Starting phenix.real_space_refine on Fri Dec 27 10:58:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gtn_34258/12_2024/8gtn_34258.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gtn_34258/12_2024/8gtn_34258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gtn_34258/12_2024/8gtn_34258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gtn_34258/12_2024/8gtn_34258.map" model { file = "/net/cci-nas-00/data/ceres_data/8gtn_34258/12_2024/8gtn_34258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gtn_34258/12_2024/8gtn_34258.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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 189 5.16 5 C 30753 2.51 5 N 8559 2.21 5 O 8802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 48303 Number of models: 1 Model: "" Number of chains: 1 Chain: "AA" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: BA, A, C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T, W, V, Y, X, Z Time building chain proxies: 7.74, per 1000 atoms: 0.16 Number of scatterers: 48303 At special positions: 0 Unit cell: (288.36, 288.36, 72.36, 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 189 16.00 O 8802 8.00 N 8559 7.00 C 30753 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: 9.43 Conformation dependent library (CDL) restraints added in 4.9 seconds 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11070 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 1 sheets defined 17.5% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 Processing helix chain 'A' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG A 35 " --> pdb=" O ASP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU A 62 " --> pdb=" O MET A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 59 through 62' Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG B 35 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 62 removed outlier: 3.710A pdb=" N LEU B 62 " --> pdb=" O MET B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 59 through 62' Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'C' and resid 3 through 17 Processing helix chain 'C' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG C 35 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU C 62 " --> pdb=" O MET C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 59 through 62' Processing helix chain 'C' and resid 126 through 133 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'D' and resid 3 through 17 Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG D 35 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU D 62 " --> pdb=" O MET D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 126 through 133 Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'E' and resid 3 through 17 Processing helix chain 'E' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG E 35 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU E 62 " --> pdb=" O MET E 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 59 through 62' Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'F' and resid 3 through 17 Processing helix chain 'F' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG F 35 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU F 62 " --> pdb=" O MET F 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 59 through 62' Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 143 through 148 Processing helix chain 'G' and resid 3 through 17 Processing helix chain 'G' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG G 35 " --> pdb=" O ASP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU G 62 " --> pdb=" O MET G 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 59 through 62' Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 143 through 148 Processing helix chain 'H' and resid 3 through 17 Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG H 35 " --> pdb=" O ASP H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU H 62 " --> pdb=" O MET H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 59 through 62' Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 143 through 148 Processing helix chain 'I' and resid 3 through 17 Processing helix chain 'I' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG I 35 " --> pdb=" O ASP I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU I 62 " --> pdb=" O MET I 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 59 through 62' Processing helix chain 'I' and resid 126 through 133 Processing helix chain 'I' and resid 143 through 148 Processing helix chain 'J' and resid 3 through 17 Processing helix chain 'J' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG J 35 " --> pdb=" O ASP J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU J 62 " --> pdb=" O MET J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 143 through 148 Processing helix chain 'K' and resid 3 through 17 Processing helix chain 'K' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG K 35 " --> pdb=" O ASP K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU K 62 " --> pdb=" O MET K 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 59 through 62' Processing helix chain 'K' and resid 126 through 133 Processing helix chain 'K' and resid 143 through 148 Processing helix chain 'L' and resid 3 through 17 Processing helix chain 'L' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG L 35 " --> pdb=" O ASP L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU L 62 " --> pdb=" O MET L 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 59 through 62' Processing helix chain 'L' and resid 126 through 133 Processing helix chain 'L' and resid 143 through 148 Processing helix chain 'M' and resid 3 through 17 Processing helix chain 'M' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG M 35 " --> pdb=" O ASP M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 62 removed outlier: 3.710A pdb=" N LEU M 62 " --> pdb=" O MET M 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 59 through 62' Processing helix chain 'M' and resid 126 through 133 Processing helix chain 'M' and resid 143 through 148 Processing helix chain 'N' and resid 3 through 17 Processing helix chain 'N' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG N 35 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU N 62 " --> pdb=" O MET N 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 59 through 62' Processing helix chain 'N' and resid 126 through 133 Processing helix chain 'N' and resid 143 through 148 Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG O 35 " --> pdb=" O ASP O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU O 62 " --> pdb=" O MET O 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 59 through 62' Processing helix chain 'O' and resid 126 through 133 Processing helix chain 'O' and resid 143 through 148 Processing helix chain 'P' and resid 3 through 17 Processing helix chain 'P' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG P 35 " --> pdb=" O ASP P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 62 removed outlier: 3.710A pdb=" N LEU P 62 " --> pdb=" O MET P 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 59 through 62' Processing helix chain 'P' and resid 126 through 133 Processing helix chain 'P' and resid 143 through 148 Processing helix chain 'Q' and resid 3 through 17 Processing helix chain 'Q' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG Q 35 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU Q 62 " --> pdb=" O MET Q 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 59 through 62' Processing helix chain 'Q' and resid 126 through 133 Processing helix chain 'Q' and resid 143 through 148 Processing helix chain 'R' and resid 3 through 17 Processing helix chain 'R' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG R 35 " --> pdb=" O ASP R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU R 62 " --> pdb=" O MET R 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 59 through 62' Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 143 through 148 Processing helix chain 'S' and