Starting phenix.real_space_refine on Tue Aug 26 16:11:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jyz_36734/08_2025/8jyz_36734.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jyz_36734/08_2025/8jyz_36734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jyz_36734/08_2025/8jyz_36734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jyz_36734/08_2025/8jyz_36734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jyz_36734/08_2025/8jyz_36734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jyz_36734/08_2025/8jyz_36734.map" } resolution = 3.63 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= 0.086 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 231 5.16 5 C 24970 2.51 5 N 6930 2.21 5 O 7029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39160 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1863 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 12, 'TRANS': 221} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 13, 'TRANS': 200} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, V, D, F, H, J, L, N, P, R, T, W Time building chain proxies: 5.02, per 1000 atoms: 0.13 Number of scatterers: 39160 At special positions: 0 Unit cell: (251.45, 251.45, 85.6, 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 231 16.00 O 7029 8.00 N 6930 7.00 C 24970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8954 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 1 sheets defined 12.7% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 128 through 137 Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 137 through 151 Processing helix chain 'C' and resid 17 through 24 Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 128 through 137 Processing helix chain 'C' and resid 138 through 147 Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 137 through 151 Processing helix chain 'E' and resid 17 through 24 Processing helix chain 'E' and resid 38 through 42 Processing helix chain 'E' and resid 128 through 137 Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'F' and resid 127 through 135 Processing helix chain 'F' and resid 137 through 151 Processing helix chain 'G' and resid 17 through 24 Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'G' and resid 128 through 137 Processing helix chain 'G' and resid 138 through 147 Processing helix chain 'H' and resid 127 through 135 Processing helix chain 'H' and resid 137 through 151 Processing helix chain 'I' and resid 17 through 24 Processing helix chain 'I' and resid 38 through 42 Processing helix chain 'I' and resid 128 through 137 Processing helix chain 'I' and resid 138 through 147 Processing helix chain 'J' and resid 127 through 135 Processing helix chain 'J' and resid 137 through 151 Processing helix chain 'K' and resid 17 through 24 Processing helix chain 'K' and resid 38 through 42 Processing helix chain 'K' and resid 128 through 137 Processing helix chain 'K' and resid 138 through 147 Processing helix chain 'L' and resid 127 through 135 Processing helix chain 'L' and resid 137 through 151 Processing helix chain 'M' and resid 17 through 24 Processing helix chain 'M' and resid 38 through 42 Processing helix chain 'M' and resid 128 through 137 Processing helix chain 'M' and resid 138 through 147 Processing helix chain 'N' and resid 127 through 135 Processing helix chain 'N' and resid 137 through 151 Processing helix chain 'O' and resid 17 through 24 Processing helix chain 'O' and resid 38 through 42 Processing helix chain 'O' and resid 128 through 137 Processing helix chain 'O' and resid 138 through 147 Processing helix chain 'P' and resid 127 through 135 Processing helix chain 'P' and resid 137 through 151 Processing helix chain 'Q' and resid 17 through 24 Processing helix chain 'Q' and resid 38 through 42 Processing helix chain 'Q' and resid 128 through 137 Processing helix chain 'Q' and resid 138 through 147 Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 137 through 151 Processing helix chain 'S' and resid 17 through 24 Processing helix chain 'S' and resid 38 through 42 Processing helix chain 'S' and resid 128 through 137 Processing helix chain 'S' and resid 138 through 147 Processing helix chain 'T' and resid 127 through 135 Processing helix chain 'T' and resid 137 through 151 Processing helix chain 'V' and resid 17 through 24 Processing helix chain 'V' and resid 38 through 42 Processing helix chain 'V' and resid 128 through 137 Processing helix chain 'V' and resid 138 through 147 Processing helix chain 'W' and resid 127 through 135 Processing helix chain 'W' and resid 137 through 151 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 6 through 7 current: chain 'A' and resid 101 through 124 removed outlier: 4.382A pdb=" N ARG A 119 " --> pdb=" O ARG A 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 157 through 169 current: chain 'A' and resid 201 through 216 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 201 through 216 current: chain 'A' and resid 239 through 242 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 239 through 242 current: chain 'B' and resid 102 through 115 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 102 through 115 current: chain 'B' and resid 154 through 165 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 154 through 165 current: chain 'B' and resid 198 through 213 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 198 through 213 current: chain 'B' and resid 236 through 239 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 236 through 239 current: chain 'C' and resid 101 through 124 removed outlier: 4.382A pdb=" N ARG C 119 " --> pdb=" O ARG C 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 157 through 169 current: chain 'C' and resid 201 through 216 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 201 through 216 current: chain 'C' and resid 239 through 242 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 239 through 242 current: chain 'D' and resid 102 through 115 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 102 through 115 current: chain 'D' and resid 154 through 165 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 154 through 165 current: chain 'D' and resid 198 through 213 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 198 through 213 current: chain 'D' and resid 236 through 239 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 236 through 239 current: chain 'E' and resid 101 through 124 removed outlier: 4.381A pdb=" N ARG E 119 " --> pdb=" O ARG E 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 157 through 169 current: chain 'E' and resid 201 through 216 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 201 through 216 current: chain 'E' and resid 239 through 242 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 239 through 242 current: chain 'F' and resid 102 through 115 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 102 through 115 current: chain 'F' and resid 154 through 165 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 154 through 165 current: chain 'F' and resid 198 through 213 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 198 through 213 current: chain 'F' and resid 236 through 239 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 236 through 239 current: chain 'G' and resid 101 through 124 removed outlier: 4.382A pdb=" N ARG G 119 " --> pdb=" O ARG G 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 157 through 169 current: chain 'G' and resid 201 through 216 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 201 through 216 current: chain 'G' and resid 239 through 242 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 239 through 242 current: chain 'H' and resid 102 through 115 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 102 through 115 current: chain 'H' and resid 154 through 165 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 154 through 165 current: chain 'H' and resid 198 through 213 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 198 through 213 current: chain 'H' and resid 236 through 239 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 236 through 239 current: chain 'I' and resid 101 through 124 removed outlier: 4.382A pdb=" N ARG I 119 " --> pdb=" O ARG I 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 157 through 169 current: chain 'I' and resid 201 through 216 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 201 through 216 current: chain 'I' and resid 239 through 242 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 239 through 242 current: chain 'J' and resid 102 through 115 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 102 through 115 current: chain 'J' and resid 154 through 165 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 154 through 165 current: chain 'J' and resid 198 through 213 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 198 through 213 current: chain 'J' and resid 236 through 239 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 236 through 239 current: chain 'K' and resid 101 through 124 removed outlier: 4.382A pdb=" N ARG K 119 " --> pdb=" O ARG K 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 157 through 169 current: chain 'K' and resid 201 through 216 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 201 through 216 current: chain 'K' and resid 239 through 242 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 239 through 242 current: chain 'L' and resid 102 through 115 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 102 through 115 current: chain 'L' and resid 154 through 165 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 154 through 165 current: chain 'L' and resid 198 through 213 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 198 through 213 current: chain 'L' and resid 236 through 239 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 236 through 239 current: chain 'M' and resid 101 through 124 removed outlier: 4.382A pdb=" N ARG M 119 " --> pdb=" O ARG M 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 157 through 169 current: chain 'M' and resid 201 through 216 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 201 through 216 current: chain 'M' and resid 239 through 242 