Starting phenix.real_space_refine on Wed Mar 4 13:57:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sd5_10149/03_2026/6sd5_10149.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sd5_10149/03_2026/6sd5_10149.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6sd5_10149/03_2026/6sd5_10149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sd5_10149/03_2026/6sd5_10149.map" model { file = "/net/cci-nas-00/data/ceres_data/6sd5_10149/03_2026/6sd5_10149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sd5_10149/03_2026/6sd5_10149.cif" } 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 22 5.16 5 C 8844 2.51 5 N 2530 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14212 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, M, O, P, R, T, U, W, X, Z, a, c, d, f, g Time building chain proxies: 1.25, per 1000 atoms: 0.09 Number of scatterers: 14212 At special positions: 0 Unit cell: (171.798, 170.154, 41.1, 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 22 16.00 O 2816 8.00 N 2530 7.00 C 8844 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: 0.98 Conformation dependent library (CDL) restraints added in 542.3 milliseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 44 sheets defined 38.6% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 194 " --> pdb=" O GLN A 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 194 " --> pdb=" O GLN D 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR F 146 " --> pdb=" O ARG F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL F 194 " --> pdb=" O GLN F 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 198 " --> pdb=" O VAL F 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 200 removed outlier: 4.400A pdb=" N SER G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 193 " --> pdb=" O GLY G 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL G 194 " --> pdb=" O GLN G 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL G 198 " --> pdb=" O VAL G 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR I 146 " --> pdb=" O ARG I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA I 193 " --> pdb=" O GLY I 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL I 198 " --> pdb=" O VAL I 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER J 192 " --> pdb=" O GLU J 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA J 193 " --> pdb=" O GLY J 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL J 194 " --> pdb=" O GLN J 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL J 198 " --> pdb=" O VAL J 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER L 192 " --> pdb=" O GLU L 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA L 193 " --> pdb=" O GLY L 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL L 194 " --> pdb=" O GLN L 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL L 198 " --> pdb=" O VAL L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'M' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR M 146 " --> pdb=" O ARG M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER M 192 " --> pdb=" O GLU M 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA M 193 " --> pdb=" O GLY M 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL M 194 " --> pdb=" O GLN M 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL M 198 " --> pdb=" O VAL M 194 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 132 Processing helix chain 'O' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR O 146 " --> pdb=" O ARG O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER O 192 " --> pdb=" O GLU O 188 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA O 193 " --> pdb=" O GLY O 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL O 194 " --> pdb=" O GLN O 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL O 198 " --> pdb=" O VAL O 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR P 146 " --> pdb=" O ARG P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER P 192 " --> pdb=" O GLU P 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA P 193 " --> pdb=" O GLY P 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL P 194 " --> pdb=" O GLN P 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL P 198 " --> pdb=" O VAL P 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR R 146 " --> pdb=" O ARG R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 193 " --> pdb=" O GLY R 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL R 194 " --> pdb=" O GLN R 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 132 Processing helix chain 'T' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR T 146 " --> pdb=" O ARG T 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER T 192 " --> pdb=" O GLU T 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA T 193 " --> pdb=" O GLY T 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL T 194 " --> pdb=" O GLN T 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL T 198 " --> pdb=" O VAL T 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 132 Processing helix chain 'U' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR U 146 " --> pdb=" O ARG U 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER U 192 " --> pdb=" O GLU U 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA U 193 " --> pdb=" O GLY U 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL U 194 " --> pdb=" O GLN U 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL U 198 " --> pdb=" O VAL U 194 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 132 Processing helix chain 'W' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR W 146 " --> pdb=" O ARG W 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA W 193 " --> pdb=" O GLY W 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL W 194 " --> pdb=" O GLN W 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL W 198 " --> pdb=" O VAL W 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 132 Processing helix chain 'X' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR X 146 " --> pdb=" O ARG X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER X 192 " --> pdb=" O GLU X 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA X 193 " --> pdb=" O GLY X 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL X 194 " --> pdb=" O GLN X 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL X 198 " --> pdb=" O VAL X 194 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 132 Processing helix chain 'Z' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR Z 146 " --> pdb=" O ARG Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER Z 192 " --> pdb=" O GLU Z 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA Z 193 " --> pdb=" O GLY Z 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL Z 198 " --> pdb=" O VAL Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 132 Processing helix chain 'a' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR a 146 " --> pdb=" O ARG a 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER a 192 " --> pdb=" O GLU a 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA a 193 " --> pdb=" O GLY a 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL a 194 " --> pdb=" O GLN a 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL a 198 " --> pdb=" O VAL a 194 " (cutoff:3.500A) Processing helix chain 'c' and resid 127 through 132 Processing helix chain 'c' and resid 132 through 146 removed outlier: 3.632A pdb=" N THR c 146 " --> pdb=" O