resid 3 through 17 Processing helix chain 'S' and resid 31 through 35 removed outlier: 3.595A pdb=" N ARG S 35 " --> pdb=" O ASP S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 62 removed outlier: 3.710A pdb=" N LEU S 62 " --> pdb=" O MET S 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 59 through 62' Processing helix chain 'S' and resid 126 through 133 Processing helix chain 'S' and resid 143 through 148 Processing helix chain 'T' and resid 3 through 17 Processing helix chain 'T' and resid 31 through 35 removed outlier: 3.593A pdb=" N ARG T 35 " --> pdb=" O ASP T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU T 62 " --> pdb=" O MET T 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 59 through 62' Processing helix chain 'T' and resid 126 through 133 Processing helix chain 'T' and resid 143 through 148 Processing helix chain 'V' and resid 3 through 17 Processing helix chain 'V' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG V 35 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU V 62 " --> pdb=" O MET V 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 59 through 62' Processing helix chain 'V' and resid 126 through 133 Processing helix chain 'V' and resid 143 through 148 Processing helix chain 'W' and resid 3 through 17 Processing helix chain 'W' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG W 35 " --> pdb=" O ASP W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU W 62 " --> pdb=" O MET W 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 59 through 62' Processing helix chain 'W' and resid 126 through 133 Processing helix chain 'W' and resid 143 through 148 Processing helix chain 'X' and resid 3 through 17 Processing helix chain 'X' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG X 35 " --> pdb=" O ASP X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU X 62 " --> pdb=" O MET X 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 59 through 62' Processing helix chain 'X' and resid 126 through 133 Processing helix chain 'X' and resid 143 through 148 Processing helix chain 'Y' and resid 3 through 17 Processing helix chain 'Y' and resid 31 through 35 removed outlier: 3.593A pdb=" N ARG Y 35 " --> pdb=" O ASP Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU Y 62 " --> pdb=" O MET Y 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 59 through 62' Processing helix chain 'Y' and resid 126 through 133 Processing helix chain 'Y' and resid 143 through 148 Processing helix chain 'Z' and resid 3 through 17 Processing helix chain 'Z' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU Z 62 " --> pdb=" O MET Z 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 59 through 62' Processing helix chain 'Z' and resid 126 through 133 Processing helix chain 'Z' and resid 143 through 148 Processing helix chain 'AA' and resid 3 through 17 Processing helix chain 'AA' and resid 31 through 35 removed outlier: 3.593A pdb=" N ARGAA 35 " --> pdb=" O ASPAA 32 " (cutoff:3.500A) Processing helix chain 'AA' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEUAA 62 " --> pdb=" O METAA 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 59 through 62' Processing helix chain 'AA' and resid 126 through 133 Processing helix chain 'AA' and resid 143 through 148 Processing helix chain 'BA' and resid 3 through 17 Processing helix chain 'BA' and resid 31 through 35 removed outlier: 3.595A pdb=" N ARGBA 35 " --> pdb=" O ASPBA 32 " (cutoff:3.500A) Processing helix chain 'BA' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEUBA 62 " --> pdb=" O METBA 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'BA' and resid 59 through 62' Processing helix chain 'BA' and resid 126 through 133 Processing helix chain 'BA' and resid 143 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 23 through 24 current: chain 'A' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 49 through 57 current: chain 'A' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 155 through 164 current: chain 'A' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 186 through 199 current: chain 'A' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 221 through 223 current: chain 'B' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 49 through 57 current: chain 'B' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 155 through 164 current: chain 'B' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 186 through 199 current: chain 'B' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 221 through 223 current: chain 'C' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 49 through 57 current: chain 'C' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 155 through 164 current: chain 'C' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 186 through 199 current: chain 'C' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 221 through 223 current: chain 'D' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 49 through 57 current: chain 'D' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 155 through 164 current: chain 'D' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 186 through 199 current: chain 'D' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 221 through 223 current: chain 'E' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 49 through 57 current: chain 'E' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 155 through 164 current: chain 'E' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 186 through 199 current: chain 'E' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 221 through 223 current: chain 'F' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 49 through 57 current: chain 'F' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 155 through 164 current: chain 'F' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 186 through 199 current: chain 'F' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 221 through 223 current: chain 'G' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 49 through 57 current: chain 'G' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 155 through 164 current: chain 'G' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 186 through 199 current: chain 'G' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 221 through 223 current: chain 'H' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 49 through 57 current: chain 'H' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 155 through 164 current: chain 'H' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 186 through 199 current: chain 'H' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 221 through 223 current: chain 'I' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 49 through 57 current: chain 'I' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 155 through 164 current: chain 'I' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 186 through 199 current: chain 'I' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 221 through 223 current: chain 'J' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 49 through 57 current: chain 'J' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 155 through 164 current: chain 'J' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 186 through 199 current: chain 'J' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 221 through 223 current: chain 'K' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 49 through 57 current: chain 'K' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 155 through 164 current: chain 'K' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 186 through 199 current: chain 'K' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 221 through 223 current: chain 'L' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 49 through 57 current: chain 'L' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 155 through 164 current: chain 'L' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 186 through 199 current: chain 'L' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 221 through 223 current: chain 