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 239 through 242 current: chain 'N' and resid 102 through 115 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 102 through 115 current: chain 'N' and resid 154 through 165 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 154 through 165 current: chain 'N' and resid 198 through 213 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 198 through 213 current: chain 'N' and resid 236 through 239 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 236 through 239 current: chain 'O' and resid 101 through 124 removed outlier: 4.382A pdb=" N ARG O 119 " --> pdb=" O ARG O 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 157 through 169 current: chain 'O' and resid 201 through 216 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 201 through 216 current: chain 'O' and resid 239 through 242 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 239 through 242 current: chain 'P' and resid 102 through 115 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 102 through 115 current: chain 'P' and resid 154 through 165 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 154 through 165 current: chain 'P' and resid 198 through 213 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 198 through 213 current: chain 'P' and resid 236 through 239 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 236 through 239 current: chain 'Q' and resid 101 through 124 removed outlier: 4.382A pdb=" N ARG Q 119 " --> pdb=" O ARG Q 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 157 through 169 current: chain 'Q' and resid 201 through 216 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 201 through 216 current: chain 'Q' and resid 239 through 242 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 239 through 242 current: chain 'R' and resid 102 through 115 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 102 through 115 current: chain 'R' and resid 154 through 165 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 154 through 165 current: chain 'R' and resid 198 through 213 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 198 through 213 current: chain 'R' and resid 236 through 239 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 236 through 239 current: chain 'S' and resid 101 through 124 removed outlier: 4.382A pdb=" N ARG S 119 " --> pdb=" O ARG S 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 157 through 169 current: chain 'S' and resid 201 through 216 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 201 through 216 current: chain 'S' and resid 239 through 242 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 239 through 242 current: chain 'T' and resid 102 through 115 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 102 through 115 current: chain 'T' and resid 154 through 165 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 154 through 165 current: chain 'T' and resid 198 through 213 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 198 through 213 current: chain 'T' and resid 236 through 239 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 236 through 239 current: chain 'V' and resid 101 through 124 removed outlier: 4.382A pdb=" N ARG V 119 " --> pdb=" O ARG V 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 157 through 169 current: chain 'V' and resid 201 through 216 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 201 through 216 current: chain 'V' and resid 239 through 242 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 239 through 242 current: chain 'W' and resid 102 through 115 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 102 through 115 current: chain 'W' and resid 154 through 165 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 154 through 165 current: chain 'W' and resid 198 through 213 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 198 through 213 current: chain 'W' and resid 236 through 239 429 hydrogen bonds defined for protein. 1221 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: 6.56 Time building geometry restraints manager: 5.30 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: 12531 1.34 - 1.46: 9093 1.46 - 1.58: 18196 1.58 - 1.69: 0 1.69 - 1.81: 396 Bond restraints: 40216 Sorted by residual: bond pdb=" N HIS F 13 " pdb=" CA HIS F 13 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.18e-02 7.18e+03 8.30e+00 bond pdb=" N HIS T 13 " pdb=" CA HIS T 13 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.18e-02 7.18e+03 8.21e+00 bond pdb=" N HIS R 13 " pdb=" CA HIS R 13 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.18e-02 7.18e+03 8.19e+00 bond pdb=" N HIS W 13 " pdb=" CA HIS W 13 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.18e-02 7.18e+03 8.13e+00 bond pdb=" N THR H 12 " pdb=" CA THR H 12 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.08e-02 8.57e+03 8.07e+00 ... (remaining 40211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 53396 1.18 - 2.36: 594 2.36 - 3.53: 284 3.53 - 4.71: 22 4.71 - 5.89: 11 Bond angle restraints: 54307 Sorted by residual: angle pdb=" C TYR L 14 " pdb=" N PRO L 15 " pdb=" CA PRO L 15 " ideal model delta sigma weight residual 119.66 121.98 -2.32 7.20e-01 1.93e+00 1.04e+01 angle pdb=" C TYR F 14 " pdb=" N PRO F 15 " pdb=" CA PRO F 15 " ideal model delta sigma weight residual 119.66 121.98 -2.32 7.20e-01 1.93e+00 1.04e+01 angle pdb=" C TYR J 14 " pdb=" N PRO J 15 " pdb=" CA PRO J 15 " ideal model delta sigma weight residual 119.66 121.95 -2.29 7.20e-01 1.93e+00 1.01e+01 angle pdb=" C TYR R 14 " pdb=" N PRO R 15 " pdb=" CA PRO R 15 " ideal model delta sigma weight residual 119.66 121.95 -2.29 7.20e-01 1.93e+00 1.01e+01 angle pdb=" C TYR D 14 " pdb=" N PRO D 15 " pdb=" CA PRO D 15 " ideal model delta sigma weight residual 119.66 121.94 -2.28 7.20e-01 1.93e+00 1.00e+01 ... (remaining 54302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.17: 21748 11.17 - 22.35: 1426 22.35 - 33.52: 432 33.52 - 44.70: 77 44.70 - 55.87: 33 Dihedral angle restraints: 23716 sinusoidal: 9746 harmonic: 13970 Sorted by residual: dihedral pdb=" N ARG W 166 " pdb=" CA ARG W 166 " pdb=" CB ARG W 166 " pdb=" CG ARG W 166 " ideal model delta sinusoidal sigma weight residual -60.00 -113.66 53.66 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N ARG F 166 " pdb=" CA ARG F 166 " pdb=" CB ARG F 166 " pdb=" CG ARG F 166 " ideal model delta sinusoidal sigma weight residual -60.00 -113.63 53.63 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N ARG J 166 " pdb=" CA ARG J 166 " pdb=" CB ARG J 166 " pdb=" CG ARG J 166 " ideal model delta sinusoidal sigma weight residual -60.00 -113.63 53.63 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 23713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 3287 0.025 - 0.051: 1618 0.051 - 0.076: 224 0.076 - 0.102: 371 0.102 - 0.127: 231 Chirality restraints: 5731 Sorted by residual: chirality pdb=" CA VAL J 124 " pdb=" N VAL J 124 " pdb=" C VAL J 124 " pdb=" CB VAL J 124 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA VAL P 124 " pdb=" N VAL P 124 " pdb=" C VAL P 124 " pdb=" CB VAL P 124 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA VAL N 124 " pdb=" N VAL N 124 " pdb=" C VAL N 124 " pdb=" CB VAL N 124 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 5728 not shown) Planarity restraints: 6864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE W 55 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO W 56 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO W 56 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO W 56 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE P 55 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO P 56 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO P 56 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO P 56 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 55 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO D 56 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO D 56 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 56 " 0.014 5.00e-02 4.00e+02 ... (remaining 6861 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6328 2.78 - 3.31: 35171 3.31 - 3.84: 60938 3.84 - 4.37: 67384 4.37 - 4.90: 122392 Nonbonded interactions: 292213 Sorted by model distance: nonbonded pdb=" OE2 GLU E 177 " pdb=" OG1 THR E 179 " model vdw 2.251 3.040 nonbonded pdb=" OE2 GLU O 177 " pdb=" OG1 THR O 179 " model vdw 2.251 3.040 nonbonded pdb=" OE2 GLU I 177 " pdb=" OG1 THR I 179 " model vdw 2.251 3.040 nonbonded pdb=" OE2 GLU A 177 " pdb=" OG1 THR A 179 " model vdw 2.251 3.040 nonbonded pdb=" OE2 GLU Q 177 " pdb=" OG1 THR Q 179 " model vdw 2.251 3.040 ... (remaining 292208 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'W' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 32.740 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.120 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:1.390 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 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 : 0.002 0.034 40216 Z= 0.117 Angle : 0.404 5.891 54307 Z= 0.215 Chirality : 0.041 0.127 5731 Planarity : 0.003 0.026 6864 Dihedral : 8.704 55.873 14762 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.26 % Allowed : 4.25 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.12), residues: 4796 helix: 1.05 (0.22), residues: 561 sheet: 0.44 (0.11), residues: 2332 loop : 0.23 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 225 TYR 0.006 0.001 TYR M 13 PHE 0.005 0.001 PHE C 250 TRP 0.009 0.001 TRP R 201 HIS 0.002 0.000 HIS F 213 Details of bonding type rmsd covalent geometry : bond 0.00175 (40216) covalent geometry : angle 0.40399 (54307) hydrogen bonds : bond 0.15969 ( 429) hydrogen bonds : angle 5.06604 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 642 time to evaluate : 1.614 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU W 4 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8097 (tpp) cc_final: 0.7891 (mpp) REVERT: A 158 GLU cc_start: 0.7666 (tt0) cc_final: 0.7046 (mp0) REVERT: B 68 GLN cc_start: 0.8008 (mp10) cc_final: 0.7776 (mp10) REVERT: C 158 GLU cc_start: 0.7766 (tt0) cc_final: 0.7171 (mp0) REVERT: E 158 GLU cc_start: 0.7644 (tt0) cc_final: 0.7051 (mp0) REVERT: F 68 GLN cc_start: 