Starting phenix.real_space_refine on Tue Nov 18 10:41:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sd2_10146/11_2025/6sd2_10146.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sd2_10146/11_2025/6sd2_10146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sd2_10146/11_2025/6sd2_10146.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sd2_10146/11_2025/6sd2_10146.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sd2_10146/11_2025/6sd2_10146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sd2_10146/11_2025/6sd2_10146.map" } resolution = 3.1 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= 0.001 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 21 5.16 5 C 8442 2.51 5 N 2415 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13566 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Restraints were copied for chains: C, D, F, G, I, J, L, N, O, Q, R, T, U, W, Y, Z, b, c, e, f Time building chain proxies: 1.35, per 1000 atoms: 0.10 Number of scatterers: 13566 At special positions: 0 Unit cell: (166.866, 166.044, 38.634, 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 21 16.00 O 2688 8.00 N 2415 7.00 C 8442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 680.8 milliseconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3402 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 21 sheets defined 40.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG C 142 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'D' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'F' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA F 135 " --> pdb=" O ASN F 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG F 142 " --> pdb=" O GLY F 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR F 146 " --> pdb=" O ARG F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'G' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA G 135 " --> pdb=" O ASN G 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY G 138 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG G 142 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'I' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA I 135 " --> pdb=" O ASN I 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY I 138 " --> pdb=" O ARG I 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG I 142 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR I 146 " --> pdb=" O ARG I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'J' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA J 135 " --> pdb=" O ASN J 131 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY J 138 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG J 142 " --> pdb=" O GLY J 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER J 192 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 208 No H-bonds generated for 'chain 'J' and resid 206 through 208' Processing helix chain 'L' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA L 135 " --> pdb=" O ASN L 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY L 138 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG L 142 " --> pdb=" O GLY L 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER L 192 " --> pdb=" O GLU L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'N' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA N 135 " --> pdb=" O ASN N 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY N 138 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG N 142 " --> pdb=" O GLY N 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR N 146 " --> pdb=" O ARG N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER N 192 " --> pdb=" O GLU N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 208 No H-bonds generated for 'chain 'N' and resid 206 through 208' Processing helix chain 'O' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA O 135 " --> pdb=" O ASN O 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY O 138 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG O 142 " --> pdb=" O GLY O 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR O 146 " --> pdb=" O ARG O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER O 192 " --> pdb=" O GLU O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 208 No H-bonds generated for 'chain 'O' and resid 206 through 208' Processing helix chain 'Q' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA Q 135 " --> pdb=" O ASN Q 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY Q 138 " --> pdb=" O ARG Q 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG Q 142 " --> pdb=" O GLY Q 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR Q 146 " --> pdb=" O ARG Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER Q 192 " --> pdb=" O GLU Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 208 No H-bonds generated for 'chain 'Q' and resid 206 through 208' Processing helix chain 'R' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA R 135 " --> pdb=" O ASN R 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY R 138 " --> pdb=" O ARG R 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG R 142 " --> pdb=" O GLY R 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR R 146 " --> pdb=" O ARG R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 208 No H-bonds generated for 'chain 'R' and resid 206 through 208' Processing helix chain 'T' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA T 135 " --> pdb=" O ASN T 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY T 138 " --> pdb=" O ARG T 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG T 142 " --> pdb=" O GLY T 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR T 146 " --> pdb=" O ARG T 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER T 192 " --> pdb=" O GLU T 188 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 208 No H-bonds generated for 'chain 'T' and resid 206 through 208' Processing helix chain 'U' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA U 135 " --> pdb=" O ASN U 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY U 138 " --> pdb=" O ARG U 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG U 142 " --> pdb=" O GLY U 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR U 146 " --> pdb=" O ARG U 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER U 192 " --> pdb=" O GLU U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 208 No H-bonds generated for 'chain 'U' and resid 206 through 208' Processing helix chain 'W' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA W 135 " --> pdb=" O ASN W 131 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY W 138 " --> pdb=" O ARG W 