final: 0.9435 (pp) REVERT: c 91 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8883 (mm-30) REVERT: f 22 ASP cc_start: 0.9054 (t0) cc_final: 0.8752 (p0) REVERT: f 30 ASP cc_start: 0.8838 (t0) cc_final: 0.8563 (t0) REVERT: f 42 ASP cc_start: 0.9313 (t0) cc_final: 0.9042 (t0) REVERT: f 63 GLN cc_start: 0.9073 (tm-30) cc_final: 0.8447 (tm-30) REVERT: f 91 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8855 (mm-30) REVERT: f 112 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9002 (ttp) REVERT: f 122 GLU cc_start: 0.9237 (tp30) cc_final: 0.8980 (tp30) REVERT: i 22 ASP cc_start: 0.9226 (t0) cc_final: 0.8882 (p0) REVERT: i 45 GLN cc_start: 0.8936 (tp40) cc_final: 0.8050 (tm-30) REVERT: i 47 ASP cc_start: 0.9104 (m-30) cc_final: 0.8576 (m-30) REVERT: i 60 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8799 (mm-30) REVERT: i 86 ILE cc_start: 0.9741 (pt) cc_final: 0.9497 (pp) REVERT: i 111 GLN cc_start: 0.8357 (tt0) cc_final: 0.8106 (tt0) REVERT: k 139 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8399 (tm-30) REVERT: k 146 LEU cc_start: 0.8994 (mm) cc_final: 0.8784 (mm) REVERT: k 147 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.9045 (ttp80) REVERT: l 30 ASP cc_start: 0.8976 (t0) cc_final: 0.8653 (t0) REVERT: l 59 GLU cc_start: 0.9013 (tt0) cc_final: 0.8182 (tt0) REVERT: l 63 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8887 (tp-100) REVERT: l 111 GLN cc_start: 0.8564 (tt0) cc_final: 0.8129 (tt0) REVERT: n 139 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8513 (pp20) REVERT: o 63 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8917 (tp-100) REVERT: o 112 MET cc_start: 0.9350 (tpp) cc_final: 0.9006 (ttp) REVERT: z 22 ASP cc_start: 0.9049 (t0) cc_final: 0.8792 (p0) REVERT: z 30 ASP cc_start: 0.8832 (t0) cc_final: 0.8574 (t0) REVERT: z 42 ASP cc_start: 0.9328 (t0) cc_final: 0.9081 (t0) REVERT: z 63 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8405 (tm-30) REVERT: z 92 LEU cc_start: 0.9739 (OUTLIER) cc_final: 0.9536 (mm) REVERT: z 112 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.9115 (ttp) REVERT: z 120 MET cc_start: 0.9546 (OUTLIER) cc_final: 0.9250 (ttp) outliers start: 47 outliers final: 23 residues processed: 609 average time/residue: 1.1844 time to fit residues: 810.8594 Evaluate side-chains 582 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 550 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain u residue 135 LYS Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Z residue 114 ASN Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 50 LEU Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain f residue 112 MET Chi-restraints excluded: chain k residue 147 ARG Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 120 MET Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 140 LEU Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 92 LEU Chi-restraints excluded: chain z residue 112 MET Chi-restraints excluded: chain z residue 120 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 80 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN Q 89 GLN W 89 GLN Z 89 GLN f 89 GLN l 89 GLN z 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.055276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.041712 restraints weight = 60379.415| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.95 r_work: 0.2506 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 17792 