'M' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 49 through 57 current: chain 'M' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 155 through 164 current: chain 'M' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 186 through 199 current: chain 'M' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 221 through 223 current: chain 'N' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 49 through 57 current: chain 'N' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 155 through 164 current: chain 'N' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 186 through 199 current: chain 'N' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 221 through 223 current: chain 'O' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 49 through 57 current: chain 'O' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 155 through 164 current: chain 'O' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 186 through 199 current: chain 'O' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 221 through 223 current: chain 'P' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 49 through 57 current: chain 'P' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 155 through 164 current: chain 'P' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 186 through 199 current: chain 'P' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 221 through 223 current: chain 'Q' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 49 through 57 current: chain 'Q' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 155 through 164 current: chain 'Q' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 186 through 199 current: chain 'Q' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 221 through 223 current: chain 'R' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 49 through 57 current: chain 'R' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 155 through 164 current: chain 'R' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 186 through 199 current: chain 'R' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 221 through 223 current: chain 'S' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 49 through 57 current: chain 'S' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 155 through 164 current: chain 'S' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 186 through 199 current: chain 'S' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 221 through 223 current: chain 'T' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 49 through 57 current: chain 'T' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 155 through 164 current: chain 'T' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 186 through 199 current: chain 'T' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 221 through 223 current: chain 'V' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 49 through 57 current: chain 'V' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 155 through 164 current: chain 'V' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 186 through 199 current: chain 'V' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 221 through 223 current: chain 'W' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 49 through 57 current: chain 'W' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 155 through 164 current: chain 'W' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 186 through 199 current: chain 'W' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 221 through 223 current: chain 'X' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 49 through 57 current: chain 'X' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 155 through 164 current: chain 'X' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 186 through 199 current: chain 'X' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 221 through 223 current: chain 'Y' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 49 through 57 current: chain 'Y' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 155 through 164 current: chain 'Y' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 186 through 199 current: chain 'Y' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 221 through 223 current: chain 'Z' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 49 through 57 current: chain 'Z' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 155 through 164 current: chain 'Z' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 186 through 199 current: chain 'Z' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 221 through 223 current: chain 'AA' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'AA' and resid 49 through 57 current: chain 'AA' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'AA' and resid 155 through 164 current: chain 'AA' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'AA' and resid 186 through 199 current: chain 'AA' and resid 221 through 223 WARNING: can't find start of bonding for strands! previous: chain 'AA' and resid 221 through 223 current: chain 'BA' and resid 49 through 57 WARNING: can't find start of bonding for strands! previous: chain 'BA' and resid 49 through 57 current: chain 'BA' and resid 104 through 124 WARNING: can't find start of bonding for strands! previous: chain 'BA' and resid 155 through 164 current: chain 'BA' and resid 186 through 199 WARNING: can't find start of bonding for strands! previous: chain 'BA' and resid 186 through 199 current: chain 'BA' and resid 221 through 223 594 hydrogen bonds defined for protein. 1701 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: 11.91 Time building geometry restraints manager: 11.04 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: 15795 1.34 - 1.46: 10574 1.46 - 1.58: 22528 1.58 - 1.69: 0 1.69 - 1.81: 324 Bond restraints: 49221 Sorted by residual: bond pdb=" N LEU H 100 " pdb=" CA LEU H 100 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.30e-02 5.92e+03 5.71e+00 bond pdb=" N LEU D 100 " pdb=" CA LEU D 100 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.30e-02 5.92e+03 5.64e+00 bond pdb=" N LEUBA 100 " pdb=" CA LEUBA 100 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.30e-02 5.92e+03 5.56e+00 bond pdb=" N LEU T 100 " pdb=" CA LEU T 100 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.30e-02 5.92e+03 5.52e+00 bond pdb=" N LEUAA 100 " pdb=" CA LEUAA 100 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.30e-02 5.92e+03 5.51e+00 ... (remaining 49216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 62938 1.13 - 2.26: 2593 2.26 - 3.38: 457 3.38 - 4.51: 27 4.51 - 5.64: 27 Bond angle restraints: 66042 Sorted by residual: angle pdb=" C LEU E 100 " pdb=" N PRO E 101 " pdb=" CA PRO E 101 " ideal model delta sigma weight residual 119.82 122.51 -2.69 9.80e-01 1.04e+00 7.53e+00 angle pdb=" C LEU V 100 " pdb=" N PRO V 101 " pdb=" CA PRO V 101 " ideal model delta sigma weight residual 119.82 122.51 -2.69 9.80e-01 1.04e+00 7.53e+00 angle pdb=" C LEU W 100 " pdb=" N PRO W 101 " pdb=" CA PRO W 101 " ideal model delta sigma weight residual 119.82 122.50 -2.68 9.80e-01 1.04e+00 7.51e+00 angle pdb=" C LEU S 100 " pdb=" N PRO S 101 " pdb=" CA PRO S 101 " ideal model delta sigma weight residual 119.82 122.50 -2.68 9.80e-01 1.04e+00 7.48e+00 angle pdb=" C LEU D 100 " pdb=" N PRO D 101 " pdb=" CA PRO D 101 " ideal model delta sigma weight residual 119.82 122.50 -2.68 9.80e-01 1.04e+00 7.47e+00 ... (remaining 66037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.39: 26002 11.39 - 22.78: 2732 22.78 - 34.17: 777 34.17 - 45.56: 189 45.56 - 56.95: 216 Dihedral angle restraints: 29916 sinusoidal: 12879 harmonic: 17037 Sorted by residual: dihedral pdb=" N ARG E 10 " pdb=" CA ARG E 10 " pdb=" CB ARG E 10 " pdb=" CG ARG E 10 " ideal model delta sinusoidal sigma weight residual -60.00 -116.95 56.95 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N ARG X 10 " pdb=" CA ARG X 10 " pdb=" CB ARG X 10 " pdb=" CG ARG X 10 " ideal model delta sinusoidal sigma weight residual -60.00 -116.94 56.94 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N