ARG c 142 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER c 192 " --> pdb=" O GLU c 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA c 193 " --> pdb=" O GLY c 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL c 198 " --> pdb=" O VAL c 194 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 132 Processing helix chain 'd' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR d 146 " --> pdb=" O ARG d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER d 192 " --> pdb=" O GLU d 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA d 193 " --> pdb=" O GLY d 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL d 194 " --> pdb=" O GLN d 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL d 198 " --> pdb=" O VAL d 194 " (cutoff:3.500A) Processing helix chain 'f' and resid 127 through 132 Processing helix chain 'f' and resid 132 through 146 removed outlier: 3.633A pdb=" N THR f 146 " --> pdb=" O ARG f 142 " (cutoff:3.500A) Processing helix chain 'f' and resid 188 through 200 removed outlier: 4.401A pdb=" N SER f 192 " --> pdb=" O GLU f 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA f 193 " --> pdb=" O GLY f 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL f 194 " --> pdb=" O GLN f 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL f 198 " --> pdb=" O VAL f 194 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 132 Processing helix chain 'g' and resid 132 through 146 removed outlier: 3.634A pdb=" N THR g 146 " --> pdb=" O ARG g 142 " (cutoff:3.500A) Processing helix chain 'g' and resid 188 through 200 removed outlier: 4.402A pdb=" N SER g 192 " --> pdb=" O GLU g 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA g 193 " --> pdb=" O GLY g 189 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL g 194 " --> pdb=" O GLN g 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL g 198 " --> pdb=" O VAL g 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR A 179 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS A 156 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR C 179 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS C 156 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR D 179 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS D 156 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR F 179 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS F 156 " --> pdb=" O SER F 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR G 179 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS G 156 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR I 179 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS I 156 " --> pdb=" O SER I 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR J 179 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS J 156 " --> pdb=" O SER J 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR L 179 " --> pdb=" O LYS L 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 156 through 157 removed outlier: 3.546A pdb=" N HIS L 156 " --> pdb=" O SER L 175 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR M 179 " --> pdb=" O LYS M 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS M 156 " --> pdb=" O SER M 175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR O 179 " --> pdb=" O LYS O 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS O 156 " --> pdb=" O SER O 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR P 179 " --> pdb=" O LYS P 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS P 156 " --> pdb=" O SER P 175 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR R 179 " --> pdb=" O LYS R 151 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS R 156 " --> pdb=" O SER R 175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR T 179 " --> pdb=" O LYS T 151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS T 156 " --> pdb=" O SER T 175 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR U 179 " --> pdb=" O LYS U 151 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS U 156 " --> pdb=" O SER U 175 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR W 179 " --> pdb=" O LYS W 151 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 156 through 157 removed outlier: 3.544A pdb=" N HIS W 156 " --> pdb=" O SER W 175 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR X 179 " --> pdb=" O LYS X 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS X 156 " --> pdb=" O SER X 175 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Z' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR Z 179 " --> pdb=" O LYS Z 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS Z 156 " --> pdb=" O SER Z 175 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'a' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR a 179 " --> pdb=" O LYS a 151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'a' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS a 156 " --> pdb=" O SER a 175 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR c 179 " --> pdb=" O LYS c 151 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS c 156 " --> pdb=" O SER c 175 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR d 179 " --> pdb=" O LYS d 151 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS d 156 " --> pdb=" O SER d 175 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'f' and resid 150 through 152 removed outlier: 6.694A pdb=" N THR f 179 " --> pdb=" O LYS f 151 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'f' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS f 156 " --> pdb=" O SER f 175 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'g' and resid 150 through 152 removed outlier: 6.695A pdb=" N THR g 179 " --> pdb=" O LYS g 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'g' and resid 156 through 157 removed outlier: 3.545A pdb=" N HIS g 156 " --> pdb=" O SER g 175 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1386 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: 2.11 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4928 1.34 - 1.46: 1742 1.46 - 1.57: 7696 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 14410 Sorted by residual: bond pdb=" CA HIS T 218 " pdb=" C HIS T 218 " ideal model delta sigma weight residual 1.532 1.519 0.014 9.60e-03 1.09e+04 2.06e+00 bond pdb=" CA HIS O 218 " pdb=" C HIS O 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.88e+00 bond pdb=" CA HIS g 218 " pdb=" C HIS g 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.86e+00 bond pdb=" CA HIS G 218 " pdb=" C HIS G 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.86e+00 bond pdb=" CA HIS A 218 " pdb=" C HIS A 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.83e+00 ... (remaining 14405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 17298 0.94 - 1.88: 1856 1.88 - 2.83: 316 2.83 - 3.77: 117 3.77 - 4.71: 59 Bond angle restraints: 19646 Sorted by residual: angle pdb=" N VAL J 130 " pdb=" CA VAL J 130 " pdb=" C VAL J 130 " ideal model delta sigma weight residual 112.12 108.28 3.84 8.40e-01 1.42e+00 2.08e+01 angle pdb=" N VAL L 130 " pdb=" CA VAL L 130 " pdb=" C VAL L 130 " ideal model delta sigma weight residual 112.12 108.30 3.82 8.40e-01 1.42e+00 2.07e+01 angle pdb=" N VAL O 130 " pdb=" CA VAL O 130 " pdb=" C VAL O 130 " ideal model delta sigma weight residual 112.12 108.30 3.82 8.40e-01 1.42e+00 2.06e+01 angle pdb=" N VAL a 130 " pdb=" CA VAL a 130 " pdb=" C VAL a 130 " ideal model delta sigma weight residual 112.12 