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG W 142 " --> pdb=" O GLY W 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR W 146 " --> pdb=" O ARG W 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 208 No H-bonds generated for 'chain 'W' and resid 206 through 208' Processing helix chain 'Y' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA Y 135 " --> pdb=" O ASN Y 131 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY Y 138 " --> pdb=" O ARG Y 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG Y 142 " --> pdb=" O GLY Y 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR Y 146 " --> pdb=" O ARG Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER Y 192 " --> pdb=" O GLU Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 208 No H-bonds generated for 'chain 'Y' and resid 206 through 208' Processing helix chain 'Z' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA Z 135 " --> pdb=" O ASN Z 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY Z 138 " --> pdb=" O ARG Z 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG Z 142 " --> pdb=" O GLY Z 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR Z 146 " --> pdb=" O ARG Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER Z 192 " --> pdb=" O GLU Z 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 206 through 208 No H-bonds generated for 'chain 'Z' and resid 206 through 208' Processing helix chain 'b' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA b 135 " --> pdb=" O ASN b 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY b 138 " --> pdb=" O ARG b 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG b 142 " --> pdb=" O GLY b 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR b 146 " --> pdb=" O ARG b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER b 192 " --> pdb=" O GLU b 188 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 208 No H-bonds generated for 'chain 'b' and resid 206 through 208' Processing helix chain 'c' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA c 135 " --> pdb=" O ASN c 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY c 138 " --> pdb=" O ARG c 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG c 142 " --> pdb=" O GLY c 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR c 146 " --> pdb=" O ARG c 142 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER c 192 " --> pdb=" O GLU c 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 206 through 208 No H-bonds generated for 'chain 'c' and resid 206 through 208' Processing helix chain 'e' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA e 135 " --> pdb=" O ASN e 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY e 138 " --> pdb=" O ARG e 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG e 142 " --> pdb=" O GLY e 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR e 146 " --> pdb=" O ARG e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER e 192 " --> pdb=" O GLU e 188 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'f' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA f 135 " --> pdb=" O ASN f 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY f 138 " --> pdb=" O ARG f 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG f 142 " --> pdb=" O GLY f 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR f 146 " --> pdb=" O ARG f 142 " (cutoff:3.500A) Processing helix chain 'f' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER f 192 " --> pdb=" O GLU f 188 " (cutoff:3.500A) Processing helix chain 'f' and resid 206 through 208 No H-bonds generated for 'chain 'f' and resid 206 through 208' Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 158 Processing sheet with id=AA2, first strand: chain 'C' and resid 152 through 158 Processing sheet with id=AA3, first strand: chain 'D' and resid 152 through 158 Processing sheet with id=AA4, first strand: chain 'F' and resid 152 through 158 Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 158 Processing sheet with id=AA6, first strand: chain 'I' and resid 152 through 158 Processing sheet with id=AA7, first strand: chain 'J' and resid 152 through 158 Processing sheet with id=AA8, first strand: chain 'L' and resid 152 through 158 Processing sheet with id=AA9, first strand: chain 'N' and resid 152 through 158 Processing sheet with id=AB1, first strand: chain 'O' and resid 152 through 158 Processing sheet with id=AB2, first strand: chain 'Q' and resid 152 through 158 Processing sheet with id=AB3, first strand: chain 'R' and resid 152 through 158 Processing sheet with id=AB4, first strand: chain 'T' and resid 152 through 158 Processing sheet with id=AB5, first strand: chain 'U' and resid 152 through 158 Processing sheet with id=AB6, first strand: chain 'W' and resid 152 through 158 Processing sheet with id=AB7, first strand: chain 'Y' and resid 152 through 158 Processing sheet with id=AB8, first strand: chain 'Z' and resid 152 through 158 Processing sheet with id=AB9, first strand: chain 'b' and resid 152 through 158 Processing sheet with id=AC1, first strand: chain 'c' and resid 152 through 158 Processing sheet with id=AC2, first strand: chain 'e' and resid 152 through 158 Processing sheet with id=AC3, first strand: chain 'f' and resid 152 through 158 672 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4685 1.34 - 1.46: 1832 1.46 - 1.57: 7196 1.57 - 1.69: 0 1.69 - 1.80: 42 Bond restraints: 13755 Sorted by residual: bond pdb=" CA HIS Q 218 " pdb=" C HIS Q 218 " ideal model delta sigma weight residual 1.532 1.518 0.014 9.60e-03 1.09e+04 2.11e+00 bond pdb=" CA HIS C 218 " pdb=" C HIS C 218 " ideal model delta sigma weight residual 1.532 1.519 0.014 9.60e-03 1.09e+04 2.05e+00 bond pdb=" CA HIS F 218 " pdb=" C HIS F 218 " ideal model delta sigma weight residual 1.532 1.519 0.014 9.60e-03 1.09e+04 2.01e+00 bond pdb=" CA HIS b 218 " pdb=" C HIS b 218 " ideal model delta sigma weight residual 1.532 1.519 0.014 9.60e-03 1.09e+04 1.99e+00 bond pdb=" CA HIS W 218 " pdb=" C HIS W 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.95e+00 ... (remaining 13750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 15901 1.04 - 2.08: 2070 2.08 - 3.12: 513 3.12 - 4.17: 185 4.17 - 5.21: 84 Bond angle restraints: 18753 Sorted by residual: angle pdb=" N VAL F 198 " pdb=" CA VAL F 198 " pdb=" C VAL F 198 " ideal model delta sigma weight residual 112.12 108.68 3.44 8.40e-01 1.42e+00 1.68e+01 angle pdb=" N VAL U 198 " pdb=" CA VAL U 198 " pdb=" C VAL U 198 " ideal model delta sigma weight residual 112.12 108.69 3.43 8.40e-01 1.42e+00 1.67e+01 angle pdb=" N VAL W 198 " pdb=" CA VAL W 198 " pdb=" C VAL W 198 " ideal model delta sigma weight residual 