Z= 0.373 Angle : 0.766 10.560 24016 Z= 0.396 Chirality : 0.053 0.298 2592 Planarity : 0.003 0.034 3152 Dihedral : 4.471 19.447 2496 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.56 % Allowed : 26.59 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2080 helix: 2.10 (0.27), residues: 320 sheet: 0.32 (0.16), residues: 944 loop : -0.57 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS c 55 PHE 0.013 0.002 PHE K 77 TYR 0.016 0.001 TYR J 138 ARG 0.003 0.000 ARG l 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 561 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASP cc_start: 0.9267 (t0) cc_final: 0.8785 (p0) REVERT: B 30 ASP cc_start: 0.8907 (t0) cc_final: 0.8629 (t0) REVERT: B 42 ASP cc_start: 0.9325 (t0) cc_final: 0.9001 (t0) REVERT: B 45 GLN cc_start: 0.9016 (tp40) cc_final: 0.8086 (tm-30) REVERT: B 47 ASP cc_start: 0.9125 (m-30) cc_final: 0.8442 (m-30) REVERT: B 59 GLU cc_start: 0.9344 (tt0) cc_final: 0.8876 (tt0) REVERT: B 63 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8935 (tm-30) REVERT: B 111 GLN cc_start: 0.8334 (tt0) cc_final: 0.8102 (tt0) REVERT: D 139 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8401 (pp20) REVERT: D 140 LEU cc_start: 0.9700 (mp) cc_final: 0.9142 (mp) REVERT: D 146 LEU cc_start: 0.8974 (mm) cc_final: 0.8660 (mm) REVERT: E 22 ASP cc_start: 0.9275 (t0) cc_final: 0.8808 (p0) REVERT: E 30 ASP cc_start: 0.8934 (t0) cc_final: 0.8645 (t0) REVERT: E 42 ASP cc_start: 0.9355 (t0) cc_final: 0.9021 (t0) REVERT: E 59 GLU cc_start: 0.9066 (tt0) cc_final: 0.8378 (tt0) REVERT: E 63 GLN cc_start: 0.9387 (mm-40) cc_final: 0.9081 (tp-100) REVERT: G 135 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7700 (ttmm) REVERT: G 139 GLU cc_start: 0.9366 (mp0) cc_final: 0.9162 (mp0) REVERT: G 142 ARG cc_start: 0.9307 (ttm-80) cc_final: 0.9064 (ttm-80) REVERT: H 22 ASP cc_start: 0.9116 (t0) cc_final: 0.8708 (p0) REVERT: H 63 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8957 (tp-100) REVERT: H 111 GLN cc_start: 0.8415 (tt0) cc_final: 0.8027 (tt0) REVERT: K 30 ASP cc_start: 0.8825 (t0) cc_final: 0.8602 (t0) REVERT: K 63 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8346 (tm-30) REVERT: K 112 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.9075 (ttp) REVERT: N 22 ASP cc_start: 0.9231 (t0) cc_final: 0.8778 (p0) REVERT: N 30 ASP cc_start: 0.8920 (t0) cc_final: 0.8653 (t0) REVERT: N 42 ASP cc_start: 0.9289 (t0) cc_final: 0.9020 (t0) REVERT: N 45 GLN cc_start: 0.8994 (tp40) cc_final: 0.8084 (tm-30) REVERT: N 47 ASP cc_start: 0.9123 (m-30) cc_final: 0.8585 (m-30) REVERT: N 59 GLU cc_start: 0.9316 (tt0) cc_final: 0.8798 (mt-10) REVERT: N 63 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8881 (tp-100) REVERT: N 86 ILE cc_start: 0.9771 (pt) cc_final: 0.9564 (pp) REVERT: N 111 GLN cc_start: 0.8366 (tt0) cc_final: 0.8144 (tt0) REVERT: P 139 GLU cc_start: 0.9221 (mp0) cc_final: 0.9017 (mp0) REVERT: P 143 GLU cc_start: 0.9319 (tp30) cc_final: 0.9048 (tp30) REVERT: Q 22 ASP cc_start: 0.9254 (t0) cc_final: 0.8735 (p0) REVERT: Q 30 ASP cc_start: 0.8942 (t0) cc_final: 0.8625 (t0) REVERT: Q 42 ASP cc_start: 0.9347 (t0) cc_final: 0.9029 (t0) REVERT: Q 59 GLU cc_start: 0.9075 (tt0) cc_final: 0.8419 (tt0) REVERT: Q 111 GLN cc_start: 0.8502 (tt0) cc_final: 0.8130 (tt0) REVERT: S 139 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8587 (pp20) REVERT: T 22 ASP cc_start: 0.9110 (t0) cc_final: 