Starting phenix.real_space_refine on Thu Sep 18 20:24:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zuj_60485/09_2025/8zuj_60485.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zuj_60485/09_2025/8zuj_60485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zuj_60485/09_2025/8zuj_60485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zuj_60485/09_2025/8zuj_60485.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zuj_60485/09_2025/8zuj_60485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zuj_60485/09_2025/8zuj_60485.map" } resolution = 2.58 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= -0.000 sd= 0.062 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 135 5.16 5 C 12750 2.51 5 N 3240 2.21 5 O 3705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 19830 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 179 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "D" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1143 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 138} Restraints were copied for chains: B, C, G, H, I, M, N, O, S, T, U, Y, Z, a, E, F, J, K, L, P, Q, R, V, W, X, b, c, d Time building chain proxies: 2.07, per 1000 atoms: 0.10 Number of scatterers: 19830 At special positions: 0 Unit cell: (162.756, 166.866, 73.98, 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 135 16.00 O 3705 8.00 N 3240 7.00 C 12750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 32 " distance=2.03 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 35 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 32 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 32 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 32 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 32 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 32 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 32 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 32 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 32 " distance=2.03 Simple disulfide: pdb=" SG CYS S 19 " - pdb=" SG CYS S 32 " distance=2.03 Simple disulfide: pdb=" SG CYS T 19 " - pdb=" SG CYS T 32 " distance=2.03 Simple disulfide: pdb=" SG CYS U 19 " - pdb=" SG CYS U 32 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 19 " - pdb=" SG CYS Y 32 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 19 " - pdb=" SG CYS Z 32 " distance=2.03 Simple disulfide: pdb=" SG CYS a 19 " - pdb=" SG CYS a 32 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 35 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 35 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 35 " distance=2.03 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 35 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 35 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 35 " distance=2.03 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 35 " distance=2.03 Simple disulfide: pdb=" SG CYS O 24 " - pdb=" SG CYS O 35 " distance=2.03 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 35 " distance=2.03 Simple disulfide: pdb=" SG CYS T 24 " - pdb=" SG CYS T 35 " distance=2.03 Simple disulfide: pdb=" SG CYS U 24 " - pdb=" SG CYS U 35 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 24 " - pdb=" SG CYS Y 35 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 24 " - pdb=" SG CYS Z 35 " distance=2.03 Simple disulfide: pdb=" SG CYS a 24 " - pdb=" SG CYS a 35 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 868.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4710 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 60 sheets defined 1.8% alpha, 45.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'C' and resid 36 through 38 No H-bonds generated for 'chain 'C' and resid 36 through 38' Processing helix chain 'G' and resid 36 through 38 No H-bonds generated for 'chain 'G' and resid 36 through 38' Processing helix chain 'H' and resid 36 through 38 No H-bonds generated for 'chain 'H' and resid 36 through 38' Processing helix chain 'I' and resid 36 through 38 No H-bonds generated for 'chain 'I' and resid 36 through 38' Processing helix chain 'M' and resid 36 through 38 No H-bonds generated for 'chain 'M' and resid 36 through 38' Processing helix chain 'N' and resid 36 through 38 No H-bonds generated for 'chain 'N' and resid 36 through 38' Processing helix chain 'O' and resid 36 through 38 No H-bonds generated for 'chain 'O' and resid 36 through 38' Processing helix chain 'S' and resid 36 through 38 No H-bonds generated for 'chain 'S' and resid 36 through 38' Processing helix chain 'T' and resid 36 through 38 No H-bonds generated for 'chain 'T' and resid 36 through 38' Processing helix chain 'U' and resid 36 through 38 No H-bonds generated for 'chain 'U' and resid 36 through 38' Processing helix chain 'Y' and resid 36 through 38 No H-bonds generated for 'chain 'Y' and resid 36 through 38' Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'a' and resid 36 through 38 No H-bonds generated for 'chain 'a' and resid 36 through 38' Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 26 Processing sheet with id=AA4, first strand: chain 'D' and resid 168 through 174 removed outlier: 6.626A pdb=" N GLN D 148 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS D 173 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N CYS D 146 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 158 through 159 Processing sheet with id=AA6, first strand: chain 'D' and resid 158 through 159 removed outlier: 6.526A pdb=" N MET D 208 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE D 233 " --> pdb=" O MET D 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS D 210 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG D 231 " --> pdb=" O HIS D 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE D 212 " --> pdb=" O LEU D 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 168 through 174 removed outlier: 6.626A pdb=" N GLN E 148 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS E 173 " --> pdb=" O CYS E 146 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS E 146 " --> pdb=" O LYS E 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 158 through 159 Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 159 removed outlier: 6.526A pdb=" N MET E 208 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE E 233 " --> pdb=" O MET E 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS E 210 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG E 231 " --> pdb=" O HIS E 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE E 212 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 168 through 174 removed outlier: 6.626A pdb=" N GLN F 148 " --> pdb=" O SER F 171 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS F 173 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N CYS F 146 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 159 Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 159 removed outlier: 6.527A pdb=" N MET F 208 " --> pdb=" O ILE F 233 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE F 233 " --> pdb=" O MET F 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS F 210 " --> pdb=" O ARG F 231 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG F 231 " --> pdb=" O HIS F 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE F 212 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 23 through 26 Processing sheet with id=AB5, first strand: chain 'H' and resid 23 through 26 Processing sheet with id=AB6, first strand: chain 'I' and resid 23 through 26 Processing sheet with id=AB7, first strand: chain 'J' and resid 168 through 174 removed outlier: 6.626A pdb=" N GLN J 148 " --> pdb=" O SER J 171 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS J 173 " --> pdb=" O CYS J 146 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS J 146 " --> pdb=" O LYS J 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 158 through 159 Processing sheet with id=AB9, first strand: chain 'J' and resid 158 through 159 removed outlier: 6.526A pdb=" N MET J 208 " --> pdb=" O ILE J 233 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE J 233 " --> pdb=" O MET J 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS J 210 " --> pdb=" O ARG J 231 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG J 231 " --> pdb=" O HIS J 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE J 212 " --> pdb=" O LEU J 229 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 168 through 174 removed outlier: 6.626A pdb=" N GLN K 148 " --> pdb=" O SER K 171 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS K 173 " --> pdb=" O CYS K 146 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS K 146 " --> pdb=" O LYS K 173 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 158 through 159 Processing sheet with id=AC3, first strand: chain 'K' and resid 158 through 159 removed outlier: 6.526A pdb=" N MET K 208 " --> pdb=" O ILE K 233 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE K 233 " --> pdb=" O MET K 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS K 210 " --> pdb=" O ARG K 231 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG K 231 " --> pdb=" O HIS K 210 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE K 212 " --> pdb=" O LEU K 229 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 168 through 174 removed outlier: 6.626A pdb=" N GLN L 148 " --> pdb=" O SER L 171 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS L 173 " --> pdb=" O CYS L 146 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS L 146 " --> pdb=" O LYS L 173 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 158 through 159 Processing sheet with id=AC6, first strand: chain 'L' and resid 158 through 159 removed outlier: 6.527A pdb=" N MET L 208 " --> pdb=" O ILE L 233 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE L 233 " --> pdb=" O MET L 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS L 210 " --> pdb=" O ARG L 231 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG L 231 " --> pdb=" O HIS L 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE L 212 " --> pdb=" O LEU L 229 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 23 through 26 Processing sheet with id=AC8, first strand: chain 'N' and resid 23 through 26 Processing sheet with id=AC9, first