108.31 3.81 8.40e-01 1.42e+00 2.06e+01 angle pdb=" N VAL M 130 " pdb=" CA VAL M 130 " pdb=" C VAL M 130 " ideal model delta sigma weight residual 112.12 108.31 3.81 8.40e-01 1.42e+00 2.06e+01 ... (remaining 19641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 7832 16.44 - 32.88: 726 32.88 - 49.32: 176 49.32 - 65.76: 44 65.76 - 82.20: 22 Dihedral angle restraints: 8800 sinusoidal: 3322 harmonic: 5478 Sorted by residual: dihedral pdb=" CB GLU J 188 " pdb=" CG GLU J 188 " pdb=" CD GLU J 188 " pdb=" OE1 GLU J 188 " ideal model delta sinusoidal sigma weight residual 0.00 -82.20 82.20 1 3.00e+01 1.11e-03 9.22e+00 dihedral pdb=" CB GLU R 188 " pdb=" CG GLU R 188 " pdb=" CD GLU R 188 " pdb=" OE1 GLU R 188 " ideal model delta sinusoidal sigma weight residual 0.00 -82.16 82.16 1 3.00e+01 1.11e-03 9.21e+00 dihedral pdb=" CB GLU D 188 " pdb=" CG GLU D 188 " pdb=" CD GLU D 188 " pdb=" OE1 GLU D 188 " ideal model delta sinusoidal sigma weight residual 0.00 -82.16 82.16 1 3.00e+01 1.11e-03 9.21e+00 ... (remaining 8797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1365 0.028 - 0.055: 656 0.055 - 0.083: 284 0.083 - 0.110: 115 0.110 - 0.138: 22 Chirality restraints: 2442 Sorted by residual: chirality pdb=" CA VAL f 213 " pdb=" N VAL f 213 " pdb=" C VAL f 213 " pdb=" CB VAL f 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA VAL W 213 " pdb=" N VAL W 213 " pdb=" C VAL W 213 " pdb=" CB VAL W 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA VAL D 213 " pdb=" N VAL D 213 " pdb=" C VAL D 213 " pdb=" CB VAL D 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 2439 not shown) Planarity restraints: 2574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU T 181 " -0.012 5.00e-02 4.00e+02 1.87e-02 5.60e-01 pdb=" N PRO T 182 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO T 182 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO T 182 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU a 181 " -0.012 5.00e-02 4.00e+02 1.87e-02 5.59e-01 pdb=" N PRO a 182 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO a 182 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO a 182 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU d 181 " -0.012 5.00e-02 4.00e+02 1.87e-02 5.59e-01 pdb=" N PRO d 182 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO d 182 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO d 182 " -0.010 5.00e-02 4.00e+02 ... (remaining 2571 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5059 2.84 - 3.35: 13320 3.35 - 3.87: 21809 3.87 - 4.38: 27851 4.38 - 4.90: 47853 Nonbonded interactions: 115892 Sorted by model distance: nonbonded pdb=" O SER D 175 " pdb=" OG SER D 175 " model vdw 2.321 3.040 nonbonded pdb=" O SER L 175 " pdb=" OG SER L 175 " model vdw 2.322 3.040 nonbonded pdb=" O SER F 175 " pdb=" OG SER F 175 " model vdw 2.322 3.040 nonbonded pdb=" O SER A 175 " pdb=" OG SER A 175 " model vdw 2.322 3.040 nonbonded pdb=" O SER I 175 " pdb=" OG SER I 175 " model vdw 2.322 3.040 ... (remaining 115887 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 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' } 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: 7.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 10.970 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 : 0.006 0.041 14410 Z= 0.290 Angle : 0.708 4.709 19646 Z= 0.428 Chirality : 0.041 0.138 2442 Planarity : 0.003 0.019 2574 Dihedral : 15.042 82.197 5236 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.39 % Allowed : 11.11 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.48 (0.16), residues: 1848 helix: -4.59 (0.08), residues: 726 sheet: -3.31 (0.23), residues: 484 loop : -2.12 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 134 TYR 0.004 0.001 TYR R 132 PHE 0.007 0.002 PHE g 126 HIS 0.003 0.001 HIS f 156 Details of bonding type rmsd covalent geometry : bond 0.00646 (14410) covalent geometry : angle 0.70811 (19646) hydrogen bonds : bond 0.32338 ( 462) hydrogen bonds : angle 12.79214 ( 1386) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 447 time to evaluate : 0.445 Fit side-chains REVERT: A 129 GLN cc_start: 0.7441 (mp10) cc_final: 0.7202 (mp10) REVERT: A 218 HIS cc_start: 0.7081 (m-70) cc_final: 0.6818 (t-90) REVERT: C 218 HIS cc_start: 0.7060 (m-70) cc_final: 0.6815 (t-90) REVERT: D 129 GLN cc_start: 0.7408 (mp10) cc_final: 0.7204 (mp10) REVERT: F 129 GLN cc_start: 0.7415 (mp10) cc_final: 0.7132 (mp10) REVERT: F 218 HIS cc_start: 0.6911 (m-70) cc_final: 0.6616 (t-90) REVERT: G 129 GLN cc_start: 0.7552 (mp10) cc_final: 0.7352 (mp10) REVERT: G 134 ARG cc_start: 0.7656 (mtp180) cc_final: 0.7405 (mtm110) REVERT: I 134 ARG cc_start: 0.7699 (mtp180) cc_final: 0.7433 (mtm110) REVERT: I 218 HIS cc_start: 0.6939 (m-70) cc_final: 0.6688 (t-90) REVERT: J 129 GLN cc_start: 0.7478 (mp10) cc_final: 0.7201 (mp10) REVERT: J 218 HIS cc_start: 0.7011 (m-70) cc_final: 0.6726 (t-90) REVERT: L 134 ARG cc_start: 0.7631 (mtp180) cc_final: 0.7406 (mtm110) REVERT: L 197 LEU cc_start: 0.8692 (tp) cc_final: 0.8357 (tt) REVERT: M 134 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7269 (mtm110) REVERT: O 134 ARG cc_start: 0.7542 (mtp180) cc_final: 0.7254 (mtm110) REVERT: P 134 ARG cc_start: 0.7467 (mtp180) cc_final: 0.7225 (mtm110) REVERT: R 129 GLN cc_start: 0.7404 (mp10) cc_final: 0.7162 (mp10) REVERT: T 134 ARG cc_start: 0.7440 (mtp180) cc_final: 0.7186 (mtm110) REVERT: U 129 GLN cc_start: 0.7535 (mp10) cc_final: 0.7334 (mp10) REVERT: U 134 ARG cc_start: 0.7495 (mtp180) cc_final: 0.7292 (mtm110) REVERT: U 142 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7384 (mmt-90) REVERT: W 129 GLN cc_start: 0.7484 (mp10) cc_final: 0.7248 (mp10) REVERT: W 134 ARG cc_start: 0.7620 (mtp180) cc_final: 0.7405 (mtm110) REVERT: X 134 ARG cc_start: 0.7667 (mtp180) cc_final: 0.7431 (mtm110) REVERT: Z 218 HIS cc_start: 0.7000 (m-70) cc_final: 0.6740 (t-90) REVERT: a 129 GLN cc_start: 0.7473 (mp10) cc_final: 0.7211 (mp10) REVERT: a 218 HIS cc_start: 0.6905 (m-70) cc_final: 0.6669 (t-90) REVERT: c 197 LEU cc_start: 0.8725 (tp) cc_final: 0.8500 (tt) REVERT: c 218 HIS cc_start: 0.6958 (m-70) cc_final: 0.6739 (t-90) REVERT: g 127 SER cc_start: 0.8706 (t) cc_final: 0.8483 (t) REVERT: g 218 HIS cc_start: 0.7003 (m-70) cc_final: 0.6643 (t-90) outliers start: 22 outliers final: 20 residues processed: 469 average time/residue: 0.1280 time to fit residues: 82.9445 Evaluate side-chains 414 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 394 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain F residue 214 ASP Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain L residue 214 ASP Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain P residue 214 ASP Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain T residue 214 ASP Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain W residue 214 ASP Chi-restraints excluded: chain X residue 214 ASP Chi-restraints excluded: chain Z residue 214 ASP Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain c residue 214 ASP Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain g residue 214 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0370 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 196 HIS C 196 HIS D 196 HIS F 190 GLN F 196 HIS G 190 GLN G 196 HIS I 190 GLN I 196 HIS J 196 HIS L 190 GLN L 196 HIS M 190 GLN M 196 HIS O 190 GLN O 196 HIS P 190 GLN P 196 HIS R 190 GLN R 196 HIS T 196 HIS U 196 HIS W 190 GLN W 196 HIS X 