0.8688 (p0) REVERT: T 63 GLN cc_start: 0.9187 (tp-100) cc_final: 0.8975 (tp-100) REVERT: u 143 GLU cc_start: 0.9366 (tp30) cc_final: 0.9130 (tp30) REVERT: v 22 ASP cc_start: 0.9162 (t0) cc_final: 0.8803 (p0) REVERT: v 30 ASP cc_start: 0.8840 (t0) cc_final: 0.8612 (t0) REVERT: v 111 GLN cc_start: 0.8527 (tt0) cc_final: 0.8212 (tt0) REVERT: v 112 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9154 (ttp) REVERT: V 143 GLU cc_start: 0.9279 (tp30) cc_final: 0.8977 (tp30) REVERT: W 22 ASP cc_start: 0.9262 (t0) cc_final: 0.8792 (p0) REVERT: W 30 ASP cc_start: 0.8911 (t0) cc_final: 0.8670 (t0) REVERT: W 42 ASP cc_start: 0.9295 (t0) cc_final: 0.9031 (t0) REVERT: W 59 GLU cc_start: 0.9313 (tt0) cc_final: 0.8944 (tt0) REVERT: W 111 GLN cc_start: 0.8637 (tt0) cc_final: 0.8132 (tt0) REVERT: Z 22 ASP cc_start: 0.9275 (t0) cc_final: 0.8796 (p0) REVERT: Z 30 ASP cc_start: 0.8961 (t0) cc_final: 0.8652 (t0) REVERT: Z 42 ASP cc_start: 0.9354 (t0) cc_final: 0.9027 (t0) REVERT: Z 59 GLU cc_start: 0.9098 (tt0) cc_final: 0.8231 (tt0) REVERT: Z 63 GLN cc_start: 0.9145 (tp-100) cc_final: 0.8938 (tp-100) REVERT: Z 111 GLN cc_start: 0.8588 (tt0) cc_final: 0.8165 (tt0) REVERT: c 22 ASP cc_start: 0.9153 (t0) cc_final: 0.8712 (p0) REVERT: c 86 ILE cc_start: 0.9700 (pt) cc_final: 0.9470 (pp) REVERT: c 91 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8870 (mm-30) REVERT: f 22 ASP cc_start: 0.9093 (t0) cc_final: 0.8729 (p0) REVERT: f 63 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8550 (tm-30) REVERT: f 91 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8926 (mm-30) REVERT: f 112 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9003 (ttp) REVERT: i 22 ASP cc_start: 0.9191 (t0) cc_final: 0.8826 (p0) REVERT: i 42 ASP cc_start: 0.9179 (t0) cc_final: 0.8824 (t0) REVERT: i 45 GLN cc_start: 0.9022 (tp40) cc_final: 0.8142 (tm-30) REVERT: i 47 ASP cc_start: 0.9127 (m-30) cc_final: 0.8607 (m-30) REVERT: i 59 GLU cc_start: 0.9211 (tt0) cc_final: 0.8684 (mt-10) REVERT: i 86 ILE cc_start: 0.9742 (pt) cc_final: 0.9502 (pp) REVERT: i 111 GLN cc_start: 0.8383 (tt0) cc_final: 0.8131 (tt0) REVERT: k 139 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8400 (tm-30) REVERT: k 142 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8721 (ptm-80) REVERT: k 146 LEU cc_start: 0.9074 (mm) cc_final: 0.8818 (mm) REVERT: l 22 ASP cc_start: 0.9216 (t0) cc_final: 0.8655 (p0) REVERT: l 30 ASP cc_start: 0.9009 (t0) cc_final: 0.8680 (t0) REVERT: l 42 ASP cc_start: 0.9337 (t0) cc_final: 0.9104 (t0) REVERT: l 59 GLU cc_start: 0.9062 (tt0) cc_final: 0.8218 (tt0) REVERT: l 63 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8921 (tp-100) REVERT: l 111 GLN cc_start: 0.8578 (tt0) cc_final: 0.8148 (tt0) REVERT: o 63 GLN cc_start: 0.9215 (tp-100) cc_final: 0.8960 (tp-100) REVERT: o 112 MET cc_start: 0.9345 (tpp) cc_final: 0.9072 (ttp) REVERT: z 22 ASP cc_start: 0.9095 (t0) cc_final: 0.8813 (p0) REVERT: z 30 ASP cc_start: 0.8853 (t0) cc_final: 0.8602 (t0) REVERT: z 42 ASP cc_start: 0.9343 (t0) cc_final: 0.9113 (t0) REVERT: z 63 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8539 (tm-30) REVERT: z 91 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8844 (mm-30) REVERT: z 92 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9505 (mm) REVERT: z 112 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9164 (ttp) outliers start: 65 outliers final: 19 residues processed: 