strand: chain 'O' and resid 23 through 26 Processing sheet with id=AD1, first strand: chain 'P' and resid 168 through 174 removed outlier: 6.626A pdb=" N GLN P 148 " --> pdb=" O SER P 171 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS P 173 " --> pdb=" O CYS P 146 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS P 146 " --> pdb=" O LYS P 173 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 158 through 159 Processing sheet with id=AD3, first strand: chain 'P' and resid 158 through 159 removed outlier: 6.526A pdb=" N MET P 208 " --> pdb=" O ILE P 233 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE P 233 " --> pdb=" O MET P 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS P 210 " --> pdb=" O ARG P 231 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG P 231 " --> pdb=" O HIS P 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE P 212 " --> pdb=" O LEU P 229 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 168 through 174 removed outlier: 6.627A pdb=" N GLN Q 148 " --> pdb=" O SER Q 171 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS Q 173 " --> pdb=" O CYS Q 146 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS Q 146 " --> pdb=" O LYS Q 173 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 158 through 159 Processing sheet with id=AD6, first strand: chain 'Q' and resid 158 through 159 removed outlier: 6.526A pdb=" N MET Q 208 " --> pdb=" O ILE Q 233 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE Q 233 " --> pdb=" O MET Q 208 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N HIS Q 210 " --> pdb=" O ARG Q 231 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG Q 231 " --> pdb=" O HIS Q 210 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE Q 212 " --> pdb=" O LEU Q 229 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 168 through 174 removed outlier: 6.625A pdb=" N GLN R 148 " --> pdb=" O SER R 171 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS R 173 " --> pdb=" O CYS R 146 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N CYS R 146 " --> pdb=" O LYS R 173 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 158 through 159 Processing sheet with id=AD9, first strand: chain 'R' and resid 158 through 159 removed outlier: 6.527A pdb=" N MET R 208 " --> pdb=" O ILE R 233 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE R 233 " --> pdb=" O MET R 208 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N HIS R 210 " --> pdb=" O ARG R 231 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG R 231 " --> pdb=" O HIS R 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE R 212 " --> pdb=" O LEU R 229 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 23 through 26 Processing sheet with id=AE2, first strand: chain 'T' and resid 23 through 26 Processing sheet with id=AE3, first strand: chain 'U' and resid 23 through 26 Processing sheet with id=AE4, first strand: chain 'V' and resid 168 through 174 removed outlier: 6.626A pdb=" N GLN V 148 " --> pdb=" O SER V 171 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS V 173 " --> pdb=" O CYS V 146 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS V 146 " --> pdb=" O LYS V 173 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 158 through 159 Processing sheet with id=AE6, first strand: chain 'V' and resid 158 through 159 removed outlier: 6.527A pdb=" N MET V 208 " --> pdb=" O ILE V 233 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE V 233 " --> pdb=" O MET V 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS V 210 " --> pdb=" O ARG V 231 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG V 231 " --> pdb=" O HIS V 210 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE V 212 " --> pdb=" O LEU V 229 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 168 through 174 removed outlier: 6.625A pdb=" N GLN W 148 " --> pdb=" O SER W 171 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS W 173 " --> pdb=" O CYS W 146 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS W 146 " --> pdb=" O LYS W 173 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 158 through 159 Processing sheet with id=AE9, first strand: chain 'W' and resid 158 through 159 removed outlier: 6.526A pdb=" N MET W 208 " --> pdb=" O ILE W 233 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE W 233 " --> pdb=" O MET W 208 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N HIS W 210 " --> pdb=" O ARG W 231 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG W 231 " --> pdb=" O HIS W 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE W 212 " --> pdb=" O LEU W 229 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 168 through 174 removed outlier: 6.626A pdb=" N GLN X 148 " --> pdb=" O SER X 171 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS X 173 " --> pdb=" O CYS X 146 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N CYS X 146 " --> pdb=" O LYS X 173 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 158 through 159 Processing sheet with id=AF3, first strand: chain 'X' and resid 158 through 159 removed outlier: 6.527A pdb=" N MET X 208 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE X 233 " --> pdb=" O MET X 208 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N HIS X 210 " --> pdb=" O ARG X 231 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ARG X 231 " --> pdb=" O HIS X 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE X 212 " --> pdb=" O LEU X 229 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 23 through 26 Processing sheet with id=AF5, first strand: chain 'Z' and resid 23 through 26 Processing sheet with id=AF6, first strand: chain 'a' and resid 23 through 26 Processing sheet with id=AF7, first strand: chain 'b' and resid 168 through 174 removed outlier: 6.627A pdb=" N GLN b 148 " --> pdb=" O SER b 171 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS b 173 " --> pdb=" O CYS b 146 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS b 146 " --> pdb=" O LYS b 173 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 158 through 159 Processing sheet with id=AF9, first strand: chain 'b' and resid 158 through 159 removed outlier: 6.526A pdb=" N MET b 208 " --> pdb=" O ILE b 233 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE b 233 " --> pdb=" O MET b 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS b 210 " --> pdb=" O ARG b 231 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG b 231 " --> pdb=" O HIS b 210 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE b 212 " --> pdb=" O LEU b 229 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 168 through 174 removed outlier: 6.626A pdb=" N GLN c 148 " --> pdb=" O SER c 171 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS c 173 " --> pdb=" O CYS c 146 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N CYS c 146 " --> pdb=" O LYS c 173 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'c' and resid 158 through 159 Processing sheet with id=AG3, first strand: chain 'c' and resid 158 through 159 removed outlier: 6.527A pdb=" N MET c 208 " --> pdb=" O ILE c 233 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE c 233 " --> pdb=" O MET c 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS c 210 " --> pdb=" O ARG c 231 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG c 231 " --> pdb=" O HIS c 210 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE c 212 " --> pdb=" O LEU c 229 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'd' and resid 168 through 174 removed outlier: 6.626A pdb=" N GLN d 148 " --> pdb=" O SER d 171 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS d 173 " --> pdb=" O CYS d 146 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N CYS d 146 " --> pdb=" O LYS d 173 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 158 through 159 Processing sheet with id=AG6, first strand: chain 'd' and resid 158 through 159 removed outlier: 6.527A pdb=" N MET d 208 " --> pdb=" O ILE d 233 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE d 233 " --> pdb=" O MET d 208 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS d 210 " --> pdb=" O ARG d 231 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ARG d 231 " --> pdb=" O HIS d 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE d 212 " --> pdb=" O LEU d 229 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6360 1.35 - 1.47: 4507 1.47 - 1.59: 9188 1.59 - 1.71: 0 1.71 - 1.83: 165 Bond restraints: 20220 Sorted by residual: bond pdb=" CB VAL M 20 " pdb=" CG2 VAL M 20 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.94e-01 bond pdb=" CB VAL Y 20 " pdb=" CG2 VAL Y 20 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.94e-01 bond pdb=" CB VAL H 20 " pdb=" CG2 VAL H 20 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.93e-01 bond pdb=" CB VAL B 20 " pdb=" CG2 VAL B 20 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.89e-01 bond pdb=" CB VAL O 20 " pdb=" CG2 VAL O 20 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.86e-01 ... (remaining 20215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 25881 1.22 - 2.45: 1233 2.45 - 3.67: 216 3.67 - 4.89: 30 4.89 - 6.11: 15 Bond angle restraints: 27375 Sorted by residual: angle pdb=" C PRO C 21 " pdb=" N ALA C 22 " pdb=" CA ALA C 22 " ideal model delta sigma weight residual 122.19 125.32 -3.13 1.41e+00 5.03e-01 4.92e+00 angle pdb=" C PRO I 21 " pdb=" N ALA I 22 " pdb=" CA ALA I 22 " ideal model delta sigma weight residual 122.19 125.29 -3.10 1.41e+00 5.03e-01 4.83e+00 angle pdb=" C PRO a 21 " pdb=" N ALA a 22 " pdb=" CA ALA a 22 " ideal model delta sigma weight residual 122.19 125.29 -3.10 1.41e+00 5.03e-01 4.82e+00 angle pdb=" N PRO M 21 " pdb=" CA PRO M 21 " pdb=" C PRO M 21 " ideal model delta sigma weight residual 111.21 114.69 -3.48 1.59e+00 3.96e-01 4.80e+00 angle pdb=" C PRO A 21 " pdb=" N ALA A 22 " pdb=" CA ALA A 22 " ideal model delta sigma weight residual 122.19 125.28 -3.09 1.41e+00 5.03e-01 4.80e+00 ... (remaining 27370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 10770 15.92 - 31.84: 1005 31.84 - 47.76: 375 47.76 - 63.68: 90 63.68 - 79.61: 30 Dihedral angle restraints: 12270 sinusoidal: 4980 harmonic: 7290 Sorted by residual: dihedral pdb=" N LYS D 204 " pdb=" CA LYS D 204 " pdb=" CB LYS D 204 " pdb=" CG LYS D 204 " ideal model delta sinusoidal sigma weight residual -60.00 -111.01 51.01 3 1.50e+01 4.44e-03 8.97e+00 dihedral pdb=" N LYS c 204 " pdb=" CA LYS c 204 " pdb=" CB LYS c 204 " pdb=" CG LYS c 204 " ideal model delta sinusoidal sigma weight residual -60.00 -111.00 51.00 3 1.50e+01 4.44e-03 8.97e+00 dihedral pdb=" N LYS K 204 " pdb=" CA LYS K 204 " pdb=" CB LYS K 204 " pdb=" CG LYS K 204 " ideal model delta sinusoidal sigma weight residual -60.00 -111.00 51.00 3 1.50e+01 4.44e-03 8.96e+00 ... (remaining 12267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1880 0.029 - 0.058: 825 0.058 - 0.087: 193 0.087 - 0.116: 228 0.116 - 0.145: 39 Chirality restraints: 3165 Sorted by residual: chirality pdb=" CA ILE K 212 " pdb=" N ILE K 212 " pdb=" C ILE K 212 " pdb=" CB ILE K 212 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE c 212 " pdb=" N ILE c 212 " pdb=" C ILE c 212 " pdb=" CB ILE c 212 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE P 212 " pdb=" N ILE P 212 " pdb=" C ILE P 212 " pdb=" CB ILE P 212 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 3162 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU c 179 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.33e+00 pdb=" C GLU c 179 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU c 179 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU c 180 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 179 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C GLU F 179 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU F 179 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU F 180 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 179 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C GLU E 179 " -0.020 2.00e-02 2.50e+03 pdb=" O GLU E 179 " 0.007 2.00e-02 2.50e+03 pdb=" N GLU E 180 " 0.007 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 220 2.60 - 3.18: 15065 3.18 - 3.75: 29585 3.75 - 4.33: 44906 4.33 - 4.90: 78401 Nonbonded interactions: 168177 Sorted by model distance: nonbonded pdb=" SG CYS Q 232 " pdb=" SG CYS Q 245 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS K 232 " pdb=" SG CYS K 245 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS E 232 " pdb=" SG CYS E 245 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS P 232 " pdb=" SG CYS P 245 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS D 232 " pdb=" SG CYS D 245 " model vdw 2.028 3.760 ... (remaining 168172 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 4.340 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.850 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 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 : 0.003 0.029 20250 Z= 0.134 Angle : 0.619 6.113 27435 Z= 0.339 Chirality : 0.043 0.145 3165 Planarity : 0.003 0.019 3480 Dihedral : 15.028 79.605 7470 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.68 % Allowed : 12.24 % Favored : 87.07 % 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: -0.31 (0.16), residues: 2460 helix: None (None), residues: 0 sheet: 1.18 (0.15), residues: 1185 loop : -1.68 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 265 TYR 0.006 0.001 TYR F 192 PHE 0.005 0.001 PHE K 230 TRP 0.003 0.001 TRP P 168 HIS 0.001 0.000 HIS P 210 Details of bonding type rmsd covalent geometry : bond 0.00260 (20220) covalent geometry : angle 0.61668 (27375) SS BOND : bond 0.00198 ( 30) SS BOND : angle 1.33732 ( 60) hydrogen bonds : bond 0.10915 ( 690) hydrogen bonds : angle 7.57678 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 413 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 236 MET cc_start: 0.6501 (mmm) cc_final: 0.6201 (mmt) REVERT: b 204 LYS cc_start: 0.7317 (mttp) cc_final: 0.6787 (mptt) outliers start: 15 outliers final: 8 residues processed: 423 average time/residue: 0.5627 time to fit residues: 271.1184 Evaluate side-chains 304 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 296 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain K residue 233 ILE Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain V residue 233 ILE Chi-restraints excluded: chain b residue 233 ILE Chi-restraints excluded: chain c residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0030 chunk 235 optimal weight: 4.9990 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 198 GLN D 242 ASN D 243 ASN D 260 GLN E 218 HIS E 243 ASN E 260 GLN F 218 HIS F 234 GLN F 235 ASN F 243 ASN H 31 HIS J 198 GLN K 218 HIS K 260 GLN L 218 HIS L 234 GLN L 235 ASN L 243 ASN P 198 GLN P 260 GLN Q 218 HIS Q 234 GLN R 218 HIS R 234 GLN R 235 ASN V 198 GLN V 243 ASN W 218 HIS W 234 GLN W 260 GLN X 218 HIS X 234 GLN X 235 ASN b 198 GLN b 260 GLN ** c 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 218 HIS c 234 GLN c 260 GLN d 218 HIS d 235 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.204556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.154118 restraints weight = 17927.481| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.77 r_work: 0.4178 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20250 Z= 0.190 Angle : 0.629 8.758 27435 Z= 0.324 Chirality : 0.044 0.153 3165 Planarity : 0.005 0.067 3480 Dihedral : 4.370 30.942 2701 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.49 % Allowed : 16.87 % Favored : 76.64 % 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: -0.54 (0.16), residues: 2460 helix: None (None), residues: 0 sheet: 0.86 (0.15), residues: 1185 loop : -1.65 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 174 TYR 0.015 0.002 TYR J 246 PHE 0.012 0.002 PHE X 194 TRP 0.008 0.002 TRP L 168 HIS 0.007 0.001 HIS c 210 Details of bonding type rmsd covalent geometry : bond 0.00422 (20220) covalent geometry : angle 0.62546 (27375) SS BOND : bond 0.00314 ( 30) SS BOND : angle 1.52049 ( 60) hydrogen bonds : bond 0.04558 ( 690) hydrogen bonds : angle 6.14645 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 338 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 231 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7023 (tmt90) REVERT: F 179 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: J 231 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7021 (tmt90) REVERT: J 242 ASN cc_start: 0.6796 (OUTLIER) cc_final: 0.6332 (p0) REVERT: K 215 LYS cc_start: 0.7132 (tptp) cc_final: 0.6857 (tptp) REVERT: L 179 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: L 257 ASP cc_start: 0.6290 (m-30) cc_final: 0.5554 (m-30) REVERT: P 231 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6989 (tmt90) REVERT: P 242 ASN cc_start: 0.6451 (OUTLIER) cc_final: 0.6160 (p0) REVERT: Q 215 LYS cc_start: 0.7171 (tptp) cc_final: 0.6968 (tptp) REVERT: R 211 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7731 (mt) REVERT: R 252 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.5563 (tmtm) REVERT: V 234 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7144 (mm-40) REVERT: W 240 LEU cc_start: 0.6391 (mt) cc_final: 0.6181 (mt) REVERT: W 267 ASN cc_start: 0.5180 (t0) cc_final: 0.4614 (p0) REVERT: X 179 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: X 232 CYS cc_start: 0.6501 (OUTLIER) cc_final: 0.6048 (t) REVERT: b 204 LYS cc_start: 0.7693 (mttp) cc_final: 0.7036 (mptt) REVERT: b 242 ASN cc_start: 0.6688 (OUTLIER) cc_final: 0.6307 (p0) REVERT: d 179 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7807 (mm-30) REVERT: d 184 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7502 (mttm) REVERT: d 235 ASN cc_start: 0.6455 (m110) cc_final: 0.6165 (m110) outliers start: 143 outliers final: 50 residues processed: 441 average time/residue: 0.5661 time to fit residues: 286.0290 Evaluate side-chains 361 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 297 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 232 CYS Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain J residue 231 ARG Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 242 ASN Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain K residue 233 ILE Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 208 MET Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 232 CYS Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain P residue 231 ARG Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 271 SER Chi-restraints excluded: chain Q residue 233 ILE Chi-restraints excluded: chain Q residue 245 CYS Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 216 LYS Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 232 CYS Chi-restraints excluded: chain R residue 242 ASN Chi-restraints excluded: chain R residue 252 LYS Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain V residue 150 ILE Chi-restraints excluded: chain V residue 233 ILE Chi-restraints excluded: chain V residue 271 SER Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain W residue 245 CYS Chi-restraints excluded: chain X residue 179 GLU Chi-restraints excluded: chain X residue 208 MET Chi-restraints excluded: chain X residue 225 SER Chi-restraints excluded: chain X residue 227 VAL Chi-restraints excluded: chain X residue 232 CYS Chi-restraints excluded: chain X residue 242 ASN Chi-restraints excluded: chain X residue 245 CYS Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain b residue 239 THR Chi-restraints excluded: chain b residue 242 ASN Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain b residue 282 LEU Chi-restraints excluded: chain c residue 233 ILE Chi-restraints excluded: chain c residue 245 CYS Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain d residue 208 MET Chi-restraints excluded: chain d residue 216 LYS Chi-restraints excluded: chain d residue 232 CYS Chi-restraints excluded: chain d residue 242 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 74 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 223 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 269 GLN F 234 GLN F 243 ASN J 260 GLN K 243 ASN K 260 GLN L 234 GLN L 243 ASN Q 243 ASN Q 269 GLN R 234 GLN R 235 ASN V 234 GLN V 242 ASN V 260 GLN W 243 ASN W 269 GLN X 234 GLN X 235 ASN ** c 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.204165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.154477 restraints weight = 18275.583| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.79 r_work: 0.4183 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20250 Z= 0.140 