196 HIS Z 190 GLN Z 196 HIS a 196 HIS c 190 GLN c 196 HIS d 190 GLN d 196 HIS f 190 GLN f 196 HIS g 190 GLN g 196 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121043 restraints weight = 16552.567| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.07 r_work: 0.3290 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14410 Z= 0.130 Angle : 0.573 6.792 19646 Z= 0.294 Chirality : 0.039 0.118 2442 Planarity : 0.004 0.017 2574 Dihedral : 4.072 11.802 2042 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.28 % Allowed : 16.54 % Favored : 80.18 % 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: -4.10 (0.17), residues: 1848 helix: -2.97 (0.14), residues: 792 sheet: -2.88 (0.24), residues: 484 loop : -1.54 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 142 TYR 0.002 0.000 TYR I 132 PHE 0.005 0.001 PHE U 126 HIS 0.003 0.001 HIS U 156 Details of bonding type rmsd covalent geometry : bond 0.00321 (14410) covalent geometry : angle 0.57303 (19646) hydrogen bonds : bond 0.03117 ( 462) hydrogen bonds : angle 5.72364 ( 1386) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 448 time to evaluate : 0.501 Fit side-chains REVERT: A 129 GLN cc_start: 0.7767 (mp10) cc_final: 0.7407 (mp10) REVERT: A 218 HIS cc_start: 0.8010 (m-70) cc_final: 0.7209 (t-90) REVERT: C 218 HIS cc_start: 0.7895 (m-70) cc_final: 0.7265 (t-90) REVERT: D 129 GLN cc_start: 0.7718 (mp10) cc_final: 0.7337 (mp10) REVERT: F 129 GLN cc_start: 0.7709 (mp10) cc_final: 0.7366 (mp10) REVERT: F 218 HIS cc_start: 0.7725 (m-70) cc_final: 0.7065 (t-90) REVERT: G 129 GLN cc_start: 0.7938 (mp10) cc_final: 0.7521 (mp10) REVERT: G 142 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7710 (ttm-80) REVERT: I 142 ARG cc_start: 0.7919 (mtp180) cc_final: 0.7642 (ttm-80) REVERT: I 218 HIS cc_start: 0.7763 (m-70) cc_final: 0.7002 (t-90) REVERT: J 129 GLN cc_start: 0.7700 (mp10) cc_final: 0.7257 (mp10) REVERT: J 142 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7674 (ttm-80) REVERT: J 218 HIS cc_start: 0.7828 (m-70) cc_final: 0.7091 (t-90) REVERT: O 142 ARG cc_start: 0.7940 (mtp180) cc_final: 0.7710 (ttm-80) REVERT: P 142 ARG cc_start: 0.8067 (mtp180) cc_final: 0.7693 (ttm-80) REVERT: R 129 GLN cc_start: 0.7713 (mp10) cc_final: 0.7310 (mp10) REVERT: R 142 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7722 (ttm-80) REVERT: U 129 GLN cc_start: 0.7759 (mp10) cc_final: 0.7352 (mp10) REVERT: U 142 ARG cc_start: 0.8095 (mtp180) cc_final: 0.7777 (ttm-80) REVERT: W 129 GLN cc_start: 0.7721 (mp10) cc_final: 0.7462 (mp10) REVERT: W 142 ARG cc_start: 0.8002 (mtp180) cc_final: 0.7656 (ttm-80) REVERT: X 142 ARG cc_start: 0.8165 (mtp180) cc_final: 0.7785 (ttm-80) REVERT: Z 142 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7715 (ttm-80) REVERT: Z 218 HIS cc_start: 0.7779 (m-70) cc_final: 0.7009 (t-90) REVERT: a 129 GLN cc_start: 0.7702 (mp10) cc_final: 0.7264 (mp10) REVERT: a 142 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7714 (ttm-80) REVERT: a 218 HIS cc_start: 0.7790 (m-70) cc_final: 0.7049 (t-90) REVERT: c 142 ARG cc_start: 0.8308 (tpp-160) cc_final: 0.7677 (ttm-80) REVERT: c 218 HIS cc_start: 0.7739 (m-70) cc_final: 0.7150 (t-90) REVERT: d 142 ARG cc_start: 0.8339 (tpp-160) cc_final: 0.7606 (ttm-80) REVERT: f 142 ARG cc_start: 0.8328 (tpp-160) cc_final: 0.7795 (ttm-80) REVERT: g 218 HIS cc_start: 0.7772 (m-70) cc_final: 0.7121 (t-90) outliers start: 52 outliers final: 33 residues processed: 480 average time/residue: 0.1159 time to fit residues: 80.7137 Evaluate side-chains 406 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 373 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 190 GLN Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 51 optimal weight: 0.0470 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 209 ASN G 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN U 209 ASN W 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122307 restraints weight = 16558.694| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.08 r_work: 0.3302 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14410 Z= 0.112 Angle : 0.550 8.681 19646 Z= 0.269 Chirality : 0.040 0.124 2442 Planarity : 0.003 0.019 2574 Dihedral : 3.692 11.098 2002 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.66 % Allowed : 20.08 % Favored : 76.26 % 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: -3.06 (0.19), residues: 1848 helix: -1.46 (0.18), residues: 770 sheet: -2.85 (0.23), residues: 528 loop : -1.43 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 154 TYR 0.001 0.000 TYR O 132 PHE 0.006 0.001 PHE T 126 HIS 0.002 0.001 HIS L 156 Details of bonding type rmsd covalent geometry : bond 0.00281 (14410) covalent geometry : angle 0.55012 (19646) hydrogen bonds : bond 0.02989 ( 462) hydrogen bonds : angle 4.97271 ( 1386) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 400 time to evaluate : 0.452 Fit side-chains REVERT: A 129 GLN cc_start: 0.7701 (mp10) cc_final: 0.7314 (mp10) REVERT: A 218 HIS cc_start: 0.7961 (m-70) cc_final: 0.7182 (t-90) REVERT: C 218 HIS cc_start: 0.7849 (m-70) cc_final: 0.7124 (t-90) REVERT: D 129 GLN cc_start: 0.7624 (mp10) cc_final: 0.7269 (mp10) REVERT: F 129 GLN cc_start: 0.7695 (mp10) cc_final: 0.7396 (mp10) REVERT: F 218 HIS cc_start: 0.7706 (m-70) cc_final: 0.7075 (t-90) REVERT: G 129 GLN cc_start: 0.7835 (mp10) cc_final: 0.7435 (mp10) REVERT: G 142 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7650 (ttm-80) REVERT: G 154 ARG cc_start: 0.8461 (ttt-90) cc_final: 0.8237 (mtp85) REVERT: I 142 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7643 (ttm-80) REVERT: I 218 HIS cc_start: 0.7662 (m-70) cc_final: 0.6946 (t-90) REVERT: J 129 GLN cc_start: 0.7650 (mp10) cc_final: 0.7298 (mp10) REVERT: J 142 ARG cc_start: 0.7895 (mtp180) cc_final: 0.7606 (ttm-80) REVERT: J 218 HIS cc_start: 0.7935 (m-70) cc_final: 0.7193 (t-90) REVERT: L 129 GLN cc_start: 0.7758 (mp10) cc_final: 0.7519 (mp10) REVERT: O 142 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7659 (ttm-80) REVERT: P 142 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7737 (ttp-110) REVERT: R 129 GLN cc_start: 0.7627 (mp10) cc_final: 0.7238 (mp10) REVERT: R 142 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7656 (ttm-80) REVERT: U 129 GLN cc_start: 0.7721 (mp10) cc_final: 0.7336 (mp10) REVERT: U 142 ARG cc_start: 0.8062 (mtp180) cc_final: 0.7710 (ttm-80) REVERT: W 129 GLN cc_start: 0.7710 (mp10) cc_final: 0.7426 (mp10) REVERT: W 142 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7602 (ttm-80) REVERT: X 142 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7691 (ttm-80) REVERT: Z 142 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7715 (ttm-80) REVERT: Z 218 HIS cc_start: 0.7787 (m-70) cc_final: 0.7066 (t-90) REVERT: a 129 GLN cc_start: 0.7654 (mp10) cc_final: 0.7217 (mp10) REVERT: a 142 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7656 (ttm-80) REVERT: a 218 HIS cc_start: 0.7800 (m-70) cc_final: 0.7119 (t-90) REVERT: c 142 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.7606 (ttm-80) REVERT: c 218 HIS cc_start: 0.7648 (m-70) cc_final: 0.7096 (t-90) REVERT: d 142 ARG cc_start: 0.8303 (tpp-160) cc_final: 0.7635 (ttm-80) REVERT: f 142 ARG cc_start: 0.8279 (tpp-160) cc_final: 0.7741 (ttm-80) REVERT: g 218 HIS cc_start: 0.7758 (m-70) cc_final: 0.7124 (t-90) outliers start: 58 outliers final: 43 residues processed: 436 average time/residue: 0.1134 time to fit residues: 71.2834 