590 average time/residue: 1.2133 time to fit residues: 804.0698 Evaluate side-chains 563 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 536 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 135 LYS Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 114 ASN Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain f residue 112 MET Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 140 LEU Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 92 LEU Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 107 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 89 GLN z 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.055061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.041269 restraints weight = 60413.361| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.96 r_work: 0.2493 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 17792 Z= 0.423 Angle : 0.823 11.535 24016 Z= 0.423 Chirality : 0.054 0.346 2592 Planarity : 0.004 0.037 3152 Dihedral : 4.650 20.287 2496 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.75 % Allowed : 28.89 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2080 helix: 1.87 (0.28), residues: 320 sheet: 0.47 (0.17), residues: 864 loop : -0.56 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS f 55 PHE 0.012 0.002 PHE v 77 TYR 0.013 0.001 TYR H 29 ARG 0.005 0.000 ARG M 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 554 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASP cc_start: 0.9293 (t0) cc_final: 0.8815 (p0) REVERT: B 30 ASP cc_start: 0.8909 (t0) cc_final: 0.8630 (t0) REVERT: B 45 GLN cc_start: 0.9059 (tp40) cc_final: 0.8180 (tm-30) REVERT: B 47 ASP cc_start: 0.9144 (m-30) cc_final: 0.8614 (m-30) REVERT: B 59 GLU cc_start: 0.9328 (tt0) cc_final: 0.8587 (mt-10) REVERT: B 63 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8963 (tp-100) REVERT: B 111 GLN cc_start: 0.8312 (tt0) cc_final: 0.8084 (tt0) REVERT: D 139 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8383 (pp20) REVERT: D 140 LEU cc_start: 0.9692 (mp) cc_final: 0.9116 (mp) REVERT: D 142 ARG cc_start: 0.9190 (ttm-80) cc_final: 0.8912 (ttm-80) REVERT: D 146 LEU cc_start: 0.8961 (mm) cc_final: 0.8709 (mm) REVERT: E 22 ASP cc_start: 0.9256 (t0) cc_final: 0.8737 (p0) REVERT: E 30 ASP cc_start: 0.8935 (t0) cc_final: 0.8629 (t0) REVERT: E 42 ASP cc_start: 0.9364 (t0) cc_final: 0.9061 (t0) REVERT: E 59 GLU cc_start: 0.9034 (tt0) cc_final: 0.8311 (tt0) REVERT: E 63 GLN cc_start: 0.9419 (mm-40) cc_final: 0.9102 (tp-100) REVERT: E 101 THR cc_start: 0.9565 (p) cc_final: 0.9358 (t) REVERT: E 111 GLN cc_start: 0.8443 (tt0) cc_final: 0.8097 (tt0) REVERT: G 142 ARG cc_start: 0.9304 (ttm-80) cc_final: 0.9082 (ttm-80) REVERT: H 22 ASP cc_start: 0.9136 (t0) cc_final: 0.8714 (p0) REVERT: H 63 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.9010 (tp-100) REVERT: H 111 GLN cc_start: 0.8373 (tt0) cc_final: 0.7985 (tt0) REVERT: J 139 GLU cc_start: 0.9220 (mp0) cc_final: 0.9000 (mp0) REVERT: K 30 ASP cc_start: 0.8841 (t0) cc_final: 0.8619 (t0) REVERT: N 22 ASP cc_start: 0.9256 (t0) cc_final: 0.8831 (p0) REVERT: N 30 ASP cc_start: 0.8917 (t0) cc_final: 0.8667 (t0) REVERT: N 47 ASP cc_start: 0.9131 (m-30) cc_final: 0.8916 (m-30) REVERT: N 59 GLU cc_start: 0.9316 (tt0) cc_final: 0.8777 (mt-10) REVERT: N 63 GLN cc_start: 0.9223 (mm-40) cc_final: 0.8919 (tm-30) REVERT: N 86 ILE cc_start: 0.9778 (pt) cc_final: 0.9568 (pp) REVERT: N 111 GLN cc_start: 0.8322 (tt0) cc_final: 0.8086 (tt0) REVERT: P 143 GLU cc_start: 0.9297 (tp30) cc_final: 0.9047 (tp30) REVERT: Q 22 ASP cc_start: 0.9257 (t0) cc_final: 0.8735 (p0) REVERT: Q 30 ASP cc_start: 0.8940 (t0) cc_final: 0.8604 (t0) REVERT: Q 42 ASP cc_start: 0.9375 (t0) cc_final: 0.9084 (t0) REVERT: Q 59 GLU cc_start: 0.9132 (tt0) cc_final: 0.8364 (tt0) REVERT: Q 111 GLN cc_start: 0.8516 (tt0) cc_final: 0.8156 (tt0) REVERT: S 139 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8554 (pp20) REVERT: T 22 ASP cc_start: 0.9116 (t0) cc_final: 0.8678 (p0) REVERT: u 143 GLU cc_start: 0.9344 (tp30) cc_final: 0.9121 (tp30) REVERT: v 22 ASP cc_start: 0.9188 (t0) cc_final: 0.8803 (p0) REVERT: v 30 ASP cc_start: 0.8833 (t0) cc_final: 0.8606 (t0) REVERT: v 42 ASP cc_start: 0.9364 (t0) cc_final: 0.9115 (t0) REVERT: v 63 GLN cc_start: 0.9115 (tp-100) cc_final: 0.8897 (tp-100) REVERT: v 111 GLN cc_start: 0.8507 (tt0) cc_final: 0.8227 (tt0) REVERT: v 112 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.9187 (ttp) REVERT: V 143 GLU cc_start: 0.9277 (tp30) cc_final: 0.8978 (tp30) REVERT: W 22 ASP cc_start: 0.9288 (t0) cc_final: 0.8798 (p0) REVERT: W 30 ASP cc_start: 0.8911 (t0) cc_final: 0.8673 (t0) REVERT: W 42 ASP cc_start: 0.9311 (t0) cc_final: 0.9073 (t0) REVERT: W 59 GLU cc_start: 0.9303 (tt0) cc_final: 0.8896 (tt0) REVERT: W 63 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8855 (tp-100) REVERT: W 111 GLN cc_start: 0.8648 (tt0) cc_final: 0.8151 (tt0) REVERT: Z 22 ASP cc_start: 0.9277 (t0) cc_final: 0.8744 (p0) REVERT: Z 30 ASP cc_start: 0.8955 (t0) cc_final: 0.8649 (t0) REVERT: Z 42 ASP cc_start: 0.9370 (t0) cc_final: 0.9071 (t0) REVERT: Z 59 GLU cc_start: 0.9140 (tt0) cc_final: 0.8223 (tt0) REVERT: Z 63 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8930 (tp-100) REVERT: Z 111 GLN cc_start: 0.8561 (tt0) cc_final: 0.8196 (tt0) REVERT: c 22 ASP cc_start: 0.9154 (t0) cc_final: 0.8720 (p0) REVERT: c 86 ILE cc_start: 0.9727 (pt) cc_final: 0.9493 (pp) REVERT: c 91 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8915 (mm-30) REVERT: c 120 MET cc_start: 0.9000 (tpp) cc_final: 0.8711 (tpt) REVERT: f 22 ASP cc_start: 0.9103 (t0) cc_final: 0.8773 (p0) REVERT: f 42 ASP cc_start: 0.9337 (t0) cc_final: 0.9088 (t0) REVERT: f 63 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8963 (tp-100) REVERT: f 91 GLU cc_start: 0.9217 (mm-30) cc_final: 0.9002 (mm-30) REVERT: f 112 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.9017 (ttp) REVERT: i 22 ASP cc_start: 0.9228 (t0) cc_final: 0.8816 (p0) REVERT: i 42 ASP cc_start: 0.9206 (t0) cc_final: 0.8975 (t0) REVERT: i 47 ASP cc_start: 0.9128 (m-30) cc_final: 0.8917 (m-30) REVERT: i 59 GLU cc_start: 0.9202 (tt0) cc_final: 0.8940 (tt0) REVERT: i 86 ILE cc_start: 0.9751 (pt) cc_final: 0.9513 (pp) REVERT: i 111 GLN cc_start: 0.8317 (tt0) cc_final: 0.8046 (tt0) REVERT: k 142 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8766 (ptm-80) REVERT: k 146 LEU cc_start: 0.9055 (mm) cc_final: 0.8810 (mm) REVERT: l 22 ASP cc_start: 0.9266 (t0) cc_final: 0.8622 (p0) REVERT: l 30 ASP cc_start: 0.8980 (t0) cc_final: 0.8616 (t0) REVERT: l 42 ASP cc_start: 0.9379 (t0) cc_final: 0.9154 (t0) REVERT: l 59 GLU cc_start: 0.9101 (tt0) cc_final: 0.8146 (tt0) REVERT: l 63 GLN cc_start: 0.9193 (tp-100) cc_final: 0.8937 (tp-100) REVERT: l 111 GLN cc_start: 0.8615 (tt0) cc_final: 0.8208 (tt0) REVERT: o 22 ASP