Starting phenix.real_space_refine on Thu Sep 18 13:56:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rt5_19479/09_2025/8rt5_19479.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rt5_19479/09_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_19479/09_2025/8rt5_19479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rt5_19479/09_2025/8rt5_19479.map" model { file = "/net/cci-nas-00/data/ceres_data/8rt5_19479/09_2025/8rt5_19479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rt5_19479/09_2025/8rt5_19479.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.021 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.25, per 1000 atoms: 0.19 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: 1.27 Conformation dependent library (CDL) restraints added in 504.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.57 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: 2.12 Time building geometry restraints manager: 1.64 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: 0.05 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 'u' selection = chain 'V' selection = chain 'Y' selection = chain 'b' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'n' 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 'v' selection = chain 'W' selection = chain 'Z' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'l' selection = chain 'o' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.010 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG G 142 TYR 0.014 0.002 TYR l 127 PHE 0.009 0.002 PHE f 77 HIS 0.005 0.002 HIS Q 83 Details of bonding type rmsd covalent geometry : bond 0.00694 (17792) covalent geometry : angle 0.78859 (24016) hydrogen bonds : bond 0.17836 ( 640) hydrogen bonds : angle 7.36231 ( 1680) *********************** 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 : 0.732 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: 0.6241 time to fit residues: 538.3667 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 : 0.663 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.0170 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.3624 ------------------------------------------------------------------------------- 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 45 GLN Z 89 GLN Z 94 ASN c 94 ASN f 94 ASN i 94 ASN l 45 GLN l 89 GLN l 94 ASN o 94 ASN z 94 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.045472 restraints weight = 58631.888| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.94 r_work: 0.2573 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17792 Z= 0.156 Angle : 0.667 7.999 24016 Z= 0.346 Chirality : 0.048 0.171 2592 Planarity : 0.005 0.044 3152 Dihedral : 4.356 15.478 2502 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 4.00 % Allowed : 16.94 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.18), residues: 2080 helix: 2.64 (0.26), residues: 320 sheet: 0.36 (0.15), residues: 944 loop : -0.68 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG l 28 TYR 0.018 0.001 TYR k 138 PHE 0.009 0.001 PHE v 77 HIS 0.002 0.000 HIS T 83 Details of bonding type rmsd covalent geometry : bond 0.00359 (17792) covalent geometry : angle 0.66715 (24016) hydrogen bonds : bond 0.04379 ( 640) hydrogen bonds : angle 5.47574 ( 1680) *********************** 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 740 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 667 time to evaluate : 0.751 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: 0.9734 (OUTLIER) cc_final: 0.9432 (mm) REVERT: B 30 ASP cc_start: 0.8713 (t0) cc_final: 0.8465 (t0) REVERT: E 63 GLN cc_start: 0.9340 (mm-40) cc_final: 0.8993 (tp-100) REVERT: E 111 GLN cc_start: 0.8572 (tt0) cc_final: 0.8336 (tt0) REVERT: E 122 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8838 (mm-30) REVERT: G 135 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8205 (tppp) REVERT: G 136 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9160 (t) REVERT: G 139 GLU cc_start: 0.9372 (mt-10) cc_final: 0.9161 (mp0) REVERT: H 111 GLN cc_start: 0.8390 (tt0) cc_final: 0.8092 (tt0) REVERT: K 30 ASP cc_start: 0.8749 (t0) cc_final: 0.8411 (t0) REVERT: K 63 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8289 (tm-30) REVERT: M 135 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8608 (ttpt) REVERT: M 139 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8785 (tm-30) REVERT: N 30 ASP cc_start: 0.8759 (t0) cc_final: 0.8527 (t0) REVERT: P 136 THR cc_start: 0.9519 (OUTLIER) cc_final: 0.9136 (t) REVERT: P 143 GLU cc_start: 0.9162 (tp30) cc_final: 0.8943 (tp30) REVERT: Q 59 GLU cc_start: 0.9247 (tt0) cc_final: 0.8779 (tt0) REVERT: Q 86 ILE cc_start: 0.9760 (pt) cc_final: 0.9471 (pp) REVERT: Q 89 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8677 (mm-40) REVERT: Q 111 GLN cc_start: 0.8406 (tt0) cc_final: 0.8134 (mt0) REVERT: S 146 LEU cc_start: 0.9159 (mt) cc_final: 0.8857 (mm) REVERT: T 63 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8942 (tp-100) REVERT: u 139 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8795 (tm-30) REVERT: v 30 ASP cc_start: 0.8798 (t0) cc_final: 0.8544 (t0) REVERT: v 111 GLN cc_start: 0.8462 (tt0) cc_final: 0.8260 (tt0) REVERT: V 136 THR cc_start: 0.9560 (t) cc_final: 0.9253 (t) REVERT: V 143 GLU cc_start: 0.9284 (tp30) cc_final: 0.9080 (tp30) REVERT: W 30 ASP cc_start: 0.8757 (t0) cc_final: 0.8424 (t0) REVERT: W 111 GLN cc_start: 0.8569 (tt0) cc_final: 0.8140 (tt0) REVERT: Y 139 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9199 (pm20) REVERT: Z 111 GLN cc_start: 0.8520 (tt0) cc_final: 0.8099 (tt0) REVERT: b 136 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9144 (t) REVERT: c 30 ASP cc_start: 0.8805 (t0) cc_final: 0.8403 (t0) REVERT: c 63 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8869 (tp-100) REVERT: c 91 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9019 (mm-30) REVERT: e 135 LYS cc_start: 0.8463 (ttmt) cc_final: 0.8248 (ttpt) REVERT: e 136 THR cc_start: 0.9498 (OUTLIER) cc_final: 0.9270 (t) REVERT: f 30 ASP cc_start: 0.8769 (t0) cc_final: 0.8487 (t0) REVERT: h 138 TYR cc_start: 0.9103 (t80) cc_final: 0.8824 (t80) REVERT: h 143 GLU cc_start: 0.9191 (tp30) cc_final: 0.8982 (tp30) REVERT: i 30 ASP cc_start: 0.8706 (t0) cc_final: 0.8425 (t0) REVERT: i 63 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8801 (tp-100) REVERT: k 143 GLU cc_start: 0.9256 (tp30) cc_final: 0.9044 (tp30) REVERT: l 30 ASP cc_start: 0.8523 (t0) cc_final: 0.8321 (t0) REVERT: l 111 GLN cc_start: 0.8650 (tt0) cc_final: 0.8201 (tt0) REVERT: o 30 ASP cc_start: 0.8747 (t0) cc_final: 0.8527 (t0) REVERT: o 63 GLN cc_start: 0.9045 (tp-100) cc_final: 0.8775 (tp-100) REVERT: o 112 MET cc_start: 0.9371 (tpp) cc_final: 0.9129 (ttm) REVERT: y 136 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9164 (t) REVERT: z 30 ASP cc_start: 0.8720 (t0) cc_final: 0.8447 (t0) outliers start: 73 outliers final: 7 residues processed: 685 average time/residue: 0.5264 time to fit residues: 407.5234 Evaluate side-chains 615 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 601 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain W residue 71 ASP 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 o residue 71 ASP Chi-restraints excluded: chain y residue 136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 30 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 89 GLN Z 45 GLN Z 89 GLN l 45 GLN l 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.055333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.041553 restraints weight = 60346.092| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 3.95 r_work: 0.2488 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 17792 Z= 0.303 Angle : 0.679 6.629 24016 Z= 0.357 Chirality : 0.049 0.186 2592 Planarity : 0.004 0.041 3152 Dihedral : 4.266 16.081 2496 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 4.22 % Allowed : 17.93 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.18), residues: 2080 helix: 2.87 (0.25), residues: 320 sheet: 0.62 (0.16), residues: 896 loop : -0.46 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG z 109 TYR 0.013 0.001 TYR o 29 PHE 0.014 0.002 PHE f 77 HIS 0.004 0.001 HIS i 55 Details of bonding type rmsd covalent geometry : bond 0.00679 (17792) covalent geometry : angle 0.67876 (24016) hydrogen bonds : bond 0.04087 ( 640) hydrogen bonds : angle 5.47261 ( 1680) *********************** 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 674 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 597 time to evaluate : 0.800 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: 0.9131 (t0) cc_final: 0.8763 (p0) REVERT: B 30 ASP cc_start: 0.8894 (t0) cc_final: 0.8580 (t0) REVERT: B 42 ASP cc_start: 0.9246 (t0) cc_final: 0.8905 (t0) REVERT: B 63 GLN cc_start: 0.9154 (tp-100) cc_final: 0.8928 (tp-100) REVERT: D 139 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8492 (pp20) REVERT: D 140 LEU cc_start: 0.9602 (mp) cc_final: 0.9083 (mp) REVERT: E 30 ASP cc_start: 