0.7951 (mp10) cc_final: 0.7409 (mp10) REVERT: F 237 MET cc_start: 0.8113 (ttp) cc_final: 0.7909 (ttm) REVERT: G 158 GLU cc_start: 0.7712 (tt0) cc_final: 0.7108 (mp0) REVERT: H 68 GLN cc_start: 0.7954 (mp10) cc_final: 0.7413 (mp10) REVERT: H 141 ARG cc_start: 0.8924 (ptm160) cc_final: 0.8537 (ttp-110) REVERT: H 237 MET cc_start: 0.7909 (ttp) cc_final: 0.7401 (ttm) REVERT: I 44 GLN cc_start: 0.7824 (mt0) cc_final: 0.7434 (mp10) REVERT: I 158 GLU cc_start: 0.7602 (tt0) cc_final: 0.7057 (mp0) REVERT: J 68 GLN cc_start: 0.8096 (mp10) cc_final: 0.7894 (mp10) REVERT: J 237 MET cc_start: 0.8078 (ttp) cc_final: 0.7636 (ttp) REVERT: K 158 GLU cc_start: 0.7852 (tt0) cc_final: 0.7227 (mp0) REVERT: L 68 GLN cc_start: 0.8006 (mp10) cc_final: 0.7625 (mp10) REVERT: L 70 HIS cc_start: 0.7511 (p90) cc_final: 0.7144 (p90) REVERT: L 237 MET cc_start: 0.7996 (ttp) cc_final: 0.7792 (ttp) REVERT: M 44 GLN cc_start: 0.7672 (mt0) cc_final: 0.7467 (mp10) REVERT: M 158 GLU cc_start: 0.7577 (tt0) cc_final: 0.7109 (mp0) REVERT: N 129 GLN cc_start: 0.8257 (pp30) cc_final: 0.7965 (pp30) REVERT: O 158 GLU cc_start: 0.7839 (tt0) cc_final: 0.7346 (mp0) REVERT: P 59 MET cc_start: 0.5415 (mmt) cc_final: 0.5165 (mmt) REVERT: P 68 GLN cc_start: 0.8019 (mp10) cc_final: 0.7679 (mp10) REVERT: P 237 MET cc_start: 0.8090 (ttp) cc_final: 0.7813 (ttm) REVERT: Q 158 GLU cc_start: 0.7725 (tt0) cc_final: 0.7215 (mp0) REVERT: R 68 GLN cc_start: 0.7937 (mp10) cc_final: 0.7513 (mp10) REVERT: R 237 MET cc_start: 0.8012 (ttp) cc_final: 0.7727 (ttp) REVERT: S 158 GLU cc_start: 0.7628 (tt0) cc_final: 0.6910 (mp0) REVERT: T 6 TRP cc_start: 0.7141 (m100) cc_final: 0.6435 (m100) REVERT: T 68 GLN cc_start: 0.7863 (mp10) cc_final: 0.7375 (mp10) REVERT: T 237 MET cc_start: 0.8090 (ttp) cc_final: 0.7864 (ttm) REVERT: V 21 MET cc_start: 0.7711 (ptm) cc_final: 0.7470 (ptm) REVERT: V 158 GLU cc_start: 0.7612 (tt0) cc_final: 0.7120 (mp0) REVERT: W 68 GLN cc_start: 0.8029 (mp10) cc_final: 0.7599 (mp10) REVERT: W 129 GLN cc_start: 0.8231 (pp30) cc_final: 0.7964 (pp30) outliers start: 11 outliers final: 11 residues processed: 653 average time/residue: 0.2683 time to fit residues: 278.3836 Evaluate side-chains 544 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 533 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain K residue 219 ASP Chi-restraints excluded: chain M residue 219 ASP Chi-restraints excluded: chain O residue 219 ASP Chi-restraints excluded: chain Q residue 219 ASP Chi-restraints excluded: chain S residue 219 ASP Chi-restraints excluded: chain V residue 219 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 0.1980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 470 optimal weight: 1.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 HIS F 145 GLN L 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.238185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4705 r_free = 0.4705 target = 0.172986 restraints weight = 41053.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 83)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.167027 restraints weight = 43390.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.162343 restraints weight = 32890.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.162606 restraints weight = 33106.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.163369 restraints weight = 30935.162| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 40216 Z= 0.221 Angle : 0.588 9.357 54307 Z= 0.311 Chirality : 0.046 0.159 5731 Planarity : 0.004 0.054 6864 Dihedral : 3.491 14.759 5302 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.23 % Allowed : 11.20 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.12), residues: 4796 helix: 0.74 (0.22), residues: 572 sheet: -0.53 (0.11), residues: 2343 loop : -0.04 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 141 TYR 0.017 0.002 TYR F 116 PHE 0.021 0.002 PHE D 217 TRP 0.040 0.002 TRP V 71 HIS 0.013 0.002 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00476 (40216) covalent geometry : angle 0.58796 (54307) hydrogen bonds : bond 0.03511 ( 429) hydrogen bonds : angle 4.06566 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 519 time to evaluate : 1.589 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU W 4 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8323 (tpp) cc_final: 0.8068 (mpp) REVERT: A 158 GLU cc_start: 0.7799 (tt0) cc_final: 0.7213 (mp0) REVERT: C 158 GLU cc_start: 0.7904 (tt0) cc_final: 0.7287 (mp0) REVERT: D 142 GLN cc_start: 0.8996 (mt0) cc_final: 0.8695 (mp10) REVERT: E 125 MET cc_start: 0.7292 (ptt) cc_final: 0.7078 (ptp) REVERT: F 68 GLN cc_start: 0.8380 (mp10) cc_final: 0.8015 (mp10) REVERT: F 141 ARG cc_start: 0.9176 (ptm-80) cc_final: 0.8564 (ptm-80) REVERT: F 142 GLN cc_start: 0.8998 (mt0) cc_final: 0.8789 (mp10) REVERT: F 145 GLN cc_start: 0.8673 (pt0) cc_final: 0.8302 (pt0) REVERT: F 235 TRP cc_start: 0.6791 (p-90) cc_final: 0.6262 (p-90) REVERT: G 154 MET cc_start: 0.7617 (ppp) cc_final: 0.7293 (ppp) REVERT: G 158 GLU cc_start: 0.7820 (tt0) cc_final: 0.7153 (mp0) REVERT: H 68 GLN cc_start: 0.8403 (mp10) cc_final: 0.8074 (mp10) REVERT: H 141 ARG cc_start: 0.9154 (ptm160) cc_final: 0.8690 (ttp-110) REVERT: H 237 MET cc_start: 0.7725 (ttp) cc_final: 0.7415 (ttm) REVERT: I 139 ASP cc_start: 0.7615 (p0) cc_final: 0.7394 (p0) REVERT: I 154 MET cc_start: 0.7776 (ppp) cc_final: 0.7558 (ppp) REVERT: I 158 GLU cc_start: 0.7754 (tt0) cc_final: 0.7134 (mp0) REVERT: J 142 GLN cc_start: 0.8978 (mt0) cc_final: 0.8684 (mp10) REVERT: J 237 MET cc_start: 0.8031 (ttp) cc_final: 0.7759 (ttp) REVERT: K 158 GLU cc_start: 0.7993 (tt0) cc_final: 0.7224 (mp0) REVERT: L 6 TRP cc_start: 0.7418 (m100) cc_final: 0.7122 (m100) REVERT: L 68 GLN cc_start: 0.8393 (mp10) cc_final: 0.7946 (mp10) REVERT: L 141 ARG cc_start: 0.8976 (ptm-80) cc_final: 0.8469 (ptm-80) REVERT: L 145 GLN cc_start: 0.8554 (pt0) cc_final: 0.8192 (pt0) REVERT: L 235 TRP cc_start: 0.6909 (p-90) cc_final: 0.6624 (p-90) REVERT: L 237 MET cc_start: 0.7814 (ttp) cc_final: 0.7571 (ttp) REVERT: M 158 GLU cc_start: 0.7750 (tt0) cc_final: 0.7230 (mp0) REVERT: N 129 GLN cc_start: 0.8180 (pp30) cc_final: 0.7916 (pp30) REVERT: N 142 GLN cc_start: 0.9054 (mt0) cc_final: 0.8829 (mp10) REVERT: O 158 GLU cc_start: 0.7905 (tt0) cc_final: 0.7387 (mp0) REVERT: P 59 MET cc_start: 0.5966 (mmt) cc_final: 0.5526 (mmt) REVERT: P 68 GLN cc_start: 0.8389 (mp10) cc_final: 0.8097 (mp10) REVERT: P 235 TRP cc_start: 0.6774 (p-90) cc_final: 0.6287 (p-90) REVERT: Q 152 MET cc_start: 0.7156 (mpp) cc_final: 0.6923 (mpp) REVERT: Q 158 GLU cc_start: 0.7912 (tt0) cc_final: 0.7182 (mp0) REVERT: R 68 GLN cc_start: 0.8237 (mp10) cc_final: 0.7990 (mp10) REVERT: R 104 LEU cc_start: 0.5173 (tt) cc_final: 0.4205 (mp) REVERT: S 158 GLU cc_start: 0.7700 (tt0) cc_final: 0.6844 (mp0) REVERT: T 6 TRP cc_start: 0.7381 (m100) cc_final: 0.6492 (m100) REVERT: T 68 GLN cc_start: 0.8235 (mp10) cc_final: 0.7939 (mp10) REVERT: T 141 ARG cc_start: 0.9053 (ptm-80) cc_final: 0.8469 (ptm-80) REVERT: T 142 GLN cc_start: 0.8950 (mt0) cc_final: 0.8632 (mp10) REVERT: V 21 MET cc_start: 0.7701 (ptm) cc_final: 0.7378 (ptm) REVERT: V 158 GLU cc_start: 0.7733 (tt0) cc_final: 0.7143 (mp0) REVERT: W 68 GLN cc_start: 0.8281 (mp10) cc_final: 0.7963 (mp10) REVERT: W 141 ARG cc_start: 0.8916 (ptm-80) cc_final: 0.8497 (ptm-80) REVERT: W 142 GLN cc_start: 0.8991 (mt0) cc_final: 0.8770 (mp10) REVERT: W 145 GLN cc_start: 0.8418 (pt0) cc_final: 0.7845 (pt0) outliers start: 52 outliers final: 20 residues processed: 558 average time/residue: 0.2738 time to fit residues: 240.0326 Evaluate side-chains 500 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 480 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain M residue 240 MET Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain P residue 132 ASP Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain V residue 162 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 435 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 chunk 417 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 378 optimal weight: 10.0000 chunk 470 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 476 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 GLN J 145 GLN ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 145 GLN R 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.232683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 140)---------------| | r_work = 0.4504 r_free = 0.4504 target = 0.155977 restraints weight = 41589.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.154941 restraints weight = 35966.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.155172 restraints weight = 31633.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.155711 restraints weight = 31622.