ARG V 10 " pdb=" CA ARG V 10 " pdb=" CB ARG V 10 " pdb=" CG ARG V 10 " ideal model delta sinusoidal sigma weight residual -60.00 -116.94 56.94 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 29913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 5111 0.040 - 0.080: 1604 0.080 - 0.120: 469 0.120 - 0.160: 79 0.160 - 0.200: 27 Chirality restraints: 7290 Sorted by residual: chirality pdb=" CA LEU P 100 " pdb=" N LEU P 100 " pdb=" C LEU P 100 " pdb=" CB LEU P 100 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA LEU S 100 " pdb=" N LEU S 100 " pdb=" C LEU S 100 " pdb=" CB LEU S 100 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA LEU Z 100 " pdb=" N LEU Z 100 " pdb=" C LEU Z 100 " pdb=" CB LEU Z 100 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.92e-01 ... (remaining 7287 not shown) Planarity restraints: 8397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 200 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO H 201 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 201 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 201 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 200 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO F 201 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO F 201 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 201 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PROAA 200 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PROAA 201 " -0.058 5.00e-02 4.00e+02 pdb=" CA PROAA 201 " 0.017 5.00e-02 4.00e+02 pdb=" CD PROAA 201 " 0.018 5.00e-02 4.00e+02 ... (remaining 8394 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5060 2.75 - 3.28: 48900 3.28 - 3.82: 79628 3.82 - 4.36: 97976 4.36 - 4.90: 168104 Nonbonded interactions: 399668 Sorted by model distance: nonbonded pdb=" O LEU R 212 " pdb=" OG SER R 230 " model vdw 2.208 3.040 nonbonded pdb=" O LEU X 212 " pdb=" OG SER X 230 " model vdw 2.208 3.040 nonbonded pdb=" O LEU C 212 " pdb=" OG SER C 230 " model vdw 2.208 3.040 nonbonded pdb=" O LEU Q 212 " pdb=" OG SER Q 230 " model vdw 2.208 3.040 nonbonded pdb=" O LEU H 212 " pdb=" OG SER H 230 " model vdw 2.208 3.040 ... (remaining 399663 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.420 Check model and map are aligned: 0.260 Set scattering table: 0.340 Process input model: 64.620 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.260 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:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 49221 Z= 0.209 Angle : 0.539 5.638 66042 Z= 0.308 Chirality : 0.043 0.200 7290 Planarity : 0.003 0.033 8397 Dihedral : 11.930 56.945 18846 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.50 % Allowed : 11.50 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.11), residues: 5751 helix: -1.14 (0.18), residues: 756 sheet: -1.79 (0.09), residues: 2538 loop : -0.51 (0.14), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 179 HIS 0.003 0.001 HISBA 186 PHE 0.012 0.001 PHE I 178 TYR 0.013 0.002 TYR L 176 ARG 0.002 0.000 ARG Q 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 872 time to evaluate : 4.512 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 111 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: B 16 MET cc_start: 0.8121 (mmp) cc_final: 0.7861 (mmp) REVERT: B 187 LEU cc_start: 0.8826 (tt) cc_final: 0.8585 (mp) REVERT: C 170 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 178 PHE cc_start: 0.7381 (p90) cc_final: 0.6973 (p90) REVERT: C 189 TYR cc_start: 0.7466 (t80) cc_final: 0.7248 (t80) REVERT: D 16 MET cc_start: 0.8303 (mmp) cc_final: 0.8064 (mmt) REVERT: D 129 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: D 178 PHE cc_start: 0.7427 (p90) cc_final: 0.6946 (p90) REVERT: D 189 TYR cc_start: 0.7320 (t80) cc_final: 0.6945 (t80) REVERT: E 16 MET cc_start: 0.8019 (mmp) cc_final: 0.7438 (mmt) REVERT: E 129 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: E 179 TRP cc_start: 0.6790 (p90) cc_final: 0.6585 (p-90) REVERT: F 16 MET cc_start: 0.8407 (mmp) cc_final: 0.7848 (mmt) REVERT: G 16 MET cc_start: 0.8268 (mmp) cc_final: 0.7787 (mmt) REVERT: G 22 MET cc_start: 0.8509 (mtt) cc_final: 0.8073 (ttm) REVERT: G 129 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: G 178 PHE cc_start: 0.7605 (p90) cc_final: 0.7264 (p90) REVERT: G 179 TRP cc_start: 0.6732 (p90) cc_final: 0.6513 (p-90) REVERT: G 189 TYR cc_start: 0.7540 (t80) cc_final: 0.7299 (t80) REVERT: H 16 MET cc_start: 0.8049 (mmp) cc_final: 0.7634 (mmt) REVERT: I 16 MET cc_start: 0.8349 (mmp) cc_final: 0.7867 (mmp) REVERT: I 111 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: K 146 PHE cc_start: 0.6292 (t80) cc_final: 0.6054 (t80) REVERT: L 110 PHE cc_start: 0.6935 (m-80) cc_final: 0.6723 (m-80) REVERT: L 129 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: M 16 MET cc_start: 0.8353 (mmp) cc_final: 0.7959 (mmp) REVERT: M 129 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: M 178 PHE cc_start: 0.7419 (p90) cc_final: 0.7193 (p90) REVERT: N 16 MET cc_start: 0.7854 (mmp) cc_final: 0.7413 (mmt) REVERT: N 110 PHE cc_start: 0.6721 (m-80) cc_final: 0.6491 (m-80) REVERT: N 129 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: N 187 LEU cc_start: 0.8777 (tt) cc_final: 0.8430 (mp) REVERT: O 16 MET cc_start: 0.7990 (mmp) cc_final: 0.7587 (mmt) REVERT: O 96 LEU cc_start: 0.8255 (pp) cc_final: 0.7924 (tt) REVERT: O 129 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: O 179 TRP cc_start: 0.6692 (p90) cc_final: 0.6468 (p-90) REVERT: P 60 ASP cc_start: 0.6724 (m-30) cc_final: 0.6494 (m-30) REVERT: P 129 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: Q 122 GLU cc_start: 0.7901 (tt0) cc_final: 0.7620 (pp20) REVERT: Q 129 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: R 16 MET cc_start: 0.8161 (mmp) cc_final: 0.7687 (mmp) REVERT: R 179 TRP cc_start: 0.6802 (p90) cc_final: 0.6570 (p-90) REVERT: S 16 MET cc_start: 0.8111 (mmp) cc_final: 0.7843 (mmt) REVERT: S 22 MET cc_start: 0.8420 (mtt) cc_final: 0.7975 (ttm) REVERT: T 16 MET cc_start: 0.8157 (mmp) cc_final: 0.7882 (mmp) REVERT: T 129 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: V 16 MET cc_start: 0.8000 (mmp) cc_final: 0.7527 (mmp) REVERT: V 129 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: V 178 PHE cc_start: 0.7504 (p90) cc_final: 0.7291 (p90) REVERT: W 16 MET cc_start: 0.8148 (mmp) cc_final: 0.7797 (mmp) REVERT: W 178 PHE cc_start: 0.7542 (p90) cc_final: 0.7118 (p90) REVERT: W 189 TYR cc_start: 0.7465 (t80) cc_final: 0.7011 (t80) REVERT: X 16 MET cc_start: 0.8044 (mmp) cc_final: 0.7656 (mmt) REVERT: X 111 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: X 129 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: X 146 PHE cc_start: 0.6296 (t80) cc_final: 0.6072 (t80) REVERT: Y 16 MET cc_start: 0.8408 (mmp) cc_final: 0.7935 (mmt) REVERT: Y 111 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: Y 178 PHE cc_start: 0.7408 (p90) cc_final: 0.6910 (p90) REVERT: Y 189 TYR cc_start: 0.7484 (t80) cc_final: 0.7065 (t80) REVERT: Z 8 ILE cc_start: 0.8858 (tp) cc_final: 0.8644 (tp) REVERT: Z 96 LEU cc_start: 0.8121 (pp) cc_final: 0.7888 (tt) REVERT: Z 178 PHE cc_start: 0.7413 (p90) cc_final: 0.7082 (p90) REVERT: AA 16 MET cc_start: 0.8290 (mmp) cc_final: 0.7943 (mmt) REVERT: AA 22 MET cc_start: 0.8437 (mtt) cc_final: 0.8227 (ttm) REVERT: AA 129 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: BA 178 PHE cc_start: 0.7407 (p90) cc_final: 0.7041 (p90) outliers start: 81 outliers final: 17 residues processed: 953 average time/residue: 0.4596 time to fit residues: 732.1435 Evaluate side-chains 531 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 496 time to evaluate : 4.