112.12 108.70 3.42 8.40e-01 1.42e+00 1.66e+01 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 112.12 108.70 3.42 8.40e-01 1.42e+00 1.65e+01 angle pdb=" N VAL J 198 " pdb=" CA VAL J 198 " pdb=" C VAL J 198 " ideal model delta sigma weight residual 112.12 108.71 3.41 8.40e-01 1.42e+00 1.65e+01 ... (remaining 18748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.35: 7082 13.35 - 26.71: 751 26.71 - 40.06: 399 40.06 - 53.42: 105 53.42 - 66.77: 63 Dihedral angle restraints: 8400 sinusoidal: 3171 harmonic: 5229 Sorted by residual: dihedral pdb=" CA GLU R 128 " pdb=" C GLU R 128 " pdb=" N GLN R 129 " pdb=" CA GLN R 129 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLU A 128 " pdb=" C GLU A 128 " pdb=" N GLN A 129 " pdb=" CA GLN A 129 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLU O 128 " pdb=" C GLU O 128 " pdb=" N GLN O 129 " pdb=" CA GLN O 129 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 8397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1230 0.032 - 0.064: 678 0.064 - 0.096: 297 0.096 - 0.128: 84 0.128 - 0.160: 42 Chirality restraints: 2331 Sorted by residual: chirality pdb=" CB THR U 179 " pdb=" CA THR U 179 " pdb=" OG1 THR U 179 " pdb=" CG2 THR U 179 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CB THR W 179 " pdb=" CA THR W 179 " pdb=" OG1 THR W 179 " pdb=" CG2 THR W 179 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CB THR e 179 " pdb=" CA THR e 179 " pdb=" OG1 THR e 179 " pdb=" CG2 THR e 179 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 2328 not shown) Planarity restraints: 2457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 179 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C THR I 179 " 0.022 2.00e-02 2.50e+03 pdb=" O THR I 179 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU I 180 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR c 179 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C THR c 179 " 0.022 2.00e-02 2.50e+03 pdb=" O THR c 179 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU c 180 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 179 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C THR C 179 " 0.022 2.00e-02 2.50e+03 pdb=" O THR C 179 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU C 180 " -0.008 2.00e-02 2.50e+03 ... (remaining 2454 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 4697 2.86 - 3.37: 12576 3.37 - 3.88: 21040 3.88 - 4.39: 26350 4.39 - 4.90: 45117 Nonbonded interactions: 109780 Sorted by model distance: nonbonded pdb=" O THR U 146 " pdb=" OG1 THR U 146 " model vdw 2.355 3.040 nonbonded pdb=" O THR I 146 " pdb=" OG1 THR I 146 " model vdw 2.355 3.040 nonbonded pdb=" O THR W 146 " pdb=" OG1 THR W 146 " model vdw 2.355 3.040 nonbonded pdb=" O THR A 146 " pdb=" OG1 THR A 146 " model vdw 2.355 3.040 nonbonded pdb=" O THR R 146 " pdb=" OG1 THR R 146 " model vdw 2.355 3.040 ... (remaining 109775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' } 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: 5.320 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.340 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.009 0.047 13755 Z= 0.394 Angle : 0.880 5.207 18753 Z= 0.514 Chirality : 0.050 0.160 2331 Planarity : 0.003 0.014 2457 Dihedral : 16.062 66.772 4998 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 5.56 % Allowed : 4.17 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.71 (0.17), residues: 1764 helix: -4.00 (0.13), residues: 693 sheet: -1.49 (0.22), residues: 504 loop : -3.06 (0.22), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c 142 TYR 0.009 0.002 TYR W 132 PHE 0.007 0.002 PHE Q 126 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00862 (13755) covalent geometry : angle 0.88036 (18753) hydrogen bonds : bond 0.27936 ( 672) hydrogen bonds : angle 9.58882 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 464 time to evaluate : 0.532 Fit side-chains REVERT: A 151 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7933 (tttm) REVERT: A 184 ARG cc_start: 0.7820 (mtt-85) cc_final: 0.6764 (mtp85) REVERT: C 151 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8088 (tttm) REVERT: D 151 LYS cc_start: 0.8525 (ttmt) cc_final: 0.7903 (tttm) REVERT: F 151 LYS cc_start: 0.8577 (ttmt) cc_final: 0.7990 (tttm) REVERT: G 151 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8076 (tttm) REVERT: G 218 HIS cc_start: 0.7715 (m-70) cc_final: 0.7486 (m170) REVERT: I 151 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8014 (tttm) REVERT: J 151 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7900 (tttm) REVERT: L 139 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: L 151 LYS cc_start: 0.8555 (ttmt) cc_final: 0.7835 (tttm) REVERT: N 151 LYS cc_start: 0.8563 (ttmt) cc_final: 0.7916 (tttm) REVERT: O 134 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7717 (ttp-170) REVERT: O 139 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: O 151 LYS cc_start: 0.8645 (ttmt) cc_final: 0.7950 (tttm) REVERT: O 218 HIS cc_start: 0.7659 (m-70) cc_final: 0.7426 (m170) REVERT: Q 151 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8066 (tttm) REVERT: R 151 LYS cc_start: 0.8547 (ttmt) cc_final: 0.7869 (tttm) REVERT: R 184 ARG cc_start: 0.7698 (mtt-85) cc_final: 0.6789 (mtp85) REVERT: R 218 HIS cc_start: 0.7724 (m-70) cc_final: 0.7505 (m170) REVERT: T 134 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7707 (ttp-170) REVERT: T 151 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7870 (tttm) REVERT: T 197 LEU cc_start: 0.8504 (tp) cc_final: 0.8262 (tt) REVERT: U 151 LYS cc_start: 0.8551 (ttmt) cc_final: 0.7809 (tttm) REVERT: W 151 LYS cc_start: 0.8493 (ttmt) cc_final: 0.7895 (tttm) REVERT: Y 151 LYS cc_start: 0.8656 (ttmt) cc_final: 0.7978 (tttm) REVERT: Z 151 LYS cc_start: 0.8554 (ttmt) cc_final: 0.7851 (tttm) REVERT: Z 184 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.6683 (mtp85) REVERT: b 151 LYS cc_start: 0.8571 (ttmt) cc_final: 0.7858 (tttm) REVERT: b 177 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8110 (m) REVERT: b 218 HIS cc_start: 0.7752 (m-70) cc_final: 0.7547 (m170) REVERT: c 151 LYS cc_start: 0.8538 (ttmt) cc_final: 0.7934 (tttm) REVERT: c 218 HIS cc_start: 0.7781 (m-70) cc_final: 0.7563 (m170) REVERT: e 151 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8023 (tttm) REVERT: f 151 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8070 (tttm) outliers start: 84 outliers final: 24 residues processed: 494 average time/residue: 0.1589 time to fit residues: 104.4310 Evaluate side-chains 396 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 369 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain N residue 139 GLU Chi-restraints excluded: chain O residue 139 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 139 GLU Chi-restraints excluded: chain T residue 139 GLU Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain W residue 139 GLU Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Z residue 139 GLU Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain f residue 139 GLU Chi-restraints excluded: chain f residue 177 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS C 196 HIS D 196 HIS F 196 HIS G 196 HIS I 196 HIS J 196 HIS L 196 HIS N 196 HIS O 196 HIS Q 196 HIS R 196 HIS T 190 GLN T 196 HIS U 190 GLN U 196 HIS W 196 HIS Y 196 HIS Z 196 HIS b 196 HIS c 196 HIS e 196 HIS f 196 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.136889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.112151 restraints weight = 15907.597| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.35 r_work: 0.3075 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13755 Z= 0.122 Angle : 0.612 8.843 18753 Z= 0.301 Chirality : 0.043 0.124 2331 Planarity : 0.004 0.030 2457 Dihedral : 5.489 28.993 1980 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.93 % Allowed : 8.33 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.20), residues: 1764 helix: -2.32 (0.16), residues: 714 sheet: 0.40 (0.27), residues: 462 loop : -2.25 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 142 TYR 0.011 0.001 TYR D 132 PHE 0.001 0.000 PHE b 126 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00298 (13755) covalent geometry : angle 0.61215 (18753) hydrogen bonds : bond 0.04691 ( 672) hydrogen bonds : angle 5.34659 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 422 time to evaluate : 0.519 Fit side-chains REVERT: A 151 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8027 (tttm) REVERT: A 184 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.6885 (mtp85) REVERT: C 131 ASN cc_start: 0.8003 (t0) cc_final: 0.7738 (t0) REVERT: C 151 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8114 (tttm) REVERT: C 184 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.6883 (mtp85) REVERT: D 151 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8014 (tttm) REVERT: F 131 ASN cc_start: 0.7972 (t0) cc_final: 0.7769 (t0) REVERT: F 151 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8038 (tttm) REVERT: F 222 GLN cc_start: 0.6232 (mm110) cc_final: 0.5963 (mm110) REVERT: G 142 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7710 (mtm110) REVERT: G 151 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8182 (tttm) REVERT: J 151 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8107 (tttm) REVERT: L 131 ASN cc_start: 0.7853 (t0) cc_final: 0.7549 (t0) REVERT: L 151 LYS cc_start: 0.8601 (ttmt) cc_final: 0.7915 (tttm) REVERT: N 151 LYS cc_start: 0.8701 (ttmt) cc_final: 0.8112 (tttm) REVERT: O 134 ARG cc_start: 0.8460 (mtp180) cc_final: 0.8245 (ttp-170) REVERT: O 151 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8052 (tttm) REVERT: Q 151 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8116 (tttm) REVERT: R 151 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8028 (tttm) REVERT: T 151 LYS cc_start: 0.8638 (ttmt) cc_final: 0.7988 (tttm) REVERT: U 142 ARG cc_start: 0.8056 (mmt-90) cc_final: 0.7806 (mtm110) REVERT: U 151 LYS cc_start: 0.8708 (ttmt) cc_final: 0.8088 (tttm) REVERT: W 151 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8033 (tttm) REVERT: Y 151 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8052 (tttm) REVERT: Z 151 LYS cc_start: 0.8595 (ttmt) cc_final: 0.7935 (tttm) REVERT: Z 184 ARG cc_start: 0.7846 (mtt-85) cc_final: 0.6815 (mtp85) REVERT: b 151 LYS cc_start: 0.8664 (ttmt) cc_final: 0.8027 (tttm) REVERT: b 177 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8180 (m) REVERT: c 151 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8031 (tttm) REVERT: e 151 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8114 (tttm) REVERT: e 216 SER cc_start: 0.8944 (m) cc_final: 0.8688 (p) REVERT: f 151 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8005 (tttm) REVERT: f 184 ARG cc_start: 0.7829 (mtt-85) cc_final: 0.6721 (mtp85) outliers start: 14 outliers final: 4 residues processed: 434 average time/residue: 0.1743 time to fit residues: 98.7885 Evaluate side-chains 341 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 336 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 157 optimal weight: 0.3980 chunk 131 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 GLN G 190 GLN L 190 GLN O 218 HIS U 190 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.106959 restraints weight = 16134.420| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.36 r_work: 0.3017 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13755 Z= 0.170 Angle : 0.610 9.953 18753 Z= 0.294 Chirality : 0.043 0.120 2331 Planarity : 0.004 0.034 2457 Dihedral : 4.628 14.295 1912 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.78 % Allowed : 9.99 % Favored : 87.24 % 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 are not related in a simple way. whole: -1.90 (0.21), residues: 1764 helix: -1.67 (0.17), residues: 735 sheet: 0.12 (0.25), residues: 504 loop : -1.73 (0.30), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 184 TYR 0.008 0.001 TYR F 132 PHE 0.004 0.001 PHE c 126 HIS 0.003 0.001 HIS Y 156 Details of bonding type rmsd covalent geometry : bond 0.00418 (13755) covalent geometry : angle 0.60950 (18753) hydrogen bonds : bond 0.04080 ( 672) hydrogen bonds : angle 4.85411 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 332 time to evaluate : 0.529 Fit side-chains REVERT: A 151 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8117 (tttm) REVERT: A 184 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.6870 (mtp85) REVERT: C 131 ASN cc_start: 0.7892 (t0) cc_final: 0.7631 (t0) REVERT: C 151 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8180 (tttm) REVERT: C 184 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.6866 (mtp85) REVERT: C 188 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7671 (mt-10) REVERT: D 151 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8034 (tttm) REVERT: F 131 ASN cc_start: 0.7993 (t0) cc_final: 0.7758 (t0) REVERT: F 151 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8070 (tttm) REVERT: G 151 LYS cc_start: 0.8713 (ttmt) cc_final: 0.8175 (tttm) REVERT: I 151 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8174 (tttm) REVERT: J 151 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8160 (tttm) REVERT: L 131 ASN cc_start: 0.7849 (t0) cc_final: 0.7540 (t0) REVERT: L 151 