Starting phenix.real_space_refine on Sun Jun 15 11:30:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rt5_19479/06_2025/8rt5_19479.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rt5_19479/06_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_19479/06_2025/8rt5_19479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rt5_19479/06_2025/8rt5_19479.map" model { file = "/net/cci-nas-00/data/ceres_data/8rt5_19479/06_2025/8rt5_19479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rt5_19479/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.60, per 1000 atoms: 0.55 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: 4.95 Conformation dependent library (CDL) restraints added in 3.1 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: 2.50 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: 6.16 Time building geometry restraints manager: 4.79 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: 0.16 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: 0.010 Normalize map: mean=0, sd=1: 2.200 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: 0.130 Set scattering table: 0.140 Process input model: 39.710 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.340 ------------------------------------------------------------------------------- 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= 0.289 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 Details of bonding type rmsd hydrogen bonds : bond 0.17836 ( 640) hydrogen bonds : angle 7.36231 ( 1680) covalent geometry : bond 0.00694 (17792) covalent geometry : angle 0.78859 (24016) *********************** 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 : 1.862 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: 1.2716 time to fit residues: 1099.5720 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 : 2.045 ------------------------------------------------------------------------------- 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: 7.9990 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: 3.1388 ------------------------------------------------------------------------------- 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 K 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.057618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.043775 restraints weight = 59074.273| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.93 r_work: 0.2524 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3143 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= 0.205 Angle : 0.672 7.808 24016 Z= 0.351 Chirality : 0.048 0.183 2592 Planarity : 0.005 0.045 3152 Dihedral : 4.377 16.003 2502 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.63 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: 0.61 (0.18), residues: 2080 helix: 2.67 (0.26), residues: 320 sheet: 0.70 (0.16), residues: 864 loop : -0.72 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Z 83 PHE 0.011 0.002 PHE v 77 TYR 0.017 0.001 TYR n 138 ARG 0.008 0.001 ARG c 28 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 640) hydrogen bonds : angle 5.60065 ( 1680) covalent geometry : bond 0.00460 (17792) covalent geometry : angle 0.67212 (24016) *********************** 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 : 1.944 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: A 140 LEU cc_start: 0.9731 (OUTLIER) cc_final: 0.9439 (mm) REVERT: B 22 ASP cc_start: 0.9169 (t0) cc_final: 0.8754 (p0) REVERT: B 30 ASP cc_start: 0.8755 (t0) cc_final: 0.8531 (t0) REVERT: B 42 ASP cc_start: 0.9244 (t0) cc_final: 0.8882 (t0) REVERT: B 63 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8857 (tp-100) REVERT: E 63 GLN cc_start: 0.9355 (mm-40) cc_final: 0.8997 (tp-100) REVERT: E 111 GLN cc_start: 0.8556 (tt0) cc_final: 0.8177 (tt0) REVERT: G 135 LYS cc_start: 0.8641 (ttmm) cc_final: 0.8229 (tppp) REVERT: H 111 GLN cc_start: 0.8378 (tt0) cc_final: 0.8087 (tt0) REVERT: J 136 THR cc_start: 0.9576 (t) cc_final: 0.8930 (t) REVERT: K 30 ASP cc_start: 0.8793 (t0) cc_final: 0.8519 (t0) REVERT: M 139 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8759 (tm-30) REVERT: M 142 ARG cc_start: 0.9092 (ttm-80) cc_final: 0.8877 (ptm-80) REVERT: N 30 ASP cc_start: 0.8802 (t0) cc_final: 0.8567 (t0) REVERT: N 63 GLN cc_start: 0.9107 (tp-100) cc_final: 0.8890 (tp-100) REVERT: P 136 THR cc_start: 0.9499 (OUTLIER) cc_final: 0.9108 (t) REVERT: Q 30 ASP cc_start: 0.8683 (t0) cc_final: 0.8482 (t0) REVERT: Q 59 GLU cc_start: 0.9306 (tt0) cc_final: 0.8768 (tt0) REVERT: Q 86 ILE cc_start: 0.9777 (pt) cc_final: 0.9505 (pp) REVERT: Q 89 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8741 (mm-40) REVERT: Q 111 GLN cc_start: 0.8402 (tt0) cc_final: 0.8112 (mt0) REVERT: S 146 LEU cc_start: 0.9213 (mt) cc_final: 0.8949 (mm) REVERT: T 63 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8961 (tp-100) REVERT: u 139 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8787 (tm-30) REVERT: v 30 ASP cc_start: 0.8799 (t0) cc_final: 0.8583 (t0) REVERT: v 111 GLN cc_start: 0.8447 (tt0) cc_final: 0.8242 (tt0) REVERT: V 136 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9233 (t) REVERT: V 143 GLU cc_start: 0.9279 (tp30) cc_final: 0.9075 (tp30) REVERT: W 30 ASP cc_start: 0.8737 (t0) cc_final: 0.8517 (t0) REVERT: W 63 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8850 (tp-100) REVERT: W 111 GLN cc_start: 0.8556 (tt0) cc_final: 0.8117 (tt0) REVERT: Y 136 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.9034 (t) REVERT: Z 30 ASP cc_start: 0.8763 (t0) cc_final: 0.8523 (t0) REVERT: Z 59 GLU cc_start: 0.9300 (tt0) cc_final: 0.8695 (tt0) REVERT: Z 63 GLN cc_start: 0.9107 (tp-100) cc_final: 0.8901 (tp-100) REVERT: Z 111 GLN cc_start: 0.8549 (tt0) cc_final: 0.8101 (tt0) REVERT: b 136 THR cc_start: 0.9459 (OUTLIER) cc_final: 0.9109 (t) REVERT: c 63 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8887 (tp-100) REVERT: c 91 GLU cc_start: 0.9305 (mm-30) cc_final: 0.9004 (mm-30) REVERT: e 135 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8301 (ttpt) REVERT: e 136 THR cc_start: 0.9486 (OUTLIER) cc_final: 0.9250 (t) REVERT: f 30 ASP cc_start: 0.8788 (t0) cc_final: 0.8524 (t0) REVERT: f 63 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8276 (tm-30) REVERT: f 91 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8944 (mm-30) REVERT: h 138 TYR cc_start: 0.9150 (t80) cc_final: 0.8857 (t80) REVERT: i 30 ASP cc_start: 0.8763 (t0) cc_final: 0.8509 (t0) REVERT: l 30 ASP cc_start: 0.8624 (t0) cc_final: 0.8367 (t0) REVERT: l 59 GLU cc_start: 0.9152 (tt0) cc_final: 0.8491 (tt0) REVERT: l 111 GLN cc_start: 0.8597 (tt0) cc_final: 0.8288 (tt0) REVERT: o 63 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8830 (tp-100) REVERT: y 136 THR cc_start: 0.9524 (OUTLIER) cc_final: 0.9192 (t) REVERT: z 30 ASP cc_start: 0.8851 (t0) cc_final: 0.8568 (t0) REVERT: z 87 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9109 (pttt) REVERT: z 92 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9475 (mm) outliers start: 82 outliers final: 17 residues processed: 677 average time/residue: 1.0954 time to fit residues: 837.7384 Evaluate side-chains 619 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 592 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 57 MET 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 V residue 136 THR Chi-restraints excluded: chain W residue 71 ASP 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 b residue 136 THR Chi-restraints excluded: chain b residue 143 GLU Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain e residue 151 THR Chi-restraints excluded: chain i residue 57 MET Chi-restraints excluded: chain i residue 71 ASP Chi-restraints excluded: chain i residue 130 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 87 LYS 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: 5.9990 chunk 13 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 89 GLN Z 89 GLN l 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.055268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.041492 restraints weight = 59900.343| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.91 r_work: 0.2482 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 17792 Z= 0.294 Angle : 0.676 6.853 24016 Z= 0.354 Chirality : 0.049 0.208 2592 Planarity : 0.004 0.044 3152 Dihedral : 4.269 15.852 2496 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 4.50 % Allowed : 18.64 % Favored : 76.86 % 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: 0.81 (0.18), residues: 2080 helix: 2.89 (0.25), residues: 320 sheet: 0.66 (0.16), residues: 896 loop : -0.47 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS i 55 PHE 0.013 0.002 PHE f 77 TYR 0.012 0.001 TYR o 29 ARG 0.004 0.001 ARG z 109 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 640) hydrogen bonds : angle 5.50189 ( 1680) covalent geometry : bond 0.00665 (17792) covalent geometry : angle 0.67579 (24016) *********************** 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 682 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 600 time to evaluate : 1.910 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: 0.9190 (t0) cc_final: 0.8752 (p0) REVERT: B 30 ASP cc_start: 0.8742 (t0) cc_final: 0.8452 (t0) REVERT: B 42 ASP cc_start: 0.9298 (t0) cc_final: 0.8925 (t0) REVERT: B 59 GLU cc_start: 0.9326 (tt0) cc_final: 0.8947 (tt0) REVERT: D 139 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8485 (pp20) REVERT: D 140 LEU cc_start: 0.9605 (mp) cc_final: 0.9088 (mp) REVERT: E 59 GLU cc_start: 0.9310 (tt0) cc_final: 0.8687 (tt0) REVERT: E 63 GLN cc_start: 0.9336 (mm-40) cc_final: 0.9072 (tm-30) REVERT: E 111 GLN cc_start: 0.8632 (tt0) cc_final: 0.8405 (tt0) REVERT: G 135 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8050 (tppp) REVERT: H 50 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9072 (tm) REVERT: H 63 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8941 (tp-100) REVERT: H 111 GLN cc_start: 0.8405 (tt0) cc_final: 0.8086 (tt0) REVERT: K 30 ASP cc_start: 0.8850 (t0) cc_final: 0.8571 (t0) REVERT: K 50 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9282 (tm) REVERT: K 57 MET cc_start: 0.8969 (ttp) cc_final: 0.8749 (ttp) REVERT: K 63 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8521 (tm-30) REVERT: K 122 GLU cc_start: 0.9404 (tp30) cc_final: 0.9039 (tp30) REVERT: N 22 ASP cc_start: 0.9143 (t0) cc_final: 0.8812 (p0) REVERT: N 30 ASP cc_start: 0.8757 (t0) cc_final: 0.8492 (t0) REVERT: N 42 ASP cc_start: 0.9237 (t0) cc_final: 0.8985 (t0) REVERT: N 59 GLU cc_start: 0.9327 (tt0) cc_final: 0.8961 (tt0) REVERT: Q 30 ASP cc_start: 0.8870 (t0) cc_final: 0.8557 (t0) REVERT: Q 86 ILE cc_start: 0.9792 (pt) cc_final: 0.9583 (pp) REVERT: Q 111 GLN cc_start: 0.8464 (tt0) cc_final: 0.8148 (tt0) REVERT: S 139 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8726 (tm-30) REVERT: T 63 GLN cc_start: 0.9156 (tp-100) cc_final: 0.8953 (tp-100) REVERT: T 122 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8951 (tp30) REVERT: v 30 ASP cc_start: 0.8889 (t0) cc_final: 0.8652 (t0) REVERT: v 111 GLN cc_start: 0.8489 (tt0) cc_final: 0.8274 (tt0) REVERT: v 122 GLU cc_start: 0.9398 (tp30) cc_final: 0.9160 (tp30) REVERT: V 143 GLU cc_start: 0.9259 (tp30) cc_final: 0.9019 (tp30) REVERT: W 22 ASP cc_start: 0.9240 (t0) cc_final: 0.8845 (p0) REVERT: W 30 ASP cc_start: 0.8712 (t0) cc_final: 0.8463 (t0) REVERT: W 42 ASP cc_start: 0.9229 (t0) cc_final: 0.8990 (t0) REVERT: W 59 GLU cc_start: 0.9305 (tt0) cc_final: 0.8920 (tt0) REVERT: W 63 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8819 (tp-100) REVERT: W 111 GLN cc_start: 0.8560 (tt0) cc_final: 0.8079 (tt0) REVERT: Z 30 ASP cc_start: 0.8895 (t0) cc_final: 0.8560 (t0) REVERT: Z 59 GLU cc_start: 0.9241 (tt0) cc_final: 0.8531 (tt0) REVERT: Z 111 GLN cc_start: 0.8542 (tt0) cc_final: 0.8079 (tt0) REVERT: Z 112 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9113 (ttp) REVERT: b 138 TYR cc_start: 0.9232 (t80) cc_final: 0.8998 (t80) REVERT: c 63 GLN cc_start: 0.9223 (tp-100) cc_final: 0.8982 (tp-100) REVERT: c 86 ILE cc_start: 0.9703 (pt) cc_final: 0.9486 (pp) REVERT: c 91 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8973 (mm-30) REVERT: c 122 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8852 (tp30) REVERT: f 30 ASP cc_start: 0.8838 (t0) cc_final: 0.8569 (t0) REVERT: f 63 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8235 (tm-30) REVERT: f 91 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8925 (mm-30) REVERT: f 92 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9490 (mm) REVERT: f 122 GLU cc_start: 0.9365 (tp30) cc_final: 0.9065 (tp30) REVERT: i 22 ASP cc_start: 0.9163 (t0) cc_final: 0.8807 (p0) REVERT: i 42 ASP cc_start: 0.9238 (t0) cc_final: 0.8928 (t0) REVERT: i 59 GLU cc_start: 0.9367 (tt0) cc_final: 0.8973 (tt0) REVERT: i 63 GLN cc_start: 0.9142 (tp-100) cc_final: 0.8940 (tp-100) REVERT: i 122 GLU cc_start: 0.9202 (tt0) cc_final: 0.8991 (tp30) REVERT: k 135 LYS cc_start: 0.8521 (mttt) cc_final: 0.7922 (ttpt) REVERT: k 139 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8933 (tm-30) REVERT: k 143 GLU cc_start: 0.9310 (tp30) cc_final: 0.9092 (tp30) REVERT: k 147 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8941 (ttp80) REVERT: l 30 ASP cc_start: 0.8806 (t0) cc_final: 0.8440 (t0) REVERT: l 59 GLU cc_start: 0.9171 (tt0) cc_final: 0.8431 (tt0) REVERT: l 63 GLN cc_start: 0.9074 (tp-100) cc_final: 0.8872 (tp-100) REVERT: l 111 GLN cc_start: 0.8490 (tt0) cc_final: 0.8188 (tt0) REVERT: o 30 ASP cc_start: 0.8892 (t0) cc_final: 0.8680 (t0) REVERT: o 63 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8949 (tp-100) REVERT: o 122 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8840 (tp30) REVERT: y 142 ARG cc_start: 0.9331 (ttm-80) cc_final: 0.9102 (ttm-80) REVERT: z 30 ASP cc_start: 0.8860 (t0) cc_final: 0.8579 (t0) REVERT: z 63 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8552 (tm-30) REVERT: z 92 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9464 (mm) REVERT: z 122 GLU cc_start: 0.9355 (tp30) cc_final: 0.8912 (tp30) outliers start: 82 outliers final: 24 residues processed: 622 average time/residue: 1.1712 time to fit residues: 816.2517 Evaluate side-chains 588 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 556 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 92 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 50 LEU 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 97 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 u residue 151 THR Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 112 MET Chi-restraints excluded: chain c residue 122 GLU Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 151 THR 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 k residue 147 ARG Chi-restraints excluded: chain l residue 114 ASN Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 151 THR 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: 1.9990 chunk 107 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 181 optimal weight: 0.0010 chunk 46 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 overall best weight: 4.7994 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.041239 restraints weight = 59525.955| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.92 r_work: 0.2483 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17792 Z= 0.263 Angle : 0.651 7.234 24016 Z= 0.341 Chirality : 0.049 0.237 2592 Planarity : 0.003 0.031 3152 Dihedral : 4.223 15.155 2496 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 4.44 % Allowed : 19.79 % Favored : 75.77 % 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: 0.71 (0.18), residues: 2080 helix: 2.74 (0.26), residues: 320 sheet: 0.60 (0.17), residues: 896 loop : -0.49 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS i 55 PHE 0.013 0.002 PHE v 77 TYR 0.016 0.001 TYR A 138 ARG 0.005 0.000 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 640) hydrogen bonds : angle 5.28518 ( 1680) covalent geometry : bond 0.00596 (17792) covalent geometry : angle 0.65085 (24016) *********************** 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 673 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 592 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASP cc_start: 0.9193 (t0) cc_final: 0.8767 (p0) REVERT: B 30 ASP cc_start: 0.8848 (t0) cc_final: 0.8558 (t0) REVERT: B 42 ASP cc_start: 0.9343 (t0) cc_final: 0.9051 (t0) REVERT: B 59 GLU cc_start: 0.9325 (tt0) cc_final: 0.8915 (tt0) REVERT: B 63 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8906 (tp-100) REVERT: D 139 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8392 (pp20) REVERT: D 140 LEU cc_start: 0.9645 (mp) cc_final: 0.9125 (mp) REVERT: E 59 GLU cc_start: 0.9252 (tt0) cc_final: 0.8612 (tt0) REVERT: E 63 GLN cc_start: 0.9346 (mm-40) cc_final: 0.8951 (tp-100) REVERT: E 71 ASP cc_start: 0.8888 (t0) cc_final: 0.8631 (t0) REVERT: E 122 GLU cc_start: 0.9340 (tp30) cc_final: 0.9084 (tp30) REVERT: G 139 GLU cc_start: 0.9487 (OUTLIER) cc_final: 0.9269 (mp0) REVERT: H 50 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9204 (tm) REVERT: H 63 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8896 (tp-100) REVERT: H 111 GLN cc_start: 0.8382 (tt0) cc_final: 0.8064 (tt0) REVERT: H 122 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8928 (tp30) REVERT: J 139 GLU cc_start: 0.9515 (OUTLIER) cc_final: 0.9311 (mp0) REVERT: K 30 ASP cc_start: 0.8853 (t0) cc_final: 0.8572 (t0) REVERT: K 63 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8901 (tp-100) REVERT: K 122 GLU cc_start: 0.9386 (tp30) cc_final: 0.9087 (tp30) REVERT: N 22 ASP cc_start: 0.9212 (t0) cc_final: 0.8788 (p0) REVERT: N 30 ASP cc_start: 0.8837 (t0) cc_final: 0.8537 (t0) REVERT: N 42 ASP cc_start: 0.9278 (t0) cc_final: 0.9027 (t0) REVERT: N 47 ASP cc_start: 0.9148 (m-30) cc_final: 0.8945 (m-30) REVERT: N 63 GLN cc_start: 0.9167 (tp-100) cc_final: 0.8927 (tp-100) REVERT: P 139 GLU cc_start: 0.9337 (mt-10) cc_final: 0.8892 (pt0) REVERT: Q 22 ASP cc_start: 0.9258 (t0) cc_final: 0.8664 (p0) REVERT: Q 30 ASP cc_start: 0.8951 (t0) cc_final: 0.8635 (t0) REVERT: Q 42 ASP cc_start: 0.9336 (t0) cc_final: 0.8918 (t0) REVERT: Q 59 GLU cc_start: 0.9243 (tt0) cc_final: 0.8619 (tt0) REVERT: Q 63 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8919 (tp-100) REVERT: Q 86 ILE cc_start: 0.9798 (pt) cc_final: 0.9586 (pp) REVERT: Q 111 GLN cc_start: 0.8454 (tt0) cc_final: 0.8113 (tt0) REVERT: Q 122 GLU cc_start: 0.9314 (tp30) cc_final: 0.9007 (tp30) REVERT: S 139 