Starting phenix.real_space_refine on Fri Mar 6 05:13:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xnc_67046/03_2026/9xnc_67046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xnc_67046/03_2026/9xnc_67046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xnc_67046/03_2026/9xnc_67046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xnc_67046/03_2026/9xnc_67046.map" model { file = "/net/cci-nas-00/data/ceres_data/9xnc_67046/03_2026/9xnc_67046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xnc_67046/03_2026/9xnc_67046.cif" } resolution = 3.37 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= 0.002 sd= 0.031 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 168 5.16 5 C 17784 2.51 5 N 4680 2.21 5 O 5448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28080 Number of models: 1 Model: "" Number of chains: 1 Chain: "G" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1170 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 3, 'TRANS': 167} Restraints were copied for chains: H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d Time building chain proxies: 2.22, per 1000 atoms: 0.08 Number of scatterers: 28080 At special positions: 0 Unit cell: (73.233, 73.233, 329.085, 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 168 16.00 O 5448 8.00 N 4680 7.00 C 17784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 183 " distance=2.03 Simple disulfide: pdb=" SG CYS I 153 " - pdb=" SG CYS I 183 " distance=2.03 Simple disulfide: pdb=" SG CYS J 153 " - pdb=" SG CYS J 183 " distance=2.03 Simple disulfide: pdb=" SG CYS K 153 " - pdb=" SG CYS K 183 " distance=2.03 Simple disulfide: pdb=" SG CYS L 153 " - pdb=" SG CYS L 183 " distance=2.03 Simple disulfide: pdb=" SG CYS M 153 " - pdb=" SG CYS M 183 " distance=2.03 Simple disulfide: pdb=" SG CYS N 153 " - pdb=" SG CYS N 183 " distance=2.03 Simple disulfide: pdb=" SG CYS O 153 " - pdb=" SG CYS O 183 " distance=2.03 Simple disulfide: pdb=" SG CYS P 153 " - pdb=" SG CYS P 183 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 153 " - pdb=" SG CYS Q 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 153 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 153 " - pdb=" SG CYS S 183 " distance=2.03 Simple disulfide: pdb=" SG CYS T 153 " - pdb=" SG CYS T 183 " distance=2.03 Simple disulfide: pdb=" SG CYS U 153 " - pdb=" SG CYS U 183 " distance=2.03 Simple disulfide: pdb=" SG CYS V 153 " - pdb=" SG CYS V 183 " distance=2.03 Simple disulfide: pdb=" SG CYS W 153 " - pdb=" SG CYS W 183 " distance=2.03 Simple disulfide: pdb=" SG CYS X 153 " - pdb=" SG CYS X 183 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 153 " - pdb=" SG CYS Y 183 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 153 " - pdb=" SG CYS Z 183 " distance=2.03 Simple disulfide: pdb=" SG CYS a 153 " - pdb=" SG CYS a 183 " distance=2.03 Simple disulfide: pdb=" SG CYS b 153 " - pdb=" SG CYS b 183 " distance=2.03 Simple disulfide: pdb=" SG CYS c 153 " - pdb=" SG CYS c 183 " distance=2.03 Simple disulfide: pdb=" SG CYS d 153 " - pdb=" SG CYS d 183 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.3 seconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7248 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 48 sheets defined 45.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'G' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR G 42 " --> pdb=" O TYR G 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY G 50 " --> pdb=" O ARG G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 63 Processing helix chain 'G' and resid 66 through 79 Processing helix chain 'G' and resid 137 through 144 Processing helix chain 'G' and resid 158 through 164 Processing helix chain 'G' and resid 175 through 179 Processing helix chain 'H' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR H 42 " --> pdb=" O TYR H 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY H 50 " --> pdb=" O ARG H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 63 Processing helix chain 'H' and resid 66 through 79 Processing helix chain 'H' and resid 137 through 144 Processing helix chain 'H' and resid 158 through 164 Processing helix chain 'H' and resid 175 through 179 Processing helix chain 'I' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU I 20 " --> pdb=" O THR I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR I 42 " --> pdb=" O TYR I 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY I 50 " --> pdb=" O ARG I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 63 Processing helix chain 'I' and resid 66 through 79 Processing helix chain 'I' and resid 137 through 144 Processing helix chain 'I' and resid 158 through 164 Processing helix chain 'I' and resid 175 through 179 Processing helix chain 'J' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU J 20 " --> pdb=" O THR J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR J 42 " --> pdb=" O TYR J 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU J 49 " --> pdb=" O ALA J 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY J 50 " --> pdb=" O ARG J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 63 Processing helix chain 'J' and resid 66 through 79 Processing helix chain 'J' and resid 137 through 144 Processing helix chain 'J' and resid 158 through 164 Processing helix chain 'J' and resid 175 through 179 Processing helix chain 'K' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR K 42 " --> pdb=" O TYR K 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY K 50 " --> pdb=" O ARG K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 63 Processing helix chain 'K' and resid 66 through 79 Processing helix chain 'K' and resid 137 through 144 Processing helix chain 'K' and resid 158 through 164 Processing helix chain 'K' and resid 175 through 179 Processing helix chain 'L' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR L 42 " --> pdb=" O TYR L 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU L 49 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY L 50 " --> pdb=" O ARG L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 63 Processing helix chain 'L' and resid 66 through 79 Processing helix chain 'L' and resid 137 through 144 Processing helix chain 'L' and resid 158 through 164 Processing helix chain 'L' and resid 175 through 179 Processing helix chain 'M' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR M 42 " --> pdb=" O TYR M 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY M 50 " --> pdb=" O ARG M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 63 Processing helix chain 'M' and resid 66 through 79 Processing helix chain 'M' and resid 137 through 144 Processing helix chain 'M' and resid 158 through 164 Processing helix chain 'M' and resid 175 through 179 Processing helix chain 'N' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR N 42 " --> pdb=" O TYR N 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY N 50 " --> pdb=" O ARG N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 63 Processing helix chain 'N' and resid 66 through 79 Processing helix chain 'N' and resid 137 through 144 Processing helix chain 'N' and resid 158 through 164 Processing helix chain 'N' and resid 175 through 179 Processing helix chain 'O' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU O 20 " --> pdb=" O THR O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR O 42 " --> pdb=" O TYR O 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY O 50 " --> pdb=" O ARG O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 63 Processing helix chain 'O' and resid 66 through 79 Processing helix