cc_start: 0.9105 (t0) cc_final: 0.8672 (p0) REVERT: o 63 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8956 (tp-100) REVERT: o 112 MET cc_start: 0.9362 (tpp) cc_final: 0.9132 (ttp) REVERT: z 22 ASP cc_start: 0.9179 (t0) cc_final: 0.8773 (p0) REVERT: z 30 ASP cc_start: 0.8859 (t0) cc_final: 0.8625 (t0) REVERT: z 63 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8933 (tp-100) REVERT: z 112 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9175 (ttp) outliers start: 32 outliers final: 17 residues processed: 568 average time/residue: 1.1846 time to fit residues: 757.8794 Evaluate side-chains 558 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 536 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain f residue 112 MET Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 92 LEU Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 170 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 163 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 89 GLN T 45 GLN Z 45 GLN z 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.044018 restraints weight = 60249.066| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 4.00 r_work: 0.2580 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17792 Z= 0.255 Angle : 0.842 13.930 24016 Z= 0.429 Chirality : 0.055 0.417 2592 Planarity : 0.003 0.030 3152 Dihedral : 4.601 20.434 2496 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.32 % Allowed : 29.71 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 2080 helix: 1.75 (0.29), residues: 320 sheet: 0.30 (0.16), residues: 944 loop : -0.46 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS i 83 PHE 0.011 0.001 PHE l 77 TYR 0.015 0.001 TYR V 138 ARG 0.009 0.000 ARG o 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 591 time to evaluate : 2.001 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: A 147 ARG cc_start: 0.9538 (ttp-110) cc_final: 0.9038 (ttp-110) REVERT: B 22 ASP cc_start: 0.9144 (t0) cc_final: 0.8804 (p0) REVERT: B 30 ASP cc_start: 0.8940 (t0) cc_final: 0.8678 (t0) REVERT: B 42 ASP cc_start: 0.9136 (t0) cc_final: 0.8777 (t0) REVERT: B 45 GLN cc_start: 0.8850 (tp40) cc_final: 0.7942 (tm-30) REVERT: B 47 ASP cc_start: 0.9069 (m-30) cc_final: 0.8468 (m-30) REVERT: B 59 GLU cc_start: 0.9319 (tt0) cc_final: 0.8787 (mt-10) REVERT: B 63 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8907 (tp-100) REVERT: B 111 GLN cc_start: 0.8307 (tt0) cc_final: 0.8093 (tt0) REVERT: D 139 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8431 (pp20) REVERT: D 140 LEU cc_start: 0.9709 (mp) cc_final: 0.9087 (mp) REVERT: E 22 ASP cc_start: 0.9212 (t0) cc_final: 0.8844 (p0) REVERT: E 30 ASP cc_start: 0.8955 (t0) cc_final: 0.8674 (t0) REVERT: E 42 ASP cc_start: 0.9345 (t0) cc_final: 0.9089 (t0) REVERT: E 59 GLU cc_start: 0.8866 (tt0) cc_final: 0.8275 (tt0) REVERT: E 63 GLN cc_start: 0.9359 (mm-40) cc_final: 0.9041 (tp-100) REVERT: E 86 ILE cc_start: 0.9725 (pt) cc_final: 0.9516 (pp) REVERT: E 111 GLN cc_start: 0.8478 (tt0) cc_final: 0.8120 (tt0) REVERT: H 45 GLN cc_start: 0.8852 (tp40) cc_final: 0.8141 (tm-30) REVERT: H 111 GLN cc_start: 0.8397 (tt0) cc_final: 0.8119 (tt0) REVERT: J 139 GLU cc_start: 0.9209 (mp0) cc_final: 0.8913 (mp0) REVERT: K 30 ASP cc_start: 0.8887 (t0) cc_final: 0.8621 (t0) REVERT: K 120 MET cc_start: 0.9508 (ttp) cc_final: 0.9293 (ttp) REVERT: N 22 ASP cc_start: 0.9141 (t0) cc_final: 0.8789 (p0) REVERT: N 