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8670 (pp20) REVERT: T 22 ASP cc_start: 0.9103 (t0) cc_final: 0.8698 (p0) REVERT: T 63 GLN cc_start: 0.9189 (tp-100) cc_final: 0.8962 (tp-100) REVERT: T 122 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8885 (tp30) REVERT: u 143 GLU cc_start: 0.9344 (tp30) cc_final: 0.9133 (tp30) REVERT: v 30 ASP cc_start: 0.8898 (t0) cc_final: 0.8625 (t0) REVERT: v 111 GLN cc_start: 0.8536 (tt0) cc_final: 0.8229 (tt0) REVERT: v 112 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.9126 (ttp) REVERT: V 139 GLU cc_start: 0.9347 (mt-10) cc_final: 0.9014 (pm20) REVERT: V 143 GLU cc_start: 0.9268 (tp30) cc_final: 0.8998 (tp30) REVERT: W 22 ASP cc_start: 0.9218 (t0) cc_final: 0.8804 (p0) REVERT: W 30 ASP cc_start: 0.8831 (t0) cc_final: 0.8557 (t0) REVERT: W 42 ASP cc_start: 0.9284 (t0) cc_final: 0.9023 (t0) REVERT: W 47 ASP cc_start: 0.9116 (m-30) cc_final: 0.8897 (m-30) REVERT: W 59 GLU cc_start: 0.9315 (tt0) cc_final: 0.8889 (tt0) REVERT: W 63 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8879 (tp-100) REVERT: W 111 GLN cc_start: 0.8590 (tt0) cc_final: 0.8090 (tt0) REVERT: Y 139 GLU cc_start: 0.9359 (mt-10) cc_final: 0.9061 (pm20) REVERT: Z 30 ASP cc_start: 0.8935 (t0) cc_final: 0.8582 (t0) REVERT: Z 59 GLU cc_start: 0.9230 (tt0) cc_final: 0.8507 (tt0) REVERT: Z 63 GLN cc_start: 0.9099 (tp-100) cc_final: 0.8874 (tp-100) REVERT: Z 111 GLN cc_start: 0.8554 (tt0) cc_final: 0.8097 (tt0) REVERT: b 147 ARG cc_start: 0.9504 (ttp-110) cc_final: 0.9275 (ttp-110) REVERT: c 22 ASP cc_start: 0.9091 (t0) cc_final: 0.8758 (p0) REVERT: c 50 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9141 (tm) REVERT: c 86 ILE cc_start: 0.9687 (pt) cc_final: 0.9460 (pp) REVERT: c 91 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8971 (mm-30) REVERT: e 139 GLU cc_start: 0.9312 (mt-10) cc_final: 0.9002 (pt0) REVERT: f 30 ASP cc_start: 0.8843 (t0) cc_final: 0.8574 (t0) REVERT: f 63 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8273 (tm-30) REVERT: f 91 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8952 (mm-30) REVERT: f 122 GLU cc_start: 0.9324 (tp30) cc_final: 0.8910 (tp30) REVERT: i 22 ASP cc_start: 0.9166 (t0) cc_final: 0.8806 (p0) REVERT: i 42 ASP cc_start: 0.9299 (t0) cc_final: 0.9032 (t0) REVERT: i 59 GLU cc_start: 0.9350 (tt0) cc_final: 0.8918 (tt0) REVERT: i 63 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8872 (tp-100) REVERT: i 65 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9362 (mp) REVERT: k 135 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8391 (ttpt) REVERT: k 139 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8876 (tm-30) REVERT: k 143 GLU cc_start: 0.9324 (tp30) cc_final: 0.9046 (tp30) REVERT: k 147 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.8792 (ttp80) REVERT: l 30 ASP cc_start: 0.8897 (t0) cc_final: 0.8525 (t0) REVERT: l 59 GLU cc_start: 0.9189 (tt0) cc_final: 0.8427 (tt0) REVERT: l 63 GLN cc_start: 0.9107 (tp-100) cc_final: 0.8903 (tp-100) REVERT: l 111 GLN cc_start: 0.8552 (tt0) cc_final: 0.8256 (tt0) REVERT: n 135 LYS cc_start: 0.8727 (mttt) cc_final: 0.8443 (mtmm) REVERT: n 140 LEU cc_start: 0.9703 (mm) cc_final: 0.9437 (mm) REVERT: o 63 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8900 (tp-100) REVERT: o 111 GLN cc_start: 0.8294 (tt0) cc_final: 0.8057 (tt0) REVERT: o 112 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9075 (ttp) REVERT: z 22 ASP cc_start: 0.9086 (t0) cc_final: 0.8752 (p0) REVERT: z 30 ASP cc_start: 0.8901 (t0) cc_final: 0.8624 (t0) REVERT: z 42 ASP cc_start: 0.9360 (t0) cc_final: 0.9088 (t0) REVERT: z 63 GLN cc_start: 0.9134 (tp-100) cc_final: 0.8925 (tp-100) REVERT: z 92 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9485 (mm) REVERT: z 122 GLU cc_start: 0.9310 (tp30) cc_final: 0.8882 (tp30) outliers start: 81 outliers final: 29 residues processed: 614 average time/residue: 1.3833 time to fit residues: 949.4676 Evaluate side-chains 587 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 546 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 130 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 97 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 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 151 THR Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain c residue 50 LEU 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 h residue 151 THR 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 135 LYS Chi-restraints excluded: chain k residue 147 ARG Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 112 MET Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 65 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 W 89 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 = 0.3028 r_free = 0.3028 target = 0.054914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.041250 restraints weight = 60588.887| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 3.92 r_work: 0.2486 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17792 Z= 0.248 Angle : 0.663 8.511 24016 Z= 0.348 Chirality : 0.049 0.232 2592 Planarity : 0.003 0.029 3152 Dihedral : 4.261 15.995 2496 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.22 % Allowed : 21.49 % Favored : 74.29 % 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: 2.52 (0.26), residues: 320 sheet: 0.54 (0.17), residues: 896 loop : -0.52 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS z 55 PHE 0.012 0.002 PHE v 77 TYR 0.019 0.001 TYR k 138 ARG 0.004 0.000 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 640) hydrogen bonds : angle 5.26913 ( 1680) covalent geometry : bond 0.00567 (17792) covalent geometry : angle 0.66284 (24016) *********************** 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 653 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 576 time to evaluate : 1.979 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 143 GLU cc_start: 0.9375 (tp30) cc_final: 0.9149 (tp30) REVERT: B 22 ASP cc_start: 0.9243 (t0) cc_final: 0.8785 (p0) REVERT: B 30 ASP cc_start: 0.8847 (t0) cc_final: 0.8589 (t0) REVERT: B 42 ASP cc_start: 0.9341 (t0) cc_final: 0.9082 (t0) REVERT: B 59 GLU cc_start: 0.9308 (tt0) cc_final: 0.8899 (tt0) REVERT: B 63 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8932 (tp-100) REVERT: B 111 GLN cc_start: 0.8336 (tt0) cc_final: 0.8081 (tt0) REVERT: D 139 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8358 (pp20) REVERT: D 140 LEU cc_start: 0.9646 (mp) cc_final: 0.9085 (mp) REVERT: E 22 ASP cc_start: 0.9254 (t0) cc_final: 0.8700 (p0) REVERT: E 42 ASP cc_start: 0.9308 (t0) cc_final: 0.8918 (t0) REVERT: E 59 GLU cc_start: 0.9180 (tt0) cc_final: 0.8821 (tt0) REVERT: E 63 GLN cc_start: 0.9348 (mm-40) cc_final: 0.8963 (tp-100) REVERT: E 111 GLN cc_start: 0.8370 (tt0) cc_final: 0.8068 (tt0) REVERT: H 22 ASP cc_start: 0.9103 (t0) cc_final: 0.8692 (p0) REVERT: H 50 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9164 (tm) REVERT: H 63 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8905 (tp-100) REVERT: H 111 GLN cc_start: 0.8379 (tt0) cc_final: 0.8025 (tt0) REVERT: H 122 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8936 (tp30) REVERT: J 139 GLU cc_start: 0.9537 (OUTLIER) cc_final: 0.9322 (mp0) REVERT: K 30 ASP cc_start: 0.8880 (t0) cc_final: 0.8617 (t0) REVERT: K 122 GLU cc_start: 0.9353 (tp30) cc_final: 0.8874 (tp30) REVERT: N 22 ASP cc_start: 0.9204 (t0) cc_final: 0.8806 (p0) REVERT: N 30 ASP cc_start: 0.8850 (t0) cc_final: 0.8593 (t0) REVERT: N 42 ASP cc_start: 0.9288 (t0) cc_final: 0.9054 (t0) REVERT: N 47 ASP cc_start: 0.9151 (m-30) cc_final: 0.8951 (m-30) REVERT: N 59 GLU cc_start: 0.9324 (tt0) cc_final: 0.8589 (mt-10) REVERT: N 63 GLN cc_start: 0.9177 (tp-100) cc_final: 0.8935 (tp-100) REVERT: N 111 GLN cc_start: 0.8370 (tt0) cc_final: 0.8138 (tt0) REVERT: P 146 LEU cc_start: 0.9038 (mm) cc_final: 0.8826 (mm) REVERT: Q 22 ASP cc_start: 0.9240 (t0) cc_final: 0.8734 (p0) REVERT: Q 30 ASP cc_start: 0.8956 (t0) cc_final: 0.8624 (t0) REVERT: Q 42 ASP cc_start: 0.9379 (t0) cc_final: 0.9004 (t0) REVERT: Q 59 GLU cc_start: 0.9210 (tt0) cc_final: 0.8574 (tt0) REVERT: Q 63 GLN cc_start: 0.9150 (tp-100) cc_final: 0.8916 (tp-100) REVERT: Q 111 GLN cc_start: 0.8462 (tt0) cc_final: 0.8128 (tt0) REVERT: S 139 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8653 (pp20) REVERT: T 22 ASP cc_start: 0.9105 (t0) cc_final: 0.8684 (p0) REVERT: T 50 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9105 (tm) REVERT: T 63 GLN cc_start: 0.9189 (tp-100) cc_final: 0.8964 (tp-100) REVERT: T 122 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8895 (tp30) REVERT: v 30 ASP cc_start: 0.8854 (t0) cc_final: 0.8626 (t0) REVERT: v 63 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8860 (tp-100) REVERT: v 92 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9504 (mm) REVERT: v 111 GLN cc_start: 0.8565 (tt0) cc_final: 0.8272 (tt0) REVERT: v 112 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.9124 (ttp) REVERT: V 136 THR cc_start: 0.9572 (t) cc_final: 0.9311 (t) REVERT: V 143 GLU cc_start: 0.9261 (tp30) cc_final: 0.8957 (tp30) REVERT: W 22 ASP cc_start: 0.9234 (t0) cc_final: 0.8791 (p0) REVERT: W 30 ASP cc_start: 0.8838 (t0) cc_final: 0.8590 (t0) REVERT: W 42 ASP cc_start: 0.9294 (t0) cc_final: 0.9068 (t0) REVERT: W 59 GLU cc_start: 0.9298 (tt0) cc_final: 0.8872 (tt0) REVERT: W 63 GLN cc_start: 0.9157 (tp-100) cc_final: 0.8886 (tp-100) REVERT: W 111 GLN cc_start: 0.8624 (tt0) cc_final: 0.8129 (tt0) REVERT: Y 136 THR cc_start: 0.9555 (t) cc_final: 0.9323 (t) REVERT: Z 22 ASP cc_start: 0.9228 (t0) cc_final: 0.8737 (p0) REVERT: Z 30 ASP cc_start: 0.8976 (t0) cc_final: 0.8625 (t0) REVERT: Z 42 ASP cc_start: 0.9327 (t0) cc_final: 0.8963 (t0) REVERT: Z 59 GLU cc_start: 0.9205 (tt0) cc_final: 0.8439 (tt0) REVERT: Z 63 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8867 (tp-100) REVERT: Z 111 GLN cc_start: 0.8584 (tt0) cc_final: 0.8093 (tt0) REVERT: c 22 ASP cc_start: 0.9113 (t0) cc_final: 0.8710 (p0) REVERT: c 50 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9176 (tm) REVERT: c 86 ILE cc_start: 0.9678 (pt) cc_final: 0.9446 (pp) REVERT: c 91 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8926 (mm-30) REVERT: e 135 LYS cc_start: 0.8242 (ttmt) cc_final: 0.8003 (tppp) REVERT: e 139 GLU cc_start: 0.9346 (mt-10) cc_final: 0.9001 (pt0) REVERT: e 143 GLU cc_start: 0.9246 (tp30) cc_final: 0.9027 (tp30) REVERT: f 30 ASP cc_start: 0.8891 (t0) cc_final: 0.8638 (t0) REVERT: f 63 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8334 (tm-30) REVERT: f 91 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8974 (mm-30) REVERT: f 112 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.9075 (ttp) REVERT: i 22 ASP cc_start: 0.9235 (t0) cc_final: 0.8818 (p0) REVERT: i 59 GLU cc_start: 0.9343 (tt0) cc_final: 0.8773 (mt-10) REVERT: i 63 GLN cc_start: 0.9149 (tp-100) cc_final: 0.8886 (tp-100) REVERT: i 111 GLN cc_start: 0.8373 (tt0) cc_final: 0.8128 (tt0) REVERT: k 143 GLU cc_start: 0.9327 (tp30) cc_final: 0.9064 (tp30) REVERT: k 147 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8855 (ttp80) REVERT: l 30 ASP cc_start: 0.8933 (t0) cc_final: 0.8571 (t0) REVERT: l 59 GLU cc_start: 0.9190 (tt0) cc_final: 0.8412 (tt0) REVERT: l 63 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8913 (tp-100) REVERT: l 111 GLN cc_start: 0.8563 (tt0) cc_final: 0.7513 (tm-30) REVERT: o 63 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8907 (tp-100) REVERT: o 111 GLN cc_start: 0.8366 (tt0) cc_final: 0.8100 (tt0) REVERT: o 112 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9109 (ttp) REVERT: z 22 ASP cc_start: 0.9126 (t0) cc_final: 0.8773 (p0) REVERT: z 30 ASP cc_start: 0.8878 (t0) cc_final: 0.8654 (t0) REVERT: z 63 GLN cc_start: 0.9144 (tp-100) cc_final: 0.8897 (tp-100) REVERT: z 92 LEU cc_start: 0.9735 (OUTLIER) cc_final: 0.9443 (mm) REVERT: z 112 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.9126 (ttp) REVERT: z 122 GLU cc_start: 0.9228 (tp30) cc_final: 0.8917 (tp30) outliers start: 77 outliers final: 29 residues processed: 601 average time/residue: 1.2868 time to fit residues: 867.1176 Evaluate side-chains 583 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 541 time to evaluate : 1.991 ------------------------------------------------------------------------------- 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 H residue 50 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain N residue 57 MET 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 120 MET Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 122 GLU Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 151 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 50 LEU Chi-restraints excluded: chain c residue 130 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 120 MET Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 112 MET Chi-restraints excluded: chain y residue 136 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: 9.9990 chunk 163 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 89 GLN v 89 GLN v 131 GLN ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 131 GLN o 89 GLN z 89 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 = 0.3050 r_free = 0.3050 target = 0.055748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.042224 restraints weight = 60266.378| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.92 r_work: 0.2513 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.4400 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= 0.183 Angle : 0.670 9.860 24016 Z= 0.349 Chirality : 0.049 0.268 2592 Planarity : 0.003 0.057 3152 Dihedral : 4.211 15.235 2496 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.11 % Allowed : 22.37 % Favored : 73.52 % 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: 0.47 (0.19), residues: 2080 helix: 2.26 (0.27), residues: 320 sheet: 0.42 (0.16), residues: 944 loop : -0.54 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS c 55 PHE 0.011 0.002 PHE l 77 TYR 0.021 0.001 TYR u 138 ARG 0.012 0.000 ARG b 147 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 640) hydrogen bonds : angle 5.12264 ( 1680) covalent geometry : bond 0.00425 (17792) covalent geometry : angle 0.66952 (24016) *********************** 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 668 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 593 time to evaluate : 1.891 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: A 143 GLU cc_start: 0.9346 (tp30) cc_final: 0.9141 (tp30) REVERT: B 22 ASP cc_start: 0.9255 (t0) cc_final: 0.8776 (p0) REVERT: B 30 ASP cc_start: 0.8895 (t0) cc_final: 0.8610 (t0) REVERT: B 42 ASP cc_start: 0.9332 (t0) cc_final: 0.9043 (t0) REVERT: B 45 GLN cc_start: 0.9046 (tp40) cc_final: 0.8332 (tm-30) REVERT: B 47 ASP cc_start: 0.9113 (m-30) cc_final: 0.8493 (m-30) REVERT: B 59 GLU cc_start: 0.9306 (tt0) cc_final: 0.8529 (mt-10) REVERT: B 63 GLN cc_start: 0.9161 (tp-100) cc_final: 0.8883 (tp-100) REVERT: B 111 GLN cc_start: 0.8313 (tt0) cc_final: 0.8076 (tt0) REVERT: D 139 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8381 (pp20) REVERT: D 140 LEU cc_start: 0.9645 (mp) cc_final: 0.9097 (mp) REVERT: D 146 LEU cc_start: 0.8975 (mm) cc_final: 0.8651 (mm) REVERT: E 22 ASP cc_start: 0.9229 (t0) cc_final: 0.8741 (p0) REVERT: E 42 ASP cc_start: 0.9317 (t0) cc_final: 0.8920 (t0) REVERT: E 59 GLU cc_start: 0.9117 (tt0) cc_final: 0.8504 (tt0) REVERT: E 63 GLN cc_start: 0.9313 (mm-40) cc_final: 0.9030 (tm-30) REVERT: E 111 GLN cc_start: 0.8418 (tt0) cc_final: 0.8093 (tt0) REVERT: H 50 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9130 (tm) REVERT: H 63 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8933 (tp-100) REVERT: H 111 GLN cc_start: 0.8372 (tt0) cc_final: 0.8013 (tt0) REVERT: J 139 GLU cc_start: 0.9527 (OUTLIER) cc_final: 0.9294 (mp0) REVERT: K 30 ASP cc_start: 0.8813 (t0) cc_final: 0.8583 (t0) REVERT: K 63 GLN cc_start: 0.9042 (tp-100) cc_final: 0.8836 (tp-100) REVERT: K 112 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9108 (ttp) REVERT: K 122 GLU cc_start: 0.9299 (tp30) cc_final: 0.8940 (tp30) REVERT: M 139 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8411 (pp20) REVERT: N 22 ASP cc_start: 0.9220 (t0) cc_final: 0.8798 (p0) REVERT: N 30 ASP cc_start: 0.8873 (t0) cc_final: 0.8599 (t0) REVERT: N 42 ASP cc_start: 0.9280 (t0) cc_final: 0.9011 (t0) REVERT: N 45 GLN cc_start: 0.8990 (tp40) cc_final: 0.8092 (tm-30) REVERT: N 47 ASP cc_start: 0.9098 (m-30) cc_final: 0.8548 (m-30) REVERT: N 59 GLU cc_start: 0.9311 (tt0) cc_final: 0.8725 (mt-10) REVERT: N 63 GLN cc_start: 0.9179 (tp-100) cc_final: 0.8902 (tp-100) REVERT: N 111 GLN cc_start: 0.8334 (tt0) cc_final: 0.8120 (tt0) REVERT: P 146 LEU cc_start: 0.8984 (mm) cc_final: 0.8739 (mm) REVERT: Q 22 ASP cc_start: 0.9229 (t0) cc_final: 0.8760 (p0) REVERT: Q 30 ASP cc_start: 0.8927 (t0) cc_final: 0.8591 (t0) REVERT: Q 42 ASP cc_start: 0.9380 (t0) cc_final: 0.9014 (t0) REVERT: Q 59 GLU cc_start: 0.9143 (tt0) cc_final: 0.8507 (tt0) REVERT: Q 63 GLN cc_start: 0.9130 (tp-100) cc_final: 0.8902 (tp-100) REVERT: Q 111 GLN cc_start: 0.8462 (tt0) cc_final: 0.8100 (tt0) REVERT: S 139 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8627 (pp20) REVERT: T 22 ASP cc_start: 0.9112 (t0) cc_final: 0.8693 (p0) REVERT: T 50 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9064 (tm) REVERT: T 63 GLN cc_start: 0.9174 (tp-100) cc_final: 0.8924 (tp-100) REVERT: v 22 ASP cc_start: 0.9106 (t0) cc_final: 0.8780 (p0) REVERT: v 30 ASP cc_start: 0.8841 (t0) cc_final: 0.8613 (t0) REVERT: v 42 ASP cc_start: 0.9360 (t0) cc_final: 0.9103 (t0) REVERT: v 63 GLN cc_start: 0.9107 (tp-100) cc_final: 0.8877 (tp-100) REVERT: v 111 GLN cc_start: 0.8526 (tt0) cc_final: 0.8207 (tt0) REVERT: v 112 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.9044 (ttp) REVERT: V 143 GLU cc_start: 0.9271 (tp30) cc_final: 0.8967 (tp30) REVERT: W 22 ASP cc_start: 0.9223 (t0) cc_final: 0.8801 (p0) REVERT: W 30 ASP cc_start: 0.8837 (t0) cc_final: 0.8573 (t0) REVERT: W 42 ASP cc_start: 0.9285 (t0) cc_final: 0.9071 (t0) REVERT: W 59 GLU cc_start: 0.9277 (tt0) cc_final: 0.8875 (tt0) REVERT: W 63 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8882 (tp-100) REVERT: W 111 GLN cc_start: 0.8571 (tt0) cc_final: 0.8149 (tt0) REVERT: W 122 GLU cc_start: 0.9388 (tp30) cc_final: 0.9187 (tp30) REVERT: Z 22 ASP cc_start: 0.9232 (t0) cc_final: 0.8750 (p0) REVERT: Z 30 ASP cc_start: 0.8950 (t0) cc_final: 0.8628 (t0) REVERT: Z 42 ASP cc_start: 0.9346 (t0) cc_final: 0.8986 (t0) REVERT: Z 59 