chain 'O' and resid 137 through 144 Processing helix chain 'O' and resid 158 through 164 Processing helix chain 'O' and resid 175 through 179 Processing helix chain 'P' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU P 20 " --> pdb=" O THR P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 54 removed outlier: 3.658A pdb=" N THR P 42 " --> pdb=" O TYR P 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU P 49 " --> pdb=" O ALA P 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY P 50 " --> pdb=" O ARG P 46 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 63 Processing helix chain 'P' and resid 66 through 79 Processing helix chain 'P' and resid 137 through 144 Processing helix chain 'P' and resid 158 through 164 Processing helix chain 'P' and resid 175 through 179 Processing helix chain 'Q' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU Q 20 " --> pdb=" O THR Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR Q 42 " --> pdb=" O TYR Q 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY Q 50 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 63 Processing helix chain 'Q' and resid 66 through 79 Processing helix chain 'Q' and resid 137 through 144 Processing helix chain 'Q' and resid 158 through 164 Processing helix chain 'Q' and resid 175 through 179 Processing helix chain 'R' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU R 20 " --> pdb=" O THR R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR R 42 " --> pdb=" O TYR R 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY R 50 " --> pdb=" O ARG R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 63 Processing helix chain 'R' and resid 66 through 79 Processing helix chain 'R' and resid 137 through 144 Processing helix chain 'R' and resid 158 through 164 Processing helix chain 'R' and resid 175 through 179 Processing helix chain 'S' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU S 20 " --> pdb=" O THR S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR S 42 " --> pdb=" O TYR S 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY S 50 " --> pdb=" O ARG S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 63 Processing helix chain 'S' and resid 66 through 79 Processing helix chain 'S' and resid 137 through 144 Processing helix chain 'S' and resid 158 through 164 Processing helix chain 'S' and resid 175 through 179 Processing helix chain 'T' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU T 20 " --> pdb=" O THR T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR T 42 " --> pdb=" O TYR T 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY T 50 " --> pdb=" O ARG T 46 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 63 Processing helix chain 'T' and resid 66 through 79 Processing helix chain 'T' and resid 137 through 144 Processing helix chain 'T' and resid 158 through 164 Processing helix chain 'T' and resid 175 through 179 Processing helix chain 'U' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU U 20 " --> pdb=" O THR U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR U 42 " --> pdb=" O TYR U 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY U 50 " --> pdb=" O ARG U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 63 Processing helix chain 'U' and resid 66 through 79 Processing helix chain 'U' and resid 137 through 144 Processing helix chain 'U' and resid 158 through 164 Processing helix chain 'U' and resid 175 through 179 Processing helix chain 'V' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU V 20 " --> pdb=" O THR V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR V 42 " --> pdb=" O TYR V 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU V 49 " --> pdb=" O ALA V 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY V 50 " --> pdb=" O ARG V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 63 Processing helix chain 'V' and resid 66 through 79 Processing helix chain 'V' and resid 137 through 144 Processing helix chain 'V' and resid 158 through 164 Processing helix chain 'V' and resid 175 through 179 Processing helix chain 'W' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU W 20 " --> pdb=" O THR W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 54 removed outlier: 3.658A pdb=" N THR W 42 " --> pdb=" O TYR W 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU W 49 " --> pdb=" O ALA W 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY W 50 " --> pdb=" O ARG W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 54 through 63 Processing helix chain 'W' and resid 66 through 79 Processing helix chain 'W' and resid 137 through 144 Processing helix chain 'W' and resid 158 through 164 Processing helix chain 'W' and resid 175 through 179 Processing helix chain 'X' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU X 20 " --> pdb=" O THR X 16 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR X 42 " --> pdb=" O TYR X 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU X 49 " --> pdb=" O ALA X 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY X 50 " --> pdb=" O ARG X 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 63 Processing helix chain 'X' and resid 66 through 79 Processing helix chain 'X' and resid 137 through 144 Processing helix chain 'X' and resid 158 through 164 Processing helix chain 'X' and resid 175 through 179 Processing helix chain 'Y' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU Y 20 " --> pdb=" O THR Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR Y 42 " --> pdb=" O TYR Y 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU Y 49 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY Y 50 " --> pdb=" O ARG Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 54 through 63 Processing helix chain 'Y' and resid 66 through 79 Processing helix chain 'Y' and resid 137 through 144 Processing helix chain 'Y' and resid 158 through 164 Processing helix chain 'Y' and resid 175 through 179 Processing helix chain 'Z' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU Z 20 " --> pdb=" O THR Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR Z 42 " --> pdb=" O TYR Z 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU Z 49 " --> pdb=" O ALA Z 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY Z 50 " --> pdb=" O ARG Z 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 54 through 63 Processing helix chain 'Z' and resid 66 through 79 Processing helix chain 'Z' and resid 137 through 144 Processing helix chain 'Z' and resid 158 through 164 Processing helix chain 'Z' and resid 175 through 179 Processing helix chain 'a' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU a 20 " --> pdb=" O THR a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR a 42 " --> pdb=" O TYR a 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU a 49 " --> pdb=" O ALA a 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY a 50 " --> pdb=" O ARG a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 63 Processing helix chain 'a' and resid 66 through 79 Processing helix chain 'a' and resid 137 through 144 Processing helix chain 'a' and resid 158 through 164 Processing helix chain 'a' and resid 175 through 179 Processing helix chain 'b' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU b 20 " --> pdb=" O THR b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR b 42 " --> pdb=" O TYR b 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU b 49 " --> pdb=" O ALA b 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY b 50 " --> pdb=" O ARG b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 54 through 63 Processing