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.156136 restraints weight = 28787.071| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40216 Z= 0.208 Angle : 0.561 10.939 54307 Z= 0.299 Chirality : 0.044 0.157 5731 Planarity : 0.004 0.027 6864 Dihedral : 3.925 25.583 5280 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.80 % Allowed : 12.98 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.12), residues: 4796 helix: 0.59 (0.22), residues: 572 sheet: -1.06 (0.11), residues: 2321 loop : -0.25 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG R 222 TYR 0.015 0.002 TYR F 116 PHE 0.017 0.002 PHE J 217 TRP 0.032 0.002 TRP R 6 HIS 0.027 0.002 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00441 (40216) covalent geometry : angle 0.56139 (54307) hydrogen bonds : bond 0.03304 ( 429) hydrogen bonds : angle 4.10592 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 508 time to evaluate : 1.588 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 151 MET cc_start: 0.6555 (pmm) cc_final: 0.6305 (pmm) REVERT: C 152 MET cc_start: 0.7163 (mpp) cc_final: 0.6591 (mpp) REVERT: D 104 LEU cc_start: 0.5373 (tt) cc_final: 0.4362 (mp) REVERT: E 58 MET cc_start: 0.6503 (mmt) cc_final: 0.6293 (mmt) REVERT: E 125 MET cc_start: 0.7287 (ptt) cc_final: 0.7066 (ptp) REVERT: F 6 TRP cc_start: 0.7387 (m100) cc_final: 0.7131 (m100) REVERT: F 141 ARG cc_start: 0.9041 (ptm-80) cc_final: 0.8132 (ptm-80) REVERT: F 145 GLN cc_start: 0.8498 (pt0) cc_final: 0.7998 (pt0) REVERT: G 158 GLU cc_start: 0.7871 (tt0) cc_final: 0.7108 (mp0) REVERT: H 68 GLN cc_start: 0.8510 (mp10) cc_final: 0.8095 (mp10) REVERT: H 141 ARG cc_start: 0.9067 (ptm160) cc_final: 0.8604 (ttp-110) REVERT: I 58 MET cc_start: 0.6476 (mmt) cc_final: 0.6203 (mmt) REVERT: I 152 MET cc_start: 0.7443 (mpp) cc_final: 0.6912 (mpp) REVERT: J 237 MET cc_start: 0.8044 (ttp) cc_final: 0.7729 (ttp) REVERT: L 141 ARG cc_start: 0.8988 (ptm-80) cc_final: 0.8270 (ptm-80) REVERT: L 145 GLN cc_start: 0.8407 (pt0) cc_final: 0.7950 (pt0) REVERT: L 237 MET cc_start: 0.7868 (ttp) cc_final: 0.7631 (ttp) REVERT: M 158 GLU cc_start: 0.7810 (tt0) cc_final: 0.7313 (mp0) REVERT: N 6 TRP cc_start: 0.7319 (m100) cc_final: 0.7083 (m100) REVERT: N 129 GLN cc_start: 0.8292 (pp30) cc_final: 0.7980 (pp30) REVERT: N 141 ARG cc_start: 0.8987 (ptm160) cc_final: 0.8710 (ttp-110) REVERT: O 139 ASP cc_start: 0.7792 (p0) cc_final: 0.7454 (p0) REVERT: O 158 GLU cc_start: 0.8007 (tt0) cc_final: 0.7508 (mp0) REVERT: P 59 MET cc_start: 0.6194 (mmt) cc_final: 0.5716 (mmt) REVERT: P 68 GLN cc_start: 0.8396 (mp10) cc_final: 0.8098 (mp10) REVERT: S 152 MET cc_start: 0.7072 (mpp) cc_final: 0.6555 (mpp) REVERT: S 158 GLU cc_start: 0.7762 (tt0) cc_final: 0.6938 (mp0) REVERT: T 12 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8752 (m) REVERT: T 68 GLN cc_start: 0.8345 (mp10) cc_final: 0.8006 (mp10) REVERT: T 141 ARG cc_start: 0.8919 (ptm-80) cc_final: 0.8329 (ptm-80) REVERT: T 142 GLN cc_start: 0.8759 (mt0) cc_final: 0.8530 (mp10) REVERT: V 21 MET cc_start: 0.7978 (ptm) cc_final: 0.7623 (ptm) REVERT: V 139 ASP cc_start: 0.7959 (p0) cc_final: 0.7517 (p0) REVERT: V 152 MET cc_start: 0.7081 (mpp) cc_final: 0.6600 (mpp) REVERT: W 104 LEU cc_start: 0.5076 (tt) cc_final: 0.4266 (mp) REVERT: W 141 ARG cc_start: 0.8819 (ptm-80) cc_final: 0.8370 (ptm-80) REVERT: W 145 GLN cc_start: 0.8186 (pt0) cc_final: 0.7769 (pt0) outliers start: 76 outliers final: 42 residues processed: 564 average time/residue: 0.2789 time to fit residues: 247.6677 Evaluate side-chains 512 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 469 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain K residue 43 ASP Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 240 MET Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 159 VAL Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain W residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 310 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 345 optimal weight: 2.9990 chunk 408 optimal weight: 10.0000 chunk 359 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 384 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN B 145 GLN D 70 HIS H 42 HIS ** J 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN N 42 HIS N 76 ASN ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 145 GLN T 76 ASN ** W 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.223836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 129)---------------| | r_work = 0.4433 r_free = 0.4433 target = 0.146997 restraints weight = 42327.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.145402 restraints weight = 44442.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.145795 restraints weight = 38781.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.146358 restraints weight = 34601.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.146598 restraints weight = 33046.919| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 40216 Z= 0.237 Angle : 0.638 10.287 54307 Z= 0.346 Chirality : 0.046 0.164 5731 Planarity : 0.005 0.053 6864 Dihedral : 4.504 26.451 5280 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.06 % Allowed : 12.94 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.13), residues: 4796 helix: 0.55 (0.22), residues: 572 sheet: -1.86 (0.11), residues: 2321 loop : -0.40 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 222 TYR 0.016 0.002 TYR F 116 PHE 0.021 0.002 PHE D 217 TRP 0.034 0.002 TRP K 71 HIS 0.009 0.002 HIS N 13 Details of bonding type rmsd covalent geometry : bond 0.00513 (40216) covalent geometry : angle 0.63787 (54307) hydrogen bonds : bond 0.03312 ( 429) hydrogen bonds : angle 4.32671 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 491 time to evaluate : 1.574 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7111 (mpp) cc_final: 0.6254 (mpp) REVERT: A 216 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: B 235 TRP cc_start: 0.6483 (p-90) cc_final: 0.5943 (p-90) REVERT: C 151 MET cc_start: 0.6619 (pmm) cc_final: 0.6324 (pmm) REVERT: C 152 MET cc_start: 0.7242 (mpp) cc_final: 0.6809 (mpp) REVERT: C 175 LYS cc_start: 0.7934 (mttt) cc_final: 0.7721 (mttp) REVERT: E 125 MET cc_start: 0.7291 (ptt) cc_final: 0.7073 (ptp) REVERT: E 166 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8350 (tt) REVERT: F 141 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8330 (ptm-80) REVERT: G 154 MET cc_start: 0.7534 (ppp) cc_final: 0.7290 (ppp) REVERT: H 68 GLN cc_start: 0.8535 (mp10) cc_final: 0.8082 (mp10) REVERT: H 222 ARG cc_start: 0.6506 (mtm110) cc_final: 0.6261 (mtm110) REVERT: I 58 MET cc_start: 0.6729 (mmt) cc_final: 0.6442 (mmt) REVERT: I 139 ASP cc_start: 0.7626 (p0) cc_final: 0.7222 (p0) REVERT: I 152 MET cc_start: 0.7426 (mpp) cc_final: 0.7052 (mpp) REVERT: J 145 GLN cc_start: 0.8349 (pt0) cc_final: 0.8105 (pt0) REVERT: J 237 MET cc_start: 0.8021 (ttp) cc_final: 0.7677 (ttp) REVERT: L 141 ARG cc_start: 0.8898 (ptm-80) cc_final: 0.8202 (ptm-80) REVERT: M 158 GLU cc_start: 0.7882 (tt0) cc_final: 0.7291 (mp0) REVERT: N 104 LEU cc_start: 0.5422 (tt) cc_final: 0.4419 (mp) REVERT: N 129 GLN cc_start: 0.8346 (pp30) cc_final: 0.7916 (pp30) REVERT: N 141 ARG cc_start: 0.8841 (ptm160) cc_final: 0.8423 (ttp-110) REVERT: O 139 ASP cc_start: 0.7621 (p0) cc_final: 0.7243 (p0) REVERT: O 158 GLU cc_start: 0.8100 (tt0) cc_final: 0.7616 (mp0) REVERT: P 59 MET cc_start: 0.6265 (mmt) cc_final: 0.5757 (mmt) REVERT: P 68 GLN cc_start: 0.8534 (mp10) cc_final: 0.8306 (mp10) REVERT: R 141 ARG cc_start: 0.8990 (ptm160) cc_final: 0.8667 (ttp-110) REVERT: S 152 MET cc_start: 0.6939 (mpp) cc_final: 0.6614 (mpp) REVERT: S 158 GLU cc_start: 0.7842 (tt0) cc_final: 0.7017 (mp0) REVERT: S 175 LYS cc_start: 0.7945 (mttt) cc_final: 0.7738 (mttm) REVERT: T 12 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8785 (m) REVERT: T 141 ARG cc_start: 0.8795 (ptm-80) cc_final: 0.8250 (ptm-80) REVERT: V 21 MET cc_start: 0.8026 (ptm) cc_final: 0.7673 (ptm) REVERT: V 139 ASP cc_start: 0.7662 (p0) cc_final: 0.7246 (p0) REVERT: V 152 MET cc_start: 0.6844 (mpp) cc_final: 0.6579 (mpp) REVERT: W 141 ARG cc_start: 0.8661 (ptm-80) cc_final: 0.8344 (ptm-80) REVERT: W 145 GLN cc_start: 0.8323 (pt0) cc_final: 0.7687 (pt0) outliers start: 129 outliers final: 96 residues processed: 588 average time/residue: 0.2721 time to fit residues: 252.3273 Evaluate side-chains 560 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 460 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 141 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain K residue 43 ASP Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 240 MET Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 216 ASP Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain O residue 71 TRP Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 159 VAL Chi-restraints excluded: chain T residue 181 VAL Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 166 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 181 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 338 optimal weight: 0.7980 chunk 343 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 481 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 259 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 HIS B 76 ASN B 145 GLN D 70 HIS ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS H 76 ASN H 145 GLN J 42 HIS L 42 HIS ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN R 42 HIS R 145 GLN T 76 ASN W 42 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.219018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.4230 r_free = 0.4230 target = 0.135360 restraints weight = 42366.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.136060 restraints weight = 36173.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.136270 restraints weight = 30759.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.136219 restraints weight = 29031.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.136258 restraints weight = 29329.436| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 40216 Z= 0.227 Angle : 0.646 11.607 54307 Z= 0.348 Chirality : 0.046 0.188 5731 Planarity : 0.004 0.040 6864 Dihedral : 4.622 26.602 5280 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.49 % Allowed : 14.46 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.13), residues: 4796 helix: 0.48 (0.22), residues: 572 sheet: -2.24 (0.11), residues: 2321 loop : -0.48 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 22 TYR 0.017 0.002 TYR A 77 PHE 0.020 0.002 PHE J 217 TRP 0.032 0.002 TRP S 71 HIS 0.010 0.002 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00493 (40216) covalent geometry : angle 0.64647 (54307) hydrogen bonds : bond 0.03263 ( 429) hydrogen bonds : angle 4.54895 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 464 time to evaluate : 1.506 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8152 (ptm) cc_final: 0.7760 (ttp) REVERT: B 141 ARG cc_start: 0.9279 (ptm160) cc_final: 0.8929 (ptm-80) REVERT: B 145 GLN cc_start: 0.8889 (pt0) cc_final: 0.8530 (pt0) REVERT: B 235 TRP cc_start: 0.6665 (p-90) cc_final: 0.6031 (p-90) REVERT: C 22 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8386 (tpp-160) REVERT: C 118 ASP cc_start: 0.7729 (t70) cc_final: 0.7441 (m-30) REVERT: C 151 MET cc_start: 0.6930 (pmm) cc_final: 0.6522 (pmm) REVERT: C 152 MET cc_start: 0.7608 (mpp) cc_final: 0.7027 (mpp) REVERT: C 216 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: D 104 LEU cc_start: 0.5146 (tt) cc_final: 0.3882 (mp) REVERT: D 214 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8649 (p) REVERT: E 125 MET cc_start: 0.7469 (ptt) cc_final: 0.7171 (ptp) REVERT: E 248 SER cc_start: 0.8204 (t) cc_final: 0.7975 (p) REVERT: F 6 TRP cc_start: 0.7364 (m100) cc_final: 0.7044 (m100) REVERT: F 141 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8859 (ptm160) REVERT: H 68 GLN cc_start: 0.8533 (mp10) cc_final: 0.8249 (mp10) REVERT: H 141 ARG cc_start: 0.9266 (ptm160) cc_final: 0.8835 (ttp-110) REVERT: I 17 SER cc_start: 0.6806 (m) cc_final: 0.6441 (t) REVERT: I 58 MET cc_start: 0.6702 (mmt) cc_final: 0.6478 (mmt) REVERT: I 152 MET cc_start: 0.7836 (mpp) cc_final: 0.7213 (mpp) REVERT: J 141 ARG cc_start: 0.9385 (ptm160) cc_final: 0.8964 (ttp-110) REVERT: J 237 MET cc_start: 0.8138 (ttp) cc_final: 0.7737 (ttp) REVERT: M 118 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: N 129 GLN cc_start: 0.8315 (pp30) cc_final: 0.7794 (pp30) REVERT: N 141 ARG cc_start: 0.9245 (ptm160) cc_final: 0.8833 (ttp-110) REVERT: O 139 ASP cc_start: 0.7996 (p0) cc_final: 0.7640 (p0) REVERT: P 59 MET cc_start: 0.6015 (mmt) cc_final: 0.5584 (mmt) REVERT: P 68 GLN cc_start: 0.8553 (mp10) cc_final: 0.8261 (mp10) REVERT: S 152 MET cc_start: 0.7368 (mpp) cc_final: 0.7001 (mpp) REVERT: S 158 GLU cc_start: 0.7878 (tt0) cc_final: 0.6739 (mp0) REVERT: T 12 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8733 (m) REVERT: T 141 ARG cc_start: 0.9171 (ptm-80) cc_final: 0.8383 (ptm-80) REVERT: V 139 ASP cc_start: 0.8035 (p0) cc_final: 0.7660 (p0) REVERT: V 152 MET cc_start: 0.7407 (mpp) cc_final: 0.6989 (mpp) REVERT: W 133 ARG cc_start: 0.8180 (ptm160) cc_final: 0.7930 (ptm160) REVERT: W 141 ARG cc_start: 0.9125 (ptm-80) cc_final: 0.8465 (ptm-80) REVERT: W 145 GLN cc_start: 0.8840 (pt0) cc_final: 0.8047 (pt0) outliers start: 147 outliers final: 113 residues processed: 571 average time/residue: 0.2694 time to fit residues: 241.9593 Evaluate side-chains 560 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 441 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 TRP Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 71 TRP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 141 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain K residue 43 ASP Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 TRP Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 163 MET Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 71 TRP Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 240 MET Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain O residue 71 TRP Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 132 ASP Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 160 THR Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain S residue 135 CYS Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 159 VAL Chi-restraints excluded: chain T residue 181 VAL Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 166 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 160 THR Chi-restraints excluded: chain W residue 181 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 241 optimal weight: 6.9990 chunk 266 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 377 optimal weight: 3.9990 chunk 264 optimal weight: 5.9990 chunk 383 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 479 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 HIS H 145 GLN J 145 GLN K 73 HIS N 76 ASN R 76 ASN S 73 HIS ** T 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.200676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.122017 restraints weight = 41063.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.120667 restraints weight = 37821.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.121049 restraints weight = 32400.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.121488 restraints weight = 27443.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.121597 restraints weight = 26391.651| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 40216 Z= 0.287 Angle : 0.730 11.899 54307 Z= 0.400 Chirality : 0.048 0.227 5731 Planarity : 0.005 0.052 6864 Dihedral : 5.094 26.342 5280 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 4.25 % Allowed : 15.69 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.12), residues: 4796 helix: 0.40 (0.22), residues: 572 sheet: -2.79 (0.11), residues: 2321 loop : -0.67 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 141 TYR 0.020 0.003 TYR F 116 PHE 0.023 0.002 PHE J 217 TRP 0.041 0.003 TRP V 71 HIS 0.011 0.002 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00633 (40216) covalent geometry : angle 0.73017 (54307) hydrogen bonds : bond 0.03628 ( 429) hydrogen bonds : angle 4.81779 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 466 time to evaluate : 1.704 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.5605 (p90) REVERT: A 152 MET cc_start: 0.7567 (mpp) cc_final: 0.6778 (mpp) REVERT: A 216 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7801 (tp-100) REVERT: A 240 MET cc_start: 0.8032 (ptm) cc_final: 0.7670 (ttp) REVERT: B 141 ARG cc_start: 0.9233 (ptm160) cc_final: 0.8870 (ptm-80) REVERT: B 145 GLN cc_start: 0.8818 (pt0) cc_final: 0.8412 (pt0) REVERT: B 214 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8874 (p) REVERT: B 235 TRP cc_start: 0.6652 (p-90) cc_final: 0.6064 (p-90) REVERT: C 22 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8338 (tpp-160) REVERT: C 77 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.5526 (p90) REVERT: C 118 ASP cc_start: 0.7927 (t70) cc_final: 0.7676 (m-30) REVERT: C 151 MET cc_start: 0.6739 (pmm) cc_final: 0.6343 (pmm) REVERT: C 152 MET cc_start: 0.7574 (mpp) cc_final: 0.7039 (mpp) REVERT: C 216 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: D 214 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8769 (p) REVERT: E 17 SER cc_start: 0.7031 (m) cc_final: 0.6576 (t) REVERT: E 77 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.5496 (p90) REVERT: E 125 MET cc_start: 0.7524 (ptt) cc_final: 0.7209 (ptp) REVERT: F 141 ARG cc_start: 0.9243 (ptm-80) cc_final: 0.8982 (ptm160) REVERT: G 154 MET cc_start: 0.7641 (ppp) cc_final: 0.7348 (ppp) REVERT: H 13 HIS cc_start: 0.7576 (OUTLIER) cc_final: 0.6512 (p-80) REVERT: H 68 GLN cc_start: 0.8636 (mp10) cc_final: 0.8244 (mp10) REVERT: H 141 ARG cc_start: 0.9299 (ptm160) cc_final: 0.8863 (ttp-110) REVERT: I 17 SER cc_start: 0.6831 (m) cc_final: 0.6464 (t) REVERT: I 58 MET cc_start: 0.6819 (mmt) cc_final: 0.6589 (mmt) REVERT: J 70 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7509 (p90) REVERT: J 237 MET cc_start: 0.8258 (ttp) cc_final: 0.7843 (ttp) REVERT: K 17 SER cc_start: 0.7023 (m) cc_final: 0.6692 (t) REVERT: K 77 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.5593 (p90) REVERT: L 145 GLN cc_start: 0.8326 (mp10) cc_final: 0.8090 (mp10) REVERT: M 77 TYR cc_start: 0.6635 (OUTLIER) cc_final: 0.5433 (p90) REVERT: M 216 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: M 248 SER cc_start: 0.8332 (t) cc_final: 0.8079 (p) REVERT: N 104 LEU cc_start: 0.5021 (tt) cc_final: 0.3937 (mp) REVERT: N 129 GLN cc_start: 0.8431 (pp30) cc_final: 0.8206 (pp30) REVERT: N 141 ARG cc_start: 0.9289 (ptm160) cc_final: 0.8842 (ttp-110) REVERT: O 77 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.5784 (p90) REVERT: O 139 ASP cc_start: 0.7924 (p0) cc_final: 0.7570 (p0) REVERT: O 216 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7671 (tp-100) REVERT: P 59 MET cc_start: 0.6015 (mmt) cc_final: 0.5567 (mmt) REVERT: Q 152 MET cc_start: 0.7251 (mpp) cc_final: 0.6868 (mpp) REVERT: Q 216 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7719 (tp-100) REVERT: R 141 ARG cc_start: 0.9277 (ptm160) cc_final: 0.8858 (ttp-110) REVERT: S 152 MET cc_start: 0.7334 (mpp) cc_final: 0.7013 (mpp) REVERT: S 154 MET cc_start: 0.7498 (ppp) cc_final: 0.7283 (ppp) REVERT: T 141 ARG cc_start: 0.9118 (ptm-80) cc_final: 0.8410 (ptm-80) REVERT: T 175 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7854 (tm-30) REVERT: V 152 MET cc_start: 0.7336 (mpp) cc_final: 0.6956 (mpp) REVERT: V 216 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7794 (tp-100) REVERT: W 59 MET cc_start: 0.5946 (mmt) cc_final: 0.5362 (mmm) REVERT: W 133 ARG cc_start: 0.8169 (ptm160) cc_final: 0.7923 (ptm160) REVERT: W 141 ARG cc_start: 0.9147 (ptm-80) cc_final: 0.8643 (ptm-80) REVERT: W 145 GLN cc_start: 0.8751 (pt0) cc_final: 0.7931 (pt0) outliers start: 179 outliers final: 143 residues processed: 600 average time/residue: 0.2737 time to fit residues: 255.1871 Evaluate side-chains 610 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 450 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 TRP Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 71 TRP Chi-restraints excluded: chain E residue 77 TYR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 71 TRP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 71 TRP Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 43 ASP Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 TRP Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 162 ILE Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 163 MET Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 216 GLN Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 70 HIS Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 216 ASP Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain O residue 71 TRP Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 77 TYR Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 216 GLN Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 117 ASP Chi-restraints excluded: chain P residue 132 ASP Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 203 THR Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain Q residue 71 TRP Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain Q residue 216 GLN Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain S residue 71 TRP Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 135 CYS Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 159 VAL Chi-restraints excluded: chain T residue 160 THR Chi-restraints excluded: chain T residue 181 VAL Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain V residue 71 TRP Chi-restraints excluded: chain V residue 72 ASP Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 166 ILE Chi-restraints excluded: chain V residue 216 GLN Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 160 THR Chi-restraints excluded: chain W residue 181 VAL Chi-restraints excluded: chain W residue 216 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 19 optimal weight: 5.9990 chunk 478 optimal weight: 4.9990 chunk 305 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 287 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 243 optimal weight: 0.9980 chunk 473 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 HIS F 145 GLN H 76 ASN L 76 ASN N 76 ASN ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.201249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.120501 restraints weight = 40199.