GLU cc_start: 0.9100 (tt0) cc_final: 0.8397 (tt0) REVERT: Z 63 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8896 (tp-100) REVERT: Z 111 GLN cc_start: 0.8585 (tt0) cc_final: 0.8140 (tt0) REVERT: c 22 ASP cc_start: 0.9097 (t0) cc_final: 0.8771 (p0) REVERT: c 50 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9118 (tm) REVERT: c 63 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8949 (tp-100) REVERT: c 86 ILE cc_start: 0.9657 (pt) cc_final: 0.9413 (pp) REVERT: c 91 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8920 (mm-30) REVERT: c 111 GLN cc_start: 0.8327 (tt0) cc_final: 0.8118 (tt0) REVERT: e 135 LYS cc_start: 0.8358 (ttmt) cc_final: 0.7912 (tppp) REVERT: e 143 GLU cc_start: 0.9306 (tp30) cc_final: 0.9097 (tp30) REVERT: f 30 ASP cc_start: 0.8896 (t0) cc_final: 0.8626 (t0) REVERT: f 63 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8271 (tm-30) REVERT: f 65 LEU cc_start: 0.9571 (mp) cc_final: 0.9370 (mp) REVERT: f 112 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9058 (ttp) REVERT: i 22 ASP cc_start: 0.9179 (t0) cc_final: 0.8847 (p0) REVERT: i 45 GLN cc_start: 0.9038 (tp40) cc_final: 0.8167 (tm-30) REVERT: i 47 ASP cc_start: 0.9136 (m-30) cc_final: 0.8535 (m-30) REVERT: i 86 ILE cc_start: 0.9722 (pt) cc_final: 0.9491 (pp) REVERT: i 111 GLN cc_start: 0.8345 (tt0) cc_final: 0.8113 (tt0) REVERT: k 143 GLU cc_start: 0.9357 (tp30) cc_final: 0.9103 (tp30) REVERT: k 147 ARG cc_start: 0.9373 (OUTLIER) cc_final: 0.8893 (ttp80) REVERT: l 30 ASP cc_start: 0.8976 (t0) cc_final: 0.8621 (t0) REVERT: l 59 GLU cc_start: 0.9110 (tt0) cc_final: 0.8335 (tt0) REVERT: l 63 GLN cc_start: 0.9143 (tp-100) cc_final: 0.8890 (tp-100) REVERT: l 111 GLN cc_start: 0.8583 (tt0) cc_final: 0.8122 (tt0) REVERT: n 135 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8609 (mtmm) REVERT: o 22 ASP cc_start: 0.9106 (t0) cc_final: 0.8709 (p0) REVERT: o 63 GLN cc_start: 0.9179 (tp-100) cc_final: 0.8888 (tp-100) REVERT: o 111 GLN cc_start: 0.8411 (tt0) cc_final: 0.8136 (tt0) REVERT: z 22 ASP cc_start: 0.9122 (t0) cc_final: 0.8780 (p0) REVERT: z 30 ASP cc_start: 0.8834 (t0) cc_final: 0.8593 (t0) REVERT: z 42 ASP cc_start: 0.9343 (t0) cc_final: 0.9087 (t0) REVERT: z 92 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9488 (mm) REVERT: z 112 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.9091 (ttp) REVERT: z 122 GLU cc_start: 0.9237 (tp30) cc_final: 0.8756 (tp30) outliers start: 75 outliers final: 28 residues processed: 614 average time/residue: 1.2600 time to fit residues: 866.6147 Evaluate side-chains 582 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 542 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 56 ILE 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 50 LEU Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 92 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 50 LEU Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain f residue 92 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 114 ASN Chi-restraints excluded: chain l residue 120 MET Chi-restraints excluded: chain n residue 135 LYS 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: 1.9990 chunk 36 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 89 GLN K 131 GLN v 89 GLN f 89 GLN z 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.055457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.041675 restraints weight = 60084.368| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 3.94 r_work: 0.2501 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17792 Z= 0.227 Angle : 0.733 11.076 24016 Z= 0.381 Chirality : 0.050 0.288 2592 Planarity : 0.003 0.032 3152 Dihedral : 4.385 17.642 2496 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 4.17 % Allowed : 24.40 % Favored : 71.44 % 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: 0.36 (0.18), residues: 2080 helix: 2.03 (0.27), residues: 320 sheet: 0.39 (0.16), residues: 944 loop : -0.59 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS W 55 PHE 0.012 0.002 PHE K 77 TYR 0.013 0.001 TYR z 29 ARG 0.008 0.000 ARG b 147 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 640) hydrogen bonds : angle 5.21253 ( 1680) covalent geometry : bond 0.00532 (17792) covalent geometry : angle 0.73270 (24016) *********************** 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 641 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 565 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ASP cc_start: 0.9266 (t0) cc_final: 0.8785 (p0) REVERT: B 30 ASP cc_start: 0.8901 (t0) cc_final: 0.8619 (t0) REVERT: B 42 ASP cc_start: 0.9328 (t0) cc_final: 0.9024 (t0) REVERT: B 59 GLU cc_start: 0.9294 (tt0) cc_final: 0.8510 (mt-10) REVERT: B 60 GLU cc_start: 0.8975 (mp0) cc_final: 0.8639 (mm-30) REVERT: B 63 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8973 (tp-100) REVERT: B 111 GLN cc_start: 0.8345 (tt0) cc_final: 0.8076 (tt0) REVERT: D 139 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8333 (pp20) REVERT: D 140 LEU cc_start: 0.9654 (mp) cc_final: 0.9104 (mp) REVERT: D 146 LEU cc_start: 0.9020 (mm) cc_final: 0.8733 (mm) REVERT: E 22 ASP cc_start: 0.9240 (t0) cc_final: 0.8715 (p0) REVERT: E 42 ASP cc_start: 0.9341 (t0) cc_final: 0.8997 (t0) REVERT: E 59 GLU cc_start: 0.9116 (tt0) cc_final: 0.8428 (tt0) REVERT: E 63 GLN cc_start: 0.9333 (mm-40) cc_final: 0.8970 (tp-100) REVERT: E 111 GLN cc_start: 0.8437 (tt0) cc_final: 0.8124 (tt0) REVERT: H 22 ASP cc_start: 0.9113 (t0) cc_final: 0.8684 (p0) REVERT: H 50 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9154 (tm) REVERT: H 63 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8932 (tp-100) REVERT: H 111 GLN cc_start: 0.8381 (tt0) cc_final: 0.8031 (tt0) REVERT: J 139 GLU cc_start: 0.9539 (OUTLIER) cc_final: 0.9327 (mp0) REVERT: K 22 ASP cc_start: 0.9152 (t0) cc_final: 0.8793 (p0) REVERT: K 30 ASP cc_start: 0.8849 (t0) cc_final: 0.8623 (t0) REVERT: K 42 ASP cc_start: 0.9344 (t0) cc_final: 0.9085 (t0) REVERT: K 63 GLN cc_start: 0.9118 (tp-100) cc_final: 0.8874 (tp-100) REVERT: K 112 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.9116 (ttp) REVERT: N 22 ASP cc_start: 0.9238 (t0) cc_final: 0.8785 (p0) REVERT: N 30 ASP cc_start: 0.8904 (t0) cc_final: 0.8642 (t0) REVERT: N 42 ASP cc_start: 0.9291 (t0) cc_final: 0.9035 (t0) REVERT: N 47 ASP cc_start: 0.9105 (m-30) cc_final: 0.8903 (m-30) REVERT: N 59 GLU cc_start: 0.9335 (tt0) cc_final: 0.8766 (tt0) REVERT: N 60 GLU cc_start: 0.8929 (mp0) cc_final: 0.8595 (mm-30) REVERT: N 63 GLN cc_start: 0.9215 (tp-100) cc_final: 0.9009 (tp-100) REVERT: N 86 ILE cc_start: 0.9760 (pt) cc_final: 0.9548 (pp) REVERT: N 111 GLN cc_start: 0.8292 (tt0) cc_final: 0.8069 (tt0) REVERT: P 146 LEU cc_start: 0.9018 (mm) cc_final: 0.8817 (mm) REVERT: Q 22 ASP cc_start: 0.9244 (t0) cc_final: 0.8712 (p0) REVERT: Q 30 ASP cc_start: 0.8930 (t0) cc_final: 0.8609 (t0) REVERT: Q 42 ASP cc_start: 0.9373 (t0) cc_final: 0.9036 (t0) REVERT: Q 59 GLU cc_start: 0.9145 (tt0) cc_final: 0.8451 (tt0) REVERT: Q 63 GLN cc_start: 0.9168 (tp-100) cc_final: 0.8929 (tp-100) REVERT: Q 111 GLN cc_start: 0.8501 (tt0) cc_final: 0.8128 (tt0) REVERT: S 139 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8599 (pp20) REVERT: T 22 ASP cc_start: 0.9129 (t0) cc_final: 0.8694 (p0) REVERT: T 50 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9158 (tm) REVERT: T 59 GLU cc_start: 0.9188 (tt0) cc_final: 0.8523 (tt0) REVERT: T 63 GLN cc_start: 0.9187 (tp-100) cc_final: 0.8981 (tp-100) REVERT: v 22 ASP cc_start: 0.9141 (t0) cc_final: 0.8798 (p0) REVERT: v 30 ASP cc_start: 0.8866 (t0) cc_final: 0.8656 (t0) REVERT: v 42 ASP cc_start: 0.9363 (t0) cc_final: 0.9093 (t0) REVERT: v 111 GLN cc_start: 0.8521 (tt0) cc_final: 0.8210 (tt0) REVERT: v 112 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.9079 (ttp) REVERT: V 143 GLU cc_start: 0.9306 (tp30) cc_final: 0.8989 (tp30) REVERT: W 22 ASP cc_start: 0.9259 (t0) cc_final: 0.8797 (p0) REVERT: W 30 ASP cc_start: 0.8888 (t0) cc_final: 0.8642 (t0) REVERT: W 42 ASP cc_start: 0.9296 (t0) cc_final: 0.9040 (t0) REVERT: W 60 GLU cc_start: 0.8954 (mp0) cc_final: 0.8705 (mm-30) REVERT: W 63 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8926 (tp-100) REVERT: W 111 GLN cc_start: 0.8560 (tt0) cc_final: 0.8174 (tt0) REVERT: Z 22 ASP cc_start: 0.9252 (t0) cc_final: 0.8793 (p0) REVERT: Z 30 ASP cc_start: 0.8944 (t0) cc_final: 0.8619 (t0) REVERT: Z 42 ASP cc_start: 0.9354 (t0) cc_final: 0.9015 (t0) REVERT: Z 59 GLU cc_start: 0.9084 (tt0) cc_final: 0.8330 (tt0) REVERT: Z 63 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8939 (tp-100) REVERT: Z 111 GLN cc_start: 0.8607 (tt0) cc_final: 0.8165 (tt0) REVERT: c 22 ASP cc_start: 0.9136 (t0) cc_final: 0.8709 (p0) REVERT: c 63 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8948 (tp-100) REVERT: c 86 ILE cc_start: 0.9681 (pt) cc_final: 0.9443 (pp) REVERT: c 91 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8919 (mm-30) REVERT: c 111 GLN cc_start: 0.8360 (tt0) cc_final: 0.8155 (tt0) REVERT: f 22 ASP cc_start: 0.9107 (t0) cc_final: 0.8740 (p0) REVERT: f 30 ASP cc_start: 0.8848 (t0) cc_final: 0.8633 (t0) REVERT: f 42 ASP cc_start: 0.9343 (t0) cc_final: 0.9050 (t0) REVERT: f 63 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8368 (tm-30) REVERT: f 112 