Evaluate side-chains 432 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 389 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 192 SER Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 159 MET Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 42 optimal weight: 1.9990 chunk 167 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 18 optimal weight: 0.0570 chunk 172 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN G 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN U 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124619 restraints weight = 16184.814| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.10 r_work: 0.3326 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14410 Z= 0.127 Angle : 0.548 8.774 19646 Z= 0.266 Chirality : 0.040 0.125 2442 Planarity : 0.003 0.019 2574 Dihedral : 3.571 10.714 2002 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.67 % Allowed : 19.13 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.19), residues: 1848 helix: -0.84 (0.19), residues: 770 sheet: -2.69 (0.23), residues: 528 loop : -1.23 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 154 TYR 0.002 0.000 TYR O 132 PHE 0.005 0.001 PHE T 126 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00318 (14410) covalent geometry : angle 0.54815 (19646) hydrogen bonds : bond 0.02926 ( 462) hydrogen bonds : angle 4.77379 ( 1386) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 393 time to evaluate : 0.490 Fit side-chains REVERT: A 129 GLN cc_start: 0.7566 (mp10) cc_final: 0.7197 (mp10) REVERT: A 218 HIS cc_start: 0.7810 (m-70) cc_final: 0.7035 (t-90) REVERT: C 218 HIS cc_start: 0.7731 (m-70) cc_final: 0.7030 (t-90) REVERT: D 129 GLN cc_start: 0.7608 (mp10) cc_final: 0.7252 (mp10) REVERT: F 129 GLN cc_start: 0.7660 (mp10) cc_final: 0.7307 (mp10) REVERT: F 218 HIS cc_start: 0.7628 (m-70) cc_final: 0.6974 (t-90) REVERT: G 129 GLN cc_start: 0.7723 (mp10) cc_final: 0.7373 (mp10) REVERT: G 142 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7544 (ttm-80) REVERT: I 142 ARG cc_start: 0.7999 (mtp180) cc_final: 0.7567 (ttm-80) REVERT: I 218 HIS cc_start: 0.7590 (m-70) cc_final: 0.6847 (t-90) REVERT: J 129 GLN cc_start: 0.7568 (mp10) cc_final: 0.7163 (mp10) REVERT: J 142 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7502 (ttm-80) REVERT: J 218 HIS cc_start: 0.7817 (m-70) cc_final: 0.7028 (t-90) REVERT: L 129 GLN cc_start: 0.7773 (mp10) cc_final: 0.7508 (mp10) REVERT: O 142 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7507 (ttm-80) REVERT: P 142 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7515 (ttm-80) REVERT: P 154 ARG cc_start: 0.8491 (ttt-90) cc_final: 0.8266 (mtp85) REVERT: R 129 GLN cc_start: 0.7511 (mp10) cc_final: 0.7139 (mp10) REVERT: R 154 ARG cc_start: 0.8478 (ttt-90) cc_final: 0.8274 (mtp85) REVERT: T 154 ARG cc_start: 0.8556 (ttt-90) cc_final: 0.8336 (mtp85) REVERT: U 129 GLN cc_start: 0.7602 (mp10) cc_final: 0.7230 (mp10) REVERT: U 142 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7651 (ttm-80) REVERT: W 129 GLN cc_start: 0.7664 (mp10) cc_final: 0.7324 (mp10) REVERT: W 142 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7525 (ttm-80) REVERT: X 142 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7523 (ttm-80) REVERT: X 154 ARG cc_start: 0.8458 (ttt-90) cc_final: 0.8210 (mtp85) REVERT: Z 142 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7580 (ttm-80) REVERT: Z 218 HIS cc_start: 0.7659 (m-70) cc_final: 0.6890 (t-90) REVERT: a 129 GLN cc_start: 0.7547 (mp10) cc_final: 0.7146 (mp10) REVERT: a 142 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7497 (ttm-80) REVERT: a 218 HIS cc_start: 0.7799 (m-70) cc_final: 0.6973 (t-90) REVERT: c 218 HIS cc_start: 0.7607 (m-70) cc_final: 0.6988 (t-90) REVERT: d 142 ARG cc_start: 0.8260 (tpp-160) cc_final: 0.7547 (ttm-80) REVERT: f 142 ARG cc_start: 0.8185 (tpp-160) cc_final: 0.7558 (ttm-80) REVERT: g 218 HIS cc_start: 0.7628 (m-70) cc_final: 0.6958 (t-90) outliers start: 74 outliers final: 60 residues processed: 442 average time/residue: 0.1130 time to fit residues: 72.2749 Evaluate side-chains 440 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 380 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 152 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 159 MET Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain d residue 176 VAL Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 173 SER Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 192 SER Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 117 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 148 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN U 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123698 restraints weight = 16163.016| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.10 r_work: 0.3308 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14410 Z= 0.142 Angle : 0.556 9.897 19646 Z= 0.269 Chirality : 0.040 0.122 2442 Planarity : 0.003 0.020 2574 Dihedral : 3.538 11.091 2002 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 6.25 % Allowed : 17.93 % Favored : 75.82 % 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: -2.07 (0.20), residues: 1848 helix: -0.68 (0.20), residues: 770 sheet: -2.44 (0.25), residues: 484 loop : -0.93 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 154 TYR 0.002 0.000 TYR O 132 PHE 0.006 0.001 PHE T 126 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00354 (14410) covalent geometry : angle 0.55601 (19646) hydrogen bonds : bond 0.02953 ( 462) hydrogen bonds : angle 4.76830 ( 1386) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 370 time to evaluate : 0.502 Fit side-chains REVERT: A 129 GLN cc_start: 0.7529 (mp10) cc_final: 0.7196 (mp10) REVERT: A 218 HIS cc_start: 0.7816 (m-70) cc_final: 0.7056 (t-90) REVERT: C 218 HIS cc_start: 0.7703 (m-70) cc_final: 0.7053 (t-90) REVERT: D 129 GLN cc_start: 0.7586 (mp10) cc_final: 0.7256 (mp10) REVERT: F 129 GLN cc_start: 0.7618 (mp10) cc_final: 0.7317 (mp10) REVERT: F 218 HIS cc_start: 0.7623 (m-70) cc_final: 0.6961 (t-90) REVERT: G 142 ARG cc_start: 0.7980 (mtp180) cc_final: 0.7503 (ttm-80) REVERT: I 142 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7542 (ttm-80) REVERT: I 218 HIS cc_start: 0.7659 (m-70) cc_final: 0.6934 (t-90) REVERT: J 129 GLN cc_start: 0.7510 (mp10) cc_final: 0.7169 (mp10) REVERT: J 142 ARG cc_start: 0.7891 (mtp180) cc_final: 0.7464 (ttm-80) REVERT: J 218 HIS cc_start: 0.7839 (m-70) cc_final: 0.7034 (t-90) REVERT: L 129 GLN cc_start: 0.7751 (mp10) cc_final: 0.7468 (mp10) REVERT: O 142 ARG cc_start: 0.7921 (mtp180) cc_final: 0.7479 (ttm-80) REVERT: P 142 ARG cc_start: 0.7989 (mtp180) cc_final: 0.7436 (ttm-80) REVERT: R 154 ARG cc_start: 0.8455 (ttt-90) cc_final: 0.8250 (mtp85) REVERT: U 142 ARG cc_start: 0.8109 (mtp180) cc_final: 0.7676 (ttm-80) REVERT: W 129 GLN cc_start: 0.7614 (mp10) cc_final: 0.7350 (mp10) REVERT: W 142 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7559 (ttm-80) REVERT: X 142 ARG cc_start: 0.7990 (mtp180) cc_final: 0.7525 (ttm-80) REVERT: Z 142 ARG cc_start: 0.7965 (mtp180) cc_final: 0.7564 (ttm-80) REVERT: Z 218 HIS cc_start: 0.7677 (m-70) cc_final: 0.6945 (t-90) REVERT: a 129 GLN cc_start: 0.7540 (mp10) cc_final: 0.7209 (mp10) REVERT: a 142 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7411 (ttm-80) REVERT: a 218 HIS cc_start: 0.7852 (m-70) cc_final: 0.7017 (t-90) REVERT: c 154 ARG cc_start: 0.8585 (ttt-90) cc_final: 0.8231 (mtp85) REVERT: c 218 HIS cc_start: 0.7609 (m-70) cc_final: 0.7017 (t-90) REVERT: d 142 ARG cc_start: 0.8273 (tpp-160) cc_final: 0.7569 (ttm-80) REVERT: g 218 HIS cc_start: 0.7643 (m-70) cc_final: 0.6892 (t-90) outliers start: 99 outliers final: 87 residues processed: 436 average time/residue: 0.1103 time to fit residues: 70.0153 Evaluate side-chains 445 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 358 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain P residue 173 SER Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 152 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 159 MET Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 175 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 159 MET Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain d residue 190 GLN Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 159 MET Chi-restraints excluded: chain g residue 173 SER Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 192 SER Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 40 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 145 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 162 optimal weight: 0.0870 chunk 58 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN F 190 GLN I 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN U 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124354 restraints weight = 15991.956| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.11 r_work: 0.3304 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14410 Z= 0.128 Angle : 0.544 9.069 19646 Z= 0.264 Chirality : 0.041 0.128 2442 Planarity : 0.003 0.022 2574 Dihedral : 3.447 11.385 2002 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.25 % Allowed : 18.43 % Favored : 75.32 % 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: -1.89 (0.20), residues: 1848 helix: -0.57 (0.20), residues: 770 sheet: -2.35 (0.25), residues: 484 loop : -0.76 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 154 TYR 0.001 0.000 TYR O 132 PHE 0.005 0.001 PHE c 126 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00321 (14410) covalent geometry : angle 0.54450 (19646) hydrogen bonds : bond 0.02899 ( 462) hydrogen bonds : angle 4.62058 ( 1386) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 360 time to evaluate : 0.481 Fit side-chains REVERT: A 218 HIS cc_start: 0.7798 (m-70) cc_final: 0.7050 (t-90) REVERT: C 218 HIS cc_start: 0.7786 (m-70) cc_final: 0.7041 (t-90) REVERT: F 129 GLN cc_start: 0.7504 (mp10) cc_final: 0.7252 (mp10) REVERT: F 218 HIS cc_start: 0.7608 (m-70) cc_final: 0.6966 (t-90) REVERT: G 142 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7486 (ttm-80) REVERT: I 142 ARG cc_start: 0.8013 (mtp180) cc_final: 0.7584 (ttm-80) REVERT: I 218 HIS cc_start: 0.7690 (m-70) cc_final: 0.6992 (t-90) REVERT: J 142 ARG cc_start: 0.7902 (mtp180) cc_final: 0.7440 (ttm-80) REVERT: J 218 HIS cc_start: 0.7734 (m-70) cc_final: 0.6974 (t-90) REVERT: L 190 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: O 142 ARG cc_start: 0.7927 (mtp180) cc_final: 0.7495 (ttm-80) REVERT: P 142 ARG cc_start: 0.7899 (mtp180) cc_final: 0.7400 (ttm-80) REVERT: U 142 ARG cc_start: 0.8114 (mtp180) cc_final: 0.7654 (ttm-80) REVERT: W 142 ARG cc_start: 0.7979 (mtp180) cc_final: 0.7558 (ttm-80) REVERT: X 142 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7498 (ttm-80) REVERT: Z 142 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7629 (ttm-80) REVERT: Z 218 HIS cc_start: 0.7703 (m-70) cc_final: 0.6998 (t-90) REVERT: a 129 GLN cc_start: 0.7444 (mp10) cc_final: 0.7149 (mp10) REVERT: a 142 ARG cc_start: 0.7884 (mtp180) cc_final: 0.7412 (ttm-80) REVERT: a 218 HIS cc_start: 0.7781 (m-70) cc_final: 0.6992 (t-90) REVERT: c 154 ARG cc_start: 0.8592 (ttt-90) cc_final: 0.8239 (mtp85) REVERT: c 218 HIS cc_start: 0.7614 (m-70) cc_final: 0.7011 (t-90) REVERT: g 218 HIS cc_start: 0.7634 (m-70) cc_final: 0.6884 (t-90) outliers start: 99 outliers final: 91 residues processed: 425 average time/residue: 0.1077 time to fit residues: 67.1338 Evaluate side-chains 443 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 351 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain P residue 175 SER Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 159 MET Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 175 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 159 MET Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain c residue 152 SER Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain d residue 176 VAL Chi-restraints excluded: chain d residue 190 GLN Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 159 MET Chi-restraints excluded: chain g residue 173 SER Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 192 SER Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 8 optimal weight: 0.9990 chunk 150 optimal weight: 0.0370 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 141 optimal weight: 0.0980 chunk 126 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN F 190 GLN I 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN U 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.147709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124797 restraints weight = 15911.171| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.09 r_work: 0.3320 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14410 Z= 0.121 Angle : 0.537 8.433 19646 Z= 0.259 Chirality : 0.040 0.122 2442 Planarity : 0.003 0.026 2574 Dihedral : 3.364 11.603 2002 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 6.12 % Allowed : 19.26 % Favored : 74.62 % 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: -1.71 (0.20), residues: 1848 helix: -0.48 (0.20), residues: 770 sheet: -2.20 (0.25), residues: 484 loop : -0.64 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 142 TYR 0.001 0.000 TYR O 132 PHE 0.006 0.001 PHE c 126 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00305 (14410) covalent geometry : angle 0.53678 (19646) hydrogen bonds : bond 0.02844 ( 462) hydrogen bonds : angle 4.48220 ( 1386) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 357 time to evaluate : 0.501 Fit side-chains REVERT: A 218 HIS cc_start: 0.7652 (m-70) cc_final: 0.7029 (t-90) REVERT: C 218 HIS cc_start: 0.7702 (m-70) cc_final: 0.6996 (t-90) REVERT: F 218 HIS cc_start: 0.7581 (m-70) cc_final: 0.6972 (t-90) REVERT: G 142 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7489 (ttm-80) REVERT: I 142 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7581 (ttm-80) REVERT: I 218 HIS cc_start: 0.7652 (m-70) cc_final: 0.7014 (t-90) REVERT: J 142 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7424 (ttm-80) REVERT: J 218 HIS cc_start: 0.7820 (m-70) cc_final: 0.7012 (t-90) REVERT: L 154 ARG cc_start: 0.8575 (ttt-90) cc_final: 0.8282 (mtp85) REVERT: L 190 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: O 142 ARG cc_start: 0.7868 (mtp180) cc_final: 0.7441 (ttm-80) REVERT: U 142 ARG cc_start: 0.8035 (mtp180) cc_final: 0.7597 (ttm-80) REVERT: W 142 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7592 (ttm-80) REVERT: X 142 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7489 (ttm-80) REVERT: Z 142 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7605 (ttm-80) REVERT: Z 218 HIS cc_start: 0.7685 (m-70) cc_final: 0.7038 (t-90) REVERT: a 142 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7421 (ttm-80) REVERT: a 218 HIS cc_start: 0.7817 (m-70) cc_final: 