helix chain 'b' and resid 66 through 79 Processing helix chain 'b' and resid 137 through 144 Processing helix chain 'b' and resid 158 through 164 Processing helix chain 'b' and resid 175 through 179 Processing helix chain 'c' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU c 20 " --> pdb=" O THR c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR c 42 " --> pdb=" O TYR c 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY c 50 " --> pdb=" O ARG c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 54 through 63 Processing helix chain 'c' and resid 66 through 79 Processing helix chain 'c' and resid 137 through 144 Processing helix chain 'c' and resid 158 through 164 Processing helix chain 'c' and resid 175 through 179 Processing helix chain 'd' and resid 16 through 31 removed outlier: 4.333A pdb=" N LEU d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 38 through 54 removed outlier: 3.657A pdb=" N THR d 42 " --> pdb=" O TYR d 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU d 49 " --> pdb=" O ALA d 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY d 50 " --> pdb=" O ARG d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 63 Processing helix chain 'd' and resid 66 through 79 Processing helix chain 'd' and resid 137 through 144 Processing helix chain 'd' and resid 158 through 164 Processing helix chain 'd' and resid 175 through 179 Processing sheet with id=AA1, first strand: chain 'G' and resid 92 through 97 Processing sheet with id=AA2, first strand: chain 'G' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR G 123 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL G 148 " --> pdb=" O LEU G 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 92 through 97 Processing sheet with id=AA4, first strand: chain 'H' and resid 92 through 97 removed outlier: 3.581A pdb=" N THR H 123 " --> pdb=" O ALA H 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL H 148 " --> pdb=" O LEU H 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 92 through 97 Processing sheet with id=AA6, first strand: chain 'I' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR I 123 " --> pdb=" O ALA I 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL I 148 " --> pdb=" O LEU I 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 92 through 97 Processing sheet with id=AA8, first strand: chain 'J' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR J 123 " --> pdb=" O ALA J 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL J 148 " --> pdb=" O LEU J 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 92 through 97 Processing sheet with id=AB1, first strand: chain 'K' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR K 123 " --> pdb=" O ALA K 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL K 148 " --> pdb=" O LEU K 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 92 through 97 Processing sheet with id=AB3, first strand: chain 'L' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR L 123 " --> pdb=" O ALA L 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL L 148 " --> pdb=" O LEU L 129 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 92 through 97 Processing sheet with id=AB5, first strand: chain 'M' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR M 123 " --> pdb=" O ALA M 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL M 148 " --> pdb=" O LEU M 129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 92 through 97 Processing sheet with id=AB7, first strand: chain 'N' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR N 123 " --> pdb=" O ALA N 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL N 148 " --> pdb=" O LEU N 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 92 through 97 Processing sheet with id=AB9, first strand: chain 'O' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR O 123 " --> pdb=" O ALA O 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL O 148 " --> pdb=" O LEU O 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 92 through 97 Processing sheet with id=AC2, first strand: chain 'P' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR P 123 " --> pdb=" O ALA P 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL P 148 " --> pdb=" O LEU P 129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 92 through 97 Processing sheet with id=AC4, first strand: chain 'Q' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR Q 123 " --> pdb=" O ALA Q 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL Q 148 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 92 through 97 Processing sheet with id=AC6, first strand: chain 'R' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR R 123 " --> pdb=" O ALA R 154 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL R 148 " --> pdb=" O LEU R 129 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 92 through 97 Processing sheet with id=AC8, first strand: chain 'S' and resid 92 through 97 removed outlier: 3.581A pdb=" N THR S 123 " --> pdb=" O ALA S 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL S 148 " --> pdb=" O LEU S 129 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 92 through 97 Processing sheet with id=AD1, first strand: chain 'T' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR T 123 " --> pdb=" O ALA T 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL T 148 " --> pdb=" O LEU T 129 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'U' and resid 92 through 97 Processing sheet with id=AD3, first strand: chain 'U' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR U 123 " --> pdb=" O ALA U 154 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL U 148 " --> pdb=" O LEU U 129 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'V' and resid 92 through 97 Processing sheet with id=AD5, first strand: chain 'V' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR V 123 " --> pdb=" O ALA V 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL V 148 " --> pdb=" O LEU V 129 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 92 through 97 Processing sheet with id=AD7, first strand: chain 'W' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR W 123 " --> pdb=" O ALA W 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL W 148 " --> pdb=" O LEU W 129 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 92 through 97 Processing sheet with id=AD9, first strand: chain 'X' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR X 123 " --> pdb=" O ALA X 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL X 148 " --> pdb=" O LEU X 129 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 92 through 97 Processing sheet with id=AE2, first strand: chain 'Y' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR Y 123 " --> pdb=" O ALA Y 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL Y 148 " --> pdb=" O LEU Y 129 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 92 through 97 Processing sheet with id=AE4, first strand: chain 'Z' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR Z 123 " --> pdb=" O ALA Z 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL Z 148 " --> pdb=" O LEU Z 129 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'a' and resid 92 through 97 Processing sheet with id=AE6, first strand: chain 'a' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR a 123 " --> pdb=" O ALA a 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL a 148 " --> pdb=" O LEU a 129 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'b' and resid 92 through 97 Processing sheet with id=AE8, first strand: chain 'b' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR b 123 " --> pdb=" O ALA b 154 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL b 148 " --> pdb=" O LEU b 129 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'c' and resid 92 through 97 Processing sheet with id=AF1, first strand: chain 'c' and resid 92 through 97 removed outlier: 3.580A pdb=" N THR c 123 " --> pdb=" O ALA c 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL c 148 " --> pdb=" O LEU c 129 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd' and resid 92 through 97 Processing sheet with id=AF3, first strand: chain 'd' and resid 92 through 97 removed outlier: 3.581A pdb=" N THR d 123 " --> pdb=" O ALA d 154 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL d 148 " --> pdb=" O LEU d 129 " (cutoff:3.500A) 1680 hydrogen bonds defined for protein. 