0.8753 (t0) cc_final: 0.8548 (t0) REVERT: E 59 GLU cc_start: 0.9291 (tt0) cc_final: 0.8614 (tt0) REVERT: E 63 GLN cc_start: 0.9340 (mm-40) cc_final: 0.9073 (tm-30) REVERT: E 111 GLN cc_start: 0.8620 (tt0) cc_final: 0.8394 (tt0) REVERT: G 135 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8293 (tppp) REVERT: H 30 ASP cc_start: 0.8820 (t0) cc_final: 0.8565 (t0) REVERT: H 63 GLN cc_start: 0.9182 (tp-100) cc_final: 0.8958 (tp-100) REVERT: H 111 GLN cc_start: 0.8410 (tt0) cc_final: 0.8082 (tt0) REVERT: H 122 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8928 (tp30) REVERT: K 30 ASP cc_start: 0.8836 (t0) cc_final: 0.8578 (t0) REVERT: K 63 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8278 (tm-30) REVERT: K 92 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9501 (mm) REVERT: K 122 GLU cc_start: 0.9383 (tp30) cc_final: 0.9104 (tp30) REVERT: N 22 ASP cc_start: 0.9136 (t0) cc_final: 0.8804 (p0) REVERT: N 30 ASP cc_start: 0.8765 (t0) cc_final: 0.8498 (t0) REVERT: N 42 ASP cc_start: 0.9229 (t0) cc_final: 0.8952 (t0) REVERT: N 59 GLU cc_start: 0.9333 (tt0) cc_final: 0.8987 (tt0) REVERT: N 63 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8895 (tp-100) REVERT: P 143 GLU cc_start: 0.9237 (tp30) cc_final: 0.8996 (tp30) REVERT: Q 30 ASP cc_start: 0.8820 (t0) cc_final: 0.8559 (t0) REVERT: Q 59 GLU cc_start: 0.9258 (tt0) cc_final: 0.8619 (tt0) REVERT: Q 111 GLN cc_start: 0.8505 (tt0) cc_final: 0.8206 (tt0) REVERT: S 139 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8695 (tm-30) REVERT: T 63 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8946 (tp-100) REVERT: T 122 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8966 (tp30) REVERT: v 30 ASP cc_start: 0.8861 (t0) cc_final: 0.8625 (t0) REVERT: v 63 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8407 (tm-30) REVERT: v 111 GLN cc_start: 0.8448 (tt0) cc_final: 0.8221 (tt0) REVERT: V 143 GLU cc_start: 0.9264 (tp30) cc_final: 0.9019 (tp30) REVERT: W 22 ASP cc_start: 0.9228 (t0) cc_final: 0.8817 (p0) REVERT: W 42 ASP cc_start: 0.9209 (t0) cc_final: 0.8962 (t0) REVERT: W 111 GLN cc_start: 0.8562 (tt0) cc_final: 0.8086 (tt0) REVERT: Y 136 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9032 (t) REVERT: Z 30 ASP cc_start: 0.8842 (t0) cc_final: 0.8586 (t0) REVERT: Z 59 GLU cc_start: 0.9237 (tt0) cc_final: 0.8521 (tt0) REVERT: Z 111 GLN cc_start: 0.8539 (tt0) cc_final: 0.8081 (tt0) REVERT: b 138 TYR cc_start: 0.9216 (t80) cc_final: 0.8990 (t80) REVERT: c 63 GLN cc_start: 0.9236 (tp-100) cc_final: 0.8992 (tp-100) REVERT: c 86 ILE cc_start: 0.9712 (pt) cc_final: 0.9501 (pp) REVERT: c 91 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8975 (mm-30) REVERT: f 30 ASP cc_start: 0.8840 (t0) cc_final: 0.8565 (t0) REVERT: f 92 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9426 (mm) REVERT: f 122 GLU cc_start: 0.9358 (tp30) cc_final: 0.9032 (tp30) REVERT: h 143 GLU cc_start: 0.9206 (tp30) cc_final: 0.8980 (tp30) REVERT: i 22 ASP cc_start: 0.9141 (t0) cc_final: 0.8761 (p0) REVERT: i 42 ASP cc_start: 0.9241 (t0) cc_final: 0.8934 (t0) REVERT: i 59 GLU cc_start: 0.9360 (tt0) cc_final: 0.8998 (tt0) REVERT: k 135 LYS cc_start: 0.8537 (mttt) cc_final: 0.7942 (ttpt) REVERT: k 139 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8905 (tm-30) REVERT: k 140 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9512 (mm) REVERT: k 143 GLU cc_start: 0.9328 (tp30) cc_final: 0.9063 (tp30) REVERT: l 30 ASP cc_start: 0.8770 (t0) cc_final: 0.8404 (t0) REVERT: l 59 GLU cc_start: 0.9152 (tt0) cc_final: 0.8405 (tt0) REVERT: l 111 GLN cc_start: 0.8570 (tt0) cc_final: 0.8274 (tt0) REVERT: l 122 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8642 (mm-30) REVERT: n 143 GLU cc_start: 0.9278 (tp30) cc_final: 0.9063 (tp30) REVERT: o 63 GLN cc_start: 0.9209 (tp-100) cc_final: 0.8956 (tp-100) REVERT: o 122 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8946 (tp30) REVERT: y 142 ARG cc_start: 0.9342 (ttm-80) cc_final: 0.9134 (ttm-80) REVERT: z 30 ASP cc_start: 0.8876 (t0) cc_final: 0.8563 (t0) REVERT: z 92 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9452 (mm) REVERT: z 122 GLU cc_start: 0.9393 (tp30) cc_final: 0.8838 (tp30) outliers start: 77 outliers final: 21 residues processed: 618 average time/residue: 0.5586 time to fit residues: 386.6474 Evaluate side-chains 584 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 554 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 H residue 122 GLU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain N residue 63 GLN Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain Q residue 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 139 GLU Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Y residue 136 THR 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 140 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain o residue 122 GLU 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 124 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 GLN E 89 GLN Q 89 GLN T 89 GLN v 89 GLN W 89 GLN Z 45 GLN Z 89 GLN l 45 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.057291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.043705 restraints weight = 59767.926| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.96 r_work: 0.2550 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17792 Z= 0.145 Angle : 0.630 7.817 24016 Z= 0.330 Chirality : 0.048 0.256 2592 Planarity : 0.003 0.037 3152 Dihedral : 4.154 15.592 2496 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 3.40 % Allowed : 21.22 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.19), residues: 2080 helix: 2.82 (0.26), residues: 320 sheet: 0.39 (0.16), residues: 944 loop : -0.44 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 34 TYR 0.015 0.001 TYR A 138 PHE 0.010 0.002 PHE l 77 HIS 0.002 0.000 HIS o 83 Details of bonding type rmsd covalent geometry : bond 0.00337 (17792) covalent geometry : angle 0.62979 (24016) hydrogen bonds : bond 0.03833 ( 640) hydrogen bonds : angle 5.01425 ( 1680) *********************** 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 697 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 635 time to evaluate : 0.708 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: B 22 ASP cc_start: 0.9104 (t0) cc_final: 0.8752 (p0) REVERT: B 30 ASP cc_start: 0.8774 (t0) cc_final: 0.8472 (t0) REVERT: B 42 ASP cc_start: 0.9248 (t0) cc_final: 0.8854 (t0) REVERT: B 45 GLN cc_start: 0.8991 (tp40) cc_final: 0.8281 (tm-30) REVERT: D 139 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8502 (pp20) REVERT: D 140 LEU cc_start: 0.9649 (mp) cc_final: 0.9157 (mp) REVERT: E 30 ASP cc_start: 0.8927 (t0) cc_final: 0.8643 (t0) REVERT: E 59 GLU cc_start: 0.9143 (tt0) cc_final: 0.8594 (tt0) REVERT: E 63 GLN cc_start: 0.9286 (mm-40) cc_final: 0.8859 (tp-100) REVERT: E 111 GLN cc_start: 0.8566 (tt0) cc_final: 0.8219 (tt0) REVERT: G 135 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8048 (tppp) REVERT: H 30 ASP cc_start: 0.8870 (t0) cc_final: 0.8642 (t0) REVERT: H 63 GLN cc_start: 0.9157 (tp-100) cc_final: 0.8917 (tp-100) REVERT: H 111 GLN cc_start: 0.8338 (tt0) cc_final: 0.7987 (tt0) REVERT: K 30 ASP cc_start: 0.8890 (t0) cc_final: 0.8597 (t0) REVERT: K 63 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8212 (tm-30) REVERT: K 112 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9128 (ttp) REVERT: N 22 ASP cc_start: 0.9085 (t0) cc_final: 0.8789 (p0) REVERT: N 30 ASP cc_start: 0.8795 (t0) cc_final: 0.8490 (t0) REVERT: N 42 ASP cc_start: 0.9242 (t0) cc_final: 0.8950 (t0) REVERT: N 45 GLN cc_start: 0.8949 (tp40) cc_final: 0.8164 (tm-30) REVERT: N 47 ASP cc_start: 0.9127 (m-30) cc_final: 0.8568 (m-30) REVERT: N 63 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8829 (tp-100) REVERT: P 139 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8964 (pt0) REVERT: P 143 GLU cc_start: 0.9272 (tp30) cc_final: 0.9033 (tp30) REVERT: P 146 LEU cc_start: 0.9024 (mm) cc_final: 0.8746 (mm) REVERT: Q 30 ASP cc_start: 0.8864 (t0) cc_final: 0.8561 (t0) REVERT: Q 59 GLU cc_start: 0.9111 (tt0) cc_final: 0.8560 (tt0) REVERT: Q 63 GLN cc_start: 0.9051 (tp-100) cc_final: 0.8817 (tp-100) REVERT: Q 111 GLN cc_start: 0.8455 (tt0) cc_final: 0.8136 (tt0) REVERT: S 139 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8688 (pp20) REVERT: S 140 LEU cc_start: 0.9661 (mm) cc_final: 0.9080 (mm) REVERT: T 45 GLN cc_start: 0.8923 (tp40) cc_final: 0.8109 (tm-30) REVERT: T 63 GLN cc_start: 0.9114 (tp-100) cc_final: 0.8874 (tp-100) REVERT: T 122 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8896 (tp30) REVERT: u 143 GLU cc_start: 0.9346 (tp30) cc_final: 0.9096 (tp30) REVERT: v 30 ASP cc_start: 0.8872 (t0) cc_final: 0.8584 (t0) REVERT: v 63 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8317 (tm-30) REVERT: v 111 GLN cc_start: 0.8562 (tt0) cc_final: 0.8280 (tt0) REVERT: v 112 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.9119 (ttp) REVERT: V 143 GLU cc_start: 0.9247 (tp30) cc_final: 