Angle : 0.576 8.937 27435 Z= 0.294 Chirality : 0.042 0.146 3165 Planarity : 0.004 0.048 3480 Dihedral : 4.206 34.213 2697 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.31 % Allowed : 19.59 % Favored : 75.10 % 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: -0.71 (0.16), residues: 2460 helix: None (None), residues: 0 sheet: 0.65 (0.15), residues: 1185 loop : -1.65 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 231 TYR 0.015 0.001 TYR V 246 PHE 0.010 0.001 PHE E 278 TRP 0.009 0.001 TRP D 168 HIS 0.004 0.001 HIS O 31 Details of bonding type rmsd covalent geometry : bond 0.00318 (20220) covalent geometry : angle 0.57279 (27375) SS BOND : bond 0.00423 ( 30) SS BOND : angle 1.38477 ( 60) hydrogen bonds : bond 0.03766 ( 690) hydrogen bonds : angle 5.77148 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 326 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 231 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6863 (tmt90) REVERT: D 245 CYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6638 (t) REVERT: E 236 MET cc_start: 0.6360 (mmm) cc_final: 0.5418 (mmt) REVERT: F 179 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: J 242 ASN cc_start: 0.6858 (OUTLIER) cc_final: 0.6314 (p0) REVERT: J 245 CYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6980 (t) REVERT: K 216 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6356 (mtpt) REVERT: L 179 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.6928 (mm-30) REVERT: L 232 CYS cc_start: 0.5932 (OUTLIER) cc_final: 0.5716 (t) REVERT: L 257 ASP cc_start: 0.6275 (m-30) cc_final: 0.5606 (m-30) REVERT: P 242 ASN cc_start: 0.6361 (OUTLIER) cc_final: 0.6096 (p0) REVERT: P 245 CYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6803 (t) REVERT: Q 215 LYS cc_start: 0.6941 (tptp) cc_final: 0.6697 (tptp) REVERT: Q 245 CYS cc_start: 0.6041 (OUTLIER) cc_final: 0.5832 (t) REVERT: R 179 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: R 190 THR cc_start: 0.6571 (m) cc_final: 0.6311 (t) REVERT: V 208 MET cc_start: 0.6192 (mtp) cc_final: 0.5818 (mtp) REVERT: V 242 ASN cc_start: 0.6388 (OUTLIER) cc_final: 0.5938 (p0) REVERT: V 245 CYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6498 (t) REVERT: V 260 GLN cc_start: 0.7746 (pt0) cc_final: 0.7377 (pt0) REVERT: W 203 ASP cc_start: 0.7614 (t0) cc_final: 0.7378 (t0) REVERT: W 240 LEU cc_start: 0.6329 (mt) cc_final: 0.6073 (mt) REVERT: X 179 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: b 204 LYS cc_start: 0.7693 (mttp) cc_final: 0.7040 (mptt) REVERT: b 242 ASN cc_start: 0.6584 (OUTLIER) cc_final: 0.6291 (p0) REVERT: b 245 CYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6993 (t) REVERT: c 245 CYS cc_start: 0.5735 (OUTLIER) cc_final: 0.5526 (t) REVERT: d 179 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7771 (mm-30) REVERT: d 211 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7696 (mp) outliers start: 117 outliers final: 40 residues processed: 400 average time/residue: 0.5699 time to fit residues: 261.4203 Evaluate side-chains 358 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 298 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 242 ASN Chi-restraints excluded: chain J residue 245 CYS Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain K residue 216 LYS Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 ILE Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 208 MET Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 232 CYS Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain P residue 239 THR Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 271 SER Chi-restraints excluded: chain Q residue 216 LYS Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 233 ILE Chi-restraints excluded: chain Q residue 245 CYS Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 242 ASN Chi-restraints excluded: chain V residue 233 ILE Chi-restraints excluded: chain V residue 242 ASN Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 271 SER Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain X residue 179 GLU Chi-restraints excluded: chain X residue 208 MET Chi-restraints excluded: chain X residue 242 ASN Chi-restraints excluded: chain b residue 233 ILE Chi-restraints excluded: chain b residue 239 THR Chi-restraints excluded: chain b residue 242 ASN Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain c residue 233 ILE Chi-restraints excluded: chain c residue 245 CYS Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 208 MET Chi-restraints excluded: chain d residue 211 LEU Chi-restraints excluded: chain d residue 216 LYS Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 225 SER Chi-restraints excluded: chain d residue 233 ILE Chi-restraints excluded: chain d residue 258 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 112 optimal weight: 1.9990 chunk 221 optimal weight: 0.0010 chunk 47 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 260 GLN F 210 HIS F 234 GLN F 243 ASN J 234 GLN K 260 GLN L 234 GLN L 243 ASN P 234 GLN Q 269 GLN R 234 GLN V 242 ASN W 243 ASN W 269 GLN X 234 GLN ** c 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 243 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.203626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.153925 restraints weight = 18328.986| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 2.81 r_work: 0.4172 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20250 Z= 0.137 Angle : 0.572 9.083 27435 Z= 0.291 Chirality : 0.042 0.147 3165 Planarity : 0.004 0.048 3480 Dihedral : 4.282 33.962 2695 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 6.21 % Allowed : 20.14 % Favored : 73.65 % 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: -0.88 (0.16), residues: 2460 helix: None (None), residues: 0 sheet: 0.50 (0.15), residues: 1185 loop : -1.72 (0.14), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 231 TYR 0.012 0.001 TYR V 246 PHE 0.016 0.001 PHE L 279 TRP 0.006 0.001 TRP D 168 HIS 0.005 0.001 HIS Y 31 Details of bonding type rmsd covalent geometry : bond 0.00314 (20220) covalent geometry : angle 0.56732 (27375) SS BOND : bond 0.00300 ( 30) SS BOND : angle 1.72851 ( 60) hydrogen bonds : bond 0.03557 ( 690) hydrogen bonds : angle 5.69404 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 314 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 245 CYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6762 (t) REVERT: E 236 MET cc_start: 0.6467 (mmm) cc_final: 0.5543 (mmt) REVERT: F 179 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: F 242 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.7106 (t0) REVERT: J 144 GLN cc_start: 0.6145 (mm110) cc_final: 0.5927 (mt0) REVERT: J 242 ASN cc_start: 0.6895 (OUTLIER) cc_final: 0.6337 (p0) REVERT: J 245 CYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7023 (t) REVERT: L 179 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.6883 (mm-30) REVERT: L 232 CYS cc_start: 0.5939 (OUTLIER) cc_final: 0.5625 (t) REVERT: L 257 ASP cc_start: 0.6311 (m-30) cc_final: 0.5656 (m-30) REVERT: P 144 GLN cc_start: 0.6587 (OUTLIER) cc_final: 0.5612 (mp10) REVERT: P 204 LYS cc_start: 0.7615 (mmmm) cc_final: 0.7328 (mmmm) REVERT: P 242 ASN cc_start: 0.6433 (OUTLIER) cc_final: 0.6227 (p0) REVERT: P 245 CYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6898 (t) REVERT: Q 224 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5991 (mm) REVERT: R 179 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: R 254 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.6055 (mm-30) REVERT: V 208 MET cc_start: 0.6395 (mtp) cc_final: 0.6140 (mtp) REVERT: V 245 CYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6486 (t) REVERT: V 260 GLN cc_start: 0.7797 (pt0) cc_final: 0.7469 (pt0) REVERT: W 203 ASP cc_start: 0.7535 (t0) cc_final: 0.7278 (t0) REVERT: W 240 LEU cc_start: 0.6382 (mt) cc_final: 0.6136 (mt) REVERT: X 179 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7719 (mm-30) REVERT: b 204 LYS cc_start: 0.7600 (mttp) cc_final: 0.6938 (mptt) REVERT: b 242 ASN cc_start: 0.6532 (OUTLIER) cc_final: 0.6274 (p0) REVERT: b 245 CYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7072 (t) REVERT: d 179 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7770 (mm-30) REVERT: d 184 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7454 (mttm) REVERT: d 208 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7466 (mmt) REVERT: d 254 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5777 (mm-30) outliers start: 137 outliers final: 50 residues processed: 413 average time/residue: 0.5703 time to fit residues: 269.8843 Evaluate side-chains 365 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 294 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain I residue 19 CYS Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 242 ASN Chi-restraints excluded: chain J residue 245 CYS Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 ILE Chi-restraints excluded: chain K residue 245 CYS Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 208 MET Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 232 CYS Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain O residue 19 CYS Chi-restraints excluded: chain P residue 144 GLN Chi-restraints excluded: chain P residue 239 THR Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 271 SER Chi-restraints excluded: chain Q residue 216 LYS Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 233 ILE Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 216 LYS Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 254 GLU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain U residue 19 CYS Chi-restraints excluded: chain V residue 233 ILE Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 271 SER Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain W residue 245 CYS Chi-restraints excluded: chain W residue 260 GLN Chi-restraints excluded: chain X residue 179 GLU Chi-restraints excluded: chain X residue 208 MET Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain b residue 233 ILE Chi-restraints excluded: chain b residue 239 THR Chi-restraints excluded: chain b residue 242 ASN Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain c residue 233 ILE Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain d residue 208 