0.7021 (t-90) REVERT: c 154 ARG cc_start: 0.8608 (ttt-90) cc_final: 0.8322 (mtp85) REVERT: c 218 HIS cc_start: 0.7473 (m-70) cc_final: 0.6978 (t-90) REVERT: g 218 HIS cc_start: 0.7653 (m-70) cc_final: 0.6913 (t-90) outliers start: 97 outliers final: 87 residues processed: 420 average time/residue: 0.1058 time to fit residues: 65.5072 Evaluate side-chains 433 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 345 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain P residue 175 SER Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 176 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 155 VAL Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 159 MET Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 159 MET Chi-restraints excluded: chain X residue 175 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain c residue 152 SER Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain d residue 176 VAL Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 159 MET Chi-restraints excluded: chain g residue 173 SER Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 192 SER Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 59 optimal weight: 0.0470 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 0.0040 chunk 171 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 105 optimal weight: 0.8980 overall best weight: 0.3668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN U 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126887 restraints weight = 15888.493| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.09 r_work: 0.3346 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14410 Z= 0.107 Angle : 0.528 7.977 19646 Z= 0.256 Chirality : 0.040 0.127 2442 Planarity : 0.003 0.033 2574 Dihedral : 3.240 11.648 2002 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.93 % Allowed : 19.82 % Favored : 74.24 % 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: -1.54 (0.20), residues: 1848 helix: -0.40 (0.19), residues: 770 sheet: -2.08 (0.24), residues: 484 loop : -0.48 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 142 TYR 0.002 0.000 TYR O 132 PHE 0.006 0.001 PHE c 126 HIS 0.002 0.000 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00272 (14410) covalent geometry : angle 0.52794 (19646) hydrogen bonds : bond 0.02729 ( 462) hydrogen bonds : angle 4.29223 ( 1386) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 368 time to evaluate : 0.490 Fit side-chains REVERT: A 218 HIS cc_start: 0.7648 (m-70) cc_final: 0.7023 (t-90) REVERT: C 218 HIS cc_start: 0.7670 (m-70) cc_final: 0.7034 (t-90) REVERT: F 218 HIS cc_start: 0.7480 (m-70) cc_final: 0.6935 (t-90) REVERT: G 142 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7466 (ttm-80) REVERT: I 142 ARG cc_start: 0.8010 (mtp180) cc_final: 0.7578 (ttm-80) REVERT: I 218 HIS cc_start: 0.7650 (m-70) cc_final: 0.7029 (t-90) REVERT: J 142 ARG cc_start: 0.7879 (mtp180) cc_final: 0.7413 (ttm-80) REVERT: J 218 HIS cc_start: 0.7787 (m-70) cc_final: 0.6991 (t-90) REVERT: L 154 ARG cc_start: 0.8535 (ttt-90) cc_final: 0.8310 (mtp85) REVERT: L 190 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: O 142 ARG cc_start: 0.7872 (mtp180) cc_final: 0.7460 (ttm-80) REVERT: P 142 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7475 (ttm-80) REVERT: W 142 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7625 (ttm-80) REVERT: X 142 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7491 (ttm-80) REVERT: Z 142 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7618 (ttm-80) REVERT: Z 218 HIS cc_start: 0.7690 (m-70) cc_final: 0.7057 (t-90) REVERT: a 142 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7436 (ttm-80) REVERT: a 218 HIS cc_start: 0.7721 (m-70) cc_final: 0.6966 (t-90) REVERT: c 154 ARG cc_start: 0.8557 (ttt-90) cc_final: 0.8311 (mtp85) REVERT: c 218 HIS cc_start: 0.7407 (m-70) cc_final: 0.6864 (t-90) REVERT: g 218 HIS cc_start: 0.7646 (m-70) cc_final: 0.6921 (t-90) outliers start: 94 outliers final: 82 residues processed: 429 average time/residue: 0.1024 time to fit residues: 65.4403 Evaluate side-chains 437 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 354 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 159 MET Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 159 MET Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 152 SER Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain P residue 173 SER Chi-restraints excluded: chain P residue 175 SER Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 159 MET Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 175 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain c residue 152 SER Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain d residue 176 VAL Chi-restraints excluded: chain d residue 190 GLN Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 159 MET Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 192 SER Chi-restraints excluded: chain g residue 197 LEU Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 172 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 63 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN F 190 GLN I 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN R 190 GLN U 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126695 restraints weight = 15737.593| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.18 r_work: 0.3329 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14410 Z= 0.116 Angle : 0.533 7.847 19646 Z= 0.258 Chirality : 0.041 0.127 2442 Planarity : 0.003 0.032 2574 Dihedral : 3.222 12.652 2002 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.12 % Allowed : 20.96 % Favored : 72.92 % 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: -1.43 (0.20), residues: 1848 helix: -0.34 (0.19), residues: 770 sheet: -1.95 (0.24), residues: 484 loop : -0.44 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 142 TYR 0.002 0.000 TYR O 132 PHE 0.006 0.001 PHE c 126 HIS 0.002 0.000 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00295 (14410) covalent geometry : angle 0.53264 (19646) hydrogen bonds : bond 0.02759 ( 462) hydrogen bonds : angle 4.27493 ( 1386) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 355 time to evaluate : 0.519 Fit side-chains REVERT: A 218 HIS cc_start: 0.7761 (m-70) cc_final: 0.7091 (t-90) REVERT: C 218 HIS cc_start: 0.7690 (m-70) cc_final: 0.7051 (t-90) REVERT: F 218 HIS cc_start: 0.7546 (m-70) cc_final: 0.6973 (t-90) REVERT: G 142 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7480 (ttm-80) REVERT: I 142 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7603 (ttm-80) REVERT: I 218 HIS cc_start: 0.7758 (m-70) cc_final: 0.7073 (t-90) REVERT: J 142 ARG cc_start: 0.7887 (mtp180) cc_final: 0.7423 (ttm-80) REVERT: J 218 HIS cc_start: 0.7848 (m-70) cc_final: 0.7057 (t-90) REVERT: L 154 ARG cc_start: 0.8571 (ttt-90) cc_final: 0.8363 (mtp85) REVERT: L 190 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: O 142 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7538 (ttm-80) REVERT: W 142 ARG cc_start: 0.8008 (mtp180) cc_final: 0.7553 (ttm-80) REVERT: X 142 ARG cc_start: 0.7882 (mtp180) cc_final: 0.7461 (ttm-80) REVERT: Z 142 ARG cc_start: 0.8071 (mtp180) cc_final: 0.7642 (ttm-80) REVERT: Z 218 HIS cc_start: 0.7743 (m-70) cc_final: 0.7047 (t-90) REVERT: a 142 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7393 (ttm-80) REVERT: a 218 HIS cc_start: 0.7761 (m-70) cc_final: 0.6996 (t-90) REVERT: c 154 ARG cc_start: 