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8037 (tttm) REVERT: N 151 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8056 (tttm) REVERT: O 134 ARG cc_start: 0.8384 (mtp180) cc_final: 0.8095 (ttp-110) REVERT: O 151 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8085 (tttm) REVERT: Q 151 LYS cc_start: 0.8741 (ttmt) cc_final: 0.8108 (tttm) REVERT: R 151 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8019 (tttm) REVERT: T 134 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8305 (ttp-170) REVERT: T 151 LYS cc_start: 0.8576 (ttmt) cc_final: 0.7950 (tttm) REVERT: U 151 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8111 (tttm) REVERT: U 154 ARG cc_start: 0.8878 (mtp-110) cc_final: 0.8671 (mtp85) REVERT: W 151 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8020 (tttm) REVERT: Y 151 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8141 (tttm) REVERT: Z 151 LYS cc_start: 0.8612 (ttmt) cc_final: 0.7985 (tttm) REVERT: b 151 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8051 (tttm) REVERT: c 151 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8020 (tttm) REVERT: e 151 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8085 (tttm) REVERT: e 216 SER cc_start: 0.8982 (m) cc_final: 0.8755 (p) REVERT: f 151 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8052 (tttm) outliers start: 42 outliers final: 27 residues processed: 367 average time/residue: 0.1955 time to fit residues: 91.7164 Evaluate side-chains 347 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 320 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 175 SER Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 15 optimal weight: 0.4980 chunk 145 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 0.0370 chunk 140 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 GLN G 190 GLN L 190 GLN U 190 GLN f 190 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.109342 restraints weight = 15926.079| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.39 r_work: 0.3032 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13755 Z= 0.143 Angle : 0.564 8.940 18753 Z= 0.272 Chirality : 0.042 0.118 2331 Planarity : 0.003 0.025 2457 Dihedral : 4.426 13.406 1911 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.12 % Allowed : 9.79 % Favored : 88.10 % 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 are not related in a simple way. whole: -0.94 (0.22), residues: 1764 helix: -0.91 (0.19), residues: 672 sheet: 0.45 (0.24), residues: 504 loop : -0.99 (0.33), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 184 TYR 0.009 0.001 TYR F 132 PHE 0.003 0.001 PHE Q 126 HIS 0.002 0.001 HIS J 156 Details of bonding type rmsd covalent geometry : bond 0.00357 (13755) covalent geometry : angle 0.56427 (18753) hydrogen bonds : bond 0.03471 ( 672) hydrogen bonds : angle 4.48419 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 321 time to evaluate : 0.488 Fit side-chains REVERT: A 151 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7933 (tttm) REVERT: C 131 ASN cc_start: 0.7891 (t0) cc_final: 0.7648 (t0) REVERT: C 151 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8153 (tttm) REVERT: D 134 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8103 (ttp-170) REVERT: D 151 LYS cc_start: 0.8488 (ttmt) cc_final: 0.7984 (tttm) REVERT: F 131 ASN cc_start: 0.7926 (t0) cc_final: 0.7704 (t0) REVERT: F 151 LYS cc_start: 0.8612 (ttmt) cc_final: 0.7962 (tttm) REVERT: G 151 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8141 (tttm) REVERT: I 151 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8108 (tttm) REVERT: J 151 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8128 (tttm) REVERT: L 131 ASN cc_start: 0.7666 (t0) cc_final: 0.7404 (t0) REVERT: L 151 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8006 (tttm) REVERT: N 151 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8088 (tttm) REVERT: O 134 ARG cc_start: 0.8373 (mtp180) cc_final: 0.8075 (ttp-170) REVERT: O 151 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8106 (tttm) REVERT: Q 151 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8011 (tttm) REVERT: Q 184 ARG cc_start: 0.7579 (mtt90) cc_final: 0.6598 (mtp85) REVERT: R 151 LYS cc_start: 0.8602 (ttmt) cc_final: 0.7957 (tttm) REVERT: T 142 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7497 (mtt90) REVERT: T 151 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7844 (tttm) REVERT: U 151 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8015 (tttm) REVERT: W 151 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8035 (tttm) REVERT: Y 151 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8044 (tttm) REVERT: Y 222 GLN cc_start: 0.6234 (mm110) cc_final: 0.5955 (mm110) REVERT: Z 151 LYS cc_start: 0.8577 (ttmt) cc_final: 0.7948 (tttm) REVERT: b 151 LYS cc_start: 0.8598 (ttmt) cc_final: 0.7951 (tttm) REVERT: c 151 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8045 (tttm) REVERT: e 151 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8112 (tttm) REVERT: f 151 LYS cc_start: 0.8499 (ttmt) cc_final: 0.7936 (tttm) outliers start: 32 outliers final: 28 residues processed: 341 average time/residue: 0.2032 time to fit residues: 87.8363 Evaluate side-chains 336 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 308 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 175 SER Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 103 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109510 restraints weight = 15953.036| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.41 r_work: 0.3022 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13755 Z= 0.139 Angle : 0.544 8.117 18753 Z= 0.261 Chirality : 0.042 0.130 2331 Planarity : 0.003 0.022 2457 Dihedral : 4.274 13.013 1911 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.25 % Allowed : 11.11 % Favored : 86.64 % 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 are not related in a simple way. whole: -0.88 (0.22), residues: 1764 helix: -0.83 (0.18), residues: 714 sheet: 0.65 (0.24), residues: 504 loop : -1.18 (0.35), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 184 TYR 0.010 0.001 TYR F 132 PHE 0.003 0.001 PHE c 126 HIS 0.002 0.001 HIS c 196 Details of bonding type rmsd covalent geometry : bond 0.00347 (13755) covalent geometry : angle 0.54395 (18753) hydrogen bonds : bond 0.03323 ( 672) hydrogen bonds : angle 4.29986 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 311 time to evaluate : 0.567 Fit side-chains REVERT: A 151 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7896 (tttm) REVERT: C 151 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8154 (tttm) REVERT: D 151 LYS cc_start: 