MET Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 254 GLU Chi-restraints excluded: chain d residue 258 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 162 optimal weight: 0.0040 chunk 163 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 111 optimal weight: 0.3980 chunk 184 optimal weight: 0.8980 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN F 234 GLN K 260 GLN ** L 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 269 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 269 GLN X 234 GLN X 242 ASN X 260 GLN ** c 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 234 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.203726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.154173 restraints weight = 18293.518| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.80 r_work: 0.4175 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20250 Z= 0.136 Angle : 0.597 9.527 27435 Z= 0.299 Chirality : 0.041 0.147 3165 Planarity : 0.004 0.068 3480 Dihedral : 4.326 33.762 2693 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.08 % Allowed : 22.18 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.16), residues: 2460 helix: None (None), residues: 0 sheet: 0.43 (0.15), residues: 1185 loop : -1.74 (0.14), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 231 TYR 0.017 0.001 TYR d 196 PHE 0.014 0.001 PHE c 279 TRP 0.006 0.001 TRP J 168 HIS 0.004 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00311 (20220) covalent geometry : angle 0.59107 (27375) SS BOND : bond 0.00498 ( 30) SS BOND : angle 1.85038 ( 60) hydrogen bonds : bond 0.03410 ( 690) hydrogen bonds : angle 5.65078 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 314 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 144 GLN cc_start: 0.6250 (mm110) cc_final: 0.6005 (mp10) REVERT: D 245 CYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6684 (t) REVERT: F 145 ASP cc_start: 0.7315 (m-30) cc_final: 0.7018 (m-30) REVERT: F 179 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: F 184 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7477 (mtmm) REVERT: F 254 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5637 (mm-30) REVERT: J 144 GLN cc_start: 0.6048 (OUTLIER) cc_final: 0.5807 (mt0) REVERT: J 242 ASN cc_start: 0.6829 (OUTLIER) cc_final: 0.6281 (p0) REVERT: J 245 CYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7108 (t) REVERT: K 148 GLN cc_start: 0.5636 (tt0) cc_final: 0.5417 (tt0) REVERT: L 179 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.6856 (mm-30) REVERT: L 232 CYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5665 (t) REVERT: L 254 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5415 (mm-30) REVERT: L 257 ASP cc_start: 0.6293 (m-30) cc_final: 0.5663 (m-30) REVERT: P 144 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.5502 (mp10) REVERT: P 204 LYS cc_start: 0.7629 (mmmm) cc_final: 0.7344 (mmmm) REVERT: P 242 ASN cc_start: 0.6660 (OUTLIER) cc_final: 0.6369 (p0) REVERT: P 245 CYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6958 (t) REVERT: Q 216 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6904 (mttt) REVERT: Q 224 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.5771 (mm) REVERT: R 179 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7755 (mm-30) REVERT: R 232 CYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5687 (t) REVERT: V 144 GLN cc_start: 0.6116 (OUTLIER) cc_final: 0.5820 (mp10) REVERT: V 208 MET cc_start: 0.6501 (mtp) cc_final: 0.6257 (mtp) REVERT: V 245 CYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6517 (t) REVERT: V 260 GLN cc_start: 0.7774 (pt0) cc_final: 0.7471 (pt0) REVERT: W 240 LEU cc_start: 0.6456 (mt) cc_final: 0.6220 (mt) REVERT: X 179 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: X 222 ASP cc_start: 0.6113 (p0) cc_final: 0.5893 (t0) REVERT: b 204 LYS cc_start: 0.7568 (mttp) cc_final: 0.6931 (mptt) REVERT: b 242 ASN cc_start: 0.6748 (OUTLIER) cc_final: 0.6413 (p0) REVERT: b 245 CYS cc_start: 0.7332 (OUTLIER) cc_final: 0.7054 (t) REVERT: d 179 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7744 (mm-30) outliers start: 112 outliers final: 51 residues processed: 388 average time/residue: 0.5346 time to fit residues: 239.0192 Evaluate side-chains 369 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 295 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain I residue 19 CYS Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 242 ASN Chi-restraints excluded: chain J residue 245 CYS Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 ILE Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 208 MET Chi-restraints excluded: chain L residue 232 CYS Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain O residue 19 CYS Chi-restraints excluded: chain P residue 144 GLN Chi-restraints excluded: chain P residue 239 THR Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 271 SER Chi-restraints excluded: chain Q residue 195 ILE Chi-restraints excluded: chain Q residue 216 LYS Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 233 ILE Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 216 LYS Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 232 CYS Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain U residue 19 CYS Chi-restraints excluded: chain V residue 144 GLN Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 271 SER Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain W residue 245 CYS Chi-restraints excluded: chain W residue 260 GLN Chi-restraints excluded: chain X residue 179 GLU Chi-restraints excluded: chain X residue 208 MET Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain b residue 239 THR Chi-restraints excluded: chain b residue 242 ASN Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain c residue 233 ILE Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 208 MET Chi-restraints excluded: chain d residue 233 ILE Chi-restraints excluded: chain d residue 258 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 205 optimal weight: 0.2980 chunk 168 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 110 optimal weight: 0.4980 chunk 23 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 267 ASN F 234 GLN F 242 ASN K 260 GLN ** L 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 269 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 269 GLN X 234 GLN X 242 ASN ** c 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 234 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.200954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.151126 restraints weight = 18290.415| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.80 r_work: 0.4138 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20250 Z= 0.174 Angle : 0.629 9.836 27435 Z= 0.316 Chirality : 0.042 0.145 3165 Planarity : 0.004 0.071 3480 Dihedral : 4.673 42.731 2691 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.62 % Allowed : 22.13 % Favored : 72.24 % 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: -1.16 (0.16), residues: 2460 helix: None (None), residues: 0 sheet: 0.22 (0.15), residues: 1185 loop : -1.80 (0.14), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 231 TYR 0.020 0.002 TYR V 246 PHE 0.014 0.002 PHE c 279 TRP 0.005 0.001 TRP V 168 HIS 0.006 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00395 (20220) covalent geometry : angle 0.62633 (27375) SS BOND : bond 0.00386 ( 30) SS BOND : angle 1.45836 ( 60) hydrogen bonds : bond 0.03652 ( 690) hydrogen bonds : angle 5.80924 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 309 time to evaluate : 0.731 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: D 245 CYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6770 (t) REVERT: E 224 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5942 (mp) REVERT: F 145 ASP cc_start: 0.7386 (m-30) cc_final: 0.7102 (m-30) REVERT: F 179 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7700 (mm-30) REVERT: F 184 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7525 (mtmm) REVERT: J 144 GLN cc_start: 0.6182 (OUTLIER) cc_final: 0.5903 (mt0) REVERT: J 208 MET cc_start: 0.6435 (mtp) cc_final: 0.6166 (ttp) REVERT: J 242 ASN cc_start: 0.6789 (OUTLIER) cc_final: 0.6159 (p0) REVERT: J 245 CYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7168 (t) REVERT: L 179 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6854 (mm-30) REVERT: L 232 CYS cc_start: 0.6359 (OUTLIER) cc_final: 0.5796 (t) REVERT: L 254 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5455 (mm-30) REVERT: L 257 ASP cc_start: 0.6327 (m-30) cc_final: 0.5677 (m-30) REVERT: P 144 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.5525 (mp10) REVERT: P 204 LYS cc_start: 0.7720 (mmmm) cc_final: 0.7240 (mmmm) REVERT: P 242 ASN cc_start: 0.6736 (OUTLIER) cc_final: 0.6343 (p0) REVERT: P 245 CYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7053 (t) REVERT: Q 224 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5824 (mm) REVERT: R 145 ASP cc_start: 0.7618 (m-30) cc_final: 0.7359 (m-30) REVERT: R 179 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: R 254 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5636 (mm-30) REVERT: V 144 GLN cc_start: 0.6210 (OUTLIER) cc_final: 0.5903 (mt0) REVERT: V 208 MET cc_start: 0.6573 (mtp) cc_final: 0.6326 (mtp) REVERT: V 245 CYS cc_start: 0.7558 (OUTLIER) cc_final: 0.6762 (t) REVERT: V 260 GLN cc_start: 0.7815 (pt0) cc_final: 0.7568 (pt0) REVERT: W 240 LEU cc_start: 0.6644 (mt) cc_final: 0.6429 (mt) REVERT: X 179 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: X 222 ASP cc_start: 0.6151 (p0) cc_final: 0.5838 (t0) REVERT: X 254 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5495 (mm-30) REVERT: b 204 LYS cc_start: 0.7631 (mttp) cc_final: 0.7017 (mptt) REVERT: b 242 ASN cc_start: 0.6773 (OUTLIER) cc_final: 0.6407 (p0) REVERT: b 245 CYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7127 (t) REVERT: c 204 LYS cc_start: 0.6834 (mppt) cc_final: 0.6512 (mttm) REVERT: d 179 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7781 (mm-30) REVERT: d 184 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7580 (mttm) outliers start: 124 outliers final: 61 residues processed: 391 average time/residue: 0.5564 time to fit residues: 250.2162 Evaluate side-chains 374 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 