4536 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: 5.37 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9216 1.34 - 1.46: 4729 1.46 - 1.57: 14159 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 28392 Sorted by residual: bond pdb=" N TYR V 91 " pdb=" CA TYR V 91 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.29e-02 6.01e+03 1.23e+01 bond pdb=" N TYR a 91 " pdb=" CA TYR a 91 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.29e-02 6.01e+03 1.23e+01 bond pdb=" N TYR S 91 " pdb=" CA TYR S 91 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.29e-02 6.01e+03 1.22e+01 bond pdb=" N TYR M 91 " pdb=" CA TYR M 91 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.29e-02 6.01e+03 1.22e+01 bond pdb=" N TYR Y 91 " pdb=" CA TYR Y 91 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.29e-02 6.01e+03 1.21e+01 ... (remaining 28387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 36544 1.09 - 2.18: 1573 2.18 - 3.27: 477 3.27 - 4.36: 190 4.36 - 5.45: 72 Bond angle restraints: 38856 Sorted by residual: angle pdb=" CA SER I 89 " pdb=" C SER I 89 " pdb=" O SER I 89 " ideal model delta sigma weight residual 121.45 118.12 3.33 1.07e+00 8.73e-01 9.67e+00 angle pdb=" CA SER c 89 " pdb=" C SER c 89 " pdb=" O SER c 89 " ideal model delta sigma weight residual 121.45 118.14 3.31 1.07e+00 8.73e-01 9.59e+00 angle pdb=" CA SER R 89 " pdb=" C SER R 89 " pdb=" O SER R 89 " ideal model delta sigma weight residual 121.45 118.14 3.31 1.07e+00 8.73e-01 9.59e+00 angle pdb=" CA SER S 89 " pdb=" C SER S 89 " pdb=" O SER S 89 " ideal model delta sigma weight residual 121.45 118.14 3.31 1.07e+00 8.73e-01 9.58e+00 angle pdb=" CA SER Y 89 " pdb=" C SER Y 89 " pdb=" O SER Y 89 " ideal model delta sigma weight residual 121.45 118.14 3.31 1.07e+00 8.73e-01 9.58e+00 ... (remaining 38851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.13: 13680 10.13 - 20.26: 1572 20.26 - 30.40: 924 30.40 - 40.53: 312 40.53 - 50.66: 96 Dihedral angle restraints: 16584 sinusoidal: 5136 harmonic: 11448 Sorted by residual: dihedral pdb=" CB CYS T 153 " pdb=" SG CYS T 153 " pdb=" SG CYS T 183 " pdb=" CB CYS T 183 " ideal model delta sinusoidal sigma weight residual 93.00 120.19 -27.19 1 1.00e+01 1.00e-02 1.06e+01 dihedral pdb=" CB CYS Q 153 " pdb=" SG CYS Q 153 " pdb=" SG CYS Q 183 " pdb=" CB CYS Q 183 " ideal model delta sinusoidal sigma weight residual 93.00 120.19 -27.19 1 1.00e+01 1.00e-02 1.06e+01 dihedral pdb=" CB CYS U 153 " pdb=" SG CYS U 153 " pdb=" SG CYS U 183 " pdb=" CB CYS U 183 " ideal model delta sinusoidal sigma weight residual 93.00 120.18 -27.18 1 1.00e+01 1.00e-02 1.06e+01 ... (remaining 16581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3208 0.029 - 0.059: 1182 0.059 - 0.088: 354 0.088 - 0.117: 223 0.117 - 0.146: 145 Chirality restraints: 5112 Sorted by residual: chirality pdb=" CB THR K 48 " pdb=" CA THR K 48 " pdb=" OG1 THR K 48 " pdb=" CG2 THR K 48 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CB THR Q 48 " pdb=" CA THR Q 48 " pdb=" OG1 THR Q 48 " pdb=" CG2 THR Q 48 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CB THR Z 48 " pdb=" CA THR Z 48 " pdb=" OG1 THR Z 48 " pdb=" CG2 THR Z 48 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 5109 not shown) Planarity restraints: 4824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 87 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C ALA Q 87 " 0.020 2.00e-02 2.50e+03 pdb=" O ALA Q 87 " -0.007 2.00e-02 2.50e+03 pdb=" N LYS Q 88 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 87 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C ALA R 87 " -0.020 2.00e-02 2.50e+03 pdb=" O ALA R 87 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS R 88 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 87 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.28e+00 pdb=" C ALA N 87 " 0.020 2.00e-02 2.50e+03 pdb=" O ALA N 87 " -0.007 2.00e-02 2.50e+03 pdb=" N LYS N 88 " -0.007 2.00e-02 2.50e+03 ... (remaining 4821 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 12425 2.92 - 3.42: 28395 3.42 - 3.91: 46845 3.91 - 4.41: 55375 4.41 - 4.90: 92600 Nonbonded interactions: 235640 Sorted by model distance: nonbonded pdb=" CA SER c 89 " pdb=" CD1 LEU d 129 " model vdw 2.429 3.890 nonbonded pdb=" CA SER a 89 " pdb=" CD1 LEU b 129 " model vdw 2.429 3.890 nonbonded pdb=" CA SER Q 89 " pdb=" CD1 LEU R 129 " model vdw 2.429 3.890 nonbonded pdb=" CA SER W 89 " pdb=" CD1 LEU X 129 " model vdw 2.429 3.890 nonbonded pdb=" CA SER N 89 " pdb=" CD1 LEU O 129 " model vdw 2.429 3.890 ... (remaining 235635 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: 0.10 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.040 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.760 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.004 0.045 28416 Z= 0.243 Angle : 0.629 5.453 38904 Z= 0.371 Chirality : 0.043 0.146 5112 Planarity : 0.003 0.021 4824 Dihedral : 12.786 49.661 9264 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 29.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.90 % Allowed : 17.15 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 4056 helix: 0.74 (0.12), residues: 1776 sheet: -1.75 (0.20), residues: 720 loop : -1.45 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG T 184 TYR 0.003 0.001 TYR S 41 PHE 0.001 0.000 PHE d 178 TRP 0.006 0.001 TRP Q 151 HIS 0.001 0.000 HIS I 164 Details of bonding type rmsd covalent geometry : bond 0.00399 (28392) covalent geometry : angle 0.62921 (38856) SS BOND : bond 0.00171 ( 24) SS BOND : angle 0.08784 ( 48) hydrogen bonds : bond 0.18144 ( 1488) hydrogen bonds : angle 6.84049 ( 4536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 398 time to evaluate : 0.831 Fit side-chains REVERT: H 60 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8671 (mtt) REVERT: I 60 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8593 (mtp) REVERT: K 60 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8580 (mtp) REVERT: L 60 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8621 (mtp) REVERT: L 135 GLN cc_start: 0.8226 (pt0) cc_final: 0.7994 (pt0) REVERT: M 60 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8492 (mtp) REVERT: N 60 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8581 (mtp) REVERT: O 135 GLN cc_start: 0.8215 (pt0) cc_final: 0.7868 (pt0) REVERT: P 60 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8511 (mtp) REVERT: P 173 THR cc_start: 0.8163 (p) cc_final: 0.7949 (p) REVERT: Q 44 ARG cc_start: 0.8784 (mtm180) cc_final: 0.8444 (mtt-85) REVERT: R 173 THR cc_start: 0.8152 (p) cc_final: 0.7941 (p) REVERT: S 60 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8716 (mtp) REVERT: T 60 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8627 (mtp) REVERT: U 60 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8621 (mtp) REVERT: W 135 GLN cc_start: 0.8165 (pt0) cc_final: 0.7916 (pt0) REVERT: Z 21 MET cc_start: 0.8571 (ttp) cc_final: 0.8183 (ttt) REVERT: Z 60 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8604 (mtp) REVERT: Z 135 GLN cc_start: 0.8151 (pt0) cc_final: 0.7861 (pt0) REVERT: Z 173 THR cc_start: 0.8379 (p) cc_final: 0.8172 (p) REVERT: a 60 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8591 (mtp) REVERT: b 60 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8572 (mtp) REVERT: c 60 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8580 (mtp) outliers start: 24 outliers final: 0 residues processed: 398 average time/residue: 0.1621 time to fit residues: 107.4001 Evaluate side-chains 376 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 362 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain U residue 60 MET Chi-restraints excluded: chain Z residue 60 MET Chi-restraints excluded: chain a residue 60 MET Chi-restraints excluded: chain b residue 60 MET Chi-restraints excluded: chain c residue 60 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 135 GLN H 135 GLN I 135 GLN J 164 HIS K 164 HIS ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 HIS N 135 GLN N 164 HIS P 135 GLN ** R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 HIS S 135 GLN ** U 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 135 GLN V 164 HIS X 135 GLN Y 135 GLN ** Z 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 HIS ** a 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.099317 restraints weight = 39431.057| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.64 r_work: 0.3062 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28416 Z= 0.156 Angle : 0.594 7.116 38904 Z= 0.289 Chirality : 0.043 0.143 5112 Planarity : 0.003 0.023 4824 Dihedral : 3.987 16.917 4314 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.54 % Allowed : 18.66 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 4056 helix: 0.75 (0.13), residues: 1800 sheet: -1.56 (0.19), residues: 720 loop : -0.87 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 44 TYR 0.006 0.001 TYR O 91 PHE 0.002 0.000 PHE L 178 TRP 0.004 0.001 TRP X 151 HIS 0.002 0.001 HIS J 164 Details of bonding type rmsd covalent geometry : bond 0.00385 (28392) covalent geometry : angle 0.59475 (38856) SS BOND : bond 0.00115 ( 24) SS BOND : angle 0.10521 ( 48) hydrogen bonds : bond 0.03890 ( 1488) hydrogen bonds : angle 4.09783 ( 4536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 384 time to evaluate : 0.887 Fit side-chains REVERT: G 57 LEU cc_start: 0.8666 (tp) cc_final: 0.8160 (tp) REVERT: H 21 MET cc_start: 0.8683 (ttp) cc_final: 0.8296 (ttp) REVERT: H 57 LEU cc_start: 0.8680 (tp) cc_final: 0.8302 (tp) REVERT: H 127 MET cc_start: 0.7693 (mtt) cc_final: 0.7389 (mtt) REVERT: I 95 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8657 (mp) REVERT: J 44 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8202 (mtt180) REVERT: J 57 LEU cc_start: 0.8757 (tp) cc_final: 0.8440 (tp) REVERT: J 95 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8661 (mp) REVERT: K 95 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8701 (mp) REVERT: L 95 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8852 (mp) REVERT: O 57 LEU cc_start: 0.8721 (tp) cc_final: 0.8382 (tp) REVERT: O 135 GLN cc_start: 0.8201 (pt0) cc_final: 0.7946 (pt0) REVERT: P 173 THR cc_start: 0.8418 (p) cc_final: 0.8180 (p) REVERT: Q 44 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8195 (mtt-85) REVERT: R 173 THR cc_start: 0.8228 (p) cc_final: 0.8009 (p) REVERT: S 173 THR cc_start: 0.8355 (p) cc_final: 0.8121 (p) REVERT: T 95 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8788 (mp) REVERT: W 99 MET cc_start: 0.7827 (ttt) cc_final: 0.7602 (ttt) REVERT: X 21 MET cc_start: 0.8535 (ttp) cc_final: 0.8210 (ttp) REVERT: X 95 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8719 (mp) REVERT: a 173 THR cc_start: 0.8437 (p) cc_final: 0.8220 (p) REVERT: d 57 LEU cc_start: 0.8870 (tp) cc_final: 0.8230 (tp) outliers start: 41 outliers final: 1 residues processed: 424 average time/residue: 0.1420 time to fit residues: 105.3965 Evaluate side-chains 373 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 366 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 95 ILE Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain X residue 95 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 350 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 366 optimal weight: 0.7980 chunk 295 optimal weight: 0.0050 chunk 190 optimal weight: 0.8980 chunk 228 optimal weight: 0.0980 chunk 386 optimal weight: 2.9990 chunk 407 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 chunk 317 optimal weight: 0.6980 chunk 343 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 135 GLN R 135 GLN ** U 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 135 GLN b 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.102894 restraints weight = 39038.589| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.75 r_work: 0.3110 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28416 Z= 0.112 Angle : 0.531 6.924 38904 Z= 0.262 Chirality : 0.041 0.144 5112 Planarity : 0.003 0.023 4824 Dihedral : 3.725 17.575 4272 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.94 % Allowed : 20.80 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 4056 helix: 0.93 (0.13), residues: 1800 sheet: -1.46 (0.19), residues: 720 loop : -0.76 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 44 TYR 0.005 0.001 TYR S 59 PHE 0.001 0.000 PHE b 178 TRP 0.007 0.001 TRP W 77 HIS 0.002 0.001 HIS S 164 Details of bonding type rmsd covalent geometry : bond 0.00271 (28392) covalent geometry : angle 0.53141 (38856) SS BOND : bond 0.00070 ( 24) SS BOND : angle 0.12521 ( 48) hydrogen bonds : bond 0.03160 ( 1488) hydrogen bonds : angle 3.69022 ( 4536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 396 time to evaluate : 0.758 Fit side-chains REVERT: G 57 LEU cc_start: 0.8675 (tp) cc_final: 0.8221 (tp) REVERT: H 21 MET cc_start: 0.8747 (ttp) cc_final: 0.8486 (ttp) REVERT: H 127 MET cc_start: 0.7554 (mtt) cc_final: 0.7304 (mtt) REVERT: I 127 MET cc_start: 0.7398 (mtt) cc_final: 0.7191 (mtt) REVERT: J 57 LEU cc_start: 0.8753 (tp) cc_final: 0.8486 (tp) REVERT: N 57 LEU cc_start: 0.8866 (tp) cc_final: 0.8539 (tp) REVERT: O 57 LEU cc_start: 0.8747 (tp) cc_final: 0.8414 (tp) REVERT: P 173 THR cc_start: 0.8326 (p) cc_final: 0.8098 (p) REVERT: R 173 THR cc_start: 0.8201 (p) cc_final: 0.7984 (p) REVERT: S 173 THR cc_start: 0.8335 (p) cc_final: 0.8111 (p) REVERT: T 21 MET cc_start: 0.8724 (ttp) cc_final: 0.8514 (ttp) REVERT: U 21 MET cc_start: 0.8784 (ttp) cc_final: 0.8575 (ttp) REVERT: V 57 LEU cc_start: 0.8777 (tp) cc_final: 0.8475 (tp) REVERT: X 21 MET cc_start: 0.8548 (ttp) cc_final: 0.8205 (ttp) REVERT: d 57 LEU cc_start: 0.8845 (tp) cc_final: 0.8206 (tp) outliers start: 25 outliers final: 8 residues processed: 413 average time/residue: 0.1409 time to fit residues: 102.5929 Evaluate side-chains 395 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 387 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain P residue 99 MET Chi-restraints excluded: chain T residue 155 SER Chi-restraints excluded: chain Y residue 155 SER Chi-restraints excluded: chain Z residue 73 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 285 optimal weight: 3.9990 chunk 345 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 382 optimal weight: 3.9990 chunk 202 optimal weight: 0.0980 chunk 87 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 