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9040 (ttp) REVERT: i 22 ASP cc_start: 0.9171 (t0) cc_final: 0.8815 (p0) REVERT: i 42 ASP cc_start: 0.9159 (t0) cc_final: 0.8816 (t0) REVERT: i 45 GLN cc_start: 0.9046 (tp40) cc_final: 0.8183 (tm-30) REVERT: i 47 ASP cc_start: 0.9131 (m-30) cc_final: 0.8558 (m-30) REVERT: i 59 GLU cc_start: 0.9334 (tt0) cc_final: 0.8778 (mt-10) REVERT: i 86 ILE cc_start: 0.9739 (pt) cc_final: 0.9512 (pp) REVERT: i 111 GLN cc_start: 0.8343 (tt0) cc_final: 0.8081 (tt0) REVERT: k 139 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8712 (tm-30) REVERT: k 143 GLU cc_start: 0.9367 (tp30) cc_final: 0.9076 (tp30) REVERT: k 147 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8867 (ttp80) REVERT: l 30 ASP cc_start: 0.8991 (t0) cc_final: 0.8654 (t0) REVERT: l 59 GLU cc_start: 0.9089 (tt0) cc_final: 0.8213 (tt0) REVERT: l 63 GLN cc_start: 0.9183 (tp-100) cc_final: 0.8964 (tp-100) REVERT: l 111 GLN cc_start: 0.8596 (tt0) cc_final: 0.7659 (tm-30) REVERT: n 139 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8465 (pp20) REVERT: n 142 ARG cc_start: 0.9242 (ttm-80) cc_final: 0.9037 (ttm-80) REVERT: o 22 ASP cc_start: 0.9120 (t0) cc_final: 0.8696 (p0) REVERT: o 63 GLN cc_start: 0.9200 (tp-100) cc_final: 0.8935 (tp-100) REVERT: o 111 GLN cc_start: 0.8405 (tt0) cc_final: 0.8096 (tt0) REVERT: o 112 MET cc_start: 0.9388 (tpp) cc_final: 0.9133 (ttp) REVERT: z 22 ASP cc_start: 0.9134 (t0) cc_final: 0.8788 (p0) REVERT: z 30 ASP cc_start: 0.8860 (t0) cc_final: 0.8624 (t0) REVERT: z 42 ASP cc_start: 0.9365 (t0) cc_final: 0.9114 (t0) REVERT: z 92 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9485 (mm) REVERT: z 112 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.9086 (ttp) REVERT: z 122 GLU cc_start: 0.9207 (tp30) cc_final: 0.8930 (tp30) outliers start: 76 outliers final: 34 residues processed: 595 average time/residue: 1.1429 time to fit residues: 764.1597 Evaluate side-chains 581 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 537 time to evaluate : 1.890 ------------------------------------------------------------------------------- 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 114 ASN 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 H residue 50 LEU Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain M residue 151 THR 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 114 ASN Chi-restraints excluded: chain Q residue 120 MET Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain W residue 50 LEU 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 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 140 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 120 MET Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 92 LEU Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 80 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 121 optimal weight: 0.0010 chunk 191 optimal weight: 2.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 89 GLN T 45 GLN v 89 GLN Z 45 GLN f 89 GLN l 45 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.056734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.043204 restraints weight = 60019.773| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.95 r_work: 0.2547 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17792 Z= 0.164 Angle : 0.759 12.165 24016 Z= 0.393 Chirality : 0.052 0.342 2592 Planarity : 0.003 0.030 3152 Dihedral : 4.421 19.467 2496 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 3.23 % Allowed : 27.69 % Favored : 69.08 % 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: 0.39 (0.19), residues: 2080 helix: 2.01 (0.28), residues: 320 sheet: 0.38 (0.16), residues: 944 loop : -0.51 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS N 55 PHE 0.011 0.001 PHE E 77 TYR 0.015 0.001 TYR G 138 ARG 0.007 0.000 ARG b 147 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 640) hydrogen bonds : angle 5.05377 ( 1680) covalent geometry : bond 0.00397 (17792) covalent geometry : angle 0.75852 (24016) *********************** 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 648 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 589 time to evaluate : 2.117 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: 0.9583 (mm) cc_final: 0.9019 (mm) REVERT: B 22 ASP cc_start: 0.9240 (t0) cc_final: 0.8795 (p0) REVERT: B 30 ASP cc_start: 0.8926 (t0) cc_final: 0.8657 (t0) REVERT: B 42 ASP cc_start: 0.9370 (t0) cc_final: 0.9043 (t0) REVERT: B 45 GLN cc_start: 0.9015 (tp40) cc_final: 0.8281 (tm-30) REVERT: B 59 GLU cc_start: 0.9305 (tt0) cc_final: 0.8556 (mt-10) REVERT: B 63 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8904 (tp-100) REVERT: B 111 GLN cc_start: 0.8341 (tt0) cc_final: 0.8095 (tt0) REVERT: D 139 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8338 (pp20) REVERT: D 140 LEU cc_start: 0.9656 (mp) cc_final: 0.9128 (mp) REVERT: D 146 LEU cc_start: 0.8989 (mm) cc_final: 0.8682 (mm) REVERT: E 22 ASP cc_start: 0.9242 (t0) cc_final: 0.8800 (p0) REVERT: E 42 ASP cc_start: 0.9333 (t0) cc_final: 0.8989 (t0) REVERT: E 59 GLU cc_start: 0.9080 (tt0) cc_final: 0.8822 (tp30) REVERT: E 63 GLN cc_start: 0.9329 (mm-40) cc_final: 0.8972 (tp-100) REVERT: E 86 ILE cc_start: 0.9736 (pt) cc_final: 0.9521 (pp) REVERT: E 111 GLN cc_start: 0.8464 (tt0) cc_final: 0.8154 (tt0) REVERT: G 139 GLU cc_start: 0.9261 (mp0) cc_final: 0.9047 (mp0) REVERT: H 22 ASP cc_start: 0.9098 (t0) cc_final: 0.8731 (p0) REVERT: H 45 GLN cc_start: 0.8851 (tp40) cc_final: 0.8183 (tm-30) REVERT: H 47 ASP cc_start: 0.8985 (m-30) cc_final: 0.8388 (m-30) REVERT: H 50 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9079 (tm) REVERT: H 63 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8929 (tp-100) REVERT: H 111 GLN cc_start: 0.8360 (tt0) cc_final: 0.8115 (tt0) REVERT: K 22 ASP cc_start: 0.9107 (t0) cc_final: 0.8808 (p0) REVERT: K 30 ASP cc_start: 0.8854 (t0) cc_final: 0.8613 (t0) REVERT: K 42 ASP cc_start: 0.9335 (t0) cc_final: 0.9078 (t0) REVERT: N 22 ASP cc_start: 0.9218 (t0) cc_final: 0.8794 (p0) REVERT: N 30 ASP cc_start: 0.8932 (t0) cc_final: 0.8690 (t0) REVERT: N 42 ASP cc_start: 0.9293 (t0) cc_final: 0.9024 (t0) REVERT: N 45 GLN cc_start: 0.8908 (tp40) cc_final: 0.8072 (tm-30) REVERT: N 47 ASP cc_start: 0.9070 (m-30) cc_final: 0.8586 (m-30) REVERT: N 60 GLU cc_start: 0.8988 (mp0) cc_final: 0.8730 (mm-30) REVERT: N 63 GLN cc_start: 0.9187 (tp-100) cc_final: 0.8889 (tp-100) REVERT: Q 22 ASP cc_start: 0.9241 (t0) cc_final: 0.8796 (p0) REVERT: Q 30 ASP cc_start: 0.8940 (t0) cc_final: 0.8636 (t0) REVERT: Q 42 ASP cc_start: 0.9373 (t0) cc_final: 0.9019 (t0) REVERT: Q 59 GLU cc_start: 0.9059 (tt0) cc_final: 0.8400 (tt0) REVERT: Q 63 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8922 (tp-100) REVERT: Q 111 GLN cc_start: 0.8504 (tt0) cc_final: 0.8160 (tt0) REVERT: S 139 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8636 (pp20) REVERT: T 22 ASP cc_start: 0.9109 (t0) cc_final: 0.8742 (p0) REVERT: T 50 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9060 (tm) REVERT: T 63 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8956 (tp-100) REVERT: v 22 ASP cc_start: 0.9116 (t0) cc_final: 0.8814 (p0) REVERT: v 30 ASP cc_start: 0.8752 (t0) cc_final: 0.8515 (t0) REVERT: v 42 ASP cc_start: 0.9361 (t0) cc_final: 0.9101 (t0) REVERT: v 111 GLN cc_start: 0.8554 (tt0) cc_final: 0.8258 (tt0) REVERT: V 143 GLU cc_start: 0.9303 (tp30) cc_final: 0.8992 (tp30) REVERT: W 22 ASP cc_start: 0.9247 (t0) cc_final: 0.8807 (p0) REVERT: W 30 ASP cc_start: 0.8907 (t0) cc_final: 0.8680 (t0) REVERT: W 42 ASP cc_start: 0.9289 (t0) cc_final: 0.9037 (t0) REVERT: W 63 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8879 (tp-100) REVERT: W 111 GLN cc_start: 0.8509 (tt0) cc_final: 0.8159 (tt0) REVERT: Z 22 ASP cc_start: 0.9229 (t0) cc_final: 0.8812 (p0) REVERT: Z 30 ASP cc_start: 0.8960 (t0) cc_final: 0.8657 (t0) REVERT: Z 42 ASP cc_start: 0.9353 (t0) cc_final: 0.9027 (t0) REVERT: Z 59 GLU cc_start: 0.9038 (tt0) cc_final: 0.8182 (tt0) REVERT: Z 60 GLU cc_start: 0.9033 (mp0) cc_final: 0.8698 (mm-30) REVERT: Z 111 GLN cc_start: 0.8616 (tt0) cc_final: 0.8220 (tt0) REVERT: c 22 ASP cc_start: 0.9123 (t0) cc_final: 0.8774 (p0) REVERT: c 45 GLN cc_start: 0.8898 (tp40) cc_final: 0.8190 (tm-30) REVERT: c 47 ASP cc_start: 0.8801 (m-30) cc_final: 0.8249 (m-30) REVERT: c 50 LEU cc_start: 0.9175 (tm) cc_final: 0.8701 (tm) REVERT: c 86 ILE cc_start: 0.9676 (pt) cc_final: 0.9431 (pp) REVERT: f 22 ASP cc_start: 0.9089 (t0) cc_final: 0.8800 (p0) REVERT: f 30 ASP cc_start: 0.8853 (t0) cc_final: 0.8637 (t0) REVERT: f 42 ASP cc_start: 0.9334 (t0) cc_final: 0.9085 (t0) REVERT: f 63 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8313 (tm-30) REVERT: f 112 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8992 (ttp) REVERT: i 22 ASP cc_start: 0.9139 (t0) cc_final: 0.8843 (p0) REVERT: i 42 ASP cc_start: 0.9152 (t0) cc_final: 0.8810 (t0) REVERT: i 45 GLN cc_start: 0.8926 (tp40) cc_final: 0.8100 (tm-30) REVERT: i 47 ASP cc_start: 0.9113 (m-30) cc_final: 0.8612 (m-30) REVERT: i 59 GLU cc_start: 0.9281 (tt0) cc_final: 0.8801 (mt-10) REVERT: i 60 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8841 (mm-30) REVERT: i 86 ILE cc_start: 0.9732 (pt) cc_final: 0.9494 (pp) REVERT: i 111 GLN cc_start: 