0.8581 (ttt-90) cc_final: 0.8357 (mtp85) REVERT: c 218 HIS cc_start: 0.7531 (m-70) cc_final: 0.6945 (t-90) REVERT: g 218 HIS cc_start: 0.7647 (m-70) cc_final: 0.6954 (t-90) outliers start: 97 outliers final: 84 residues processed: 417 average time/residue: 0.1035 time to fit residues: 63.9983 Evaluate side-chains 432 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 347 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 190 GLN Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain P residue 173 SER Chi-restraints excluded: chain P residue 175 SER Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain T residue 152 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 175 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain X residue 199 SER Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 159 MET Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain c residue 152 SER Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain d residue 176 VAL Chi-restraints excluded: chain d residue 190 GLN Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 192 SER Chi-restraints excluded: chain g residue 197 LEU Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN F 190 GLN G 190 GLN I 190 GLN L 190 GLN M 190 GLN O 190 GLN P 190 GLN U 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123679 restraints weight = 15986.413| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.09 r_work: 0.3305 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14410 Z= 0.158 Angle : 0.570 7.981 19646 Z= 0.277 Chirality : 0.042 0.123 2442 Planarity : 0.003 0.032 2574 Dihedral : 3.335 12.723 2002 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 6.25 % Allowed : 21.21 % Favored : 72.54 % 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: -1.50 (0.20), residues: 1848 helix: -0.46 (0.19), residues: 770 sheet: -1.86 (0.25), residues: 484 loop : -0.50 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 142 TYR 0.002 0.001 TYR g 132 PHE 0.006 0.001 PHE c 126 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00394 (14410) covalent geometry : angle 0.56967 (19646) hydrogen bonds : bond 0.03055 ( 462) hydrogen bonds : angle 4.53121 ( 1386) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 342 time to evaluate : 0.525 Fit side-chains REVERT: A 218 HIS cc_start: 0.7768 (m-70) cc_final: 0.7096 (t-90) REVERT: C 218 HIS cc_start: 0.7722 (m-70) cc_final: 0.7045 (t-90) REVERT: F 218 HIS cc_start: 0.7593 (m-70) cc_final: 0.6979 (t-90) REVERT: G 142 ARG cc_start: 0.7990 (mtp180) cc_final: 0.7523 (ttm-80) REVERT: I 142 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7609 (ttm-80) REVERT: I 218 HIS cc_start: 0.7726 (m-70) cc_final: 0.7061 (t-90) REVERT: J 142 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7480 (ttm-80) REVERT: J 218 HIS cc_start: 0.7818 (m-70) cc_final: 0.6986 (t-90) REVERT: L 154 ARG cc_start: 0.8572 (ttt-90) cc_final: 0.8337 (mtp85) REVERT: O 142 ARG cc_start: 0.7952 (mtp180) cc_final: 0.7510 (ttm-80) REVERT: P 142 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7488 (ttm-80) REVERT: W 142 ARG cc_start: 0.8076 (mtp180) cc_final: 0.7624 (ttm-80) REVERT: X 142 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7524 (ttm-80) REVERT: Z 142 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7674 (ttm-80) REVERT: Z 218 HIS cc_start: 0.7758 (m-70) cc_final: 0.7085 (t-90) REVERT: a 142 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7494 (ttm-80) REVERT: a 218 HIS cc_start: 0.7833 (m-70) cc_final: 0.7022 (t-90) REVERT: c 154 ARG cc_start: 0.8639 (ttt-90) cc_final: 0.8335 (mtp85) REVERT: c 218 HIS cc_start: 0.7528 (m-70) cc_final: 0.7026 (t-90) REVERT: g 218 HIS cc_start: 0.7639 (m-70) cc_final: 0.6914 (t-90) outliers start: 99 outliers final: 90 residues processed: 410 average time/residue: 0.1089 time to fit residues: 64.5751 Evaluate side-chains 433 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 343 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 190 GLN Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 190 GLN Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 190 GLN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 173 SER Chi-restraints excluded: chain I residue 190 GLN Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 152 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain M residue 152 SER Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain M residue 190 GLN Chi-restraints excluded: chain O residue 152 SER Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 190 GLN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 159 MET Chi-restraints excluded: chain P residue 173 SER Chi-restraints excluded: chain P residue 175 SER Chi-restraints excluded: chain P residue 176 VAL Chi-restraints excluded: chain P residue 190 GLN Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 190 GLN Chi-restraints excluded: chain T residue 152 SER Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain U residue 190 GLN Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain X residue 155 VAL Chi-restraints excluded: chain X residue 175 SER Chi-restraints excluded: chain X residue 176 VAL Chi-restraints excluded: chain X residue 199 SER Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 190 GLN Chi-restraints excluded: chain a residue 155 VAL Chi-restraints excluded: chain a residue 159 MET Chi-restraints excluded: chain a residue 173 SER Chi-restraints excluded: chain a residue 175 SER Chi-restraints excluded: chain c residue 152 SER Chi-restraints excluded: chain c residue 155 VAL Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 159 MET Chi-restraints excluded: chain d residue 190 GLN Chi-restraints excluded: chain f residue 152 SER Chi-restraints excluded: chain f residue 155 VAL Chi-restraints excluded: chain f residue 159 MET Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 190 GLN Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 176 VAL Chi-restraints excluded: chain g residue 199 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 52 optimal weight: 0.2980 chunk 150 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 169 optimal weight: 0.9980 chunk 109 optimal weight: 0.2980 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN D 190 GLN F 190 GLN G 190 GLN I 190 GLN ** L 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 GLN O 190 GLN P 190 GLN U 190 GLN Z 190 GLN c 190 GLN f 190 GLN g 190 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125739 restraints weight = 15656.893| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.21 r_work: 0.3322 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14410 Z= 0.122 Angle : 0.548 7.686 19646 Z= 0.267 Chirality : 0.041 0.125 2442 Planarity : 0.003 0.039 2574 Dihedral : 3.269 12.771 2002 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.06 % Allowed : 21.65 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.39 (0.20), residues: 1848 helix: -0.38 (0.19), residues: 770 sheet: -1.81 (0.24), residues: 484 loop : -0.43 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 142 TYR 0.002 0.000 TYR O 132 PHE 0.005 0.001 PHE c 126 HIS 0.002 0.000 HIS Z 156 Details of bonding type rmsd covalent geometry : bond 0.00310 (14410) covalent geometry : angle 0.54769 (19646) hydrogen bonds : bond 0.02842 ( 462) hydrogen bonds : angle 4.35522 ( 1386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3475.79 seconds wall clock time: 60 minutes 7.51 seconds (3607.51 seconds total)