289 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 267 ASN Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain I residue 19 CYS Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 242 ASN Chi-restraints excluded: chain J residue 245 CYS Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 ILE Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 208 MET Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 232 CYS Chi-restraints excluded: chain L residue 245 CYS Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain O residue 19 CYS Chi-restraints excluded: chain P residue 144 GLN Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain P residue 239 THR Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 271 SER Chi-restraints excluded: chain Q residue 216 LYS Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 233 ILE Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 216 LYS Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 232 CYS Chi-restraints excluded: chain R residue 254 GLU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain T residue 19 CYS Chi-restraints excluded: chain U residue 19 CYS Chi-restraints excluded: chain V residue 144 GLN Chi-restraints excluded: chain V residue 233 ILE Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 271 SER Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain W residue 245 CYS Chi-restraints excluded: chain W residue 253 LEU Chi-restraints excluded: chain W residue 260 GLN Chi-restraints excluded: chain X residue 179 GLU Chi-restraints excluded: chain X residue 208 MET Chi-restraints excluded: chain X residue 233 ILE Chi-restraints excluded: chain X residue 254 GLU Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain Z residue 19 CYS Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain b residue 239 THR Chi-restraints excluded: chain b residue 242 ASN Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 195 ILE Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain c residue 233 ILE Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain d residue 208 MET Chi-restraints excluded: chain d residue 258 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 196 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 50 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN K 269 GLN L 234 GLN Q 234 GLN Q 269 GLN R 234 GLN W 269 GLN ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 242 ASN c 267 ASN d 234 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.198198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.148253 restraints weight = 18501.305| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.81 r_work: 0.4097 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20250 Z= 0.238 Angle : 0.704 10.243 27435 Z= 0.355 Chirality : 0.045 0.160 3165 Planarity : 0.005 0.087 3480 Dihedral : 5.300 58.372 2691 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.67 % Allowed : 22.40 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.46 (0.16), residues: 2460 helix: None (None), residues: 0 sheet: -0.07 (0.15), residues: 1185 loop : -1.91 (0.14), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 231 TYR 0.028 0.002 TYR V 246 PHE 0.020 0.002 PHE E 279 TRP 0.005 0.002 TRP D 168 HIS 0.007 0.001 HIS E 210 Details of bonding type rmsd covalent geometry : bond 0.00543 (20220) covalent geometry : angle 0.70036 (27375) SS BOND : bond 0.00399 ( 30) SS BOND : angle 1.58693 ( 60) hydrogen bonds : bond 0.04030 ( 690) hydrogen bonds : angle 6.13213 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 295 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 144 GLN cc_start: 0.6649 (mm110) cc_final: 0.6359 (mp10) REVERT: D 231 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7303 (tmt90) REVERT: D 245 CYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6892 (t) REVERT: E 224 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.6020 (mp) REVERT: F 145 ASP cc_start: 0.7417 (m-30) cc_final: 0.7128 (m-30) REVERT: F 179 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: F 184 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7584 (mtmm) REVERT: J 144 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.6009 (mt0) REVERT: J 208 MET cc_start: 0.6640 (mtp) cc_final: 0.6420 (mtp) REVERT: J 242 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6246 (p0) REVERT: J 245 CYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7126 (t) REVERT: L 179 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.6859 (mm-30) REVERT: L 254 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5383 (mm-30) REVERT: L 257 ASP cc_start: 0.6382 (m-30) cc_final: 0.5676 (m-30) REVERT: P 144 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.5639 (mp10) REVERT: P 204 LYS cc_start: 0.7828 (mmmm) cc_final: 0.7549 (mmmm) REVERT: P 242 ASN cc_start: 0.6711 (OUTLIER) cc_final: 0.6393 (p0) REVERT: P 245 CYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7156 (t) REVERT: Q 224 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5819 (mm) REVERT: R 145 ASP cc_start: 0.7651 (m-30) cc_final: 0.7414 (m-30) REVERT: R 179 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: R 254 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5708 (mm-30) REVERT: V 144 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5944 (mt0) REVERT: V 208 MET cc_start: 0.6693 (mtp) cc_final: 0.6484 (mtp) REVERT: V 245 CYS cc_start: 0.7650 (OUTLIER) cc_final: 0.6902 (t) REVERT: W 240 LEU cc_start: 0.6855 (mt) cc_final: 0.6653 (mt) REVERT: X 179 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7650 (mm-30) REVERT: X 222 ASP cc_start: 0.6222 (p0) cc_final: 0.5871 (t0) REVERT: X 254 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.5715 (mm-30) REVERT: b 204 LYS cc_start: 0.7650 (mttp) cc_final: 0.7024 (mptt) REVERT: b 242 ASN cc_start: 0.6805 (OUTLIER) cc_final: 0.6425 (p0) REVERT: b 245 CYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7242 (t) REVERT: c 204 LYS cc_start: 0.6924 (mppt) cc_final: 0.6581 (mttm) REVERT: d 145 ASP cc_start: 0.7568 (m-30) cc_final: 0.7354 (m-30) REVERT: d 179 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7811 (mm-30) REVERT: d 184 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7586 (mttm) REVERT: d 211 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7963 (mt) outliers start: 125 outliers final: 73 residues processed: 383 average time/residue: 0.5413 time to fit residues: 239.3517 Evaluate side-chains 375 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 277 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain I residue 19 CYS Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 242 ASN Chi-restraints excluded: chain J residue 245 CYS Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 ILE Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 184 LYS Chi-restraints excluded: chain L residue 208 MET Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 232 CYS Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain N residue 19 CYS Chi-restraints excluded: chain O residue 19 CYS Chi-restraints excluded: chain P residue 144 GLN Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain P residue 239 THR Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 271 SER Chi-restraints excluded: chain Q residue 216 LYS Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 233 ILE Chi-restraints excluded: chain Q residue 236 MET Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 216 LYS Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 232 CYS Chi-restraints excluded: chain R residue 254 GLU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain T residue 19 CYS Chi-restraints excluded: chain U residue 19 CYS Chi-restraints excluded: chain V residue 144 GLN Chi-restraints excluded: chain V residue 233 ILE Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 271 SER Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain W residue 245 CYS Chi-restraints excluded: chain W residue 253 LEU Chi-restraints excluded: chain X residue 179 GLU Chi-restraints excluded: chain X residue 208 MET Chi-restraints excluded: chain X residue 225 SER Chi-restraints excluded: chain X residue 227 VAL Chi-restraints excluded: chain X residue 233 ILE Chi-restraints excluded: chain X residue 254 GLU Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain Z residue 19 CYS Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain b residue 233 ILE Chi-restraints excluded: chain b residue 239 THR Chi-restraints excluded: chain b residue 242 ASN Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 195 ILE Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain c residue 233 ILE Chi-restraints excluded: chain d residue 152 ASP Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain d residue 208 MET Chi-restraints excluded: chain d residue 211 LEU Chi-restraints excluded: chain d residue 225 SER Chi-restraints excluded: chain d residue 258 GLU Chi-restraints excluded: chain d residue 276 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 130 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN L 234 GLN Q 234 GLN Q 269 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 ASN W 260 GLN ** W 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 242 ASN b 234 GLN c 183 ASN c 234 GLN c 267 ASN d 234 GLN d 243 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.202230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.152697 restraints weight = 18361.860| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 2.81 r_work: 0.4155 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20250 Z= 0.132 Angle : 0.613 10.675 27435 Z= 0.302 Chirality : 0.042 0.162 3165 Planarity : 0.004 0.051 3480 Dihedral : 4.598 47.662 2691 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.08 % Allowed : 23.90 % Favored : 71.02 % 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: -1.33 (0.16), residues: 2460 helix: None (None), residues: 0 sheet: 0.06 (0.15), residues: 1185 loop : -1.86 (0.14), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 265 TYR 0.015 0.001 TYR V 246 PHE 0.022 0.001 PHE Q 279 TRP 0.008 0.001 TRP F 168 HIS 0.004 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00303 (20220) covalent geometry : angle 0.61041 (27375) SS BOND : bond 0.00337 ( 30) SS BOND : angle 1.28734 ( 