0.8954 (tp30) REVERT: W 22 ASP cc_start: 0.9174 (t0) cc_final: 0.8789 (p0) REVERT: W 42 ASP cc_start: 0.9251 (t0) cc_final: 0.8979 (t0) REVERT: W 50 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9180 (tm) REVERT: W 63 GLN cc_start: 0.9082 (tp-100) cc_final: 0.8851 (tp-100) REVERT: W 111 GLN cc_start: 0.8537 (tt0) cc_final: 0.8078 (tt0) REVERT: Z 30 ASP cc_start: 0.8911 (t0) cc_final: 0.8595 (t0) REVERT: Z 59 GLU cc_start: 0.9101 (tt0) cc_final: 0.8489 (tt0) REVERT: Z 63 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8844 (tp-100) REVERT: Z 111 GLN cc_start: 0.8504 (tt0) cc_final: 0.8064 (tt0) REVERT: b 136 THR cc_start: 0.9584 (t) cc_final: 0.9355 (t) REVERT: c 45 GLN cc_start: 0.8957 (tp40) cc_final: 0.8185 (tm-30) REVERT: c 86 ILE cc_start: 0.9704 (pt) cc_final: 0.9466 (pp) REVERT: c 91 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8947 (mm-30) REVERT: e 139 GLU cc_start: 0.9329 (mt-10) cc_final: 0.9032 (pm20) REVERT: f 30 ASP cc_start: 0.8825 (t0) cc_final: 0.8569 (t0) REVERT: f 112 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.9051 (ttp) REVERT: f 122 GLU cc_start: 0.9266 (tp30) cc_final: 0.9032 (tp30) REVERT: h 143 GLU cc_start: 0.9189 (tp30) cc_final: 0.8869 (tp30) REVERT: i 22 ASP cc_start: 0.9108 (t0) cc_final: 0.8764 (p0) REVERT: i 42 ASP cc_start: 0.9257 (t0) cc_final: 0.8897 (t0) REVERT: i 45 GLN cc_start: 0.9034 (tp40) cc_final: 0.8333 (tm-30) REVERT: i 63 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8854 (tp-100) REVERT: i 111 GLN cc_start: 0.8375 (tt0) cc_final: 0.8172 (tt0) REVERT: k 135 LYS cc_start: 0.8752 (mttt) cc_final: 0.8283 (ttmt) REVERT: k 139 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8879 (tm-30) REVERT: k 140 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9517 (mm) REVERT: k 143 GLU cc_start: 0.9342 (tp30) cc_final: 0.9011 (tp30) REVERT: k 147 ARG cc_start: 0.9384 (OUTLIER) cc_final: 0.8860 (ttp80) REVERT: l 30 ASP cc_start: 0.8846 (t0) cc_final: 0.8476 (t0) REVERT: l 59 GLU cc_start: 0.9077 (tt0) cc_final: 0.8358 (tt0) REVERT: l 111 GLN cc_start: 0.8546 (tt0) cc_final: 0.8063 (tt0) REVERT: n 135 LYS cc_start: 0.8831 (mttp) cc_final: 0.8629 (mtmm) REVERT: o 63 GLN cc_start: 0.9122 (tp-100) cc_final: 0.8919 (tp-100) REVERT: z 30 ASP cc_start: 0.8830 (t0) cc_final: 0.8540 (t0) REVERT: z 92 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9483 (mm) REVERT: z 112 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9095 (ttp) outliers start: 62 outliers final: 10 residues processed: 646 average time/residue: 0.5645 time to fit residues: 407.4970 Evaluate side-chains 580 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 560 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 63 GLN Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 122 GLU 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 57 MET Chi-restraints excluded: chain f residue 112 MET Chi-restraints excluded: chain k residue 140 LEU Chi-restraints excluded: chain k residue 147 ARG Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain z residue 92 LEU Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 171 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 GLN v 89 GLN W 45 GLN ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 45 GLN l 45 GLN z 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.040334 restraints weight = 60641.597| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 3.89 r_work: 0.2464 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 17792 Z= 0.346 Angle : 0.717 8.236 24016 Z= 0.378 Chirality : 0.050 0.203 2592 Planarity : 0.004 0.050 3152 Dihedral : 4.401 16.452 2496 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.89 % Allowed : 21.27 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 2080 helix: 2.40 (0.26), residues: 320 sheet: 0.52 (0.17), residues: 896 loop : -0.52 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG b 147 TYR 0.020 0.002 TYR S 138 PHE 0.014 0.002 PHE f 77 HIS 0.005 0.001 HIS z 55 Details of bonding type rmsd covalent geometry : bond 0.00785 (17792) covalent geometry : angle 0.71742 (24016) hydrogen bonds : bond 0.04110 ( 640) hydrogen bonds : angle 5.43817 ( 1680) *********************** 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 629 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 558 time to evaluate : 0.488 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 139 GLU cc_start: 0.8636 (pp20) cc_final: 0.8398 (pp20) REVERT: A 143 GLU cc_start: 0.9391 (tp30) cc_final: 0.9176 (tp30) REVERT: B 22 ASP cc_start: 0.9245 (t0) cc_final: 0.8766 (p0) REVERT: B 30 ASP cc_start: 0.8850 (t0) cc_final: 0.8589 (t0) REVERT: B 42 ASP cc_start: 0.9306 (t0) cc_final: 0.9029 (t0) REVERT: B 63 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8951 (tp-100) REVERT: D 139 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8344 (pp20) REVERT: D 140 LEU cc_start: 0.9636 (mp) cc_final: 0.9087 (mp) REVERT: E 22 ASP cc_start: 0.9268 (t0) cc_final: 0.8632 (p0) REVERT: E 30 ASP cc_start: 0.8937 (t0) cc_final: 0.8591 (t0) REVERT: E 42 ASP cc_start: 0.9344 (t0) cc_final: 0.8981 (t0) REVERT: E 59 GLU cc_start: 0.9235 (tt0) cc_final: 0.8531 (tt0) REVERT: E 63 GLN cc_start: 0.9347 (mm-40) cc_final: 0.9041 (tm-30) REVERT: E 111 GLN cc_start: 0.8594 (tt0) cc_final: 0.8360 (tt0) REVERT: H 22 ASP cc_start: 0.9118 (t0) cc_final: 0.8685 (p0) REVERT: H 63 GLN cc_start: 0.9231 (tp-100) cc_final: 0.8965 (tp-100) REVERT: H 111 GLN cc_start: 0.8462 (tt0) cc_final: 0.8095 (tt0) REVERT: J 142 ARG cc_start: 0.9350 (ttm-80) cc_final: 0.9140 (ttm-80) REVERT: K 30 ASP cc_start: 0.8945 (t0) cc_final: 0.8632 (t0) REVERT: K 63 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8370 (tm-30) REVERT: K 112 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9123 (ttp) REVERT: N 22 ASP cc_start: 0.9232 (t0) cc_final: 0.8799 (p0) REVERT: N 30 ASP cc_start: 0.8868 (t0) cc_final: 0.8607 (t0) REVERT: N 47 ASP cc_start: 0.9169 (m-30) cc_final: 0.8953 (m-30) REVERT: N 59 GLU cc_start: 0.9332 (tt0) cc_final: 0.8950 (tt0) REVERT: N 63 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8865 (tp-100) REVERT: N 111 GLN cc_start: 0.8378 (tt0) cc_final: 0.8145 (tt0) REVERT: P 143 GLU cc_start: 0.9281 (tp30) cc_final: 0.9016 (tp30) REVERT: Q 22 ASP cc_start: 0.9269 (t0) cc_final: 0.8642 (p0) REVERT: Q 30 ASP cc_start: 0.8941 (t0) cc_final: 0.8592 (t0) REVERT: Q 42 ASP cc_start: 0.9348 (t0) cc_final: 0.9013 (t0) REVERT: Q 59 GLU cc_start: 0.9264 (tt0) cc_final: 0.8523 (tt0) REVERT: Q 63 GLN cc_start: 0.9167 (tp-100) cc_final: 0.8936 (tp-100) REVERT: Q 111 GLN cc_start: 0.8488 (tt0) cc_final: 0.8128 (tt0) REVERT: S 139 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8630 (pp20) REVERT: S 140 LEU cc_start: 0.9637 (mm) cc_final: 0.8979 (mm) REVERT: S 142 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8974 (ptm-80) REVERT: T 22 ASP cc_start: 0.9147 (t0) cc_final: 0.8689 (p0) REVERT: T 63 GLN cc_start: 0.9196 (tp-100) cc_final: 0.8949 (tp-100) REVERT: u 139 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9133 (pt0) REVERT: u 143 GLU cc_start: 0.9349 (tp30) cc_final: 0.9148 (tp30) REVERT: v 30 ASP cc_start: 0.8846 (t0) cc_final: 0.8630 (t0) REVERT: v 63 GLN cc_start: 0.9200 (tm-30) cc_final: 0.8572 (tm-30) REVERT: v 111 GLN cc_start: 0.8557 (tt0) cc_final: 0.8301 (tt0) REVERT: v 112 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.9183 (ttp) REVERT: V 139 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9178 (mp0) REVERT: V 143 GLU cc_start: 0.9302 (tp30) cc_final: 0.9048 (tp30) REVERT: W 22 ASP cc_start: 0.9251 (t0) cc_final: 0.8825 (p0) REVERT: W 59 GLU cc_start: 0.9281 (tt0) cc_final: 0.8882 (tt0) REVERT: W 63 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8900 (tp-100) REVERT: W 111 GLN cc_start: 0.8634 (tt0) cc_final: 0.8127 (tt0) REVERT: Z 30 ASP cc_start: 0.8983 (t0) cc_final: 0.8618 (t0) REVERT: Z 59 GLU cc_start: 0.9214 (tt0) cc_final: 0.8375 (tt0) REVERT: Z 63 GLN cc_start: 0.9165 (tp-100) cc_final: 0.8919 (tp-100) REVERT: Z 111 GLN cc_start: 0.8586 (tt0) cc_final: 0.7659 (tm-30) REVERT: c 22 ASP cc_start: 0.9145 (t0) cc_final: 0.8723 (p0) REVERT: c 86 ILE cc_start: 0.9720 (pt) cc_final: 0.9509 (pp) REVERT: c 91 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8935 (mm-30) REVERT: e 135 LYS cc_start: 0.8390 (ttmt) cc_final: 0.7952 (tppp) REVERT: f 30 ASP cc_start: 0.8855 (t0) cc_final: 0.8604 (t0) REVERT: f 112 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.9116 (ttp) REVERT: f 122 GLU cc_start: 0.9236 (tp30) cc_final: 0.8976 (tp30) REVERT: h 143 GLU cc_start: 0.9208 (tp30) cc_final: 0.8908 (tp30) REVERT: i 22 ASP cc_start: 0.9241 (t0) cc_final: 0.8833 (p0) REVERT: i 59 GLU cc_start: 0.9279 (tt0) cc_final: 0.8913 (tt0) REVERT: i 63 GLN cc_start: 0.9264 (mm-40) cc_final: 0.8951 (tp-100) REVERT: i 86 ILE cc_start: 0.9745 (pt) cc_final: 0.9530 (pp) REVERT: i 111 GLN cc_start: 0.8398 (tt0) cc_final: 0.8153 (tt0) REVERT: k 135 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8394 (ttmt) REVERT: k 139 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8749 (tm-30) REVERT: k 140 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9491 (mm) REVERT: k 143 GLU cc_start: 0.9377 (tp30) cc_final: 0.9071 (tp30) REVERT: k 147 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.8892 (ttp80) REVERT: l 30 ASP cc_start: 0.8935 (t0) cc_final: 0.8562 (t0) REVERT: l 59 GLU cc_start: 0.9156 (tt0) cc_final: 0.8346 (tt0) REVERT: l 63 GLN cc_start: 0.9160 (tp-100) cc_final: 0.8909 (tp-100) REVERT: n 135 LYS cc_start: 0.8817 (mttp) cc_final: 0.8476 (mtmm) REVERT: n 140 LEU cc_start: 0.9694 (OUTLIER) cc_final: 0.9378 (mm) REVERT: o 30 ASP cc_start: 0.8941 (t0) cc_final: 0.8741 (t0) REVERT: o 63 GLN cc_start: 0.9212 (tp-100) cc_final: 0.8968 (tp-100) REVERT: z 30 ASP cc_start: 0.8831 (t0) cc_final: 0.8603 (t0) REVERT: z 112 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.9173 (ttp) outliers start: 71 outliers final: 30 residues processed: 582 average time/residue: 0.5676 time to fit residues: 369.2263 Evaluate side-chains 564 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 523 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 114 ASN Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain N residue 63 GLN Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain S residue 142 ARG Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 139 GLU Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 151 THR 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 135 LYS Chi-restraints excluded: chain k residue 140 LEU Chi-restraints excluded: chain k residue 147 ARG Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain n residue 140 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 151 THR Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 GLN H 89 GLN Q 89 GLN v 89 GLN v 131 GLN W 45 GLN W 89 GLN Z 45 GLN f 131 GLN l 45 GLN z 89 GLN z 131 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.057705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.044323 restraints weight = 59771.528| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.94 r_work: 0.2579 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17792 Z= 0.137 Angle : 0.676 9.415 24016 Z= 0.354 Chirality : 0.049 0.215 2592 Planarity : 0.003 0.043 3152 Dihedral : 4.178 14.635 2496 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.63 % Allowed : 24.40 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.19), residues: 2080 helix: 2.52 (0.27), residues: 320 sheet: 0.34 (0.16), residues: 944 loop : -0.42 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 147 TYR 0.017 0.001 TYR J 138 PHE 0.010 0.001 PHE c 77 HIS 0.003 0.000 HIS c 55 Details of bonding type rmsd covalent geometry : bond 0.00319 (17792) covalent geometry : angle 0.67641 (24016) hydrogen bonds : bond 0.03895 ( 640) hydrogen bonds : angle 4.91282 ( 1680) *********************** 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 670 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 622 time to evaluate : 0.756 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: A 139 GLU cc_start: 0.8636 (pp20) cc_final: 0.8430 (pp20) REVERT: A 140 LEU cc_start: 0.9658 (mm) cc_final: 0.9401 (mm) REVERT: A 143 GLU cc_start: 0.9329 (tp30) cc_final: 0.9124 (tp30) REVERT: B 22 ASP cc_start: 0.9154 (t0) cc_final: 0.8781 (p0) REVERT: B 30 ASP cc_start: 0.8899 (t0) cc_final: 0.8621 (t0) REVERT: B 42 ASP cc_start: 0.9272 (t0) cc_final: 0.9017 (t0) REVERT: B 45 GLN cc_start: 0.8955 (tp40) cc_final: 0.8212 (tm-30) REVERT: B 47 ASP cc_start: 0.9091 (m-30) cc_final: 0.8539 (m-30) REVERT: B 63 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8797 (tp-100) REVERT: B 111 GLN cc_start: 0.8324 (tt0) cc_final: 0.8112 (tt0) REVERT: D 139 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8421 (pp20) REVERT: D 140 LEU cc_start: 0.9660 (mp) cc_final: 0.9121 (mp) REVERT: D 142 ARG cc_start: 0.9251 (ttm-80) cc_final: 0.8893 (ttm-80) REVERT: D 146 LEU cc_start: 0.8973 (mm) cc_final: 0.8666 (mm) REVERT: E 22 ASP cc_start: 0.9209 (t0) cc_final: 0.8768 (p0) REVERT: E 30 ASP cc_start: 0.8927 (t0) cc_final: 0.8614 (t0) REVERT: E 42 ASP cc_start: 0.9315 (t0) cc_final: 0.8915 (t0) REVERT: E 59 GLU cc_start: 0.8993 (tt0) cc_final: 0.8335 (tt0) REVERT: E 63 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8890 (tp-100) REVERT: E 111 GLN cc_start: 0.8609 (tt0) cc_final: 0.8264 (tt0) REVERT: G 142 ARG cc_start: 0.9283 (ttm-80) cc_final: 0.9048 (ttm-80) REVERT: H 45 GLN cc_start: 0.8889 (tp40) cc_final: 0.8114 (tm-30) REVERT: H 47 ASP cc_start: 0.8943 (m-30) cc_final: 0.8258 (m-30) REVERT: H 63 GLN cc_start: 0.9145 (tp-100) cc_final: 0.8823 (tp-100) REVERT: H 111 GLN cc_start: 0.8361 (tt0) cc_final: 0.8052 (tt0) REVERT: K 30 ASP cc_start: 0.8875 (t0) cc_final: 0.8565 (t0) REVERT: K 63 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8282 (tm-30) REVERT: K 112 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.9050 (ttp) REVERT: M 139 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8474 (pp20) REVERT: N 22 ASP cc_start: 0.9093 (t0) cc_final: 0.8777 (p0) REVERT: N 30 ASP cc_start: 0.8874 (t0) cc_final: 0.8600 (t0) REVERT: N 42 ASP cc_start: 0.9144 (t0) cc_final: 0.8845 (t0) REVERT: N 45 GLN cc_start: 0.8862 (tp40) cc_final: 0.7968 (tm-30) REVERT: N 47 ASP cc_start: 0.9083 (m-30) cc_final: 0.8467 (m-30) REVERT: N 63 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8796 (tp-100) REVERT: N 111 GLN cc_start: 0.8356 (tt0) cc_final: 0.8148 (tt0) REVERT: P 143 GLU cc_start: 0.9270 (tp30) cc_final: 0.8971 (tp30) REVERT: Q 22 ASP cc_start: 0.9202 (t0) cc_final: 0.8772 (p0) REVERT: Q 30 ASP cc_start: 0.8918 (t0) cc_final: 0.8583 (t0) REVERT: Q 42 ASP cc_start: 0.9350 (t0) cc_final: 0.8994 (t0) REVERT: Q 59 GLU cc_start: 0.9019 (tt0) cc_final: 0.8325 (tt0) REVERT: Q 63 GLN cc_start: 0.9048 (tp-100) cc_final: 0.8804 (tp-100) REVERT: Q 111 GLN cc_start: 0.8473 (tt0) cc_final: 0.8138 (tt0) REVERT: S 139 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8598 (pp20) REVERT: S 140 LEU cc_start: 0.9661 (mm) cc_final: 0.8949 (mm) REVERT: T 22 ASP cc_start: 0.9083 (t0) cc_final: 0.8743 (p0) REVERT: T 45 GLN cc_start: 0.8880 (tp40) cc_final: 0.8065 (tm-30) REVERT: T 47 ASP cc_start: 0.8957 (m-30) cc_final: 0.8396 (m-30) REVERT: T 63 GLN cc_start: 0.9132 (tp-100) cc_final: 0.8894 (tp-100) REVERT: u 136 THR cc_start: 0.9636 (t) cc_final: 0.9423 (t) REVERT: u 143 GLU cc_start: 0.9340 (tp30) cc_final: 0.9121 (tp30) REVERT: v 30 ASP cc_start: 0.8860 (t0) cc_final: 0.8620 (t0) REVERT: v 42 ASP cc_start: 0.9338 (t0) cc_final: 0.9057 (t0) REVERT: v 63 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8431 (tm-30) REVERT: v 111 GLN cc_start: 0.8577 (tt0) cc_final: 0.8303 (tt0) REVERT: v 112 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.9104 (ttp) REVERT: V 143 GLU cc_start: 0.9242 (tp30) cc_final: 0.8920 (tp30) REVERT: W 22 ASP cc_start: 0.9139 (t0) cc_final: 0.8797 (p0) REVERT: W 42 ASP cc_start: 0.9166 (t0) cc_final: 0.8808 (t0) REVERT: W 63 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8846 (tp-100) REVERT: W 111 GLN cc_start: 0.8545 (tt0) cc_final: 0.8107 (tt0) REVERT: Z 22 ASP cc_start: 0.9188 (t0) cc_final: 0.8778 (p0) REVERT: Z 30 ASP cc_start: 0.8951 (t0) cc_final: 0.8608 (t0) REVERT: Z 42 ASP cc_start: 0.9338 (t0) cc_final: 0.9067 (t0) REVERT: Z 59 GLU cc_start: 0.9037 (tt0) cc_final: 0.8337 (tt0) REVERT: Z 63 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8837 (tp-100) REVERT: Z 86 ILE cc_start: 0.9782 (pt) cc_final: 0.9535 (pp) REVERT: Z 111 GLN cc_start: 0.8511 (tt0) cc_final: 0.8144 (tt0) REVERT: c 22 ASP cc_start: 0.9063 (t0) cc_final: 0.8770 (p0) REVERT: c 45 GLN cc_start: 0.8828 (tp40) cc_final: 0.8108 (tm-30) REVERT: c 47 ASP cc_start: 0.8932 (m-30) cc_final: 0.8334 (m-30) REVERT: c 50 LEU cc_start: 0.9211 (tm) cc_final: 0.8652 (tm) REVERT: c 63 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8869 (tp-100) REVERT: c 86 ILE cc_start: 0.9709 (pt) cc_final: 0.9479 (pp) REVERT: c 91 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8853 (mm-30) REVERT: f 22 ASP cc_start: 0.8975 (t0) cc_final: 0.8764 (p0) REVERT: f 30 ASP cc_start: 0.8876 (t0) cc_final: 0.8604 (t0) REVERT: f 42 ASP cc_start: 0.9362 (t0) cc_final: 0.9076 (t0) REVERT: f 112 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.9023 (ttp) REVERT: f 120 MET cc_start: 0.9511 (ttp) cc_final: 0.9241 (ttp) REVERT: h 143 GLU cc_start: 0.9199 (tp30) cc_final: 0.8847 (tp30) REVERT: i 22 ASP cc_start: 0.9149 (t0) cc_final: 0.8827 (p0) REVERT: i 42 ASP cc_start: 0.9199 (t0) cc_final: 0.8890 (t0) REVERT: i 45 GLN cc_start: 0.8915 (tp40) cc_final: 0.8033 (tm-30) REVERT: i 47 ASP cc_start: 0.9114 (m-30) cc_final: 0.8490 (m-30) REVERT: i 63 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8845 (tp-100) REVERT: i 86 ILE cc_start: 0.9741 (pt) cc_final: 0.9500 (pp) REVERT: i 111 GLN cc_start: 0.8375 (tt0) cc_final: 0.8137 (tt0) REVERT: k 135 LYS cc_start: 0.8959 (mttt) cc_final: 0.8632 (ttmt) REVERT: k 