0.8453 (ttmt) cc_final: 0.7961 (tttm) REVERT: F 151 LYS cc_start: 0.8530 (ttmt) cc_final: 0.7889 (tttm) REVERT: F 218 HIS cc_start: 0.7903 (m170) cc_final: 0.7625 (m90) REVERT: G 151 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8099 (tttm) REVERT: I 151 LYS cc_start: 0.8587 (ttmt) cc_final: 0.8122 (tttm) REVERT: J 151 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8159 (tttm) REVERT: L 131 ASN cc_start: 0.7617 (t0) cc_final: 0.7352 (t0) REVERT: L 151 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8006 (tttm) REVERT: N 151 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8037 (tttm) REVERT: O 134 ARG cc_start: 0.8211 (mtp180) cc_final: 0.7932 (ttp-170) REVERT: O 151 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8063 (tttm) REVERT: Q 151 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8020 (tttm) REVERT: Q 184 ARG cc_start: 0.7645 (mtt90) cc_final: 0.6636 (mtp85) REVERT: R 151 LYS cc_start: 0.8546 (ttmt) cc_final: 0.7892 (tttm) REVERT: T 151 LYS cc_start: 0.8388 (ttmt) cc_final: 0.7842 (tttm) REVERT: U 151 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8119 (tttm) REVERT: W 151 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8015 (tttm) REVERT: Y 151 LYS cc_start: 0.8579 (ttmt) cc_final: 0.7998 (tttm) REVERT: Y 222 GLN cc_start: 0.6215 (mm110) cc_final: 0.5918 (mm110) REVERT: Z 131 ASN cc_start: 0.7840 (t0) cc_final: 0.7592 (t0) REVERT: Z 151 LYS cc_start: 0.8534 (ttmt) cc_final: 0.7917 (tttm) REVERT: b 151 LYS cc_start: 0.8447 (ttmt) cc_final: 0.7891 (tttm) REVERT: c 151 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8020 (tttm) REVERT: e 151 LYS cc_start: 0.8505 (ttmt) cc_final: 0.8078 (tttm) REVERT: f 151 LYS cc_start: 0.8489 (ttmt) cc_final: 0.7934 (tttm) outliers start: 34 outliers final: 31 residues processed: 332 average time/residue: 0.2062 time to fit residues: 86.6202 Evaluate side-chains 337 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 306 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 175 SER Chi-restraints excluded: chain c residue 180 LEU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 20 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 GLN G 190 GLN e 218 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109886 restraints weight = 15873.078| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.37 r_work: 0.3041 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13755 Z= 0.120 Angle : 0.521 7.589 18753 Z= 0.250 Chirality : 0.042 0.128 2331 Planarity : 0.003 0.018 2457 Dihedral : 4.126 12.786 1911 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.51 % Allowed : 11.31 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1764 helix: -0.44 (0.18), residues: 735 sheet: 0.76 (0.23), residues: 504 loop : -0.99 (0.36), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 184 TYR 0.010 0.001 TYR F 132 PHE 0.003 0.001 PHE T 126 HIS 0.002 0.000 HIS e 218 Details of bonding type rmsd covalent geometry : bond 0.00304 (13755) covalent geometry : angle 0.52144 (18753) hydrogen bonds : bond 0.03044 ( 672) hydrogen bonds : angle 4.08923 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 300 time to evaluate : 0.517 Fit side-chains REVERT: A 151 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7881 (tttm) REVERT: C 151 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8111 (tttm) REVERT: D 151 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8045 (tttm) REVERT: F 151 LYS cc_start: 0.8525 (ttmt) cc_final: 0.7996 (tttm) REVERT: G 151 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8156 (tttm) REVERT: I 151 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8115 (tttm) REVERT: J 151 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8167 (tttm) REVERT: L 131 ASN cc_start: 0.7596 (t0) cc_final: 0.7345 (t0) REVERT: L 151 LYS cc_start: 0.8584 (ttmt) cc_final: 0.7982 (tttm) REVERT: N 151 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8026 (tttm) REVERT: O 134 ARG cc_start: 0.8342 (mtp180) cc_final: 0.8060 (ttp-170) REVERT: O 151 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8067 (tttm) REVERT: Q 151 LYS cc_start: 0.8580 (ttmt) cc_final: 0.8068 (tttm) REVERT: R 151 LYS cc_start: 0.8495 (ttmt) cc_final: 0.7836 (tttm) REVERT: T 151 LYS cc_start: 0.8382 (ttmt) cc_final: 0.7863 (tttm) REVERT: U 151 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8126 (tttm) REVERT: W 151 LYS cc_start: 0.8532 (ttmt) cc_final: 0.7986 (tttm) REVERT: Y 151 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8018 (tttm) REVERT: Y 222 GLN cc_start: 0.6290 (mm110) cc_final: 0.6011 (mm110) REVERT: Z 151 LYS cc_start: 0.8485 (ttmt) cc_final: 0.7926 (tttm) REVERT: b 151 LYS cc_start: 0.8475 (ttmt) cc_final: 0.7894 (tttm) REVERT: c 151 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8060 (tttm) REVERT: e 151 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8068 (tttm) REVERT: f 151 LYS cc_start: 0.8510 (ttmt) cc_final: 0.7929 (tttm) outliers start: 38 outliers final: 31 residues processed: 325 average time/residue: 0.2053 time to fit residues: 84.1583 Evaluate side-chains 327 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain c residue 175 SER Chi-restraints excluded: chain c residue 180 LEU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 0.0470 chunk 101 optimal weight: 0.0770 chunk 113 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 190 GLN e 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109396 restraints weight = 15863.209| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.41 r_work: 0.3024 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13755 Z= 0.149 Angle : 0.534 7.512 18753 Z= 0.256 Chirality : 0.042 0.118 2331 Planarity : 0.003 0.018 2457 Dihedral : 4.134 12.668 1911 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.38 % Allowed : 11.77 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.22), residues: 1764 helix: -0.11 (0.18), residues: 735 sheet: 0.77 (0.23), residues: 504 loop : -0.94 (0.35), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 184 TYR 0.011 0.001 TYR F 132 PHE 0.004 0.001 PHE Z 126 HIS 0.003 0.001 HIS e 218 Details of bonding type rmsd covalent geometry : bond 0.00369 (13755) covalent geometry : angle 0.53443 (18753) hydrogen bonds : bond 0.03273 ( 672) hydrogen bonds : angle 4.15251 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 308 time to evaluate : 0.565 Fit side-chains REVERT: A 151 LYS cc_start: 0.8409 (ttmt) cc_final: 0.7873 (tttm) REVERT: C 151 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8100 (tttm) REVERT: D 151 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8051 (tttm) REVERT: F 151 