165 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 135 GLN ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 GLN O 135 GLN P 135 GLN U 135 GLN V 135 GLN d 135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.101021 restraints weight = 39146.173| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.73 r_work: 0.3084 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28416 Z= 0.124 Angle : 0.545 7.374 38904 Z= 0.268 Chirality : 0.042 0.147 5112 Planarity : 0.003 0.028 4824 Dihedral : 3.742 17.350 4272 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.05 % Allowed : 22.41 % Favored : 76.54 % 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: -0.31 (0.14), residues: 4056 helix: 0.90 (0.13), residues: 1800 sheet: -1.34 (0.19), residues: 720 loop : -0.84 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 44 TYR 0.010 0.001 TYR V 59 PHE 0.002 0.000 PHE S 178 TRP 0.009 0.001 TRP W 77 HIS 0.002 0.001 HIS U 164 Details of bonding type rmsd covalent geometry : bond 0.00303 (28392) covalent geometry : angle 0.54492 (38856) SS BOND : bond 0.00112 ( 24) SS BOND : angle 0.10886 ( 48) hydrogen bonds : bond 0.03200 ( 1488) hydrogen bonds : angle 3.53796 ( 4536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 385 time to evaluate : 0.937 Fit side-chains REVERT: G 57 LEU cc_start: 0.8668 (tp) cc_final: 0.8173 (tp) REVERT: H 21 MET cc_start: 0.8817 (ttp) cc_final: 0.8424 (ttp) REVERT: H 127 MET cc_start: 0.7607 (mtt) cc_final: 0.7342 (mtt) REVERT: J 57 LEU cc_start: 0.8782 (tp) cc_final: 0.8469 (tp) REVERT: K 95 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8727 (mp) REVERT: L 95 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8817 (mp) REVERT: N 57 LEU cc_start: 0.8841 (tp) cc_final: 0.8451 (tp) REVERT: P 173 THR cc_start: 0.8397 (p) cc_final: 0.8192 (p) REVERT: R 173 THR cc_start: 0.8287 (p) cc_final: 0.8071 (p) REVERT: T 95 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8730 (mp) REVERT: V 57 LEU cc_start: 0.8814 (tp) cc_final: 0.8585 (tp) REVERT: X 21 MET cc_start: 0.8566 (ttp) cc_final: 0.8223 (ttp) REVERT: d 57 LEU cc_start: 0.8826 (tp) cc_final: 0.8143 (tp) outliers start: 28 outliers final: 15 residues processed: 399 average time/residue: 0.1426 time to fit residues: 100.1738 Evaluate side-chains 399 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 381 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 155 SER Chi-restraints excluded: chain O residue 155 SER Chi-restraints excluded: chain P residue 99 MET Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain W residue 155 SER Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 155 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 221 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 263 optimal weight: 0.3980 chunk 243 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 239 optimal weight: 0.0970 chunk 117 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 GLN ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 135 GLN Y 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101102 restraints weight = 39336.514| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.67 r_work: 0.3093 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28416 Z= 0.122 Angle : 0.538 7.953 38904 Z= 0.266 Chirality : 0.042 0.155 5112 Planarity : 0.002 0.022 4824 Dihedral : 3.727 17.571 4272 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.69 % Allowed : 22.79 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 4056 helix: 0.89 (0.13), residues: 1800 sheet: -1.22 (0.19), residues: 720 loop : -0.91 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 44 TYR 0.011 0.001 TYR V 59 PHE 0.003 0.000 PHE L 178 TRP 0.006 0.001 TRP a 151 HIS 0.002 0.001 HIS U 164 Details of bonding type rmsd covalent geometry : bond 0.00296 (28392) covalent geometry : angle 0.53838 (38856) SS BOND : bond 0.00122 ( 24) SS BOND : angle 0.14929 ( 48) hydrogen bonds : bond 0.03113 ( 1488) hydrogen bonds : angle 3.45227 ( 4536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 387 time to evaluate : 0.874 Fit side-chains REVERT: G 57 LEU cc_start: 0.8644 (tp) cc_final: 0.8147 (tp) REVERT: G 127 MET cc_start: 0.7837 (mtt) cc_final: 0.7525 (mtt) REVERT: J 57 LEU cc_start: 0.8664 (tp) cc_final: 0.8344 (tp) REVERT: K 95 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8751 (mp) REVERT: L 95 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8792 (mp) REVERT: N 57 LEU cc_start: 0.8813 (tp) cc_final: 0.8390 (tp) REVERT: P 173 THR cc_start: 0.8475 (p) cc_final: 0.8266 (p) REVERT: R 173 THR cc_start: 0.8318 (p) cc_final: 0.8104 (p) REVERT: T 95 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8749 (mp) REVERT: V 57 LEU cc_start: 0.8803 (tp) cc_final: 0.8585 (tp) REVERT: W 57 LEU cc_start: 0.8753 (tp) cc_final: 0.8543 (tp) REVERT: X 21 MET cc_start: 0.8568 (ttp) cc_final: 0.8282 (ttp) REVERT: Y 95 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8734 (mp) REVERT: d 57 LEU cc_start: 0.8805 (tp) cc_final: 0.8126 (tp) outliers start: 45 outliers final: 18 residues processed: 419 average time/residue: 0.1374 time to fit residues: 102.2189 Evaluate side-chains 403 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 381 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 155 SER Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain N residue 155 SER Chi-restraints excluded: chain O residue 155 SER Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 166 ILE Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain W residue 155 SER Chi-restraints excluded: chain X residue 155 SER Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 155 SER Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 155 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 202 optimal weight: 0.0060 chunk 171 optimal weight: 0.9990 chunk 374 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 195 optimal weight: 0.0040 chunk 75 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 overall best weight: 0.5810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.101808 restraints weight = 38979.593| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.76 r_work: 0.3098 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28416 Z= 0.118 Angle : 0.533 8.187 38904 Z= 0.264 Chirality : 0.042 0.152 5112 Planarity : 0.002 0.024 4824 Dihedral : 3.708 17.822 4272 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.54 % Allowed : 23.65 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 4056 helix: 0.88 (0.13), residues: 1800 sheet: -1.18 (0.19), residues: 720 loop : -0.97 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 44 TYR 0.010 0.001 TYR V 59 PHE 0.003 0.000 PHE K 178 TRP 0.006 0.001 TRP O 151 HIS 0.002 0.001 HIS a 164 Details of bonding type rmsd covalent geometry : bond 0.00292 (28392) covalent geometry : angle 0.53293 (38856) SS BOND : bond 0.00108 ( 24) SS BOND : angle 0.14558 ( 48) hydrogen bonds : bond 0.03025 ( 1488) hydrogen bonds : angle 3.38156 ( 4536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 401 time to evaluate : 0.922 Fit side-chains REVERT: G 57 LEU cc_start: 0.8648 (tp) cc_final: 0.8150 (tp) REVERT: G 127 MET cc_start: 0.7942 (mtt) cc_final: 0.7297 (mtt) REVERT: H 53 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8223 (tt) REVERT: H 57 LEU cc_start: 0.8615 (tp) cc_final: 0.8220 (tp) REVERT: J 57 LEU cc_start: 0.8709 (tp) cc_final: 0.8496 (tp) REVERT: L 95 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8787 (mp) REVERT: M 150 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8420 (m-30) REVERT: N 57 LEU cc_start: 0.8883 (tp) cc_final: 