143 GLU cc_start: 0.9336 (tp30) cc_final: 0.8943 (tp30) REVERT: k 147 ARG cc_start: 0.9487 (OUTLIER) cc_final: 0.9004 (ttp80) REVERT: l 30 ASP cc_start: 0.8984 (t0) cc_final: 0.8642 (t0) REVERT: l 59 GLU cc_start: 0.9054 (tt0) cc_final: 0.8293 (tt0) REVERT: l 63 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8768 (tp-100) REVERT: l 111 GLN cc_start: 0.8605 (tt0) cc_final: 0.8155 (tt0) REVERT: o 30 ASP cc_start: 0.8996 (t0) cc_final: 0.8761 (t0) REVERT: o 45 GLN cc_start: 0.8825 (tp40) cc_final: 0.8129 (tm-30) REVERT: o 47 ASP cc_start: 0.9006 (m-30) cc_final: 0.8449 (m-30) REVERT: o 63 GLN cc_start: 0.9150 (tp-100) cc_final: 0.8892 (tp-100) REVERT: z 30 ASP cc_start: 0.8833 (t0) cc_final: 0.8566 (t0) REVERT: z 42 ASP cc_start: 0.9317 (t0) cc_final: 0.9045 (t0) REVERT: z 63 GLN cc_start: 0.8951 (tp-100) cc_final: 0.8676 (tp-100) REVERT: z 86 ILE cc_start: 0.9766 (pt) cc_final: 0.9554 (pp) REVERT: z 112 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.9055 (ttp) REVERT: z 120 MET cc_start: 0.9535 (ttp) cc_final: 0.9334 (ttp) outliers start: 48 outliers final: 16 residues processed: 638 average time/residue: 0.5627 time to fit residues: 402.2298 Evaluate side-chains 584 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 563 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Z residue 114 ASN Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain e residue 136 THR 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 123 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR 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 97 optimal weight: 9.9990 chunk 135 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 24 optimal weight: 0.1980 chunk 104 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 131 GLN T 89 GLN W 89 GLN f 89 GLN l 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.056237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.042577 restraints weight = 60267.171| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.98 r_work: 0.2527 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17792 Z= 0.197 Angle : 0.724 9.804 24016 Z= 0.379 Chirality : 0.051 0.240 2592 Planarity : 0.003 0.028 3152 Dihedral : 4.342 17.050 2496 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.41 % Allowed : 26.70 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.19), residues: 2080 helix: 2.23 (0.27), residues: 320 sheet: 0.33 (0.16), residues: 944 loop : -0.48 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 147 TYR 0.016 0.001 TYR G 138 PHE 0.011 0.002 PHE v 77 HIS 0.004 0.001 HIS l 55 Details of bonding type rmsd covalent geometry : bond 0.00469 (17792) covalent geometry : angle 0.72430 (24016) hydrogen bonds : bond 0.04173 ( 640) hydrogen bonds : angle 5.06427 ( 1680) *********************** 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 617 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 573 time to evaluate : 0.732 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 139 GLU cc_start: 0.8663 (pp20) cc_final: 0.8430 (pp20) REVERT: A 140 LEU cc_start: 0.9642 (mm) cc_final: 0.9257 (mm) REVERT: B 22 ASP cc_start: 0.9197 (t0) cc_final: 0.8798 (p0) REVERT: B 30 ASP cc_start: 0.8922 (t0) cc_final: 0.8649 (t0) REVERT: B 42 ASP cc_start: 0.9283 (t0) cc_final: 0.8976 (t0) REVERT: B 45 GLN cc_start: 0.9036 (tp40) cc_final: 0.8300 (tm-30) REVERT: B 47 ASP cc_start: 0.9107 (m-30) cc_final: 0.8403 (m-30) REVERT: B 59 GLU cc_start: 0.9228 (tt0) cc_final: 0.8791 (mt-10) REVERT: B 111 GLN cc_start: 0.8403 (tt0) cc_final: 0.8155 (tt0) REVERT: D 139 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8361 (pp20) REVERT: D 140 LEU cc_start: 0.9649 (mp) cc_final: 0.9093 (mp) REVERT: D 146 LEU cc_start: 0.8982 (mm) cc_final: 0.8647 (mm) REVERT: E 22 ASP cc_start: 0.9237 (t0) cc_final: 0.8824 (p0) REVERT: E 30 ASP cc_start: 0.8967 (t0) cc_final: 0.8665 (t0) REVERT: E 42 ASP cc_start: 0.9327 (t0) cc_final: 0.8967 (t0) REVERT: E 59 GLU cc_start: 0.9050 (tt0) cc_final: 0.8345 (tt0) REVERT: E 63 GLN cc_start: 0.9288 (mm-40) cc_final: 0.8983 (tp-100) REVERT: E 111 GLN cc_start: 0.8634 (tt0) cc_final: 0.8278 (tt0) REVERT: G 135 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7724 (ttmm) REVERT: G 142 ARG cc_start: 0.9315 (ttm-80) cc_final: 0.9096 (ttm-80) REVERT: H 22 ASP cc_start: 0.9079 (t0) cc_final: 0.8717 (p0) REVERT: H 63 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8962 (tp-100) REVERT: H 111 GLN cc_start: 0.8427 (tt0) cc_final: 0.8060 (tt0) REVERT: J 139 GLU cc_start: 0.9348 (mp0) cc_final: 0.9141 (mp0) REVERT: K 22 ASP cc_start: 0.9079 (t0) cc_final: 0.8805 (p0) REVERT: K 30 ASP cc_start: 0.8879 (t0) cc_final: 0.8658 (t0) REVERT: K 42 ASP cc_start: 0.9355 (t0) cc_final: 0.9117 (t0) REVERT: K 63 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8348 (tm-30) REVERT: K 112 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9061 (ttp) REVERT: M 139 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8416 (pp20) REVERT: M 142 ARG cc_start: 0.9415 (ttm-80) cc_final: 0.8962 (ttm-80) REVERT: N 22 ASP cc_start: 0.9177 (t0) cc_final: 0.8804 (p0) REVERT: N 30 ASP cc_start: 0.8908 (t0) cc_final: 0.8653 (t0) REVERT: N 42 ASP cc_start: 0.9205 (t0) cc_final: 0.8965 (t0) REVERT: N 45 GLN cc_start: 0.8948 (tp40) cc_final: 0.8017 (tm-30) REVERT: N 47 ASP cc_start: 0.9105 (m-30) cc_final: 0.8518 (m-30) REVERT: N 59 GLU cc_start: 0.9229 (tt0) cc_final: 0.8892 (tt0) REVERT: N 63 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8911 (tm-30) REVERT: N 111 GLN cc_start: 0.8424 (tt0) cc_final: 0.8197 (tt0) REVERT: P 143 GLU cc_start: 0.9329 (tp30) cc_final: 0.9067 (tp30) REVERT: Q 22 ASP cc_start: 0.9232 (t0) cc_final: 0.8815 (p0) REVERT: Q 30 ASP cc_start: 0.8951 (t0) cc_final: 0.8634 (t0) REVERT: Q 42 ASP cc_start: 0.9357 (t0) cc_final: 0.9011 (t0) REVERT: Q 59 GLU cc_start: 0.9056 (tt0) cc_final: 0.8336 (tt0) REVERT: Q 63 GLN cc_start: 0.9122 (tp-100) cc_final: 0.8885 (tp-100) REVERT: Q 111 GLN cc_start: 0.8535 (tt0) cc_final: 0.8171 (tt0) REVERT: S 139 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8621 (pp20) REVERT: S 140 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.8887 (mm) REVERT: T 22 ASP cc_start: 0.9104 (t0) cc_final: 0.8771 (p0) REVERT: T 45 GLN cc_start: 0.8930 (tp40) cc_final: 0.8210 (tm-30) REVERT: T 47 ASP cc_start: 0.9021 (m-30) cc_final: 0.8418 (m-30) REVERT: T 63 GLN cc_start: 0.9173 (tp-100) cc_final: 0.8937 (tp-100) REVERT: u 143 GLU cc_start: 0.9383 (tp30) cc_final: 0.9154 (tp30) REVERT: v 30 ASP cc_start: 0.8834 (t0) cc_final: 0.8605 (t0) REVERT: v 63 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8538 (tm-30) REVERT: v 111 GLN cc_start: 0.8594 (tt0) cc_final: 0.8301 (tt0) REVERT: v 112 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.9129 (ttp) REVERT: V 143 GLU cc_start: 0.9299 (tp30) cc_final: 0.9003 (tp30) REVERT: V 150 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8708 (mm) REVERT: W 22 ASP cc_start: 0.9163 (t0) cc_final: 0.8824 (p0) REVERT: W 42 ASP cc_start: 0.9228 (t0) cc_final: 0.9001 (t0) REVERT: W 59 GLU cc_start: 0.9181 (tt0) cc_final: 0.8787 (mt-10) REVERT: W 63 GLN cc_start: 0.9181 (tp-100) cc_final: 0.8908 (tp-100) REVERT: W 111 GLN cc_start: 0.8613 (tt0) cc_final: 0.8244 (tt0) REVERT: Z 22 ASP cc_start: 0.9228 (t0) cc_final: 0.8719 (p0) REVERT: Z 30 ASP cc_start: 0.8999 (t0) cc_final: 0.8665 (t0) REVERT: Z 42 ASP cc_start: 0.9361 (t0) cc_final: 0.9094 (t0) REVERT: Z 59 GLU cc_start: 0.9013 (tt0) cc_final: 0.8256 (tt0) REVERT: Z 111 GLN cc_start: 0.8573 (tt0) cc_final: 0.8219 (tt0) REVERT: b 142 ARG cc_start: 0.9280 (ttm-80) cc_final: 0.9049 (ttm-80) REVERT: c 22 ASP cc_start: 0.9107 (t0) cc_final: 0.8778 (p0) REVERT: c 91 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8872 (mm-30) REVERT: f 22 ASP cc_start: 0.9008 (t0) cc_final: 0.8790 (p0) REVERT: f 30 ASP cc_start: 0.8849 (t0) cc_final: 0.8642 (t0) REVERT: f 42 ASP cc_start: 0.9402 (t0) cc_final: 0.9129 (t0) REVERT: f 112 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.9038 (ttp) REVERT: h 143 GLU cc_start: 0.9219 (tp30) cc_final: 0.8886 (tp30) REVERT: i 22 ASP cc_start: 0.9172 (t0) cc_final: 0.8822 (p0) REVERT: i 42 ASP cc_start: 0.9250 (t0) cc_final: 0.8999 (t0) REVERT: i 45 GLN cc_start: 0.8963 (tp40) cc_final: 0.8092 (tm-30) REVERT: i 47 ASP cc_start: 0.9141 (m-30) cc_final: 0.8533 (m-30) REVERT: i 59 GLU cc_start: 0.9287 (tt0) cc_final: 0.8762 (mt-10) REVERT: i 63 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8847 (tp-100) REVERT: i 86 ILE cc_start: 0.9746 (pt) cc_final: 0.9535 (pp) REVERT: i 111 GLN cc_start: 0.8424 (tt0) cc_final: 0.8175 (tt0) REVERT: k 139 GLU cc_start: 0.9442 (mt-10) cc_final: 0.9230 (pt0) REVERT: k 143 GLU cc_start: 0.9310 (tp30) cc_final: 0.9046 (tp30) REVERT: k 147 ARG cc_start: 0.9458 (OUTLIER) cc_final: 0.9045 (ttp80) REVERT: l 30 ASP cc_start: 0.8982 (t0) cc_final: 0.8646 (t0) REVERT: l 59 GLU cc_start: 0.9029 (tt0) cc_final: 0.8255 (tt0) REVERT: l 63 GLN cc_start: 0.9137 (tp-100) cc_final: 0.8861 (tp-100) REVERT: l 111 GLN cc_start: 0.8647 (tt0) cc_final: 0.8197 (tt0) REVERT: n 142 ARG cc_start: 0.9212 (ttm-80) cc_final: 0.8901 (ttm-80) REVERT: o 63 GLN cc_start: 0.9208 (tp-100) cc_final: 0.8978 (tp-100) REVERT: z 30 ASP cc_start: 0.8879 (t0) cc_final: 0.8641 (t0) REVERT: z 112 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9147 (ttp) outliers start: 44 outliers final: 20 residues processed: 586 average time/residue: 0.5506 time to fit residues: 361.0152 Evaluate side-chains 566 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 537 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain G residue 135 LYS Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain H residue 114 ASN Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 114 ASN Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 89 GLN Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Z residue 114 ASN Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain e residue 136 THR 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 n residue 151 THR Chi-restraints excluded: chain y residue 136 THR 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 110 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 GLN f 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.055096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.041420 restraints weight = 60601.933| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 3.95 r_work: 0.2500 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 17792 Z= 0.253 Angle : 0.771 10.275 24016 Z= 0.403 Chirality : 0.053 0.336 2592 Planarity : 0.004 0.031 3152 Dihedral : 4.509 18.651 2496 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.25 % Allowed : 28.89 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.18), residues: 2080 helix: 2.08 (0.28), residues: 320 sheet: 0.31 (0.16), residues: 944 loop : -0.56 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 147 TYR 0.015 0.001 TYR c 29 PHE 0.012 0.002 PHE v 77 HIS 0.004 0.001 HIS W 55 Details of bonding type rmsd covalent geometry : bond 0.00598 (17792) covalent geometry : angle 0.77100 (24016) hydrogen bonds : bond 0.04443 ( 640) hydrogen bonds : angle 5.23559 ( 1680) *********************** 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 603 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 562 time to evaluate : 0.458 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 139 GLU cc_start: 0.8679 (pp20) cc_final: 0.8466 (pp20) REVERT: A 140 LEU cc_start: 0.9619 (mm) cc_final: 0.9194 (mm) REVERT: B 22 ASP cc_start: 0.9227 (t0) cc_final: 0.8841 (p0) REVERT: B 30 ASP cc_start: 0.8916 (t0) cc_final: 0.8645 (t0) REVERT: B 59 GLU cc_start: 0.9331 (tt0) cc_final: 0.8684 (mt-10) REVERT: B 111 GLN cc_start: 0.8385 (tt0) cc_final: 0.8117 (tt0) REVERT: D 139 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8360 (pp20) REVERT: D 140 LEU cc_start: 0.9656 (mp) cc_final: 0.9113 (mp) REVERT: D 142 ARG cc_start: 0.9254 (ttm-80) cc_final: 0.8957 (ttm-80) REVERT: D 146 LEU cc_start: 0.8982 (mm) cc_final: 0.8686 (mm) REVERT: E 22 ASP cc_start: 0.9238 (t0) cc_final: 0.8751 (p0) REVERT: E 30 ASP cc_start: 0.8958 (t0) cc_final: 0.8660 (t0) REVERT: E 42 ASP cc_start: 0.9360 (t0) cc_final: 0.9044 (t0) REVERT: E 59 GLU cc_start: 0.9058 (tt0) cc_final: 0.8375 (tt0) REVERT: E 63 GLN cc_start: 0.9377 (mm-40) cc_final: 0.9091 (tp-100) REVERT: E 111 GLN cc_start: 0.8623 (tt0) cc_final: 0.8270 (tt0) REVERT: G 135 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7692 (ttmm) REVERT: G 142 ARG cc_start: 0.9344 (ttm-80) cc_final: 0.9102 (ttm-80) REVERT: H 22 ASP cc_start: 0.9111 (t0) cc_final: 0.8696 (p0) REVERT: H 63 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8999 (tp-100) REVERT: H 111 GLN cc_start: 0.8395 (tt0) cc_final: 0.8098 (tt0) REVERT: J 139 GLU cc_start: 0.9356 (mp0) cc_final: 0.9123 (mp0) REVERT: K 22 ASP cc_start: 0.9124 (t0) cc_final: 0.8813 (p0) REVERT: K 30 ASP cc_start: 0.8872 (t0) cc_final: 0.8654 (t0) REVERT: K 63 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8380 (tm-30) REVERT: K 112 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.9102 (ttp) REVERT: N 22 ASP cc_start: 0.9211 (t0) cc_final: 0.8777 (p0) REVERT: N 30 ASP cc_start: 0.8918 (t0) cc_final: 0.8678 (t0) REVERT: N 42 ASP cc_start: 0.9258 (t0) cc_final: 0.9010 (t0) REVERT: N 47 ASP cc_start: 0.9130 (m-30) cc_final: 0.8929 (m-30) REVERT: N 59 GLU cc_start: 0.9327 (tt0) cc_final: 0.8714 (mt-10) REVERT: N 63 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8896 (tp-100) REVERT: N 111 GLN cc_start: 0.8369 (tt0) cc_final: 0.8128 (tt0) REVERT: P 143 GLU cc_start: 0.9313 (tp30) cc_final: 0.9057 (tp30) REVERT: Q 22 ASP cc_start: 0.9233 (t0) cc_final: 0.8745 (p0) REVERT: Q 30 ASP cc_start: 0.8954 (t0) cc_final: 0.8635 (t0) REVERT: Q 42 ASP cc_start: 0.9377 (t0) cc_final: 0.9071 (t0) REVERT: Q 59 GLU cc_start: 0.9094 (tt0) cc_final: 0.8403 (tt0) REVERT: Q 63 GLN cc_start: 0.9188 (tp-100) cc_final: 0.8964 (tp-100) REVERT: Q 111 GLN cc_start: 0.8532 (tt0) cc_final: 0.8145 (tt0) REVERT: S 139 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8593 (pp20) REVERT: S 140 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.8892 (mm) REVERT: T 22 ASP cc_start: 0.9136 (t0) cc_final: 0.8712 (p0) REVERT: T 63 GLN cc_start: 0.9208 (tp-100) cc_final: 0.8997 (tp-100) REVERT: T 120 MET cc_start: 0.9324 (tpp) cc_final: 0.8853 (tpp) REVERT: u 143 GLU cc_start: 0.9420 (tp30) cc_final: 0.9182 (tp30) REVERT: v 30 ASP cc_start: 0.8835 (t0) cc_final: 0.8618 (t0) REVERT: v 63 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8590 (tm-30) REVERT: v 111 GLN cc_start: 0.8569 (tt0) cc_final: 0.8307 (tt0) REVERT: v 112 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9148 (ttp) REVERT: V 143 GLU cc_start: 0.9287 (tp30) cc_final: 0.8992 (tp30) REVERT: W 22 ASP cc_start: 0.9196 (t0) cc_final: 0.8806 (p0) REVERT: W 42 ASP cc_start: 0.9261 (t0) cc_final: 0.8992 (t0) REVERT: W 59 GLU cc_start: 0.9277 (tt0) cc_final: 0.8713 (mt-10) REVERT: W 63 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8909 (tp-100) REVERT: W 111 GLN cc_start: 0.8623 (tt0) cc_final: 0.8252 (tt0) REVERT: Z 22 ASP cc_start: 0.9243 (t0) cc_final: 0.8636 (p0) REVERT: Z 30 ASP cc_start: 0.8988 (t0) cc_final: 0.8660 (t0) REVERT: Z 42 ASP cc_start: 0.9376 (t0) cc_final: 0.9120 (t0) REVERT: Z 59 GLU cc_start: 0.9089 (tt0) cc_final: 0.8424 (tt0) REVERT: Z 111 GLN cc_start: 0.8592 (tt0) cc_final: 0.8228 (tt0) REVERT: b 142 ARG cc_start: 0.9274 (ttm-80) cc_final: 0.9043 (ttm-80) REVERT: c 22 ASP cc_start: 0.9146 (t0) cc_final: 0.8721 (p0) REVERT: c 91 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8904 (mm-30) REVERT: f 22 ASP cc_start: 0.9036 (t0) cc_final: 0.8795 (p0) REVERT: f 30 ASP cc_start: 0.8869 (t0) cc_final: 0.8661 (t0) REVERT: f 42 ASP cc_start: 0.9414 (t0) cc_final: 0.9143 (t0) REVERT: f 112 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.9105 (ttp) REVERT: h 143 GLU cc_start: 0.9235 (tp30) cc_final: 0.8909 (tp30) REVERT: i 22 ASP cc_start: 0.9215 (t0) cc_final: 0.8825 (p0) REVERT: i 42 ASP cc_start: 0.9262 (t0) cc_final: 0.8996 (t0) REVERT: i 45 GLN cc_start: 0.9044 (tp40) cc_final: 0.8128 (tm-30) REVERT: i 47 ASP cc_start: 0.9160 (m-30) cc_final: 0.8527 (m-30) REVERT: i 59 GLU cc_start: 0.9289 (tt0) cc_final: 0.8855 (tt0) REVERT: i 63 GLN cc_start: 0.9262 (mm-40) cc_final: 0.8969 (tp-100) REVERT: i 86 ILE cc_start: 0.9748 (pt) cc_final: 0.9537 (pp) REVERT: i 111 GLN cc_start: 0.8418 (tt0) cc_final: 0.8156 (tt0) REVERT: k 139 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9109 (pt0) REVERT: k 143 GLU cc_start: 0.9277 (tp30) cc_final: 0.9034 (tp30) REVERT: k 147 ARG cc_start: 0.9426 (OUTLIER) cc_final: 0.8929 (ttp80) REVERT: l 22 ASP cc_start: 0.9193 (t0) cc_final: 0.8669 (p0) REVERT: l 30 ASP cc_start: 0.8990 (t0) cc_final: 0.8673 (t0) REVERT: l 42 ASP cc_start: 0.9385 (t0) cc_final: 0.9160 (t0) REVERT: l 59 GLU cc_start: 0.9071 (tt0) cc_final: 0.8137 (tt0) REVERT: l 63 GLN cc_start: 0.9188 (tp-100) cc_final: 0.8956 (tp-100) REVERT: n 139 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8483 (pp20) REVERT: o 63 GLN cc_start: 0.9237 (tp-100) cc_final: 0.8990 (tp-100) REVERT: y 139 GLU cc_start: 0.9312 (mp0) cc_final: 0.9107 (mp0) REVERT: z 30 ASP cc_start: 0.8844 (t0) cc_final: 0.8608 (t0) REVERT: z 63 GLN cc_start: 0.9043 (tp-100) cc_final: 0.8818 (tp-100) REVERT: z 91 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8913 (mm-30) REVERT: z 112 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.9167 (ttp) outliers start: 41 outliers final: 18 residues processed: 579 average time/residue: 0.5612 time to fit residues: 363.2360 Evaluate side-chains 557 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 531 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 LYS Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 146 LEU Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain f residue 112 MET Chi-restraints excluded: chain k residue 147 