60) hydrogen bonds : bond 0.03360 ( 690) hydrogen bonds : angle 5.64974 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 305 time to evaluate : 0.816 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: D 144 GLN cc_start: 0.6689 (mm110) cc_final: 0.6416 (mp10) REVERT: D 245 CYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6768 (t) REVERT: F 145 ASP cc_start: 0.7239 (m-30) cc_final: 0.6961 (m-30) REVERT: F 179 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: J 144 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.6003 (mt0) REVERT: J 208 MET cc_start: 0.6520 (mtp) cc_final: 0.6246 (ttp) REVERT: J 242 ASN cc_start: 0.6768 (OUTLIER) cc_final: 0.6104 (p0) REVERT: J 245 CYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7140 (t) REVERT: K 204 LYS cc_start: 0.6771 (mppt) cc_final: 0.6484 (mttm) REVERT: L 179 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.6850 (mm-30) REVERT: L 254 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5401 (mm-30) REVERT: L 257 ASP cc_start: 0.6257 (m-30) cc_final: 0.5654 (m-30) REVERT: P 149 LEU cc_start: 0.7809 (mt) cc_final: 0.7571 (mm) REVERT: P 204 LYS cc_start: 0.7739 (mmmm) cc_final: 0.7459 (mmmm) REVERT: P 242 ASN cc_start: 0.6872 (OUTLIER) cc_final: 0.6403 (p0) REVERT: P 245 CYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7085 (t) REVERT: Q 216 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6972 (mttt) REVERT: Q 224 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5879 (mp) REVERT: Q 267 ASN cc_start: 0.5261 (t0) cc_final: 0.5027 (t0) REVERT: R 179 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: R 245 CYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6353 (t) REVERT: V 144 GLN cc_start: 0.6381 (OUTLIER) cc_final: 0.6058 (mt0) REVERT: V 245 CYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6682 (t) REVERT: W 203 ASP cc_start: 0.7678 (t0) cc_final: 0.7368 (t0) REVERT: W 204 LYS cc_start: 0.6943 (mppt) cc_final: 0.6672 (mttm) REVERT: W 240 LEU cc_start: 0.6670 (mt) cc_final: 0.6462 (mt) REVERT: X 179 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: X 222 ASP cc_start: 0.6236 (p0) cc_final: 0.5912 (t0) REVERT: Z 31 HIS cc_start: 0.7033 (t-170) cc_final: 0.6700 (m-70) REVERT: b 204 LYS cc_start: 0.7709 (mttp) cc_final: 0.7110 (mptt) REVERT: b 208 MET cc_start: 0.6498 (mtp) cc_final: 0.6266 (ttp) REVERT: b 242 ASN cc_start: 0.6690 (OUTLIER) cc_final: 0.6234 (p0) REVERT: b 245 CYS cc_start: 0.7357 (OUTLIER) cc_final: 0.7128 (t) REVERT: c 204 LYS cc_start: 0.6791 (mppt) cc_final: 0.6531 (mttm) REVERT: d 179 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: d 184 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7514 (mttm) REVERT: d 236 MET cc_start: 0.6387 (mmp) cc_final: 0.6187 (mmp) outliers start: 112 outliers final: 57 residues processed: 382 average time/residue: 0.5552 time to fit residues: 244.2487 Evaluate side-chains 362 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 285 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain I residue 19 CYS Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 242 ASN Chi-restraints excluded: chain J residue 245 CYS Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 ILE Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 208 MET Chi-restraints excluded: chain L residue 219 VAL Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain N residue 19 CYS Chi-restraints excluded: chain O residue 19 CYS Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain P residue 239 THR Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain Q residue 216 LYS Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 224 LEU Chi-restraints excluded: chain Q residue 233 ILE Chi-restraints excluded: chain Q residue 236 MET Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 216 LYS Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 245 CYS Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain T residue 19 CYS Chi-restraints excluded: chain U residue 19 CYS Chi-restraints excluded: chain V residue 144 GLN Chi-restraints excluded: chain V residue 233 ILE Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 271 SER Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain W residue 245 CYS Chi-restraints excluded: chain X residue 179 GLU Chi-restraints excluded: chain X residue 208 MET Chi-restraints excluded: chain X residue 233 ILE Chi-restraints excluded: chain Z residue 19 CYS Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain b residue 239 THR Chi-restraints excluded: chain b residue 242 ASN Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain c residue 233 ILE Chi-restraints excluded: chain d residue 152 ASP Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain d residue 242 ASN Chi-restraints excluded: chain d residue 258 GLU Chi-restraints excluded: chain d residue 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 214 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 213 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.1980 chunk 142 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 242 ASN ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 260 GLN L 234 GLN ** Q 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 243 ASN V 242 ASN W 269 GLN ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 242 ASN c 267 ASN d 234 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.200040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.150368 restraints weight = 18365.294| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.82 r_work: 0.4128 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20250 Z= 0.179 Angle : 0.667 11.269 27435 Z= 0.330 Chirality : 0.043 0.152 3165 Planarity : 0.004 0.072 3480 Dihedral : 4.819 47.701 2691 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.72 % Allowed : 24.44 % Favored : 70.84 % 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: -1.61 (0.16), residues: 2460 helix: None (None), residues: 0 sheet: -0.44 (0.15), residues: 1260 loop : -1.75 (0.15), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 265 TYR 0.022 0.002 TYR V 246 PHE 0.021 0.002 PHE V 172 TRP 0.006 0.001 TRP F 168 HIS 0.006 0.001 HIS E 210 Details of bonding type rmsd covalent geometry : bond 0.00413 (20220) covalent geometry : angle 0.66041 (27375) SS BOND : bond 0.00376 ( 30) SS BOND : angle 2.11060 ( 60) hydrogen bonds : bond 0.03620 ( 690) hydrogen bonds : angle 5.83683 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 299 time to evaluate : 0.831 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: D 144 GLN cc_start: 0.6711 (mm110) cc_final: 0.6400 (mp10) REVERT: D 245 CYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6957 (t) REVERT: F 145 ASP cc_start: 0.7247 (m-30) cc_final: 0.6988 (m-30) REVERT: F 179 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: J 144 GLN cc_start: 0.6259 (OUTLIER) cc_final: 0.6021 (mt0) REVERT: J 174 ARG cc_start: 0.7112 (mtm180) cc_final: 0.6612 (mtm180) REVERT: J 208 MET cc_start: 0.6620 (mtp) cc_final: 0.6388 (mtp) REVERT: J 242 ASN cc_start: 0.6830 (OUTLIER) cc_final: 0.6113 (p0) REVERT: J 245 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7227 (t) REVERT: K 204 LYS cc_start: 0.6825 (mppt) cc_final: 0.6508 (mttm) REVERT: L 179 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.6828 (mm-30) REVERT: L 254 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5374 (mm-30) REVERT: L 257 ASP cc_start: 0.6255 (m-30) cc_final: 0.5619 (m-30) REVERT: P 144 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.5959 (mp10) REVERT: P 204 LYS cc_start: 0.7816 (mmmm) cc_final: 0.7533 (mmmm) REVERT: P 242 ASN cc_start: 0.6768 (OUTLIER) cc_final: 0.6284 (p0) REVERT: P 245 CYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7190 (t) REVERT: R 145 ASP cc_start: 0.7597 (m-30) cc_final: 0.7353 (m-30) REVERT: R 179 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: R 254 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5621 (mm-30) REVERT: V 144 GLN cc_start: 0.6337 (OUTLIER) cc_final: 0.6048 (mt0) REVERT: V 208 MET cc_start: 0.6728 (mtp) cc_final: 0.6444 (mtp) REVERT: V 245 CYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6780 (t) REVERT: W 203 ASP cc_start: 0.7640 (t0) cc_final: 0.7315 (t0) REVERT: W 204 LYS cc_start: 0.7038 (mppt) cc_final: 0.6786 (mttm) REVERT: W 240 LEU cc_start: 0.6679 (mt) cc_final: 0.6472 (mt) REVERT: X 179 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7728 (mm-30) REVERT: X 222 ASP cc_start: 0.6261 (p0) cc_final: 0.5938 (t0) REVERT: Z 31 HIS cc_start: 0.7045 (t-170) cc_final: 0.6710 (m-70) REVERT: Z 37 LEU cc_start: 0.7407 (mm) cc_final: 0.6937 (mm) REVERT: b 204 LYS cc_start: 0.7697 (mttp) cc_final: 0.7092 (mptt) REVERT: b 208 MET cc_start: 0.6566 (mtp) cc_final: 0.6319 (ttp) REVERT: b 242 ASN cc_start: 0.6728 (OUTLIER) cc_final: 0.6087 (p0) REVERT: b 245 CYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7197 (t) REVERT: c 204 LYS cc_start: 0.6849 (mppt) cc_final: 0.6595 (mttm) REVERT: d 145 ASP cc_start: 0.7480 (m-30) cc_final: 0.7274 (m-30) REVERT: d 179 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: d 184 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7542 (mttm) outliers start: 104 outliers final: 67 residues processed: 371 average time/residue: 0.5580 time to fit residues: 237.9333 Evaluate side-chains 366 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 280 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain E residue 267 ASN Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain I residue 19 CYS Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 242 ASN Chi-restraints excluded: chain J residue 245 CYS Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 ILE Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 184 LYS Chi-restraints excluded: chain L residue 208 MET Chi-restraints excluded: chain L residue 219 VAL Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain N residue 19 CYS Chi-restraints excluded: chain O residue 19 CYS Chi-restraints excluded: chain P residue 144 GLN Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain P residue 239 THR Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 271 SER Chi-restraints excluded: chain Q residue 216 LYS Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 233 ILE Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 