0.8626 (tp) REVERT: R 173 THR cc_start: 0.8324 (p) cc_final: 0.8115 (p) REVERT: T 21 MET cc_start: 0.8857 (ttp) cc_final: 0.8528 (ttp) REVERT: T 57 LEU cc_start: 0.8764 (tp) cc_final: 0.8503 (tp) REVERT: T 95 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8731 (mp) REVERT: V 57 LEU cc_start: 0.8846 (tp) cc_final: 0.8481 (tp) REVERT: W 57 LEU cc_start: 0.8812 (tp) cc_final: 0.8610 (tp) REVERT: X 21 MET cc_start: 0.8602 (ttp) cc_final: 0.8294 (ttp) REVERT: d 57 LEU cc_start: 0.8810 (tp) cc_final: 0.8178 (tp) outliers start: 41 outliers final: 16 residues processed: 433 average time/residue: 0.1386 time to fit residues: 106.4152 Evaluate side-chains 412 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 392 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain K residue 155 SER Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain P residue 99 MET Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 166 ILE Chi-restraints excluded: chain W residue 155 SER Chi-restraints excluded: chain Y residue 150 ASP Chi-restraints excluded: chain Y residue 155 SER Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 155 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 123 optimal weight: 0.9980 chunk 335 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 407 optimal weight: 1.9990 chunk 377 optimal weight: 0.6980 chunk 329 optimal weight: 4.9990 chunk 177 optimal weight: 0.0570 chunk 201 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.100779 restraints weight = 39048.004| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.67 r_work: 0.3090 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28416 Z= 0.130 Angle : 0.547 8.431 38904 Z= 0.271 Chirality : 0.042 0.157 5112 Planarity : 0.002 0.023 4824 Dihedral : 3.732 17.629 4272 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.46 % Allowed : 24.92 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.13), residues: 4056 helix: 0.81 (0.13), residues: 1800 sheet: -1.14 (0.19), residues: 720 loop : -1.00 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 44 TYR 0.012 0.001 TYR V 59 PHE 0.002 0.000 PHE K 178 TRP 0.006 0.001 TRP Y 151 HIS 0.002 0.001 HIS R 164 Details of bonding type rmsd covalent geometry : bond 0.00326 (28392) covalent geometry : angle 0.54724 (38856) SS BOND : bond 0.00132 ( 24) SS BOND : angle 0.14747 ( 48) hydrogen bonds : bond 0.03167 ( 1488) hydrogen bonds : angle 3.37190 ( 4536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 399 time to evaluate : 0.886 Fit side-chains REVERT: G 57 LEU cc_start: 0.8616 (tp) cc_final: 0.8133 (tp) REVERT: G 127 MET cc_start: 0.7842 (mtt) cc_final: 0.7154 (mtt) REVERT: H 53 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8162 (tt) REVERT: H 57 LEU cc_start: 0.8615 (tp) cc_final: 0.8223 (tp) REVERT: J 57 LEU cc_start: 0.8701 (tp) cc_final: 0.8473 (tp) REVERT: L 95 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8781 (mp) REVERT: M 150 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: N 57 LEU cc_start: 0.8864 (tp) cc_final: 0.8373 (tp) REVERT: O 57 LEU cc_start: 0.8687 (tp) cc_final: 0.8294 (tp) REVERT: R 173 THR cc_start: 0.8275 (p) cc_final: 0.8067 (p) REVERT: T 21 MET cc_start: 0.8845 (ttp) cc_final: 0.8507 (ttp) REVERT: T 57 LEU cc_start: 0.8753 (tp) cc_final: 0.8528 (tp) REVERT: T 95 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8756 (mp) REVERT: U 150 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8277 (m-30) REVERT: V 150 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8263 (m-30) REVERT: W 57 LEU cc_start: 0.8743 (tp) cc_final: 0.8525 (tp) REVERT: X 21 MET cc_start: 0.8618 (ttp) cc_final: 0.8190 (ttp) REVERT: d 57 LEU cc_start: 0.8844 (tp) cc_final: 0.8208 (tp) outliers start: 39 outliers final: 24 residues processed: 426 average time/residue: 0.1360 time to fit residues: 102.7639 Evaluate side-chains 422 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 392 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain K residue 155 SER Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain O residue 155 SER Chi-restraints excluded: chain P residue 99 MET Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 166 ILE Chi-restraints excluded: chain U residue 150 ASP Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain W residue 90 LYS Chi-restraints excluded: chain W residue 155 SER Chi-restraints excluded: chain Y residue 127 MET Chi-restraints excluded: chain Y residue 150 ASP Chi-restraints excluded: chain Y residue 155 SER Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 155 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 375 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 178 optimal weight: 0.0270 chunk 160 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 406 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 337 optimal weight: 3.9990 chunk 260 optimal weight: 0.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.105102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.096836 restraints weight = 39855.496| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.63 r_work: 0.3031 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28416 Z= 0.169 Angle : 0.602 8.939 38904 Z= 0.296 Chirality : 0.044 0.173 5112 Planarity : 0.002 0.022 4824 Dihedral : 3.945 17.427 4272 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.69 % Allowed : 25.34 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 4056 helix: 0.65 (0.13), residues: 1800 sheet: -1.18 (0.19), residues: 720 loop : -0.99 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 44 TYR 0.014 0.001 TYR V 59 PHE 0.003 0.000 PHE K 178 TRP 0.006 0.001 TRP J 151 HIS 0.003 0.001 HIS a 164 Details of bonding type rmsd covalent geometry : bond 0.00421 (28392) covalent geometry : angle 0.60212 (38856) SS BOND : bond 0.00188 ( 24) SS BOND : angle 0.14158 ( 48) hydrogen bonds : bond 0.03702 ( 1488) hydrogen bonds : angle 3.49204 ( 4536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 404 time to evaluate : 0.707 Fit side-chains REVERT: G 57 LEU cc_start: 0.8550 (tp) cc_final: 0.8087 (tp) REVERT: G 127 MET cc_start: 0.7726 (mtt) cc_final: 0.7435 (mtt) REVERT: H 53 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8108 (tt) REVERT: H 57 LEU cc_start: 0.8617 (tp) cc_final: 0.8227 (tp) REVERT: I 57 LEU cc_start: 0.8511 (tp) cc_final: 0.8110 (tp) REVERT: J 57 LEU cc_start: 0.8702 (tp) cc_final: 0.8397 (tp) REVERT: L 95 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8814 (mp) REVERT: N 57 LEU cc_start: 0.8836 (tp) cc_final: 0.8561 (tp) REVERT: O 57 LEU cc_start: 0.8656 (tp) cc_final: 0.8289 (tp) REVERT: P 44 ARG cc_start: 0.8500 (mtm180) cc_final: 0.8192 (mtt90) REVERT: Q 44 ARG cc_start: 0.8365 (mtm180) cc_final: 0.8000 (mtt-85) REVERT: T 57 LEU cc_start: 0.8700 (tp) cc_final: 0.8498 (tp) REVERT: T 95 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8785 (mp) REVERT: V 150 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8348 (m-30) REVERT: X 21 MET cc_start: 0.8588 (ttp) cc_final: 0.8177 (ttp) REVERT: a 127 MET cc_start: 0.7495 (mtt) cc_final: 0.7253 (mtt) REVERT: d 57 LEU cc_start: 0.8755 (tp) cc_final: 0.8154 (tp) outliers start: 45 outliers final: 23 residues processed: 431 average time/residue: 0.1430 time to fit residues: 108.0895 Evaluate side-chains 424 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 397 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain K residue 155 SER Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain O residue 155 SER Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 150 ASP Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 