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8031 (tttm) REVERT: G 151 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8111 (tttm) REVERT: I 151 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8117 (tttm) REVERT: J 151 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8165 (tttm) REVERT: L 131 ASN cc_start: 0.7647 (t0) cc_final: 0.7407 (t0) REVERT: L 151 LYS cc_start: 0.8488 (ttmt) cc_final: 0.7865 (tttm) REVERT: L 188 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7385 (mt-10) REVERT: N 151 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8026 (tttm) REVERT: O 134 ARG cc_start: 0.8249 (mtp180) cc_final: 0.7972 (ttp-170) REVERT: O 151 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8056 (tttm) REVERT: Q 151 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8064 (tttm) REVERT: R 151 LYS cc_start: 0.8537 (ttmt) cc_final: 0.7946 (tttm) REVERT: T 151 LYS cc_start: 0.8406 (ttmt) cc_final: 0.7873 (tttm) REVERT: U 151 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8122 (tttm) REVERT: W 151 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7977 (tttm) REVERT: Y 151 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8005 (tttm) REVERT: Y 222 GLN cc_start: 0.6260 (mm110) cc_final: 0.6009 (mm110) REVERT: Z 151 LYS cc_start: 0.8438 (ttmt) cc_final: 0.7874 (tttm) REVERT: b 151 LYS cc_start: 0.8502 (ttmt) cc_final: 0.7900 (tttm) REVERT: c 151 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8052 (tttm) REVERT: e 151 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8062 (tttm) REVERT: f 151 LYS cc_start: 0.8550 (ttmt) cc_final: 0.7954 (tttm) outliers start: 36 outliers final: 34 residues processed: 329 average time/residue: 0.2099 time to fit residues: 87.2159 Evaluate side-chains 340 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 306 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain c residue 175 SER Chi-restraints excluded: chain c residue 180 LEU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 138 optimal weight: 0.0570 chunk 101 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 GLN G 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.135819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109738 restraints weight = 15805.146| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.42 r_work: 0.3023 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13755 Z= 0.145 Angle : 0.530 7.237 18753 Z= 0.254 Chirality : 0.042 0.138 2331 Planarity : 0.003 0.020 2457 Dihedral : 4.124 12.739 1911 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.38 % Allowed : 12.10 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.22), residues: 1764 helix: 0.17 (0.18), residues: 735 sheet: 0.78 (0.23), residues: 504 loop : -0.91 (0.35), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 142 TYR 0.011 0.001 TYR F 132 PHE 0.004 0.001 PHE U 126 HIS 0.002 0.001 HIS c 196 Details of bonding type rmsd covalent geometry : bond 0.00359 (13755) covalent geometry : angle 0.53036 (18753) hydrogen bonds : bond 0.03206 ( 672) hydrogen bonds : angle 4.08470 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 309 time to evaluate : 0.522 Fit side-chains REVERT: A 151 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7893 (tttm) REVERT: C 151 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8090 (tttm) REVERT: D 151 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8033 (tttm) REVERT: F 151 LYS cc_start: 0.8498 (ttmt) cc_final: 0.7983 (tttm) REVERT: G 151 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8049 (tttm) REVERT: I 151 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8101 (tttm) REVERT: J 151 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8128 (tttm) REVERT: L 131 ASN cc_start: 0.7625 (t0) cc_final: 0.7399 (t0) REVERT: L 151 LYS cc_start: 0.8471 (ttmt) cc_final: 0.7865 (tttm) REVERT: L 188 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7287 (mt-10) REVERT: N 151 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7986 (tttm) REVERT: O 134 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7814 (ttp-170) REVERT: O 151 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8056 (tttm) REVERT: Q 151 LYS cc_start: 0.8582 (ttmt) cc_final: 0.7996 (tttm) REVERT: R 151 LYS cc_start: 0.8526 (ttmt) cc_final: 0.7937 (tttm) REVERT: T 151 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7870 (tttm) REVERT: U 151 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8117 (tttm) REVERT: W 151 LYS cc_start: 0.8536 (ttmt) cc_final: 0.7988 (tttm) REVERT: Y 151 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7915 (tttm) REVERT: Y 222 GLN cc_start: 0.6231 (mm110) cc_final: 0.5969 (mm110) REVERT: Z 151 LYS cc_start: 0.8431 (ttmt) cc_final: 0.7873 (tttm) REVERT: b 151 LYS cc_start: 0.8477 (ttmt) cc_final: 0.7876 (tttm) REVERT: c 151 LYS cc_start: 0.8497 (ttmt) cc_final: 0.8032 (tttm) REVERT: e 151 LYS cc_start: 0.8538 (ttmt) cc_final: 0.8054 (tttm) REVERT: f 151 LYS cc_start: 0.8541 (ttmt) cc_final: 0.7944 (tttm) outliers start: 36 outliers final: 34 residues processed: 330 average time/residue: 0.1979 time to fit residues: 82.5563 Evaluate side-chains 336 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 302 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain c residue 175 SER Chi-restraints excluded: chain c residue 180 LEU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 93 optimal weight: 0.2980 chunk 99 optimal weight: 0.6980 chunk 8 optimal weight: 0.0270 chunk 139 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111687 restraints weight = 15809.821| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.41 r_work: 0.3052 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13755 Z= 0.108 Angle : 0.508 6.874 18753 Z= 0.244 Chirality : 0.042 0.137 2331 Planarity : 0.003 0.016 2457 Dihedral : 4.016 12.616 1911 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.25 % Allowed : 12.57 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.22), residues: 1764 helix: 0.71 (0.19), residues: 735 sheet: 0.83 (0.23), residues: 504 loop : -0.91 (0.35), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 184 TYR 0.011 0.001 TYR F 132 PHE 0.002 0.001 PHE U 126 HIS 0.001 0.000 HIS Q 196 Details of bonding type rmsd covalent geometry : bond 0.00280 (13755) covalent geometry : angle 0.50774 (18753) hydrogen bonds : bond 0.02853 ( 672) hydrogen bonds : angle 3.85897 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 301 time to evaluate : 0.530 Fit side-chains REVERT: A 151 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7881 (tttm) REVERT: C 151 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8033 (tttm) REVERT: C 154 ARG cc_start: 0.8533 (mtp85) cc_final: 0.8321 (mtp85) REVERT: D 151 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8021 (tttm) REVERT: F 151 LYS cc_start: 0.8464 (ttmt) cc_final: 0.7951 (tttm) REVERT: G 151 LYS cc_start: 0.8469 (ttmt) cc_final: 0.7991 (tttm) REVERT: I 151 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8020 (tttm) REVERT: J 151 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8146 (tttm) REVERT: L 131 ASN cc_start: 0.7521 (t0) cc_final: 0.7300 (t0) REVERT: L 151 LYS cc_start: 0.8434 (ttmt) cc_final: 0.7845 (tttm) REVERT: N 151 LYS cc_start: 0.8440 (ttmt) cc_final: 0.7988 (tttm) REVERT: O 134 ARG cc_start: 0.8015 (mtp180) cc_final: 0.7781 (ttp-170) REVERT: O 151 LYS cc_start: 0.8581 (ttmt) cc_final: 0.8012 (tttm) REVERT: Q 151 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8046 (tttm) REVERT: R 151 LYS cc_start: 0.8442 (ttmt) cc_final: 0.7864 (tttm) REVERT: T 151 LYS cc_start: 0.8365 (ttmt) cc_final: 0.7856 (tttm) REVERT: U 151 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8011 (tttm) REVERT: W 151 LYS cc_start: 0.8522 (ttmt) cc_final: 0.7995 (tttm) REVERT: Y 151 LYS cc_start: 0.8487 (ttmt) cc_final: 0.7929 (tttm) REVERT: Y 222 GLN cc_start: 0.6211 (mm110) cc_final: 0.5946 (mm110) REVERT: Z 151 LYS cc_start: 0.8385 (ttmt) cc_final: 0.7830 (tttm) REVERT: b 151 LYS cc_start: 0.8409 (ttmt) cc_final: 0.7861 (tttm) REVERT: c 151 LYS cc_start: 0.8429 (ttmt) cc_final: 0.7999 (tttm) REVERT: e 151 LYS cc_start: 0.8505 (ttmt) cc_final: 0.8049 (tttm) REVERT: f 151 LYS cc_start: 0.8530 (ttmt) cc_final: 0.7941 (tttm) outliers start: 34 outliers final: 33 residues processed: 320 average time/residue: 0.1981 time to fit residues: 79.8838 Evaluate side-chains 330 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 297 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain c residue 175 SER Chi-restraints excluded: chain c residue 180 LEU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 146 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 114 optimal weight: 0.2980 chunk 143 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.2980 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 190 GLN G 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110904 restraints weight = 15831.934| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.46 r_work: 0.3037 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13755 Z= 0.119 Angle : 0.514 6.974 18753 Z= 0.246 Chirality : 0.042 0.141 2331 Planarity : 0.003 0.026 2457 Dihedral : 4.008 12.552 1911 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.38 % Allowed : 12.57 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1764 helix: 0.89 (0.19), residues: 735 sheet: 0.88 (0.23), residues: 504 loop : -0.95 (0.34), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 142 TYR 0.014 0.001 TYR F 132 PHE 0.003 0.001 PHE U 126 HIS 0.001 0.000 HIS c 196 Details of bonding type rmsd covalent geometry : bond 0.00305 (13755) covalent geometry : angle 0.51389 (18753) hydrogen bonds : bond 0.02933 ( 672) hydrogen bonds : angle 3.87378 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 290 time to evaluate : 0.513 Fit side-chains REVERT: A 151 LYS cc_start: 0.8389 (ttmt) cc_final: 0.7875 (tttm) REVERT: C 151 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8013 (tttm) REVERT: C 154 ARG cc_start: 0.8558 (mtp85) cc_final: 0.8334 (mtp85) REVERT: D 151 LYS cc_start: 0.8400 (ttmt) cc_final: 0.8006 (tttm) REVERT: F 151 LYS cc_start: 0.8459 (ttmt) cc_final: 0.7943 (tttm) REVERT: G 151 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8002 (tttm) REVERT: I 151 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8000 (tttm) REVERT: J 151 LYS cc_start: 0.8452 (ttmt) cc_final: 0.8011 (tttm) REVERT: L 131 ASN cc_start: 0.7619 (t0) cc_final: 0.7358 (t0) REVERT: L 151 LYS cc_start: 0.8404 (ttmt) cc_final: 0.7808 (tttm) REVERT: N 151 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7969 (tttm) REVERT: O 134 ARG cc_start: 0.7937 (mtp180) cc_final: 0.7699 (ttp-170) REVERT: O 151 LYS cc_start: 0.8537 (ttmt) cc_final: 0.7955 (tttm) REVERT: Q 151 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8029 (tttm) REVERT: R 151 LYS cc_start: 0.8409 (ttmt) cc_final: 0.7831 (tttm) REVERT: T 151 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7833 (tttm) REVERT: U 151 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8002 (tttm) REVERT: W 151 LYS cc_start: 0.8523 (ttmt) cc_final: 0.7988 (tttm) REVERT: Y 151 LYS cc_start: 0.8476 (ttmt) cc_final: 0.7914 (tttm) REVERT: Y 222 GLN cc_start: 0.6187 (mm110) cc_final: 0.5930 (mm110) REVERT: Z 151 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7821 (tttm) REVERT: b 151 LYS cc_start: 0.8378 (ttmt) cc_final: 0.7833 (tttm) REVERT: b 184 ARG cc_start: 0.7736 (mtt-85) cc_final: 0.6798 (mtp85) REVERT: c 151 LYS cc_start: 0.8414 (ttmt) cc_final: 0.7982 (tttm) REVERT: e 151 LYS cc_start: 0.8501 (ttmt) cc_final: 0.8032 (tttm) REVERT: f 151 LYS cc_start: 0.8524 (ttmt) cc_final: 0.7927 (tttm) outliers start: 36 outliers final: 36 residues processed: 311 average time/residue: 0.2128 time to fit residues: 82.9637 Evaluate side-chains 326 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 290 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 173 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain c residue 175 SER Chi-restraints excluded: chain c residue 180 LEU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 173 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 115 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 167 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 165 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111050 restraints weight = 15924.896| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.36 r_work: 0.3047 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13755 Z= 0.129 Angle : 0.517 7.353 18753 Z= 0.248 Chirality : 0.042 0.130 2331 Planarity : 0.003 0.025 2457 Dihedral : 4.020 12.854 1911 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.38 % Allowed : 12.57 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.21), residues: 1764 helix: 0.85 (0.18), residues: 735 sheet: 0.91 (0.23), residues: 504 loop : -0.98 (0.34), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 142 TYR 0.014 0.001 TYR F 132 PHE 0.003 0.001 PHE D 126 HIS 0.005 0.000 HIS e 218 Details of bonding type rmsd covalent geometry : bond 0.00326 (13755) covalent geometry : angle 0.51697 (18753) hydrogen bonds : bond 0.03014 ( 672) hydrogen bonds : angle 3.90587 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3480.53 seconds wall clock time: 60 minutes 20.92 seconds (3620.92 seconds total)