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain E residue 129 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 129 TYR Chi-restraints excluded: chain J residue 129 TYR Chi-restraints excluded: chain K residue 129 TYR Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain M residue 129 TYR Chi-restraints excluded: chain N residue 129 TYR Chi-restraints excluded: chain O residue 129 TYR Chi-restraints excluded: chain P residue 129 TYR Chi-restraints excluded: chain Q residue 129 TYR Chi-restraints excluded: chain R residue 129 TYR Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 129 TYR Chi-restraints excluded: chain T residue 129 TYR Chi-restraints excluded: chain V residue 129 TYR Chi-restraints excluded: chain W residue 129 TYR Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 129 TYR Chi-restraints excluded: chain Y residue 111 GLN Chi-restraints excluded: chain Y residue 129 TYR Chi-restraints excluded: chain Z residue 129 TYR Chi-restraints excluded: chain AA residue 129 TYR Chi-restraints excluded: chain BA residue 129 TYR Chi-restraints excluded: chain BA residue 170 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 478 optimal weight: 10.0000 chunk 429 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 289 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 444 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 270 optimal weight: 0.1980 chunk 330 optimal weight: 0.9990 chunk 514 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 HIS ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 HIS ** J 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 GLN N 175 GLN N 186 HIS ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 GLN O 175 GLN ** O 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 186 HIS ** Q 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 175 GLN T 186 HIS ** T 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 111 GLN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 175 GLN ** V 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 186 HIS ** X 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN Y 186 HIS ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 49221 Z= 0.187 Angle : 0.566 8.034 66042 Z= 0.287 Chirality : 0.043 0.164 7290 Planarity : 0.004 0.032 8397 Dihedral : 5.481 49.956 6500 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.26 % Allowed : 14.54 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.11), residues: 5751 helix: -0.23 (0.20), residues: 594 sheet: -1.79 (0.10), residues: 2376 loop : -0.41 (0.13), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP M 179 HIS 0.003 0.001 HIS B 223 PHE 0.023 0.002 PHE K 47 TYR 0.014 0.001 TYR M 189 ARG 0.003 0.000 ARG N 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 621 time to evaluate : 4.678 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 B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. 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 P 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 R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 110 PHE cc_start: 0.6950 (m-80) cc_final: 0.6465 (m-80) REVERT: B 16 MET cc_start: 0.8202 (mmp) cc_final: 0.7795 (mmt) REVERT: C 16 MET cc_start: 0.8196 (mmp) cc_final: 0.7823 (mmt) REVERT: C 187 LEU cc_start: 0.8768 (mp) cc_final: 0.8557 (mp) REVERT: D 16 MET cc_start: 0.8290 (mmp) cc_final: 0.7957 (mmp) REVERT: D 122 GLU cc_start: 0.7593 (pp20) cc_final: 0.7351 (pp20) REVERT: D 129 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: E 16 MET cc_start: 0.8152 (mmp) cc_final: 0.7487 (mmt) REVERT: E 179 TRP cc_start: 0.6935 (p90) cc_final: 0.6727 (p-90) REVERT: F 16 MET cc_start: 0.8422 (mmp) cc_final: 0.7942 (mmt) REVERT: H 16 MET cc_start: 0.7966 (mmp) cc_final: 0.7465 (mmt) REVERT: I 16 MET cc_start: 0.8359 (mmp) cc_final: 0.7789 (mmp) REVERT: K 60 ASP cc_start: 0.6784 (m-30) cc_final: 0.6475 (m-30) REVERT: L 16 MET cc_start: 0.8187 (mmp) cc_final: 0.7860 (mmp) REVERT: L 110 PHE cc_start: 0.7008 (m-80) cc_final: 0.6746 (m-80) REVERT: L 146 PHE cc_start: 0.6666 (t80) cc_final: 0.6456 (t80) REVERT: L 217 LYS cc_start: 0.8868 (mttt) cc_final: 0.8518 (mmtt) REVERT: M 16 MET cc_start: 0.8257 (mmp) cc_final: 0.7877 (mmt) REVERT: M 187 LEU cc_start: 0.8650 (mp) cc_final: 0.8427 (mp) REVERT: N 16 MET cc_start: 0.7825 (mmp) cc_final: 0.7345 (mmt) REVERT: N 110 PHE cc_start: 0.6874 (m-80) cc_final: 0.6635 (m-80) REVERT: N 129 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6744 (m-80) REVERT: P 60 ASP cc_start: 0.6713 (m-30) cc_final: 0.6438 (m-30) REVERT: Q 16 MET cc_start: 0.8464 (mmp) cc_final: 0.7986 (mmt) REVERT: R 16 MET cc_start: 0.8302 (mmp) cc_final: 0.7689 (mmp) REVERT: R 96 LEU cc_start: 0.8073 (pp) cc_final: 0.7869 (tt) REVERT: R 179 TRP cc_start: 0.6810 (p90) cc_final: 0.6559 (p-90) REVERT: S 16 MET cc_start: 0.8111 (mmp) cc_final: 0.7814 (mmt) REVERT: S 187 LEU cc_start: 0.8604 (mp) cc_final: 0.8391 (mp) REVERT: T 16 MET cc_start: 0.8233 (mmp) cc_final: 0.7655 (mmp) REVERT: T 129 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: V 16 MET cc_start: 0.7949 (mmp) cc_final: 0.7260 (mmp) REVERT: W 16 MET cc_start: 0.8168 (mmp) cc_final: 0.7692 (mmp) REVERT: W 122 GLU cc_start: 0.7355 (pp20) cc_final: 0.7145 (pp20) REVERT: X 16 MET cc_start: 0.8120 (mmp) cc_final: 0.7729 (mmt) REVERT: Y 16 MET cc_start: 0.8361 (mmp) cc_final: 0.7720 (mmp) REVERT: Y 96 LEU cc_start: 0.8140 (pp) cc_final: 0.7917 (tt) REVERT: Y 187 LEU cc_start: 0.8832 (mp) cc_final: 0.8619 (mp) REVERT: Z 16 MET cc_start: 0.7922 (mmp) cc_final: 0.7598 (mmp) REVERT: AA 22 MET cc_start: 0.8463 (mtt) cc_final: 0.8185 (ttm) REVERT: AA 129 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.6950 (m-80) REVERT: AA 146 PHE cc_start: 0.6838 (t80) cc_final: 0.6372 (t80) REVERT: AA 217 LYS cc_start: 0.8850 (mttt) cc_final: 0.8425 (mmtt) REVERT: BA 16 MET cc_start: 0.8199 (mmp) cc_final: 0.7826 (mmt) REVERT: BA 178 PHE cc_start: 0.7447 (p90) cc_final: 0.7212 (p90) outliers start: 68 outliers final: 42 residues processed: 688 average time/residue: 0.4378 time to fit residues: 524.7511 Evaluate side-chains 539 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 493 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 129 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain I residue 129 TYR Chi-restraints excluded: chain J residue 129 TYR Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 129 TYR Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 129 TYR Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 129 TYR Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain P residue 129 TYR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 129 TYR Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain T residue 129 TYR Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain V residue 129 TYR Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 129 TYR Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 129 TYR Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain AA residue 129 TYR Chi-restraints excluded: chain BA residue 120 ILE Chi-restraints excluded: chain BA residue 129 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 286 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 428 optimal weight: 20.0000 chunk 350 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 515 optimal weight: 2.9990 chunk 557 optimal weight: 5.9990 chunk 459 optimal weight: 2.9990 chunk 511 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 413 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN B 114 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 194 GLN C 111 GLN C 114 HIS ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN D 111 GLN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN E 175 GLN E 194 GLN F 114 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN I 114 HIS ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 GLN J 111 GLN J 114 HIS ** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 GLN K 111 GLN K 175 GLN K 194 GLN ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 GLN M 194 GLN N 194 GLN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 194 GLN P 111 GLN P 175 GLN ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 GLN R 114 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 194 GLN S 111 GLN S 175 GLN ** S 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN ** T 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 