0.8339 (tt0) cc_final: 0.8101 (tt0) REVERT: k 139 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8684 (tm-30) REVERT: k 143 GLU cc_start: 0.9345 (tp30) cc_final: 0.9074 (tp30) REVERT: k 147 ARG cc_start: 0.9370 (OUTLIER) cc_final: 0.8839 (ttp80) REVERT: l 30 ASP cc_start: 0.8969 (t0) cc_final: 0.8638 (t0) REVERT: l 59 GLU cc_start: 0.8934 (tt0) cc_final: 0.8214 (tt0) REVERT: l 63 GLN cc_start: 0.9168 (tp-100) cc_final: 0.8958 (tp-100) REVERT: l 111 GLN cc_start: 0.8586 (tt0) cc_final: 0.8208 (tt0) REVERT: n 143 GLU cc_start: 0.9166 (tp30) cc_final: 0.8885 (tp30) REVERT: n 147 ARG cc_start: 0.9345 (ttm110) cc_final: 0.8987 (ttm110) REVERT: o 22 ASP cc_start: 0.9120 (t0) cc_final: 0.8776 (p0) REVERT: o 45 GLN cc_start: 0.8848 (tp40) cc_final: 0.8133 (tm-30) REVERT: o 47 ASP cc_start: 0.8994 (m-30) cc_final: 0.8491 (m-30) REVERT: o 63 GLN cc_start: 0.9209 (tp-100) cc_final: 0.8978 (tp-100) REVERT: o 112 MET cc_start: 0.9364 (tpp) cc_final: 0.9052 (ttp) REVERT: z 22 ASP cc_start: 0.9127 (t0) cc_final: 0.8803 (p0) REVERT: z 30 ASP cc_start: 0.8814 (t0) cc_final: 0.8574 (t0) REVERT: z 42 ASP cc_start: 0.9347 (t0) cc_final: 0.9106 (t0) REVERT: z 63 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8745 (tp-100) REVERT: z 92 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9514 (mm) REVERT: z 112 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.9053 (ttp) outliers start: 59 outliers final: 19 residues processed: 615 average time/residue: 1.2977 time to fit residues: 898.2167 Evaluate side-chains 577 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 551 time to evaluate : 3.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 63 GLN 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 P residue 136 THR Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain b residue 136 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 h residue 151 THR 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 n residue 150 LEU Chi-restraints excluded: chain y residue 140 LEU 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: 0.2980 chunk 176 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 89 GLN o 45 GLN z 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.057145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.043532 restraints weight = 60213.125| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.99 r_work: 0.2562 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 17792 Z= 0.167 Angle : 0.812 11.883 24016 Z= 0.418 Chirality : 0.054 0.315 2592 Planarity : 0.003 0.033 3152 Dihedral : 4.489 22.416 2496 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.48 % Allowed : 30.59 % 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: 0.33 (0.19), residues: 2080 helix: 1.80 (0.29), residues: 320 sheet: 0.37 (0.16), residues: 944 loop : -0.50 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS N 55 PHE 0.011 0.001 PHE f 77 TYR 0.010 0.001 TYR v 29 ARG 0.006 0.000 ARG b 147 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 640) hydrogen bonds : angle 5.02826 ( 1680) covalent geometry : bond 0.00412 (17792) covalent geometry : angle 0.81151 (24016) *********************** 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 608 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 581 time to evaluate : 4.502 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: 0.9218 (t0) cc_final: 0.8802 (p0) REVERT: B 30 ASP cc_start: 0.8969 (t0) cc_final: 0.8706 (t0) REVERT: B 42 ASP cc_start: 0.9376 (t0) cc_final: 0.9050 (t0) REVERT: B 45 GLN cc_start: 0.8964 (tp40) cc_final: 0.8232 (tm-30) REVERT: B 47 ASP cc_start: 0.9064 (m-30) cc_final: 0.8497 (m-30) REVERT: B 59 GLU cc_start: 0.9286 (tt0) cc_final: 0.8650 (mt-10) REVERT: B 63 GLN cc_start: 0.9168 (tp-100) cc_final: 0.8900 (tp-100) REVERT: B 111 GLN cc_start: 0.8303 (tt0) cc_final: 0.8051 (tt0) REVERT: D 139 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8335 (pp20) REVERT: D 140 LEU cc_start: 0.9659 (mp) cc_final: 0.9141 (mp) REVERT: D 142 ARG cc_start: 0.9210 (ttm-80) cc_final: 0.8909 (ttm-80) REVERT: D 146 LEU cc_start: 0.8968 (mm) cc_final: 0.8686 (mm) REVERT: E 22 ASP cc_start: 0.9237 (t0) cc_final: 0.8819 (p0) REVERT: E 42 ASP cc_start: 0.9343 (t0) cc_final: 0.9025 (t0) REVERT: E 59 GLU cc_start: 0.9005 (tt0) cc_final: 0.8241 (tt0) REVERT: E 63 GLN cc_start: 0.9366 (mm-40) cc_final: 0.9051 (tp-100) REVERT: E 86 ILE cc_start: 0.9721 (pt) cc_final: 0.9510 (pp) REVERT: E 111 GLN cc_start: 0.8458 (tt0) cc_final: 0.8146 (tt0) REVERT: H 22 ASP cc_start: 0.9098 (t0) cc_final: 0.8748 (p0) REVERT: H 45 GLN cc_start: 0.8771 (tp40) cc_final: 0.8128 (tm-30) REVERT: H 47 ASP cc_start: 0.8988 (m-30) cc_final: 0.8363 (m-30) REVERT: H 50 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9076 (tm) REVERT: H 63 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8931 (tp-100) REVERT: H 111 GLN cc_start: 0.8381 (tt0) cc_final: 0.8136 (tt0) REVERT: K 22 ASP cc_start: 0.9098 (t0) cc_final: 0.8826 (p0) REVERT: K 30 ASP cc_start: 0.8880 (t0) cc_final: 0.8636 (t0) REVERT: K 42 ASP cc_start: 0.9336 (t0) cc_final: 0.9072 (t0) REVERT: N 22 ASP cc_start: 0.9202 (t0) cc_final: 0.8795 (p0) REVERT: N 30 ASP cc_start: 0.8957 (t0) cc_final: 0.8713 (t0) REVERT: N 42 ASP cc_start: 0.9265 (t0) cc_final: 0.8992 (t0) REVERT: N 45 GLN cc_start: 0.8846 (tp40) cc_final: 0.7983 (tm-30) REVERT: N 47 ASP cc_start: 0.9046 (m-30) cc_final: 0.8532 (m-30) REVERT: N 60 GLU cc_start: 0.8999 (mp0) cc_final: 0.8731 (mm-30) REVERT: N 63 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8874 (tp-100) REVERT: P 143 GLU cc_start: 0.9177 (tp30) cc_final: 0.8951 (tm-30) REVERT: P 147 ARG cc_start: 0.9321 (ttp80) cc_final: 0.9095 (ttp-110) REVERT: Q 22 ASP cc_start: 0.9251 (t0) cc_final: 0.8821 (p0) REVERT: Q 30 ASP cc_start: 0.8956 (t0) cc_final: 0.8663 (t0) REVERT: Q 42 ASP cc_start: 0.9382 (t0) cc_final: 0.9063 (t0) REVERT: Q 45 GLN cc_start: 0.8835 (tp40) cc_final: 0.8414 (tm-30) REVERT: Q 59 GLU cc_start: 0.8932 (tt0) cc_final: 0.8490 (tt0) REVERT: Q 111 GLN cc_start: 0.8508 (tt0) cc_final: 0.8210 (tt0) REVERT: S 139 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8642 (pp20) REVERT: T 22 ASP cc_start: 0.9120 (t0) cc_final: 0.8752 (p0) REVERT: T 50 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9045 (tm) REVERT: v 22 ASP cc_start: 0.9106 (t0) cc_final: 0.8838 (p0) REVERT: v 30 ASP cc_start: 0.8779 (t0) cc_final: 0.8540 (t0) REVERT: v 42 ASP cc_start: 0.9360 (t0) cc_final: 0.9116 (t0) REVERT: v 57 MET cc_start: 0.8861 (mmt) cc_final: 0.8636 (mmm) REVERT: v 86 ILE cc_start: 0.9734 (pt) cc_final: 0.9507 (pp) REVERT: v 111 GLN cc_start: 0.8571 (tt0) cc_final: 0.8272 (tt0) REVERT: V 143 GLU cc_start: 0.9280 (tp30) cc_final: 0.8962 (tp30) REVERT: W 22 ASP cc_start: 0.9247 (t0) cc_final: 0.8817 (p0) REVERT: W 30 ASP cc_start: 0.8945 (t0) cc_final: 0.8707 (t0) REVERT: W 42 ASP cc_start: 0.9272 (t0) cc_final: 0.9015 (t0) REVERT: W 59 GLU cc_start: 0.9275 (tt0) cc_final: 0.8676 (mt-10) REVERT: W 63 GLN cc_start: 0.9124 (tp-100) cc_final: 0.8878 (tp-100) REVERT: W 111 GLN cc_start: 0.8508 (tt0) cc_final: 0.8169 (tt0) REVERT: Z 22 ASP cc_start: 0.9245 (t0) cc_final: 0.8856 (p0) REVERT: Z 30 ASP cc_start: 0.8980 (t0) cc_final: 0.8692 (t0) REVERT: Z 42 ASP cc_start: 0.9352 (t0) cc_final: 0.9093 (t0) REVERT: Z 59 GLU cc_start: 0.9043 (tt0) cc_final: 0.8273 (tt0) REVERT: Z 111 GLN cc_start: 0.8562 (tt0) cc_final: 0.8215 (tt0) REVERT: c 22 ASP cc_start: 0.9114 (t0) cc_final: 0.8799 (p0) REVERT: c 45 GLN cc_start: 0.8822 (tp40) cc_final: 0.8341 (tp-100) REVERT: c 86 ILE cc_start: 0.9687 (pt) cc_final: 0.9450 (pp) REVERT: f 22 ASP cc_start: 0.9080 (t0) cc_final: 0.8817 (p0) REVERT: f 30 ASP cc_start: 0.8828 (t0) cc_final: 0.8597 (t0) REVERT: f 42 ASP cc_start: 0.9340 (t0) cc_final: 0.9108 (t0) REVERT: f 60 GLU cc_start: 0.8858 (mp0) cc_final: 0.7815 (mp0) REVERT: f 63 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8357 (tm-30) REVERT: i 22 ASP cc_start: 0.9131 (t0) cc_final: 0.8845 (p0) REVERT: i 42 ASP cc_start: 0.9153 (t0) cc_final: 0.8817 (t0) REVERT: i 45 GLN cc_start: 0.8857 (tp40) cc_final: 0.8008 (tm-30) REVERT: i 47 ASP cc_start: 0.9088 (m-30) cc_final: 0.8579 (m-30) REVERT: i 86 ILE cc_start: 0.9738 (pt) cc_final: 0.9501 (pp) REVERT: i 111 GLN cc_start: 0.8311 (tt0) cc_final: 0.8084 (tt0) REVERT: k 139 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8720 (tm-30) REVERT: k 143 GLU cc_start: 0.9348 (tp30) cc_final: 0.9049 (tp30) REVERT: l 30 ASP cc_start: 0.9011 (t0) cc_final: 0.8693 (t0) REVERT: l 59 GLU cc_start: 0.8806 (tt0) cc_final: 0.8218 (tt0) REVERT: l 63 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8962 (tp-100) REVERT: l 111 GLN cc_start: 0.8591 (tt0) cc_final: 0.8261 (tt0) REVERT: o 22 ASP cc_start: 0.9106 (t0) cc_final: 0.8905 (p0) REVERT: o 63 GLN cc_start: 0.9240 (tp-100) cc_final: 0.9014 (tp-100) REVERT: o 112 MET cc_start: 0.9380 (tpp) cc_final: 0.9084 (ttp) REVERT: y 138 TYR cc_start: 0.9374 (t80) cc_final: 0.9165 (t80) REVERT: y 139 GLU cc_start: 0.9342 (mp0) cc_final: 0.9137 (pt0) REVERT: z 22 ASP cc_start: 0.9103 (t0) cc_final: 0.8808 (p0) REVERT: z 30 ASP cc_start: 0.8830 (t0) cc_final: 0.8569 (t0) REVERT: z 42 ASP cc_start: 0.9348 (t0) cc_final: 0.9127 (t0) REVERT: z 92 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9505 (mm) outliers start: 27 outliers final: 20 residues processed: 590 average time/residue: 1.2202 time to fit residues: 809.0733 Evaluate side-chains 573 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 549 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain u residue 140 LEU 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 Y residue 150 LEU Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain e residue 136 THR 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 z residue 92 LEU 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: 4.9990 chunk 82 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 161 optimal weight: 0.0270 chunk 112 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 overall best weight: 1.