30 ASP cc_start: 0.8928 (t0) cc_final: 0.8676 (t0) REVERT: N 42 ASP cc_start: 0.9115 (t0) cc_final: 0.8778 (t0) REVERT: N 45 GLN cc_start: 0.8806 (tp40) cc_final: 0.7908 (tm-30) REVERT: N 47 ASP cc_start: 0.9069 (m-30) cc_final: 0.8487 (m-30) REVERT: N 63 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8908 (tp-100) REVERT: N 111 GLN cc_start: 0.8310 (tt0) cc_final: 0.8092 (tt0) REVERT: P 138 TYR cc_start: 0.9340 (t80) cc_final: 0.9118 (t80) REVERT: P 143 GLU cc_start: 0.9306 (tp30) cc_final: 0.9051 (tp30) REVERT: Q 22 ASP cc_start: 0.9236 (t0) cc_final: 0.8861 (p0) REVERT: Q 30 ASP cc_start: 0.8955 (t0) cc_final: 0.8665 (t0) REVERT: Q 42 ASP cc_start: 0.9365 (t0) cc_final: 0.9135 (t0) REVERT: Q 45 GLN cc_start: 0.8850 (tp40) cc_final: 0.8361 (tm-30) REVERT: Q 47 ASP cc_start: 0.9027 (m-30) cc_final: 0.8782 (m-30) REVERT: Q 59 GLU cc_start: 0.9132 (tt0) cc_final: 0.8436 (tt0) REVERT: Q 86 ILE cc_start: 0.9759 (pt) cc_final: 0.9556 (pp) REVERT: Q 111 GLN cc_start: 0.8526 (tt0) cc_final: 0.8214 (tt0) REVERT: S 139 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8639 (pp20) REVERT: T 22 ASP cc_start: 0.9071 (t0) cc_final: 0.8681 (p0) REVERT: T 63 GLN cc_start: 0.9107 (tp-100) cc_final: 0.8904 (tp-100) REVERT: u 143 GLU cc_start: 0.9337 (tp30) cc_final: 0.9119 (tp30) REVERT: v 22 ASP cc_start: 0.9103 (t0) cc_final: 0.8823 (p0) REVERT: v 30 ASP cc_start: 0.8771 (t0) cc_final: 0.8545 (t0) REVERT: v 42 ASP cc_start: 0.9356 (t0) cc_final: 0.9111 (t0) REVERT: v 63 GLN cc_start: 0.9082 (tp-100) cc_final: 0.8835 (tp-100) REVERT: v 86 ILE cc_start: 0.9750 (pt) cc_final: 0.9536 (pp) REVERT: v 111 GLN cc_start: 0.8552 (tt0) cc_final: 0.8263 (tt0) REVERT: v 112 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8972 (ttp) REVERT: V 143 GLU cc_start: 0.9260 (tp30) cc_final: 0.8967 (tp30) REVERT: W 22 ASP cc_start: 0.9211 (t0) cc_final: 0.8799 (p0) REVERT: W 30 ASP cc_start: 0.8935 (t0) cc_final: 0.8709 (t0) REVERT: W 42 ASP cc_start: 0.9282 (t0) cc_final: 0.9017 (t0) REVERT: W 45 GLN cc_start: 0.8743 (tp-100) cc_final: 0.7986 (tm-30) REVERT: W 47 ASP cc_start: 0.8988 (m-30) cc_final: 0.8384 (m-30) REVERT: W 59 GLU cc_start: 0.9293 (tt0) cc_final: 0.8834 (mt-10) REVERT: W 63 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8662 (tp-100) REVERT: W 111 GLN cc_start: 0.8583 (tt0) cc_final: 0.8178 (tt0) REVERT: Y 138 TYR cc_start: 0.9377 (t80) cc_final: 0.9151 (t80) REVERT: Z 22 ASP cc_start: 0.9225 (t0) cc_final: 0.8841 (p0) REVERT: Z 30 ASP cc_start: 0.8997 (t0) cc_final: 0.8695 (t0) REVERT: Z 42 ASP cc_start: 0.9346 (t0) cc_final: 0.9093 (t0) REVERT: Z 59 GLU cc_start: 0.8993 (tt0) cc_final: 0.8298 (tt0) REVERT: Z 63 GLN cc_start: 0.9137 (tp-100) cc_final: 0.8873 (tp-100) REVERT: Z 86 ILE cc_start: 0.9778 (pt) cc_final: 0.9552 (pp) REVERT: Z 111 GLN cc_start: 0.8560 (tt0) cc_final: 0.8322 (tt0) REVERT: b 139 GLU cc_start: 0.9344 (pm20) cc_final: 0.9142 (pm20) REVERT: b 147 ARG cc_start: 0.9541 (ttp-110) cc_final: 0.9294 (ttp-110) REVERT: c 22 ASP cc_start: 0.9125 (t0) cc_final: 0.8743 (p0) REVERT: c 45 GLN cc_start: 0.8845 (tp40) cc_final: 0.8304 (tp-100) REVERT: c 86 ILE cc_start: 0.9710 (pt) cc_final: 0.9471 (pp) REVERT: c 91 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8889 (mm-30) REVERT: e 139 GLU cc_start: 0.9334 (pt0) cc_final: 0.9121 (mp0) REVERT: e 147 ARG cc_start: 0.9392 (ttp-110) cc_final: 0.9147 (ttp-110) REVERT: f 42 ASP