HIS ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 111 GLN W 175 GLN ** W 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 194 GLN Y 194 GLN ** Y 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 111 GLN ** AA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 175 GLN AA 194 GLN BA 111 GLN BA 114 HIS ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 175 GLN ** BA 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 49221 Z= 0.481 Angle : 0.780 15.981 66042 Z= 0.397 Chirality : 0.049 0.161 7290 Planarity : 0.005 0.031 8397 Dihedral : 5.906 47.169 6466 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.26 % Allowed : 16.07 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.11), residues: 5751 helix: -0.85 (0.20), residues: 621 sheet: -2.17 (0.10), residues: 2430 loop : -1.01 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP O 179 HIS 0.010 0.002 HIS C 114 PHE 0.023 0.003 PHE W 178 TYR 0.026 0.003 TYR M 52 ARG 0.005 0.001 ARG N 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 481 time to evaluate : 5.102 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 111 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: E 96 LEU cc_start: 0.7392 (mp) cc_final: 0.7100 (tt) REVERT: F 16 MET cc_start: 0.8399 (mmp) cc_final: 0.8194 (mmp) REVERT: G 8 ILE cc_start: 0.8884 (tp) cc_final: 0.8666 (tp) REVERT: H 16 MET cc_start: 0.8237 (mmp) cc_final: 0.7550 (mmt) REVERT: I 16 MET cc_start: 0.8558 (mmp) cc_final: 0.7735 (mmp) REVERT: I 111 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6185 (pp30) REVERT: L 11 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7696 (mp) REVERT: L 217 LYS cc_start: 0.8878 (mttt) cc_final: 0.8540 (mmtt) REVERT: M 16 MET cc_start: 0.8323 (mmp) cc_final: 0.7801 (mmt) REVERT: M 22 MET cc_start: 0.8537 (mtt) cc_final: 0.8155 (ttm) REVERT: N 16 MET cc_start: 0.7953 (mmp) cc_final: 0.7338 (mmt) REVERT: N 129 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: O 8 ILE cc_start: 0.8836 (tp) cc_final: 0.8608 (tp) REVERT: P 60 ASP cc_start: 0.6793 (m-30) cc_final: 0.6524 (m-30) REVERT: P 168 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7337 (mm-30) REVERT: Q 60 ASP cc_start: 0.6603 (m-30) cc_final: 0.6369 (m-30) REVERT: Q 171 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8451 (mptt) REVERT: S 11 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7685 (mp) REVERT: S 16 MET cc_start: 0.8265 (mmp) cc_final: 0.7785 (mmt) REVERT: T 8 ILE cc_start: 0.8708 (tp) cc_final: 0.8492 (tp) REVERT: T 16 MET cc_start: 0.8324 (mmp) cc_final: 0.7439 (mmt) REVERT: V 168 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6988 (mm-30) REVERT: W 11 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7782 (mp) REVERT: W 16 MET cc_start: 0.8242 (mmp) cc_final: 0.7643 (mmp) REVERT: X 16 MET cc_start: 0.8261 (mmp) cc_final: 0.7517 (mmt) REVERT: AA 16 MET cc_start: 0.8221 (mmt) cc_final: 0.7794 (mmt) REVERT: AA 129 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.6863 (m-80) REVERT: BA 8 ILE cc_start: 0.8934 (tp) cc_final: 0.8712 (tp) REVERT: BA 16 MET cc_start: 0.8364 (mmp) cc_final: 0.7772 (mmt) REVERT: BA 178 PHE cc_start: 0.7526 (p90) cc_final: 0.7286 (p90) outliers start: 176 outliers final: 85 residues processed: 640 average time/residue: 0.4138 time to fit residues: 462.8050 Evaluate side-chains 525 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 433 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 114 HIS Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 129 TYR Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 129 TYR Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain P residue 96 LEU Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain Q residue 87 LEU Chi-restraints excluded: chain Q residue 96 LEU Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 96 LEU Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain V residue 205 LEU Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 158 VAL Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 96 LEU Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 158 VAL Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain AA residue 87 LEU Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain AA residue 129 TYR Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain BA residue 87 LEU Chi-restraints excluded: chain BA residue 96 LEU Chi-restraints excluded: chain BA residue 120 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 509 optimal weight: 0.9990 chunk 387 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 346 optimal weight: 0.7980 chunk 517 optimal weight: 2.9990 chunk 548 optimal weight: 1.9990 chunk 270 optimal weight: 0.7980 chunk 490 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS F 114 HIS ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN H 114 HIS I 186 HIS J 114 HIS ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN L 114 HIS ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 GLN L 186 HIS ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 HIS ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS R 186 HIS ** S 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS ** T 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 HIS V 186 HIS ** V 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 111 GLN Z 175 GLN ** Z 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN ** AA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 186 HIS BA 194 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 49221 Z= 0.230 Angle : 0.619 9.529 66042 Z= 0.309 Chirality : 0.044 0.145 7290 Planarity : 0.004 0.031 8397 Dihedral : 4.703 45.350 6434 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.54 % Allowed : 20.67 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.11), residues: 5751 helix: -0.49 (0.20), residues: 594 sheet: -2.07 (0.10), residues: 2376 loop : -0.67 (0.12), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP R 179 HIS 0.012 0.001 HIS J 114 PHE 0.021 0.002 PHE E 178 TYR 0.012 0.001 TYR H 176 ARG 0.004 0.000 ARGBA 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 493 time to evaluate : 4.486 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 B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 96 LEU cc_start: 0.7482 (mp) cc_final: 0.7129 (tt) REVERT: C 96 LEU cc_start: 0.7449 (mp) cc_final: 0.7128 (tt) REVERT: C 146 PHE cc_start: 0.6544 (t80) cc_final: 0.6338 (t80) REVERT: D 16 MET cc_start: 0.8237 (mmp) cc_final: 0.7924 (mmp) REVERT: D 96 LEU cc_start: 0.7587 (mp) cc_final: 0.7203 (tt) REVERT: D 190 LYS cc_start: 0.9054 (mttt) cc_final: 0.8796 (mmtt) REVERT: D 217 LYS cc_start: 0.8892 (mttt) cc_final: 0.8537 (mmtt) REVERT: E 96 LEU cc_start: 0.7521 (mp) cc_final: 0.7200 (tt) REVERT: F 16 MET cc_start: 0.8377 (mmp) cc_final: 0.7810 (mmt) REVERT: F 120 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8072 (pt) REVERT: F 231 PHE cc_start: 0.6286 (m-10) cc_final: 0.6074 (m-10) REVERT: G 96 LEU cc_start: 0.7429 (mp) cc_final: 0.7038 (tt) REVERT: H 16 MET cc_start: 0.8208 (mmp) cc_final: 0.7597 (mmt) REVERT: I 16 MET cc_start: 0.8527 (mmp) cc_final: 0.7721 (mmp) REVERT: J 16 MET cc_start: 0.7855 (mmp) cc_final: 0.7484 (mmt) REVERT: J 120 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8153 (pt) REVERT: L 16 MET cc_start: 0.8221 (mmp) cc_final: 0.7775 (mmp) REVERT: L 217 LYS cc_start: 0.8851 (mttt) cc_final: 0.8500 (mmtt) REVERT: M 16 MET cc_start: 0.8417 (mmp) cc_final: 0.7830 (mmt) REVERT: N 16 MET cc_start: 0.7865 (mmp) cc_final: 0.7233 (mmt) REVERT: O 11 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7953 (mp) REVERT: O 110 PHE cc_start: 0.7194 (m-80) cc_final: 0.6993 (m-80) REVERT: P 16 MET cc_start: 0.8168 (mmp) cc_final: 0.7521 (mmp) REVERT: P 60 ASP cc_start: 0.6849 (m-30) cc_final: 0.6549 (m-30) REVERT: P 168 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7193 (mm-30) REVERT: Q 11 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7704 (mp) REVERT: Q 16 MET cc_start: 0.8391 (mmp) cc_final: 0.7920 (mmt) REVERT: Q 60 ASP cc_start: 0.6557 (m-30) cc_final: 0.6296 (m-30) REVERT: Q 171 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8424 (mptt) REVERT: R 96 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7943 (tt) REVERT: S 16 MET cc_start: 0.8334 (mmp) cc_final: 0.7741 (mmt) REVERT: T 8 ILE cc_start: 0.8626 (tp) cc_final: 0.8418 (tp) REVERT: T 16 MET cc_start: 0.8373 (mmp) cc_final: 0.7394 (mmt) REVERT: T 110 PHE cc_start: 0.6858 (m-80) cc_final: 0.6572 (m-80) REVERT: V 16 MET cc_start: 0.8061 (mmp) cc_final: 0.7355 (mmp) REVERT: W 16 MET cc_start: 0.8085 (mmp) cc_final: 0.7600 (mmp) REVERT: X 11 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7968 (mp) REVERT: X 16 MET cc_start: 0.8136 (mmp) cc_final: 0.7606 (mmt) REVERT: Y 16 MET cc_start: 0.8318 (mmp) cc_final: 0.7581 (mmt) REVERT: Y 111 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6548 (pp30) REVERT: Z 16 MET cc_start: 0.7955 (mmp) cc_final: 0.7489 (mmt) REVERT: AA 16 MET cc_start: 0.8181 (mmt) cc_final: 0.7710 (mmt) REVERT: AA 22 MET cc_start: 0.8508 (mtt) cc_final: 0.8220 (ttm) REVERT: AA 129 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: AA 146 PHE cc_start: 0.6944 (t80) cc_final: 0.6462 (t80) REVERT: AA 217 LYS cc_start: 0.8884 (mttt) cc_final: 0.8491 (mmtt) REVERT: BA 8 ILE cc_start: 0.8865 (tp) cc_final: 0.8616 (tp) REVERT: BA 16 MET cc_start: 0.8351 (mmp) cc_final: 0.7782 (mmt) REVERT: BA 118 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8479 (mm) outliers start: 83 outliers final: 41 residues processed: 568 average time/residue: 0.3962 time to fit residues: 403.7569 Evaluate side-chains 514 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 464 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 114 HIS Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 114 HIS Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 114 HIS Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 114 HIS Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain R residue 96 LEU Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain Y residue 111 GLN Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain AA residue 129 TYR Chi-restraints excluded: chain BA residue 22 MET Chi-restraints excluded: chain BA residue 118 ILE Chi-restraints excluded: chain BA residue 120 ILE Chi-restraints excluded: chain BA residue 158 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 456 optimal weight: 1.9990 chunk 311 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 408 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 467 optimal weight: 0.5980 chunk 378 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 279 optimal weight: 0.0470 chunk 491 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN F 114 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 HIS L 194 GLN ** M 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 HIS ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS ** S 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS T 194 GLN V 114 HIS ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS ** X 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 49221 Z= 0.253 Angle : 0.620 9.231 66042 Z= 0.310 Chirality : 0.044 0.144 7290 Planarity : 0.004 0.033 8397 Dihedral : 4.530 43.592 6428 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.98 % Allowed : 21.56 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.11), residues: 5751 helix: -0.48 (0.20), residues: 594 sheet: -2.03 (0.10), residues: 2430 loop : -0.75 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 179 HIS 0.010 0.001 HIS H 114 PHE 0.020 0.002 PHEAA 178 TYR 0.013 0.002 TYR M 52 ARG 0.003 0.000 ARG S 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 494 time to evaluate : 4.735 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 61 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6013 (mm) REVERT: A 96 LEU cc_start: 0.7487 (mp) cc_final: 0.7228 (tt) REVERT: B 16 MET cc_start: 0.8035 (mmp) cc_final: 0.7728 (mmt) REVERT: C 96 LEU cc_start: 0.7469 (mp) cc_final: 0.7196 (tt) REVERT: C 146 PHE cc_start: 0.6515 (t80) cc_final: 0.6315 (t80) REVERT: D 16 MET cc_start: 0.8337 (mmp) cc_final: 0.7988 (mmp) REVERT: D 96 LEU cc_start: 0.7578 (mp) cc_final: 0.7234 (tt) REVERT: D 190 LYS cc_start: 0.9017 (mttt) cc_final: 0.8792 (mmtt) REVERT: E 11 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7648 (mp) REVERT: E 96 LEU cc_start: 0.7497 (mp) cc_final: 0.7145 (tt) REVERT: F 16 MET cc_start: 0.8248 (mmp) cc_final: 0.7892 (mmt) REVERT: F 120 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8107 (pt) REVERT: F 231 PHE cc_start: 0.6274 (m-10) cc_final: 0.6064 (m-10) REVERT: G 16 MET cc_start: 0.8237 (mmp) cc_final: 0.7587 (mmm) REVERT: G 96 LEU cc_start: 0.7592 (mp) cc_final: 0.7202 (tt) REVERT: H 16 MET cc_start: 0.8123 (mmp) cc_final: 0.7533 (mmt) REVERT: I 16 MET cc_start: 0.8506 (mmp) cc_final: 0.7742 (mmp) REVERT: I 61 ILE cc_start: 0.6783 (OUTLIER) cc_final: 0.6355 (mm) REVERT: J 16 MET cc_start: 0.7858 (mmp) cc_final: 0.7524 (mmt) REVERT: J 120 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8171 (pt) REVERT: L 11 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7707 (mp) REVERT: L 16 MET cc_start: 0.8294 (mmp) cc_final: 0.7847 (mmp) REVERT: L 217 LYS cc_start: 0.8852 (mttt) cc_final: 0.8502 (mmtt) REVERT: M 16 MET cc_start: 0.8343 (mmp) cc_final: 0.7855 (mmt) REVERT: N 16 MET cc_start: 0.7877 (mmp) cc_final: 0.7248 (mmt) REVERT: N 96 LEU cc_start: 0.7490 (mp) cc_final: 0.7048 (tt) REVERT: N 178 PHE cc_start: 0.7562 (p90) cc_final: 0.7126 (p90) REVERT: O 11 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7957 (mp) REVERT: P 16 MET cc_start: 0.8218 (mmp) cc_final: 0.7560 (mmp) REVERT: P 46 PHE cc_start: 0.4730 (m-10) cc_final: 0.4418 (m-80) REVERT: P 60 ASP cc_start: 0.6799 (m-30) cc_final: 0.6487 (m-30) REVERT: P 168 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7210 (mm-30) REVERT: P 194 GLN cc_start: 0.7317 (tm130) cc_final: 0.7071 (tm-30) REVERT: Q 11 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7692 (mp) REVERT: Q 16 MET cc_start: 0.8434 (mmp) cc_final: 0.7808 (mmt) REVERT: S 11 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7767 (mp) REVERT: S 16 MET cc_start: 0.8186 (mmp) cc_final: 0.7782 (mmt) REVERT: S 171 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7706 (tmtt) REVERT: T 16 MET cc_start: 0.8296 (mmp) cc_final: 0.7343 (mmt) REVERT: T 110 PHE cc_start: 0.6863 (m-80) cc_final: 0.6643 (m-80) REVERT: V 16 MET cc_start: 0.7930 (mmp) cc_final: 0.7192 (mmp) REVERT: W 11 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7741 (mp) REVERT: W 16 MET cc_start: 0.8157 (mmp) cc_final: 0.7657 (mmp) REVERT: X 11 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7966 (mp) REVERT: X 16 MET cc_start: 0.8192 (mmp) cc_final: 0.7668 (mmt) REVERT: Y 11 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7722 (mp) REVERT: Y 16 MET cc_start: 0.8338 (mmp) cc_final: 0.7606 (mmt) REVERT: Y 111 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6783 (pp30) REVERT: Z 16 MET cc_start: 0.7950 (mmp) cc_final: 0.7498 (mmt) REVERT: Z 61 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6532 (mm) REVERT: Z 96 LEU cc_start: 0.7521 (mp) cc_final: 0.7237 (tt) REVERT: AA 16 MET cc_start: 0.8139 (mmt) cc_final: 0.7756 (mmt) REVERT: BA 8 ILE cc_start: 0.8892 (tp) cc_final: 0.8538 (tp) REVERT: BA 16 MET cc_start: 0.8322 (mmp) cc_final: 0.7798 (mmt) outliers start: 107 outliers final: 51 residues processed: 585 average time/residue: 0.4075 time to fit residues: 432.3417 Evaluate side-chains 532 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 466 time to evaluate : 4.