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.043550 restraints weight = 60549.289| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.98 r_work: 0.2568 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 17792 Z= 0.181 Angle : 0.863 13.072 24016 Z= 0.441 Chirality : 0.056 0.363 2592 Planarity : 0.004 0.061 3152 Dihedral : 4.614 23.435 2496 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.10 % Allowed : 32.02 % Favored : 66.89 % 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: 0.29 (0.19), residues: 2080 helix: 1.54 (0.30), residues: 320 sheet: 0.39 (0.16), residues: 944 loop : -0.48 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 55 PHE 0.010 0.001 PHE E 77 TYR 0.013 0.001 TYR V 138 ARG 0.015 0.000 ARG e 147 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 640) hydrogen bonds : angle 5.14268 ( 1680) covalent geometry : bond 0.00444 (17792) covalent geometry : angle 0.86254 (24016) ********************** 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 589 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 569 time to evaluate : 1.881 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: 0.9194 (t0) cc_final: 0.8816 (p0) REVERT: B 30 ASP cc_start: 0.8980 (t0) cc_final: 0.8739 (t0) REVERT: B 42 ASP cc_start: 0.9390 (t0) cc_final: 0.9060 (t0) REVERT: B 45 GLN cc_start: 0.8953 (tp40) cc_final: 0.8246 (tm-30) REVERT: B 47 ASP cc_start: 0.9072 (m-30) cc_final: 0.8423 (m-30) REVERT: B 59 GLU cc_start: 0.9284 (tt0) cc_final: 0.8672 (mt-10) REVERT: B 63 GLN cc_start: 0.9173 (tp-100) cc_final: 0.8940 (tp-100) REVERT: B 91 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8814 (mm-30) REVERT: B 111 GLN cc_start: 0.8337 (tt0) cc_final: 0.8095 (tt0) REVERT: D 139 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8301 (pp20) REVERT: D 140 LEU cc_start: 0.9661 (mp) cc_final: 0.9013 (mp) REVERT: D 142 ARG cc_start: 0.9265 (ttm-80) cc_final: 0.9020 (ttm-80) REVERT: D 146 LEU cc_start: 0.9007 (mm) cc_final: 0.8781 (mm) REVERT: E 22 ASP cc_start: 0.9212 (t0) cc_final: 0.8835 (p0) REVERT: E 42 ASP cc_start: 0.9360 (t0) cc_final: 0.9048 (t0) REVERT: E 59 GLU cc_start: 0.8988 (tt0) cc_final: 0.8394 (tt0) REVERT: E 63 GLN cc_start: 0.9341 (mm-40) cc_final: 0.9027 (tp-100) REVERT: E 111 GLN cc_start: 0.8477 (tt0) cc_final: 0.8139 (tt0) REVERT: H 22 ASP cc_start: 0.9082 (t0) cc_final: 0.8721 (p0) REVERT: H 45 GLN cc_start: 0.8792 (tp40) cc_final: 0.8168 (tm-30) REVERT: H 47 ASP cc_start: 0.8987 (m-30) cc_final: 0.8331 (m-30) REVERT: H 50 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9111 (tm) REVERT: H 111 GLN cc_start: 0.8425 (tt0) cc_final: 0.8185 (tt0) REVERT: K 22 ASP cc_start: 0.9062 (t0) cc_final: 0.8851 (p0) REVERT: K 30 ASP cc_start: 0.8862 (t0) cc_final: 0.8641 (t0) REVERT: K 42 ASP cc_start: 0.9351 (t0) cc_final: 0.9104 (t0) REVERT: K 63 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8783 (tp-100) REVERT: N 22 ASP cc_start: 0.9189 (t0) cc_final: 0.8812 (p0) REVERT: N 30 ASP cc_start: 0.8964 (t0) cc_final: 0.8730 (t0) REVERT: N 42 ASP cc_start: 0.9275 (t0) cc_final: 0.9001 (t0) REVERT: N 45 GLN cc_start: 0.8867 (tp40) cc_final: 0.8012 (tm-30) REVERT: N 47 ASP cc_start: 0.9045 (m-30) cc_final: 0.8524 (m-30) REVERT: N 63 GLN cc_start: 0.9164 (tp-100) cc_final: 0.8931 (tp-100) REVERT: Q 22 ASP cc_start: 0.9195 (t0) cc_final: 0.8842 (p0) REVERT: Q 30 ASP cc_start: 0.8968 (t0) cc_final: 0.8716 (t0) REVERT: Q 42 ASP cc_start: 0.9396 (t0) cc_final: 0.9133 (t0) REVERT: Q 45 GLN cc_start: 0.8848 (tp40) cc_final: 0.8499 (tm-30) REVERT: Q 59 GLU cc_start: 0.9086 (tt0) cc_final: 0.8513 (tt0) REVERT: Q 63 GLN cc_start: 0.9219 (tp-100) cc_final: 0.9015 (tp-100) REVERT: Q 111 GLN cc_start: 0.8544 (tt0) cc_final: 0.8248 (tt0) REVERT: S 139 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8632 (pp20) REVERT: T 22 ASP cc_start: 0.9053 (t0) cc_final: 0.8749 (p0) REVERT: T 50 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8901 (tm) REVERT: T 63 GLN cc_start: 0.9125 (tp-100) cc_final: 0.8912 (tp-100) REVERT: v 22 ASP cc_start: 0.9071 (t0) cc_final: 0.8854 (p0) REVERT: v 30 ASP cc_start: 0.8807 (t0) cc_final: 0.8594 (t0) REVERT: v 42 ASP cc_start: 0.9373 (t0) cc_final: 0.9122 (t0) REVERT: v 86 ILE cc_start: 0.9720 (pt) cc_final: 0.9519 (pp) REVERT: v 111 GLN cc_start: 0.8627 (tt0) cc_final: 0.8357 (tt0) REVERT: V 143 GLU cc_start: 0.9271 (tp30) cc_final: 0.8953 (tp30) REVERT: W 22 ASP cc_start: 0.9207 (t0) cc_final: 0.8845 (p0) REVERT: W 30 ASP cc_start: 0.8959 (t0) cc_final: 0.8739 (t0) REVERT: W 59 GLU cc_start: 0.9265 (tt0) cc_final: 0.8699 (mt-10) REVERT: W 111 GLN cc_start: 0.8540 (tt0) cc_final: 0.8204 (tt0) REVERT: Z 22 ASP cc_start: 0.9210 (t0) cc_final: 0.8860 (p0) REVERT: Z 30 ASP cc_start: 0.8993 (t0) cc_final: 0.8727 (t0) REVERT: Z 42 ASP cc_start: 0.9356 (t0) cc_final: 0.9101 (t0) REVERT: Z 59 GLU cc_start: 0.9042 (tt0) cc_final: 0.8389 (tt0) REVERT: Z 63 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8797 (tp-100) REVERT: Z 111 GLN cc_start: 0.8619 (tt0) cc_final: 0.8272 (tt0) REVERT: c 22 ASP cc_start: 0.9095 (t0) cc_final: 0.8787 (p0) REVERT: c 45 GLN cc_start: 0.8821 (tp40) cc_final: 0.8325 (tp-100) REVERT: c 86 ILE cc_start: 0.9706 (pt) cc_final: 0.9500 (pp) REVERT: c 111 GLN cc_start: 0.8195 (tt0) cc_final: 0.7940 (mt0) REVERT: f 30 ASP cc_start: 0.8850 (t0) cc_final: 0.8638 (t0) REVERT: f 42 ASP cc_start: 0.9348 (t0) cc_final: 0.9115 (t0) REVERT: f 63 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8374 (tm-30) REVERT: i 22 ASP cc_start: 0.9100 (t0) cc_final: 0.8866 (p0) REVERT: i 42 ASP cc_start: 0.9237 (t0) cc_final: 0.9016 (t0) REVERT: i 45 GLN cc_start: 0.8856 (tp40) cc_final: 0.8008 (tm-30) REVERT: i 47 ASP cc_start: 0.9088 (m-30) cc_final: 0.8509 (m-30) REVERT: i 59 GLU cc_start: 0.9294 (tt0) cc_final: 0.8849 (mt-10) REVERT: i 86 ILE cc_start: 0.9749 (pt) cc_final: 0.9533 (pp) REVERT: i 111 GLN cc_start: 0.8328 (tt0) cc_final: 0.8087 (tt0) REVERT: k 139 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8708 (tm-30) REVERT: k 143 GLU cc_start: 0.9350 (tp30) cc_final: 0.9090 (tp30) REVERT: k 147 ARG cc_start: 0.9447 (OUTLIER) cc_final: 0.8959 (ttp80) REVERT: l 30 ASP cc_start: 0.9013 (t0) cc_final: 0.8729 (t0) REVERT: l 59 GLU cc_start: 0.8843 (tt0) cc_final: 0.8046 (tt0) REVERT: l 63 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8947 (tp-100) REVERT: l 111 GLN cc_start: 0.8588 (tt0) cc_final: 0.8292 (tt0) REVERT: o 59 GLU cc_start: 0.9374 (tt0) cc_final: 0.8790 (tt0) REVERT: o 63 GLN cc_start: 0.9234 (tp-100) cc_final: 0.9017 (tp-100) REVERT: o 112 MET cc_start: 0.9356 (tpp) cc_final: 0.9103 (ttp) REVERT: y 138 TYR cc_start: 0.9397 (t80) cc_final: 0.9197 (t80) REVERT: z 30 ASP cc_start: 0.8874 (t0) cc_final: 0.8628 (t0) REVERT: z 42 ASP cc_start: 0.9372 (t0) cc_final: 0.9137 (t0) REVERT: z 63 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8794 (tp-100) REVERT: z 112 MET cc_start: 0.9298 (ttp) cc_final: 0.9040 (ttp) outliers start: 20 outliers final: 16 residues processed: 578 average time/residue: 1.1622 time to fit residues: 755.2977 Evaluate side-chains 567 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 548 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 112 MET Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain b residue 136 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 147 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.057582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.044077 restraints weight = 60802.605| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.98 r_work: 0.2575 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17792 Z= 0.170 Angle : 0.893 14.026 24016 Z= 0.452 Chirality : 0.056 0.396 2592 Planarity : 0.003 0.033 3152 Dihedral : 4.607 23.232 2496 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.10 % Allowed : 32.40 % Favored : 66.50 % 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: 0.23 (0.19), residues: 2080 helix: 1.26 (0.30), residues: 320 sheet: 0.36 (0.16), residues: 944 loop : -0.43 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS l 55 PHE 0.010 0.001 PHE o 77 TYR 0.010 0.001 TYR l 64 ARG 0.011 0.000 ARG e 147 Details of bonding type rmsd hydrogen bonds : bond 0.04927 ( 640) hydrogen bonds : angle 5.15380 ( 1680) covalent geometry : bond 0.00413 (17792) covalent geometry : angle 0.89327 (24016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16302.80 seconds wall clock time: 282 minutes 25.19 seconds (16945.19 seconds total)