155 SER Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain W residue 155 SER Chi-restraints excluded: chain Y residue 127 MET Chi-restraints excluded: chain Y residue 155 SER Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 150 ASP Chi-restraints excluded: chain d residue 155 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 341 optimal weight: 0.5980 chunk 349 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 161 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 344 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100785 restraints weight = 39144.789| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.64 r_work: 0.3089 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28416 Z= 0.124 Angle : 0.552 9.208 38904 Z= 0.272 Chirality : 0.042 0.157 5112 Planarity : 0.002 0.020 4824 Dihedral : 3.819 17.019 4272 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.13 % Allowed : 26.20 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.13), residues: 4056 helix: 0.74 (0.13), residues: 1800 sheet: -1.19 (0.19), residues: 720 loop : -1.04 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 44 TYR 0.014 0.001 TYR V 59 PHE 0.002 0.000 PHE M 178 TRP 0.007 0.001 TRP W 77 HIS 0.003 0.001 HIS K 164 Details of bonding type rmsd covalent geometry : bond 0.00310 (28392) covalent geometry : angle 0.55276 (38856) SS BOND : bond 0.00138 ( 24) SS BOND : angle 0.15190 ( 48) hydrogen bonds : bond 0.03129 ( 1488) hydrogen bonds : angle 3.41048 ( 4536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 398 time to evaluate : 0.651 Fit side-chains REVERT: G 57 LEU cc_start: 0.8598 (tp) cc_final: 0.8119 (tp) REVERT: G 127 MET cc_start: 0.7749 (mtt) cc_final: 0.7102 (mtt) REVERT: H 53 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8139 (tt) REVERT: H 57 LEU cc_start: 0.8622 (tp) cc_final: 0.8230 (tp) REVERT: J 57 LEU cc_start: 0.8713 (tp) cc_final: 0.8484 (tp) REVERT: K 57 LEU cc_start: 0.8542 (tp) cc_final: 0.8031 (tp) REVERT: L 95 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8766 (mp) REVERT: N 57 LEU cc_start: 0.8856 (tp) cc_final: 0.8357 (tp) REVERT: O 57 LEU cc_start: 0.8695 (tp) cc_final: 0.8329 (tp) REVERT: T 21 MET cc_start: 0.8853 (ttp) cc_final: 0.8506 (ttp) REVERT: T 57 LEU cc_start: 0.8782 (tp) cc_final: 0.8557 (tp) REVERT: T 95 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8752 (mp) REVERT: V 150 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8228 (m-30) REVERT: X 21 MET cc_start: 0.8623 (ttp) cc_final: 0.8197 (ttp) REVERT: d 57 LEU cc_start: 0.8774 (tp) cc_final: 0.8138 (tp) outliers start: 30 outliers final: 20 residues processed: 417 average time/residue: 0.1382 time to fit residues: 102.1415 Evaluate side-chains 419 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 395 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain K residue 155 SER Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 95 ILE Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain O residue 155 SER Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain Q residue 155 SER Chi-restraints excluded: chain R residue 150 ASP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 155 SER Chi-restraints excluded: chain W residue 155 SER Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 155 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 250 optimal weight: 0.0770 chunk 233 optimal weight: 0.6980 chunk 52 optimal weight: 0.0770 chunk 315 optimal weight: 0.9980 chunk 263 optimal weight: 0.5980 chunk 271 optimal weight: 0.9980 chunk 371 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 404 optimal weight: 3.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 135 GLN P 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.102830 restraints weight = 38872.219| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.77 r_work: 0.3117 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28416 Z= 0.114 Angle : 0.540 9.441 38904 Z= 0.266 Chirality : 0.042 0.222 5112 Planarity : 0.002 0.028 4824 Dihedral : 3.711 16.327 4272 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.83 % Allowed : 26.80 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.13), residues: 4056 helix: 0.83 (0.13), residues: 1800 sheet: -1.20 (0.19), residues: 720 loop : -1.05 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 44 TYR 0.013 0.001 TYR V 59 PHE 0.002 0.000 PHE M 178 TRP 0.007 0.001 TRP W 77 HIS 0.004 0.001 HIS b 164 Details of bonding type rmsd covalent geometry : bond 0.00285 (28392) covalent geometry : angle 0.54014 (38856) SS BOND : bond 0.00107 ( 24) SS BOND : angle 0.14481 ( 48) hydrogen bonds : bond 0.02893 ( 1488) hydrogen bonds : angle 3.33528 ( 4536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 400 time to evaluate : 0.942 Fit side-chains REVERT: G 57 LEU cc_start: 0.8617 (tp) cc_final: 0.8142 (tp) REVERT: G 127 MET cc_start: 0.7813 (mtt) cc_final: 0.7176 (mtt) REVERT: H 53 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8191 (tt) REVERT: I 57 LEU cc_start: 0.8478 (tp) cc_final: 0.8016 (tp) REVERT: K 57 LEU cc_start: 0.8494 (tp) cc_final: 0.7942 (tp) REVERT: N 57 LEU cc_start: 0.8871 (tp) cc_final: 0.8409 (tp) REVERT: T 21 MET cc_start: 0.8877 (ttp) cc_final: 0.8574 (ttp) REVERT: T 57 LEU cc_start: 0.8786 (tp) cc_final: 0.8526 (tp) REVERT: V 57 LEU cc_start: 0.8784 (tp) cc_final: 0.8409 (tp) REVERT: V 150 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: W 99 MET cc_start: 0.7795 (ttt) cc_final: 0.7513 (ttt) REVERT: X 21 MET cc_start: 0.8611 (ttp) cc_final: 0.8177 (ttp) REVERT: d 57 LEU cc_start: 0.8766 (tp) cc_final: 0.8139 (tp) REVERT: d 99 MET cc_start: 0.7935 (ttp) cc_final: 0.7674 (mtp) outliers start: 22 outliers final: 15 residues processed: 415 average time/residue: 0.1362 time to fit residues: 100.2077 Evaluate side-chains 413 residues out of total 2664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 396 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 155 SER Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain Q residue 150 ASP Chi-restraints excluded: chain R residue 150 ASP Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain W residue 155 SER Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain d residue 155 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 61 optimal weight: 0.0970 chunk 281 optimal weight: 1.9990 chunk 330 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 199 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 168 optimal weight: 0.1980 chunk 275 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104470 restraints weight = 38660.892| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.77 r_work: 0.3140 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28416 Z= 0.110 Angle : 0.534 9.573 38904 Z= 0.263 Chirality : 0.042 0.158 5112 Planarity : 0.002 0.026 4824 Dihedral : 3.645 16.528 4272 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.68 % Allowed : 27.44 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 4056 helix: 0.89 (0.13), residues: 1800 sheet: -1.20 (0.19), residues: 720 loop : -1.05 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Z 44 TYR 0.014 0.001 TYR V 59 PHE 0.002 0.000 PHE M 178 TRP 0.013 0.001 TRP W 77 HIS 0.003 0.001 HIS K 164 Details of bonding type rmsd covalent geometry : bond 0.00274 (28392) covalent geometry : angle 0.53412 (38856) SS BOND : bond 0.00105 ( 24) SS BOND : angle 0.17338 ( 48) hydrogen bonds : bond 0.02784 ( 1488) hydrogen bonds : angle 3.27369 ( 4536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5461.16 seconds wall clock time: 94 minutes 38.98 seconds (5678.98 seconds total)