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.120748 restraints weight = 29933.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.120475 restraints weight = 26224.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.120917 restraints weight = 26290.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.121042 restraints weight = 24448.169| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 40216 Z= 0.217 Angle : 0.676 11.674 54307 Z= 0.362 Chirality : 0.046 0.236 5731 Planarity : 0.004 0.033 6864 Dihedral : 4.834 25.703 5280 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 4.13 % Allowed : 16.59 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.12), residues: 4796 helix: 0.30 (0.22), residues: 572 sheet: -2.82 (0.11), residues: 2310 loop : -0.72 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 22 TYR 0.019 0.002 TYR S 77 PHE 0.018 0.002 PHE P 71 TRP 0.042 0.002 TRP M 71 HIS 0.008 0.002 HIS N 13 Details of bonding type rmsd covalent geometry : bond 0.00477 (40216) covalent geometry : angle 0.67609 (54307) hydrogen bonds : bond 0.03450 ( 429) hydrogen bonds : angle 4.73652 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 451 time to evaluate : 1.616 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 216 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: A 240 MET cc_start: 0.7985 (ptm) cc_final: 0.7630 (ttp) REVERT: B 141 ARG cc_start: 0.9374 (ptm160) cc_final: 0.9062 (ptm-80) REVERT: B 145 GLN cc_start: 0.9061 (pt0) cc_final: 0.8650 (pt0) REVERT: B 214 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 235 TRP cc_start: 0.6597 (p-90) cc_final: 0.5943 (p-90) REVERT: C 22 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8582 (tpp-160) REVERT: C 77 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.5503 (p90) REVERT: C 151 MET cc_start: 0.7125 (pmm) cc_final: 0.6697 (pmm) REVERT: C 152 MET cc_start: 0.7791 (mpp) cc_final: 0.7152 (mpp) REVERT: C 216 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: C 248 SER cc_start: 0.8378 (t) cc_final: 0.8034 (p) REVERT: D 104 LEU cc_start: 0.4984 (tt) cc_final: 0.3751 (mp) REVERT: D 214 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8728 (p) REVERT: E 17 SER cc_start: 0.6809 (m) cc_final: 0.6348 (t) REVERT: E 125 MET cc_start: 0.7634 (ptt) cc_final: 0.7260 (ptp) REVERT: F 6 TRP cc_start: 0.7339 (m100) cc_final: 0.6948 (m100) REVERT: F 235 TRP cc_start: 0.7017 (p-90) cc_final: 0.6799 (p-90) REVERT: G 154 MET cc_start: 0.7999 (ppp) cc_final: 0.7701 (ppp) REVERT: H 13 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.6459 (p-80) REVERT: H 141 ARG cc_start: 0.9403 (ptm160) cc_final: 0.8776 (ttp-110) REVERT: I 17 SER cc_start: 0.6651 (m) cc_final: 0.6263 (t) REVERT: I 58 MET cc_start: 0.6624 (mmt) cc_final: 0.6201 (mmp) REVERT: I 77 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.5402 (p90) REVERT: K 17 SER cc_start: 0.6865 (m) cc_final: 0.6571 (t) REVERT: K 22 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8596 (tpp-160) REVERT: K 77 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.5526 (p90) REVERT: M 77 TYR cc_start: 0.6616 (OUTLIER) cc_final: 0.5436 (p90) REVERT: M 216 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: M 248 SER cc_start: 0.8376 (t) cc_final: 0.8094 (p) REVERT: N 129 GLN cc_start: 0.8343 (pp30) cc_final: 0.8119 (pp30) REVERT: N 141 ARG cc_start: 0.9482 (ptm160) cc_final: 0.9056 (ttp-110) REVERT: O 139 ASP cc_start: 0.8110 (p0) cc_final: 0.7767 (p0) REVERT: O 216 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7675 (tp-100) REVERT: P 59 MET cc_start: 0.5922 (mmt) cc_final: 0.5522 (mmt) REVERT: P 141 ARG cc_start: 0.9359 (ptm160) cc_final: 0.8910 (ttp-110) REVERT: Q 77 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.5433 (p90) REVERT: Q 152 MET cc_start: 0.7560 (mpp) cc_final: 0.7199 (mpp) REVERT: R 141 ARG cc_start: 0.9385 (ptm160) cc_final: 0.9037 (ttp-110) REVERT: R 142 GLN cc_start: 0.9308 (mp10) cc_final: 0.9036 (mp10) REVERT: S 77 TYR cc_start: 0.6501 (OUTLIER) cc_final: 0.5213 (p90) REVERT: S 125 MET cc_start: 0.7565 (ptt) cc_final: 0.7357 (ptp) REVERT: S 152 MET cc_start: 0.7578 (mpp) cc_final: 0.7241 (mpp) REVERT: S 248 SER cc_start: 0.8412 (t) cc_final: 0.8138 (p) REVERT: T 12 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8619 (m) REVERT: T 141 ARG cc_start: 0.9276 (ptm-80) cc_final: 0.8595 (ptm-80) REVERT: T 142 GLN cc_start: 0.9165 (mt0) cc_final: 0.8816 (mt0) REVERT: V 152 MET cc_start: 0.7564 (mpp) cc_final: 0.7106 (mpp) REVERT: W 59 MET cc_start: 0.5684 (mmt) cc_final: 0.5193 (mmm) REVERT: W 133 ARG cc_start: 0.8124 (ptm160) cc_final: 0.7874 (ptm160) REVERT: W 141 ARG cc_start: 0.9333 (ptm-80) cc_final: 0.8804 (ptm-80) REVERT: W 145 GLN cc_start: 0.9042 (pt0) cc_final: 0.8413 (pt0) outliers start: 174 outliers final: 133 residues processed: 581 average time/residue: 0.2787 time to fit residues: 252.3186 Evaluate side-chains 573 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 424 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 TRP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 TRP Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 71 TRP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 71 TRP Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 216 ASP Chi-restraints excluded: chain J residue 223 LEU Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 43 ASP Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 TRP Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 70 HIS Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 163 MET Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain M residue 216 GLN Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 216 ASP Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain O residue 71 TRP Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 216 GLN Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 132 ASP Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 160 THR Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 203 THR Chi-restraints excluded: chain P residue 223 LEU Chi-restraints excluded: chain Q residue 71 TRP Chi-restraints excluded: chain Q residue 77 TYR Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 216 ASP Chi-restraints excluded: chain S residue 71 TRP Chi-restraints excluded: chain S residue 77 TYR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 135 CYS Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 159 VAL Chi-restraints excluded: chain T residue 160 THR Chi-restraints excluded: chain T residue 181 VAL Chi-restraints excluded: chain T residue 216 ASP Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain V residue 71 TRP Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 166 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 140 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 160 THR Chi-restraints excluded: chain W residue 181 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 137 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 353 optimal weight: 0.0370 chunk 47 optimal weight: 10.0000 chunk 422 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 403 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 HIS ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 42 HIS ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.208520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.130499 restraints weight = 40920.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.130871 restraints weight = 29689.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.130479 restraints weight = 24731.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.130721 restraints weight = 23963.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.130789 restraints weight = 22875.593| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40216 Z= 0.144 Angle : 0.620 13.146 54307 Z= 0.323 Chirality : 0.045 0.204 5731 Planarity : 0.003 0.031 6864 Dihedral : 4.303 22.298 5280 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.35 % Allowed : 17.54 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.12), residues: 4796 helix: 0.24 (0.22), residues: 572 sheet: -2.71 (0.11), residues: 2321 loop : -0.61 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 22 TYR 0.019 0.002 TYR G 77 PHE 0.018 0.001 PHE D 71 TRP 0.036 0.002 TRP V 71 HIS 0.009 0.001 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00318 (40216) covalent geometry : angle 0.62026 (54307) hydrogen bonds : bond 0.03388 ( 429) hydrogen bonds : angle 4.68341 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 423 time to evaluate : 1.628 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 240 MET cc_start: 0.7995 (ptm) cc_final: 0.7618 (ttp) REVERT: B 141 ARG cc_start: 0.9297 (ptm160) cc_final: 0.8964 (ptm-80) REVERT: B 145 GLN cc_start: 0.8927 (pt0) cc_final: 0.8506 (pt0) REVERT: B 214 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8759 (p) REVERT: B 235 TRP cc_start: 0.6518 (p-90) cc_final: 0.5862 (p-90) REVERT: C 22 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8558 (tpp-160) REVERT: C 77 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.5471 (p90) REVERT: C 151 MET cc_start: 0.6968 (pmm) cc_final: 0.6527 (pmm) REVERT: C 152 MET cc_start: 0.7506 (mpp) cc_final: 0.6860 (mpp) REVERT: C 248 SER cc_start: 0.8345 (t) cc_final: 0.8048 (p) REVERT: D 214 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8547 (p) REVERT: E 17 SER cc_start: 0.6892 (m) cc_final: 0.6321 (t) REVERT: E 125 MET cc_start: 0.7568 (ptt) cc_final: 0.7223 (ptp) REVERT: F 6 TRP cc_start: 0.7355 (m100) cc_final: 0.7028 (m100) REVERT: H 13 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6427 (p-80) REVERT: H 141 ARG cc_start: 0.9331 (ptm160) cc_final: 0.8741 (ttp-110) REVERT: I 17 SER cc_start: 0.6674 (m) cc_final: 0.6252 (t) REVERT: I 58 MET cc_start: 0.6622 (mmt) cc_final: 0.6181 (mmp) REVERT: I 77 TYR cc_start: 0.6674 (OUTLIER) cc_final: 0.5326 (p90) REVERT: J 70 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7369 (p90) REVERT: K 22 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8562 (tpp-160) REVERT: K 71 TRP cc_start: 0.7619 (OUTLIER) cc_final: 0.7403 (t60) REVERT: L 6 TRP cc_start: 0.7106 (m100) cc_final: 0.6181 (m100) REVERT: M 77 TYR cc_start: 0.6460 (OUTLIER) cc_final: 0.5311 (p90) REVERT: M 248 SER cc_start: 0.8295 (t) cc_final: 0.8056 (p) REVERT: N 129 GLN cc_start: 0.8445 (pp30) cc_final: 0.7863 (pp30) REVERT: N 141 ARG cc_start: 0.9383 (ptm160) cc_final: 0.8951 (ttp-110) REVERT: O 77 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.5596 (p90) REVERT: O 216 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7621 (tp-100) REVERT: P 59 MET cc_start: 0.5841 (mmt) cc_final: 0.5462 (mmt) REVERT: P 68 GLN cc_start: 0.8587 (mp10) cc_final: 0.8279 (mp10) REVERT: P 141 ARG cc_start: 0.9240 (ptm160) cc_final: 0.8821 (ttp-110) REVERT: Q 77 TYR cc_start: 0.6665 (OUTLIER) cc_final: 0.5400 (p90) REVERT: Q 152 MET cc_start: 0.7412 (mpp) cc_final: 0.7062 (mpp) REVERT: R 141 ARG cc_start: 0.9238 (ptm160) cc_final: 0.8883 (ttp-110) REVERT: R 142 GLN cc_start: 0.9165 (mp10) cc_final: 0.8902 (mp10) REVERT: S 65 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8597 (pt) REVERT: S 152 MET cc_start: 0.7412 (mpp) cc_final: 0.7079 (mpp) REVERT: T 12 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8608 (m) REVERT: T 141 ARG cc_start: 0.9208 (ptm-80) cc_final: 0.8547 (ptm-80) REVERT: V 71 TRP cc_start: 0.7579 (OUTLIER) cc_final: 0.7289 (t60) REVERT: V 152 MET cc_start: 0.7395 (mpp) cc_final: 0.6995 (mpp) REVERT: W 59 MET cc_start: 0.5594 (mmt) cc_final: 0.5166 (mmm) REVERT: W 133 ARG cc_start: 0.8326 (ptm160) cc_final: 0.8044 (ptm160) REVERT: W 145 GLN cc_start: 0.9007 (pt0) cc_final: 0.8766 (pt0) outliers start: 141 outliers final: 111 residues processed: 532 average time/residue: 0.2751 time to fit residues: 229.8423 Evaluate side-chains 541 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 414 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 TRP Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 71 TRP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 71 TRP Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 43 ASP Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 TRP Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 70 HIS Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 163 MET Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 70 HIS Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain O residue 71 TRP Chi-restraints excluded: chain O residue 77 TYR Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 118 ASP Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 216 GLN Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 132 ASP Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 160 THR Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain Q residue 77 TYR Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain S residue 71 TRP Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 135 CYS Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 159 VAL Chi-restraints excluded: chain T residue 181 VAL Chi-restraints excluded: chain V residue 71 TRP Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 118 ASP Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 166 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 140 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 160 THR Chi-restraints excluded: chain W residue 181 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 391 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 374 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 352 optimal weight: 3.9990 chunk 330 optimal weight: 0.0050 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 HIS ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.204757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.121525 restraints weight = 40114.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.123910 restraints weight = 27988.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.123737 restraints weight = 22791.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.123762 restraints weight = 22393.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.123894 restraints weight = 22655.586| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 40216 Z= 0.185 Angle : 0.656 14.521 54307 Z= 0.347 Chirality : 0.046 0.244 5731 Planarity : 0.004 0.031 6864 Dihedral : 4.455 24.097 5280 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 3.63 % Allowed : 17.59 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.12), residues: 4796 helix: 0.37 (0.22), residues: 561 sheet: -2.83 (0.11), residues: 2321 loop : -0.66 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 141 TYR 0.019 0.002 TYR G 77 PHE 0.017 0.002 PHE P 71 TRP 0.042 0.002 TRP A 71 HIS 0.008 0.001 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00410 (40216) covalent geometry : angle 0.65576 (54307) hydrogen bonds : bond 0.03682 ( 429) hydrogen bonds : angle 4.78409 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 428 time to evaluate : 1.583 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 216 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: A 240 MET cc_start: 0.7967 (ptm) cc_final: 0.7602 (ttp) REVERT: B 141 ARG cc_start: 0.9339 (ptm160) cc_final: 0.8995 (ptm-80) REVERT: B 145 GLN cc_start: 0.9031 (pt0) cc_final: 0.8624 (pt0) REVERT: B 214 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8758 (p) REVERT: B 235 TRP cc_start: 0.6555 (p-90) cc_final: 0.5888 (p-90) REVERT: C 22 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8576 (tpp-160) REVERT: C 47 ASN cc_start: 0.7645 (t0) cc_final: 0.7417 (t0) REVERT: C 77 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.5449 (p90) REVERT: C 151 MET cc_start: 0.7183 (pmm) cc_final: 0.6666 (pmm) REVERT: C 152 MET cc_start: 0.7690 (mpp) cc_final: 0.6991 (mpp) REVERT: C 248 SER cc_start: 0.8389 (t) cc_final: 0.8102 (p) REVERT: D 214 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8657 (p) REVERT: E 17 SER cc_start: 0.6940 (m) cc_final: 0.6532 (t) REVERT: E 125 MET cc_start: 0.7634 (ptt) cc_final: 0.7255 (ptp) REVERT: F 6 TRP cc_start: 0.7297 (m100) cc_final: 0.6726 (m100) REVERT: F 141 ARG cc_start: 0.9448 (ptm-80) cc_final: 0.9224 (ptm160) REVERT: G 216 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7683 (tp-100) REVERT: H 13 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.6414 (p-80) REVERT: H 59 MET cc_start: 0.5709 (mmt) cc_final: 0.5494 (mmt) REVERT: H 141 ARG cc_start: 0.9404 (ptm160) cc_final: 0.8875 (ttp-110) REVERT: I 17 SER cc_start: 0.6705 (m) cc_final: 0.6297 (t) REVERT: I 58 MET cc_start: 0.6587 (mmt) cc_final: 0.6130 (mmp) REVERT: I 77 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.5369 (p90) REVERT: J 70 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7428 (p90) REVERT: K 17 SER cc_start: 0.6933 (m) cc_final: 0.6594 (t) REVERT: K 22 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8589 (tpp-160) REVERT: K 77 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.5445 (p90) REVERT: L 6 TRP cc_start: 0.7119 (m100) cc_final: 0.6291 (m100) REVERT: M 77 TYR cc_start: 0.6586 (OUTLIER) cc_final: 0.5338 (p90) REVERT: M 118 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: M 248 SER cc_start: 0.8344 (t) cc_final: 0.8082 (p) REVERT: N 129 GLN cc_start: 0.8336 (pp30) cc_final: 0.8116 (pp30) REVERT: N 141 ARG cc_start: 0.9456 (ptm160) cc_final: 0.9034 (ttp-110) REVERT: O 77 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.5550 (p90) REVERT: O 216 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7705 (tp-100) REVERT: P 59 MET cc_start: 0.5819 (mmt) cc_final: 0.5427 (mmt) REVERT: P 68 GLN cc_start: 0.8624 (mp10) cc_final: 0.8324 (mp10) REVERT: P 141 ARG cc_start: 0.9312 (ptm160) cc_final: 0.8890 (ttp-110) REVERT: Q 77 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.5378 (p90) REVERT: Q 152 MET cc_start: 0.7579 (mpp) cc_final: 0.7210 (mpp) REVERT: R 141 ARG cc_start: 0.9362 (ptm160) cc_final: 0.8992 (ttp-110) REVERT: R 142 GLN cc_start: 0.9254 (mp10) cc_final: 0.8918 (mp10) REVERT: S 65 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8608 (pt) REVERT: S 77 TYR cc_start: 0.6476 (OUTLIER) cc_final: 0.5194 (p90) REVERT: S 152 MET cc_start: 0.7514 (mpp) cc_final: 0.7168 (mpp) REVERT: S 248 SER cc_start: 0.8472 (t) cc_final: 0.8235 (p) REVERT: T 12 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8607 (m) REVERT: T 141 ARG cc_start: 0.9280 (ptm-80) cc_final: 0.8583 (ptm-80) REVERT: T 142 GLN cc_start: 0.9218 (mt0) cc_final: 0.8931 (mt0) REVERT: V 47 ASN cc_start: 0.7694 (t0) cc_final: 0.7438 (t0) REVERT: V 71 TRP cc_start: 0.7661 (OUTLIER) cc_final: 0.7333 (t60) REVERT: V 152 MET cc_start: 0.7515 (mpp) cc_final: 0.7099 (mpp) REVERT: W 141 ARG cc_start: 0.9349 (ptm-80) cc_final: 0.8900 (ttp-110) outliers start: 153 outliers final: 123 residues processed: 550 average time/residue: 0.2582 time to fit residues: 224.7825 Evaluate side-chains 565 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 422 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 216 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 71 TRP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 77 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 71 TRP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain G residue 65 ILE Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 216 GLN Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 71 TRP Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 70 HIS Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 142 GLN Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 43 ASP Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 70 HIS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 145 GLN Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 163 MET Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain M residue 162 