cc_start: 0.9320 (t0) cc_final: 0.9078 (t0) REVERT: f 63 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8473 (tm-30) REVERT: f 91 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8921 (mm-30) REVERT: i 22 ASP cc_start: 0.9169 (t0) cc_final: 0.8841 (p0) REVERT: i 42 ASP cc_start: 0.9174 (t0) cc_final: 0.8839 (t0) REVERT: i 45 GLN cc_start: 0.8832 (tp40) cc_final: 0.7997 (tm-30) REVERT: i 47 ASP cc_start: 0.9057 (m-30) cc_final: 0.8593 (m-30) REVERT: i 59 GLU cc_start: 0.9293 (tt0) cc_final: 0.8871 (mt-10) REVERT: i 63 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8620 (tp-100) REVERT: i 86 ILE cc_start: 0.9738 (pt) cc_final: 0.9487 (pp) REVERT: i 91 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8906 (mm-30) REVERT: i 111 GLN cc_start: 0.8308 (tt0) cc_final: 0.8074 (tt0) REVERT: k 142 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8843 (ttm-80) REVERT: k 143 GLU cc_start: 0.9190 (tp30) cc_final: 0.8942 (tm-30) REVERT: k 147 ARG cc_start: 0.9340 (ttp80) cc_final: 0.9112 (ttp-110) REVERT: l 22 ASP cc_start: 0.9240 (t0) cc_final: 0.8648 (p0) REVERT: l 30 ASP cc_start: 0.8960 (t0) cc_final: 0.8660 (t0) REVERT: l 42 ASP cc_start: 0.9379 (t0) cc_final: 0.9143 (t0) REVERT: l 59 GLU cc_start: 0.8995 (tt0) cc_final: 0.8137 (tt0) REVERT: l 63 GLN cc_start: 0.9144 (tp-100) cc_final: 0.8882 (tp-100) REVERT: l 111 GLN cc_start: 0.8544 (tt0) cc_final: 0.8299 (tt0) REVERT: n 147 ARG cc_start: 0.9401 (ttm110) cc_final: 0.9024 (ttm110) REVERT: o 45 GLN cc_start: 0.8867 (tp40) cc_final: 0.8158 (tm-30) REVERT: o 47 ASP cc_start: 0.8809 (m-30) cc_final: 0.8347 (m-30) REVERT: o 63 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8981 (tp-100) REVERT: z 30 ASP cc_start: 0.8899 (t0) cc_final: 0.8642 (t0) REVERT: z 42 ASP cc_start: 0.9357 (t0) cc_final: 0.9146 (t0) REVERT: z 60 GLU cc_start: 0.8835 (mp0) cc_final: 0.7800 (mp0) REVERT: z 63 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8487 (tm-30) REVERT: z 112 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9061 (ttp) outliers start: 24 outliers final: 14 residues processed: 605 average time/residue: 1.1927 time to fit residues: 810.4599 Evaluate side-chains 575 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 558 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Z residue 112 MET Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 140 LEU Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 147 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN H 89 GLN Q 89 GLN Z 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.056344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.042707 restraints weight = 60747.814| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.97 r_work: 0.2541 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 17792 Z= 0.325 Angle : 0.882 13.405 24016 Z= 0.446 Chirality : 0.057 0.351 2592 Planarity : 0.004 0.061 3152 Dihedral : 4.639 22.358 2496 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.43 % Allowed : 30.65 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.19), residues: 2080 helix: 1.35 (0.30), residues: 320 sheet: 0.32 (0.16), residues: 944 loop : -0.45 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS i 83 PHE 0.011 0.001 PHE l 77 TYR 0.013 0.001 TYR G 138 ARG 0.015 0.000 ARG h 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14868.44 seconds wall clock time: 262 minutes 28.86 seconds (15748.86 seconds total)