ARG Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 140 LEU Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 86 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 chunk 8 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 89 GLN o 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.056398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.042771 restraints weight = 58411.154| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.88 r_work: 0.2536 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 17792 Z= 0.173 Angle : 0.791 12.101 24016 Z= 0.411 Chirality : 0.053 0.315 2592 Planarity : 0.003 0.032 3152 Dihedral : 4.525 18.315 2496 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.97 % Allowed : 29.82 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.19), residues: 2080 helix: 2.01 (0.28), residues: 320 sheet: 0.31 (0.16), residues: 944 loop : -0.49 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 147 TYR 0.013 0.001 TYR c 29 PHE 0.011 0.001 PHE E 77 HIS 0.003 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00419 (17792) covalent geometry : angle 0.79103 (24016) hydrogen bonds : bond 0.04506 ( 640) hydrogen bonds : angle 5.14950 ( 1680) *********************** 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 626 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 590 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8659 (pp20) cc_final: 0.8408 (pp20) REVERT: A 140 LEU cc_start: 0.9610 (mm) cc_final: 0.8981 (mm) REVERT: B 22 ASP cc_start: 0.9128 (t0) cc_final: 0.8789 (p0) REVERT: B 30 ASP cc_start: 0.8910 (t0) cc_final: 0.8640 (t0) REVERT: B 42 ASP cc_start: 0.9066 (t0) cc_final: 0.8715 (t0) REVERT: B 45 GLN cc_start: 0.8978 (tp40) cc_final: 0.8217 (tm-30) REVERT: B 47 ASP cc_start: 0.9073 (m-30) cc_final: 0.8423 (m-30) REVERT: B 59 GLU cc_start: 0.9311 (tt0) cc_final: 0.8683 (mt-10) REVERT: B 111 GLN cc_start: 0.8273 (tt0) cc_final: 0.8049 (tt0) REVERT: D 139 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8316 (pp20) REVERT: D 140 LEU cc_start: 0.9642 (mp) cc_final: 0.9093 (mp) REVERT: E 22 ASP cc_start: 0.9232 (t0) cc_final: 0.8742 (p0) REVERT: E 30 ASP cc_start: 0.8959 (t0) cc_final: 0.8665 (t0) REVERT: E 42 ASP cc_start: 0.9341 (t0) cc_final: 0.9025 (t0) REVERT: E 59 GLU cc_start: 0.8918 (tt0) cc_final: 0.8266 (tt0) REVERT: E 63 GLN cc_start: 0.9395 (mm-40) cc_final: 0.9084 (tp-100) REVERT: E 111 GLN cc_start: 0.8598 (tt0) cc_final: 0.8273 (tt0) REVERT: G 142 ARG cc_start: 0.9286 (ttm-80) cc_final: 0.9026 (ttm-80) REVERT: H 22 ASP cc_start: 0.9100 (t0) cc_final: 0.8835 (p0) REVERT: H 63 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8978 (tp-100) REVERT: H 111 GLN cc_start: 0.8343 (tt0) cc_final: 0.8088 (tt0) REVERT: J 139 GLU cc_start: 0.9397 (mp0) cc_final: 0.9165 (mp0) REVERT: K 22 ASP cc_start: 0.9093 (t0) cc_final: 0.8843 (p0) REVERT: K 30 ASP cc_start: 0.8837 (t0) cc_final: 0.8599 (t0) REVERT: K 42 ASP cc_start: 0.9349 (t0) cc_final: 0.9115 (t0) REVERT: K 112 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.9101 (ttp) REVERT: K 120 MET cc_start: 0.9581 (ttp) cc_final: 0.9341 (ttp) REVERT: M 139 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8197 (tm-30) REVERT: N 22 ASP cc_start: 0.9189 (t0) cc_final: 0.8779 (p0) REVERT: N 30 ASP cc_start: 0.8906 (t0) cc_final: 0.8639 (t0) REVERT: N 42 ASP cc_start: 0.9250 (t0) cc_final: 0.9021 (t0) REVERT: N 45 GLN cc_start: 0.8845 (tp40) cc_final: 0.7934 (tm-30) REVERT: N 47 ASP cc_start: 0.9089 (m-30) cc_final: 0.8468 (m-30) REVERT: N 59 GLU cc_start: 0.9361 (tt0) cc_final: 0.8837 (mt-10) REVERT: N 63 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8972 (tp-100) REVERT: N 111 GLN cc_start: 0.8268 (tt0) cc_final: 0.8068 (tt0) REVERT: P 143 GLU cc_start: 0.9315 (tp30) cc_final: 0.9055 (tp30) REVERT: Q 22 ASP cc_start: 0.9255 (t0) cc_final: 0.8813 (p0) REVERT: Q 30 ASP cc_start: 0.8934 (t0) cc_final: 0.8633 (t0) REVERT: Q 42 ASP cc_start: 0.9348 (t0) cc_final: 0.9035 (t0) REVERT: Q 59 GLU cc_start: 0.8939 (tt0) cc_final: 0.8327 (tt0) REVERT: Q 111 GLN cc_start: 0.8474 (tt0) cc_final: 0.8136 (tt0) REVERT: S 139 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8646 (pp20) REVERT: S 140 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.8850 (mm) REVERT: T 22 ASP cc_start: 0.9132 (t0) cc_final: 0.8733 (p0) REVERT: T 45 GLN cc_start: 0.8905 (tp40) cc_final: 0.8121 (tm-30) REVERT: T 47 ASP cc_start: 0.8943 (m-30) cc_final: 0.8340 (m-30) REVERT: T 63 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8967 (tp-100) REVERT: T 120 MET cc_start: 0.9308 (tpp) cc_final: 0.8832 (tpp) REVERT: u 143 GLU cc_start: 0.9378 (tp30) cc_final: 0.9139 (tp30) REVERT: v 30 ASP cc_start: 0.8780 (t0) cc_final: 0.8525 (t0) REVERT: v 57 MET cc_start: 0.8971 (mmt) cc_final: 0.8711 (mmm) REVERT: v 63 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8534 (tm-30) REVERT: v 111 GLN cc_start: 0.8576 (tt0) cc_final: 0.8282 (tt0) REVERT: v 112 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.9078 (ttp) REVERT: V 143 GLU cc_start: 0.9246 (tp30) cc_final: 0.8940 (tp30) REVERT: W 22 ASP cc_start: 0.9194 (t0) cc_final: 0.8793 (p0) REVERT: W 42 ASP cc_start: 0.9225 (t0) cc_final: 0.8975 (t0) REVERT: W 59 GLU cc_start: 0.9295 (tt0) cc_final: 0.8762 (mt-10) REVERT: W 63 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8902 (tp-100) REVERT: W 111 GLN cc_start: 0.8483 (tt0) cc_final: 0.8136 (tt0) REVERT: Z 22 ASP cc_start: 0.9253 (t0) cc_final: 0.8620 (p0) REVERT: Z 30 ASP cc_start: 0.8972 (t0) cc_final: 0.8638 (t0) REVERT: Z 42 ASP cc_start: 0.9364 (t0) cc_final: 0.9109 (t0) REVERT: Z 59 GLU cc_start: 0.9144 (tt0) cc_final: 0.8428 (tt0) REVERT: Z 63 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8889 (tp-100) REVERT: Z 111 GLN cc_start: 0.8539 (tt0) cc_final: 0.8258 (tt0) REVERT: c 22 ASP cc_start: 0.9111 (t0) cc_final: 0.8751 (p0) REVERT: c 91 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8861 (mm-30) REVERT: f 22 ASP cc_start: 0.9055 (t0) cc_final: 0.8791 (p0) REVERT: f 30 ASP cc_start: 0.8829 (t0) cc_final: 0.8587 (t0) REVERT: f 42 ASP cc_start: 0.9412 (t0) cc_final: 0.9099 (t0) REVERT: f 112 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.9022 (ttp) REVERT: h 143 GLU cc_start: 0.9224 (tp30) cc_final: 0.8894 (tp30) REVERT: i 22 ASP cc_start: 0.9183 (t0) cc_final: 0.8811 (p0) REVERT: i 42 ASP cc_start: 0.9246 (t0) cc_final: 0.8974 (t0) REVERT: i 45 GLN cc_start: 0.8881 (tp40) cc_final: 0.8013 (tm-30) REVERT: i 47 ASP cc_start: 0.9111 (m-30) cc_final: 0.8572 (m-30) REVERT: i 59 GLU cc_start: 0.9292 (tt0) cc_final: 0.8738 (mt-10) REVERT: i 63 GLN cc_start: 0.9245 (mm-40) cc_final: 0.8961 (tp-100) REVERT: i 86 ILE cc_start: 0.9738 (pt) cc_final: 0.9504 (pp) REVERT: i 111 GLN cc_start: 0.8369 (tt0) cc_final: 0.8116 (tt0) REVERT: k 139 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9126 (pt0) REVERT: k 143 GLU cc_start: 0.9274 (tp30) cc_final: 0.9043 (tp30) REVERT: k 147 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.8789 (ttp80) REVERT: l 22 ASP cc_start: 0.9188 (t0) cc_final: 0.8666 (p0) REVERT: l 30 ASP cc_start: 0.8983 (t0) cc_final: 0.8664 (t0) REVERT: l 42 ASP cc_start: 0.9350 (t0) cc_final: 0.9118 (t0) REVERT: l 59 GLU cc_start: 0.9007 (tt0) cc_final: 0.8308 (tt0) REVERT: l 63 GLN cc_start: 0.9167 (tp-100) cc_final: 0.8854 (tp-100) REVERT: l 111 GLN cc_start: 0.8590 (tt0) cc_final: 0.8199 (tt0) REVERT: o 45 GLN cc_start: 0.8864 (tp40) cc_final: 0.8075 (tm-30) REVERT: o 47 ASP cc_start: 0.9004 (m-30) cc_final: 0.8469 (m-30) REVERT: o 63 GLN cc_start: 0.9247 (tp-100) cc_final: 0.9008 (tp-100) REVERT: z 30 ASP cc_start: 0.8846 (t0) cc_final: 0.8572 (t0) REVERT: z 86 ILE cc_start: 0.9769 (pt) cc_final: 0.9565 (pp) REVERT: z 112 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.9083 (ttp) outliers start: 36 outliers final: 13 residues processed: 606 average time/residue: 0.5901 time to fit residues: 400.7171 Evaluate side-chains 570 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 550 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain H residue 63 GLN Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain f residue 112 MET Chi-restraints excluded: chain k residue 147 ARG Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 19 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.057340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.043757 restraints weight = 58034.986| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.86 r_work: 0.2563 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 17792 Z= 0.169 Angle : 0.848 15.247 24016 Z= 0.432 Chirality : 0.056 0.404 2592 Planarity : 0.004 0.050 3152 Dihedral : 4.532 19.607 2496 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.15 % Allowed : 31.36 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.19), residues: 2080 helix: 1.74 (0.29), residues: 320 sheet: 0.30 (0.16), residues: 944 loop : -0.44 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG e 147 TYR 0.014 0.001 TYR V 138 PHE 0.011 0.001 PHE l 77 HIS 0.003 0.000 