ILE Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 70 HIS Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain O residue 71 TRP Chi-restraints excluded: chain O residue 77 TYR Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 162 ILE Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 216 GLN Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 132 ASP Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain P residue 159 VAL Chi-restraints excluded: chain P residue 160 THR Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain Q residue 77 TYR Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain S residue 71 TRP Chi-restraints excluded: chain S residue 77 TYR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 135 CYS Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 159 VAL Chi-restraints excluded: chain T residue 160 THR Chi-restraints excluded: chain T residue 181 VAL Chi-restraints excluded: chain T residue 223 LEU Chi-restraints excluded: chain V residue 71 TRP Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 118 ASP Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 166 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 70 HIS Chi-restraints excluded: chain W residue 140 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 160 THR Chi-restraints excluded: chain W residue 181 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 444 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 330 optimal weight: 0.6980 chunk 476 optimal weight: 8.9990 chunk 134 optimal weight: 0.7980 chunk 438 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 442 optimal weight: 1.9990 chunk 482 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 HIS ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 HIS L 76 ASN ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN W 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.207183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.127464 restraints weight = 40339.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.130324 restraints weight = 27498.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.130653 restraints weight = 20958.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.130472 restraints weight = 19758.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.130641 restraints weight = 20617.640| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 40216 Z= 0.119 Angle : 0.615 17.576 54307 Z= 0.318 Chirality : 0.045 0.255 5731 Planarity : 0.003 0.035 6864 Dihedral : 3.989 20.805 5280 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.82 % Allowed : 18.54 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.12), residues: 4796 helix: 0.26 (0.22), residues: 572 sheet: -2.63 (0.11), residues: 2354 loop : -0.50 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 141 TYR 0.018 0.002 TYR G 77 PHE 0.023 0.001 PHE D 71 TRP 0.036 0.002 TRP V 71 HIS 0.010 0.001 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00264 (40216) covalent geometry : angle 0.61499 (54307) hydrogen bonds : bond 0.03883 ( 429) hydrogen bonds : angle 4.74002 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9592 Ramachandran restraints generated. 4796 Oldfield, 0 Emsley, 4796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 435 time to evaluate : 1.170 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 240 MET cc_start: 0.7968 (ptm) cc_final: 0.7586 (ttp) REVERT: B 141 ARG cc_start: 0.9307 (ptm160) cc_final: 0.9067 (ptm-80) REVERT: B 142 GLN cc_start: 0.9308 (mp10) cc_final: 0.9082 (mp10) REVERT: B 145 GLN cc_start: 0.8940 (pt0) cc_final: 0.8550 (pt0) REVERT: B 235 TRP cc_start: 0.6531 (p-90) cc_final: 0.5859 (p-90) REVERT: C 22 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8552 (tpp-160) REVERT: C 151 MET cc_start: 0.7072 (pmm) cc_final: 0.6544 (pmm) REVERT: C 152 MET cc_start: 0.7529 (mpp) cc_final: 0.6775 (mpp) REVERT: C 248 SER cc_start: 0.8355 (t) cc_final: 0.8074 (p) REVERT: E 17 SER cc_start: 0.7009 (m) cc_final: 0.6535 (t) REVERT: E 125 MET cc_start: 0.7570 (ptt) cc_final: 0.7215 (ptp) REVERT: F 6 TRP cc_start: 0.7302 (m100) cc_final: 0.6974 (m100) REVERT: F 141 ARG cc_start: 0.9366 (ptm-80) cc_final: 0.9127 (ptm160) REVERT: H 13 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.6400 (p-80) REVERT: H 141 ARG cc_start: 0.9380 (ptm160) cc_final: 0.8884 (ttp-110) REVERT: I 17 SER cc_start: 0.6626 (m) cc_final: 0.6166 (t) REVERT: I 58 MET cc_start: 0.6546 (mmt) cc_final: 0.6104 (mmp) REVERT: J 68 GLN cc_start: 0.8566 (mp10) cc_final: 0.8346 (mp10) REVERT: J 141 ARG cc_start: 0.9292 (ptm160) cc_final: 0.8872 (ttp-110) REVERT: K 22 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8539 (tpp-160) REVERT: K 77 TYR cc_start: 0.6588 (OUTLIER) cc_final: 0.5402 (p90) REVERT: L 6 TRP cc_start: 0.7170 (m100) cc_final: 0.6349 (m100) REVERT: M 77 TYR cc_start: 0.6369 (OUTLIER) cc_final: 0.5223 (p90) REVERT: M 248 SER cc_start: 0.8295 (t) cc_final: 0.8076 (p) REVERT: N 129 GLN cc_start: 0.8387 (pp30) cc_final: 0.7950 (pp30) REVERT: N 141 ARG cc_start: 0.9395 (ptm160) cc_final: 0.8931 (ttp-110) REVERT: O 77 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.5654 (p90) REVERT: P 59 MET cc_start: 0.5782 (mmt) cc_final: 0.5439 (mmt) REVERT: P 68 GLN cc_start: 0.8533 (mp10) cc_final: 0.8158 (mp10) REVERT: P 141 ARG cc_start: 0.9271 (ptm160) cc_final: 0.9052 (ttp-110) REVERT: Q 77 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.5450 (p90) REVERT: Q 152 MET cc_start: 0.7452 (mpp) cc_final: 0.7108 (mpp) REVERT: R 141 ARG cc_start: 0.9289 (ptm160) cc_final: 0.8966 (ttp-110) REVERT: S 152 MET cc_start: 0.7461 (mpp) cc_final: 0.7128 (mpp) REVERT: S 248 SER cc_start: 0.8395 (t) cc_final: 0.8172 (p) REVERT: T 6 TRP cc_start: 0.7344 (m100) cc_final: 0.6752 (m100) REVERT: T 12 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8590 (m) REVERT: T 141 ARG cc_start: 0.9228 (ptm-80) cc_final: 0.8560 (ptm-80) REVERT: T 142 GLN cc_start: 0.9143 (mt0) cc_final: 0.8856 (mt0) REVERT: V 47 ASN cc_start: 0.7686 (t0) cc_final: 0.7451 (t0) REVERT: V 71 TRP cc_start: 0.7591 (OUTLIER) cc_final: 0.7343 (t60) REVERT: V 152 MET cc_start: 0.7319 (mpp) cc_final: 0.6934 (mpp) REVERT: W 133 ARG cc_start: 0.8370 (ptm160) cc_final: 0.8041 (ptm160) outliers start: 119 outliers final: 98 residues processed: 526 average time/residue: 0.2425 time to fit residues: 201.2240 Evaluate side-chains 526 residues out of total 4235 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 419 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 22 ARG Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 71 TRP Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 135 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain H residue 10 LYS Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 226 LEU Chi-restraints excluded: chain I residue 240 MET Chi-restraints excluded: chain J residue 63 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain K residue 22 ARG Chi-restraints excluded: chain K residue 77 TYR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 145 GLN Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 77 TYR Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 125 MET Chi-restraints excluded: chain M residue 135 CYS Chi-restraints excluded: chain M residue 166 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 CYS Chi-restraints excluded: chain N residue 70 HIS Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain O residue 71 TRP Chi-restraints excluded: chain O residue 77 TYR Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 135 CYS Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain P residue 132 ASP Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 145 GLN Chi-restraints excluded: chain P residue 160 THR Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain Q residue 77 TYR Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 135 CYS Chi-restraints excluded: chain S residue 166 ILE Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 135 LEU Chi-restraints excluded: chain T residue 140 VAL Chi-restraints excluded: chain T residue 159 VAL Chi-restraints excluded: chain T residue 160 THR Chi-restraints excluded: chain T residue 181 VAL Chi-restraints excluded: chain V residue 71 TRP Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 118 ASP Chi-restraints excluded: chain V residue 166 ILE Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 140 VAL Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 160 THR Chi-restraints excluded: chain W residue 181 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 57 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 403 optimal weight: 0.7980 chunk 472 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 418 optimal weight: 0.9980 chunk 373 optimal weight: 10.0000 chunk 478 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 HIS ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.204364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.125327 restraints weight = 40546.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.126306 restraints weight = 28675.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.126420 restraints weight = 23159.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.126880 restraints weight = 22673.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.126955 restraints weight = 21672.125| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40216 Z= 0.144 Angle : 0.626 19.028 54307 Z= 0.328 Chirality : 0.045 0.219 5731 Planarity : 0.003 0.031 6864 Dihedral : 4.005 20.939 5280 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.06 % Allowed : 18.54 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.51 (0.12), residues: 4796 helix: 0.28 (0.22), residues: 572 sheet: -2.65 (0.11), residues: 2354 loop : -0.50 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 141 TYR 0.018 0.002 TYR G 77 PHE 0.022 0.001 PHE D 71 TRP 0.036 0.002 TRP V 71 HIS 0.006 0.001 HIS D 70 Details of bonding type rmsd covalent geometry : bond 0.00320 (40216) covalent geometry : angle 0.62622 (54307) hydrogen bonds : bond 0.04178 ( 429) hydrogen bonds : angle 4.83513 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9143.22 seconds wall clock time: 158 minutes 7.58 seconds (9487.58 seconds total)