216 LYS Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 254 GLU Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain T residue 19 CYS Chi-restraints excluded: chain U residue 19 CYS Chi-restraints excluded: chain V residue 144 GLN Chi-restraints excluded: chain V residue 233 ILE Chi-restraints excluded: chain V residue 242 ASN Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 271 SER Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain W residue 245 CYS Chi-restraints excluded: chain X residue 179 GLU Chi-restraints excluded: chain X residue 208 MET Chi-restraints excluded: chain X residue 225 SER Chi-restraints excluded: chain X residue 233 ILE Chi-restraints excluded: chain Z residue 19 CYS Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain b residue 144 GLN Chi-restraints excluded: chain b residue 239 THR Chi-restraints excluded: chain b residue 242 ASN Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain c residue 233 ILE Chi-restraints excluded: chain d residue 152 ASP Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain d residue 242 ASN Chi-restraints excluded: chain d residue 258 GLU Chi-restraints excluded: chain d residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 175 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN ** Q 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 GLN V 242 ASN W 260 GLN W 269 GLN X 234 GLN X 242 ASN ** c 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 267 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.202261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.153005 restraints weight = 18403.286| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 2.81 r_work: 0.4162 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20250 Z= 0.132 Angle : 0.640 11.312 27435 Z= 0.312 Chirality : 0.042 0.150 3165 Planarity : 0.004 0.054 3480 Dihedral : 4.626 48.723 2691 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.81 % Allowed : 25.49 % Favored : 70.70 % 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: -1.53 (0.16), residues: 2460 helix: None (None), residues: 0 sheet: -0.37 (0.15), residues: 1260 loop : -1.71 (0.15), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 265 TYR 0.016 0.001 TYR V 246 PHE 0.014 0.001 PHE Q 279 TRP 0.009 0.001 TRP P 168 HIS 0.004 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00307 (20220) covalent geometry : angle 0.63340 (27375) SS BOND : bond 0.00367 ( 30) SS BOND : angle 2.02746 ( 60) hydrogen bonds : bond 0.03328 ( 690) hydrogen bonds : angle 5.62234 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 298 time to evaluate : 0.806 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: D 144 GLN cc_start: 0.6688 (mm110) cc_final: 0.6408 (mp10) REVERT: D 242 ASN cc_start: 0.6124 (p0) cc_final: 0.5680 (p0) REVERT: D 245 CYS cc_start: 0.7366 (OUTLIER) cc_final: 0.6850 (t) REVERT: D 260 GLN cc_start: 0.7845 (pt0) cc_final: 0.7410 (tt0) REVERT: E 204 LYS cc_start: 0.6801 (mppt) cc_final: 0.6548 (mttm) REVERT: F 145 ASP cc_start: 0.7229 (m-30) cc_final: 0.6950 (m-30) REVERT: F 179 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7688 (mm-30) REVERT: F 242 ASN cc_start: 0.7123 (OUTLIER) cc_final: 0.6914 (t0) REVERT: J 144 GLN cc_start: 0.6271 (OUTLIER) cc_final: 0.6036 (mt0) REVERT: J 208 MET cc_start: 0.6541 (mtp) cc_final: 0.6334 (mtp) REVERT: J 242 ASN cc_start: 0.6714 (OUTLIER) cc_final: 0.6055 (p0) REVERT: J 245 CYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7142 (t) REVERT: K 204 LYS cc_start: 0.6745 (mppt) cc_final: 0.6466 (mttm) REVERT: L 179 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6877 (mm-30) REVERT: L 254 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5419 (mm-30) REVERT: L 257 ASP cc_start: 0.6223 (m-30) cc_final: 0.5607 (m-30) REVERT: P 149 LEU cc_start: 0.7562 (mp) cc_final: 0.7324 (mm) REVERT: P 204 LYS cc_start: 0.7808 (mmmm) cc_final: 0.7508 (mmmm) REVERT: P 242 ASN cc_start: 0.6794 (OUTLIER) cc_final: 0.6335 (p0) REVERT: P 245 CYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7137 (t) REVERT: Q 267 ASN cc_start: 0.5248 (t0) cc_final: 0.5030 (t0) REVERT: R 145 ASP cc_start: 0.7537 (m-30) cc_final: 0.7297 (m-30) REVERT: R 179 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7701 (mm-30) REVERT: V 144 GLN cc_start: 0.6342 (OUTLIER) cc_final: 0.6050 (mt0) REVERT: V 208 MET cc_start: 0.6679 (mtp) cc_final: 0.6419 (mtp) REVERT: V 245 CYS cc_start: 0.7494 (OUTLIER) cc_final: 0.6739 (t) REVERT: W 203 ASP cc_start: 0.7572 (t0) cc_final: 0.7234 (t0) REVERT: W 204 LYS cc_start: 0.7010 (mppt) cc_final: 0.6728 (mttm) REVERT: W 240 LEU cc_start: 0.6608 (mt) cc_final: 0.6408 (mt) REVERT: W 269 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.6113 (mm-40) REVERT: X 179 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7726 (mm-30) REVERT: X 222 ASP cc_start: 0.6207 (p0) cc_final: 0.5897 (t0) REVERT: Z 31 HIS cc_start: 0.7050 (t-170) cc_final: 0.6728 (m-70) REVERT: b 204 LYS cc_start: 0.7701 (mttp) cc_final: 0.7087 (mptt) REVERT: b 208 MET cc_start: 0.6434 (mtp) cc_final: 0.6226 (ttp) REVERT: b 242 ASN cc_start: 0.6597 (OUTLIER) cc_final: 0.5974 (p0) REVERT: b 245 CYS cc_start: 0.7344 (OUTLIER) cc_final: 0.7089 (t) REVERT: c 204 LYS cc_start: 0.6779 (mppt) cc_final: 0.6548 (mttm) REVERT: d 179 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7726 (mm-30) REVERT: d 184 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7537 (mttm) REVERT: d 236 MET cc_start: 0.6258 (mmp) cc_final: 0.5833 (mmp) outliers start: 84 outliers final: 56 residues processed: 358 average time/residue: 0.5479 time to fit residues: 225.7932 Evaluate side-chains 355 residues out of total 2205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 280 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 245 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 245 CYS Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 242 ASN Chi-restraints excluded: chain H residue 19 CYS Chi-restraints excluded: chain I residue 19 CYS Chi-restraints excluded: chain J residue 144 GLN Chi-restraints excluded: chain J residue 233 ILE Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 242 ASN Chi-restraints excluded: chain J residue 245 CYS Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 233 ILE Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 179 GLU Chi-restraints excluded: chain L residue 208 MET Chi-restraints excluded: chain L residue 219 VAL Chi-restraints excluded: chain L residue 225 SER Chi-restraints excluded: chain L residue 254 GLU Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 276 VAL Chi-restraints excluded: chain N residue 19 CYS Chi-restraints excluded: chain O residue 19 CYS Chi-restraints excluded: chain P residue 233 ILE Chi-restraints excluded: chain P residue 239 THR Chi-restraints excluded: chain P residue 242 ASN Chi-restraints excluded: chain P residue 245 CYS Chi-restraints excluded: chain P residue 271 SER Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 233 ILE Chi-restraints excluded: chain R residue 179 GLU Chi-restraints excluded: chain R residue 208 MET Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 227 VAL Chi-restraints excluded: chain R residue 276 VAL Chi-restraints excluded: chain T residue 19 CYS Chi-restraints excluded: chain U residue 19 CYS Chi-restraints excluded: chain V residue 144 GLN Chi-restraints excluded: chain V residue 242 ASN Chi-restraints excluded: chain V residue 245 CYS Chi-restraints excluded: chain V residue 271 SER Chi-restraints excluded: chain W residue 219 VAL Chi-restraints excluded: chain W residue 233 ILE Chi-restraints excluded: chain W residue 245 CYS Chi-restraints excluded: chain W residue 253 LEU Chi-restraints excluded: chain W residue 269 GLN Chi-restraints excluded: chain X residue 179 GLU Chi-restraints excluded: chain X residue 208 MET Chi-restraints excluded: chain X residue 233 ILE Chi-restraints excluded: chain Z residue 19 CYS Chi-restraints excluded: chain a residue 19 CYS Chi-restraints excluded: chain b residue 239 THR Chi-restraints excluded: chain b residue 242 ASN Chi-restraints excluded: chain b residue 245 CYS Chi-restraints excluded: chain b residue 271 SER Chi-restraints excluded: chain c residue 216 LYS Chi-restraints excluded: chain c residue 219 VAL Chi-restraints excluded: chain c residue 233 ILE Chi-restraints excluded: chain d residue 152 ASP Chi-restraints excluded: chain d residue 179 GLU Chi-restraints excluded: chain d residue 184 LYS Chi-restraints excluded: chain d residue 242 ASN Chi-restraints excluded: chain d residue 258 GLU Chi-restraints excluded: chain d residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 62 optimal weight: 0.0870 chunk 138 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 220 optimal weight: 0.0470 chunk 130 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 260 GLN L 234 GLN ** Q 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 ASN W 269 GLN ** X 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 242 ASN ** c 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 267 ASN ** d 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.202515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.153074 restraints weight = 18426.155| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 2.83 r_work: 0.4162 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20250 Z= 0.135 Angle : 0.638 11.055 27435 Z= 0.312 Chirality : 0.042 0.149 3165 Planarity : 0.004 0.053 3480 Dihedral : 4.598 48.904 2691 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.95 % Allowed : 25.71 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.16), residues: 2460 helix: None (None), residues: 0 sheet: -0.37 (0.15), residues: 1260 loop : -1.70 (0.15), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 265 TYR 0.016 0.001 TYR V 246 PHE 0.021 0.001 PHE J 172 TRP 0.006 0.001 TRP P 168 HIS 0.004 0.001 HIS F 210 Details of bonding type rmsd covalent geometry : bond 0.00315 (20220) covalent geometry : angle 0.63316 (27375) SS BOND : bond 0.00333 ( 30) SS BOND : angle 1.86733 ( 60) hydrogen bonds : bond 0.03348 ( 690) hydrogen bonds : angle 5.59146 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8070.17 seconds wall clock time: 138 minutes 29.94 seconds (8309.94 seconds total)