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00416 (17792) covalent geometry : angle 0.84771 (24016) hydrogen bonds : bond 0.04729 ( 640) hydrogen bonds : angle 5.06687 ( 1680) ********************** 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 611 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 590 time to evaluate : 0.627 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: A 140 LEU cc_start: 0.9517 (mm) cc_final: 0.9154 (mm) REVERT: A 150 LEU cc_start: 0.9038 (mt) cc_final: 0.8784 (tp) REVERT: B 22 ASP cc_start: 0.9111 (t0) cc_final: 0.8795 (p0) REVERT: B 30 ASP cc_start: 0.8931 (t0) cc_final: 0.8677 (t0) REVERT: B 42 ASP cc_start: 0.9041 (t0) cc_final: 0.8668 (t0) REVERT: B 45 GLN cc_start: 0.8913 (tp40) cc_final: 0.8170 (tm-30) REVERT: B 47 ASP cc_start: 0.9046 (m-30) cc_final: 0.8357 (m-30) REVERT: B 59 GLU cc_start: 0.9312 (tt0) cc_final: 0.8720 (mt-10) REVERT: B 63 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8611 (tp-100) REVERT: B 111 GLN cc_start: 0.8285 (tt0) cc_final: 0.8058 (tt0) REVERT: D 139 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8281 (pp20) REVERT: D 140 LEU cc_start: 0.9659 (mp) cc_final: 0.9043 (mp) REVERT: E 22 ASP cc_start: 0.9214 (t0) cc_final: 0.8828 (p0) REVERT: E 30 ASP cc_start: 0.8952 (t0) cc_final: 0.8679 (t0) REVERT: E 42 ASP cc_start: 0.9338 (t0) cc_final: 0.9032 (t0) REVERT: E 45 GLN cc_start: 0.8759 (tp40) cc_final: 0.8425 (tm-30) REVERT: E 59 GLU cc_start: 0.8910 (tt0) cc_final: 0.8312 (tt0) REVERT: E 63 GLN cc_start: 0.9393 (mm-40) cc_final: 0.9056 (tp-100) REVERT: E 111 GLN cc_start: 0.8529 (tt0) cc_final: 0.8282 (tt0) REVERT: H 22 ASP cc_start: 0.9085 (t0) cc_final: 0.8836 (p0) REVERT: H 45 GLN cc_start: 0.8800 (tp40) cc_final: 0.8349 (tp-100) REVERT: H 63 GLN cc_start: 0.9236 (tp-100) cc_final: 0.9000 (tp-100) REVERT: H 111 GLN cc_start: 0.8343 (tt0) cc_final: 0.8090 (tt0) REVERT: K 30 ASP cc_start: 0.8809 (t0) cc_final: 0.8551 (t0) REVERT: K 42 ASP cc_start: 0.9363 (t0) cc_final: 0.9116 (t0) REVERT: K 60 GLU cc_start: 0.8859 (mp0) cc_final: 0.8618 (mm-30) REVERT: K 112 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.9082 (ttp) REVERT: K 120 MET cc_start: 0.9594 (ttp) cc_final: 0.9346 (ttp) REVERT: M 139 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8171 (tm-30) REVERT: M 143 GLU cc_start: 0.8606 (pp20) cc_final: 0.8370 (pm20) REVERT: N 22 ASP cc_start: 0.9159 (t0) cc_final: 0.8798 (p0) REVERT: N 30 ASP cc_start: 0.8948 (t0) cc_final: 0.8693 (t0) REVERT: N 42 ASP cc_start: 0.9206 (t0) cc_final: 0.8983 (t0) REVERT: N 45 GLN cc_start: 0.8773 (tp40) cc_final: 0.7949 (tm-30) REVERT: N 47 ASP cc_start: 0.9069 (m-30) cc_final: 0.8445 (m-30) REVERT: N 63 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8960 (tp-100) REVERT: P 143 GLU cc_start: 0.9329 (tp30) cc_final: 0.9069 (tp30) REVERT: Q 22 ASP cc_start: 0.9218 (t0) cc_final: 0.8829 (p0) REVERT: Q 30 ASP cc_start: 0.8989 (t0) cc_final: 0.8702 (t0) REVERT: Q 42 ASP cc_start: 0.9356 (t0) cc_final: 0.9054 (t0) REVERT: Q 45 GLN cc_start: 0.8814 (tp40) cc_final: 0.8369 (tm-30) REVERT: Q 59 GLU cc_start: 0.8970 (tt0) cc_final: 0.8244 (tt0) REVERT: Q 111 GLN cc_start: 0.8523 (tt0) cc_final: 0.8186 (tt0) REVERT: S 139 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8641 (pp20) REVERT: S 140 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.8940 (mm) REVERT: T 22 ASP cc_start: 0.9116 (t0) cc_final: 0.8746 (p0) REVERT: T 45 GLN cc_start: 0.8824 (tp40) cc_final: 0.8061 (tm-30) REVERT: T 47 ASP cc_start: 0.8943 (m-30) cc_final: 0.8356 (m-30) REVERT: T 120 MET cc_start: 0.9281 (tpp) cc_final: 0.8918 (tpp) REVERT: u 143 GLU cc_start: 0.9380 (tp30) cc_final: 0.9149 (tp30) REVERT: v 30 ASP cc_start: 0.8872 (t0) cc_final: 0.8609 (t0) REVERT: v 57 MET cc_start: 0.8923 (mmt) cc_final: 0.8702 (mmm) REVERT: v 63 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8538 (tm-30) REVERT: v 111 GLN cc_start: 0.8596 (tt0) cc_final: 0.8313 (tt0) REVERT: v 112 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.9003 (ttp) REVERT: V 143 GLU cc_start: 0.9248 (tp30) cc_final: 0.8945 (tp30) REVERT: W 22 ASP cc_start: 0.9145 (t0) cc_final: 0.8829 (p0) REVERT: W 45 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8095 (tm-30) REVERT: W 47 ASP cc_start: 0.8992 (m-30) cc_final: 0.8355 (m-30) REVERT: W 59 GLU cc_start: 0.9326 (tt0) cc_final: 0.8837 (mt-10) REVERT: W 63 GLN cc_start: 0.9145 (tp-100) cc_final: 0.8885 (tp-100) REVERT: W 111 GLN cc_start: 0.8459 (tt0) cc_final: 0.8140 (tt0) REVERT: Z 22 ASP cc_start: 0.9241 (t0) cc_final: 0.8627 (p0) REVERT: Z 30 ASP cc_start: 0.8989 (t0) cc_final: 0.8689 (t0) REVERT: Z 42 ASP cc_start: 0.9331 (t0) cc_final: 0.9093 (t0) REVERT: Z 59 GLU cc_start: 0.9109 (tt0) cc_final: 0.8364 (tt0) REVERT: Z 63 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8870 (tp-100) REVERT: Z 111 GLN cc_start: 0.8535 (tt0) cc_final: 0.8328 (tt0) REVERT: b 135 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6985 (ttmm) REVERT: c 22 ASP cc_start: 0.9084 (t0) cc_final: 0.8750 (p0) REVERT: c 91 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8884 (mm-30) REVERT: f 30 ASP cc_start: 0.8780 (t0) cc_final: 0.8535 (t0) REVERT: f 42 ASP cc_start: 0.9416 (t0) cc_final: 0.9112 (t0) REVERT: h 143 GLU cc_start: 0.9224 (tp30) cc_final: 0.8895 (tp30) REVERT: i 22 ASP cc_start: 0.9158 (t0) cc_final: 0.8828 (p0) REVERT: i 42 ASP cc_start: 0.9252 (t0) cc_final: 0.9008 (t0) REVERT: i 45 GLN cc_start: 0.8789 (tp40) cc_final: 0.7911 (tm-30) REVERT: i 47 ASP cc_start: 0.9069 (m-30) cc_final: 0.8472 (m-30) REVERT: i 59 GLU cc_start: 0.9319 (tt0) cc_final: 0.8773 (mt-10) REVERT: i 63 GLN cc_start: 0.9261 (mm-40) cc_final: 0.9027 (tp-100) REVERT: i 86 ILE cc_start: 0.9751 (pt) cc_final: 0.9523 (pp) REVERT: i 111 GLN cc_start: 0.8324 (tt0) cc_final: 0.8072 (tt0) REVERT: k 139 GLU cc_start: 0.9413 (mt-10) cc_final: 0.9144 (pt0) REVERT: k 143 GLU cc_start: 0.9287 (tp30) cc_final: 0.9044 (tp30) REVERT: k 147 ARG cc_start: 0.9394 (OUTLIER) cc_final: 0.8848 (ttp80) REVERT: l 22 ASP cc_start: 0.9201 (t0) cc_final: 0.8684 (p0) REVERT: l 30 ASP cc_start: 0.8989 (t0) cc_final: 0.8681 (t0) REVERT: l 42 ASP cc_start: 0.9345 (t0) cc_final: 0.9123 (t0) REVERT: l 59 GLU cc_start: 0.8982 (tt0) cc_final: 0.8090 (tt0) REVERT: l 63 GLN cc_start: 0.9160 (tp-100) cc_final: 0.8850 (tp-100) REVERT: l 111 GLN cc_start: 0.8578 (tt0) cc_final: 0.8214 (tt0) REVERT: n 143 GLU cc_start: 0.9134 (tp30) cc_final: 0.8890 (tm-30) REVERT: n 147 ARG cc_start: 0.9413 (ttm110) cc_final: 0.9025 (ttm110) REVERT: o 45 GLN cc_start: 0.8755 (tp40) cc_final: 0.7988 (tm-30) REVERT: o 47 ASP cc_start: 0.8981 (m-30) cc_final: 0.8393 (m-30) REVERT: o 63 GLN cc_start: 0.9214 (tp-100) cc_final: 0.8988 (tp-100) REVERT: z 30 ASP cc_start: 0.8784 (t0) cc_final: 0.8515 (t0) REVERT: z 63 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8844 (tp-100) REVERT: z 112 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.9076 (ttp) REVERT: z 120 MET cc_start: 0.9589 (ttp) cc_final: 0.9280 (ttp) outliers start: 21 outliers final: 15 residues processed: 601 average time/residue: 0.5363 time to fit residues: 362.4944 Evaluate side-chains 579 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 558 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 112 MET Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain S residue 140 LEU Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain u residue 136 THR Chi-restraints excluded: chain v residue 112 MET Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 136 THR Chi-restraints excluded: chain b residue 135 LYS Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain k residue 147 ARG Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 140 LEU Chi-restraints excluded: chain z residue 112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 84 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 135 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.056011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.042280 restraints weight = 61143.824| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.98 r_work: 0.2519 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 17792 Z= 0.223 Angle : 0.888 14.441 24016 Z= 0.450 Chirality : 0.057 0.405 2592 Planarity : 0.004 0.051 3152 Dihedral : 4.638 20.979 2496 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.26 % Allowed : 31.14 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.19), residues: 2080 helix: 1.49 (0.30), residues: 320 sheet: 0.32 (0.16), residues: 944 loop : -0.43 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 147 TYR 0.015 0.001 TYR c 29 PHE 0.011 0.002 PHE l 77 HIS 0.004 0.001 HIS H 55 Details of bonding type rmsd covalent geometry : bond 0.00539 (17792) covalent geometry : angle 0.88777 (24016) hydrogen bonds : bond 0.04817 ( 640) hydrogen bonds : angle 5.24748 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7389.52 seconds wall clock time: 126 minutes 27.00 seconds (7587.00 seconds total)