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 171 LYS Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 111 GLN Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain BA residue 22 MET Chi-restraints excluded: chain BA residue 56 LEU Chi-restraints excluded: chain BA residue 87 LEU Chi-restraints excluded: chain BA residue 120 ILE Chi-restraints excluded: chain BA residue 158 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 184 optimal weight: 20.0000 chunk 493 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 321 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 548 optimal weight: 0.9990 chunk 455 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 181 optimal weight: 0.9980 chunk 288 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS F 194 GLN H 114 HIS ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS O 186 HIS ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS V 114 HIS V 194 GLN W 114 HIS ** W 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS X 194 GLN ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 HIS ** Y 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 49221 Z= 0.171 Angle : 0.562 9.057 66042 Z= 0.281 Chirality : 0.042 0.161 7290 Planarity : 0.003 0.034 8397 Dihedral : 4.147 14.517 6426 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.70 % Allowed : 22.52 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.11), residues: 5751 helix: -0.36 (0.19), residues: 594 sheet: -1.93 (0.10), residues: 2376 loop : -0.51 (0.12), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 179 HIS 0.015 0.001 HIS V 114 PHE 0.018 0.001 PHE J 178 TYR 0.008 0.001 TYR S 176 ARG 0.003 0.000 ARG S 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 532 time to evaluate : 4.543 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 96 LEU cc_start: 0.7331 (mp) cc_final: 0.7092 (tt) REVERT: B 16 MET cc_start: 0.8036 (mmp) cc_final: 0.7781 (mmt) REVERT: B 61 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6368 (mm) REVERT: C 16 MET cc_start: 0.8228 (mmp) cc_final: 0.7730 (mmt) REVERT: C 96 LEU cc_start: 0.7594 (mp) cc_final: 0.7155 (tt) REVERT: C 146 PHE cc_start: 0.6490 (t80) cc_final: 0.6286 (t80) REVERT: D 16 MET cc_start: 0.8273 (mmp) cc_final: 0.7992 (mmp) REVERT: D 61 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6450 (mm) REVERT: D 96 LEU cc_start: 0.7659 (mp) cc_final: 0.7333 (tt) REVERT: D 190 LYS cc_start: 0.9026 (mttt) cc_final: 0.8797 (mmtt) REVERT: E 11 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7669 (mp) REVERT: E 61 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.6296 (mm) REVERT: E 96 LEU cc_start: 0.7493 (mp) cc_final: 0.7197 (tt) REVERT: F 16 MET cc_start: 0.8357 (mmp) cc_final: 0.7816 (mmt) REVERT: F 61 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.6264 (mm) REVERT: F 120 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8032 (pt) REVERT: F 231 PHE cc_start: 0.6178 (m-10) cc_final: 0.5901 (m-10) REVERT: G 22 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8079 (mtt) REVERT: G 96 LEU cc_start: 0.7561 (mp) cc_final: 0.7242 (tt) REVERT: H 16 MET cc_start: 0.8044 (mmp) cc_final: 0.7474 (mmt) REVERT: H 61 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6810 (mm) REVERT: I 16 MET cc_start: 0.8497 (mmp) cc_final: 0.7756 (mmp) REVERT: I 61 ILE cc_start: 0.6811 (OUTLIER) cc_final: 0.6437 (mm) REVERT: I 111 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6832 (pp30) REVERT: J 16 MET cc_start: 0.7851 (mmp) cc_final: 0.7515 (mmt) REVERT: J 61 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6450 (mm) REVERT: L 11 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7740 (mp) REVERT: L 16 MET cc_start: 0.8231 (mmp) cc_final: 0.7826 (mmt) REVERT: L 61 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6387 (mm) REVERT: L 217 LYS cc_start: 0.8863 (mttt) cc_final: 0.8539 (mmtt) REVERT: M 16 MET cc_start: 0.8313 (mmp) cc_final: 0.7791 (mmt) REVERT: M 61 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6471 (mm) REVERT: M 96 LEU cc_start: 0.7614 (mp) cc_final: 0.7290 (tt) REVERT: N 16 MET cc_start: 0.7856 (mmp) cc_final: 0.7204 (mmt) REVERT: N 96 LEU cc_start: 0.7411 (mp) cc_final: 0.6999 (tt) REVERT: N 178 PHE cc_start: 0.7630 (p90) cc_final: 0.7205 (p90) REVERT: O 11 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7902 (mp) REVERT: O 96 LEU cc_start: 0.7508 (mp) cc_final: 0.7136 (tt) REVERT: P 16 MET cc_start: 0.8210 (mmp) cc_final: 0.7537 (mmp) REVERT: P 46 PHE cc_start: 0.4586 (m-10) cc_final: 0.4315 (m-80) REVERT: P 60 ASP cc_start: 0.6731 (m-30) cc_final: 0.6271 (m-30) REVERT: P 114 HIS cc_start: 0.6742 (OUTLIER) cc_final: 0.6528 (m-70) REVERT: P 194 GLN cc_start: 0.7304 (tm130) cc_final: 0.7054 (tm-30) REVERT: Q 11 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7666 (mp) REVERT: Q 16 MET cc_start: 0.8372 (mmp) cc_final: 0.7768 (mmt) REVERT: Q 60 ASP cc_start: 0.6423 (m-30) cc_final: 0.6111 (m-30) REVERT: Q 96 LEU cc_start: 0.8189 (pp) cc_final: 0.7986 (tt) REVERT: Q 171 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8301 (mptt) REVERT: R 61 ILE cc_start: 0.6667 (OUTLIER) cc_final: 0.6171 (mm) REVERT: R 217 LYS cc_start: 0.8825 (mttt) cc_final: 0.8563 (mmtt) REVERT: S 11 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7767 (mp) REVERT: S 16 MET cc_start: 0.8254 (mmp) cc_final: 0.7816 (mmt) REVERT: T 16 MET cc_start: 0.8320 (mmp) cc_final: 0.7284 (mmt) REVERT: T 96 LEU cc_start: 0.7539 (mp) cc_final: 0.7159 (tt) REVERT: T 110 PHE cc_start: 0.6725 (m-80) cc_final: 0.6517 (m-80) REVERT: V 16 MET cc_start: 0.8086 (mmp) cc_final: 0.7315 (mmp) REVERT: V 61 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6556 (mm) REVERT: W 11 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7713 (mp) REVERT: W 16 MET cc_start: 0.8155 (mmp) cc_final: 0.7659 (mmp) REVERT: X 11 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7981 (mp) REVERT: X 16 MET cc_start: 0.8126 (mmp) cc_final: 0.7652 (mmt) REVERT: Y 11 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7656 (mp) REVERT: Y 16 MET cc_start: 0.8338 (mmp) cc_final: 0.7585 (mmt) REVERT: Y 61 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6798 (mm) REVERT: Y 96 LEU cc_start: 0.7648 (mp) cc_final: 0.7219 (tt) REVERT: Z 16 MET cc_start: 0.7952 (mmp) cc_final: 0.7524 (mmt) REVERT: Z 96 LEU cc_start: 0.7511 (mp) cc_final: 0.7141 (tt) REVERT: AA 16 MET cc_start: 0.8125 (mmt) cc_final: 0.7685 (mmt) REVERT: AA 22 MET cc_start: 0.8519 (mtt) cc_final: 0.8224 (ttt) REVERT: AA 61 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6261 (mm) REVERT: AA 146 PHE cc_start: 0.6895 (t80) cc_final: 0.6420 (t80) REVERT: BA 16 MET cc_start: 0.8308 (mmp) cc_final: 0.7759 (mmt) REVERT: BA 61 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6473 (mm) outliers start: 92 outliers final: 25 residues processed: 608 average time/residue: 0.3846 time to fit residues: 421.6373 Evaluate side-chains 526 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 475 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain P residue 114 HIS Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 114 HIS Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 114 HIS Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 56 LEU Chi-restraints excluded: chain AA residue 61 ILE Chi-restraints excluded: chain BA residue 22 MET Chi-restraints excluded: chain BA residue 56 LEU Chi-restraints excluded: chain BA residue 61 ILE Chi-restraints excluded: chain BA residue 120 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 528 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 312 optimal weight: 0.8980 chunk 400 optimal weight: 0.6980 chunk 310 optimal weight: 10.0000 chunk 461 optimal weight: 5.9990 chunk 306 optimal weight: 0.8980 chunk 546 optimal weight: 0.9990 chunk 342 optimal weight: 4.9990 chunk 333 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS H 114 HIS ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS V 114 HIS ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 114 HIS ** W 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 HIS ** Y 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 186 HIS ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 49221 Z= 0.161 Angle : 0.559 9.331 66042 Z= 0.279 Chirality : 0.042 0.207 7290 Planarity : 0.003 0.033 8397 Dihedral : 4.016 16.234 6426 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.78 % Allowed : 23.26 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.11), residues: 5751 helix: -0.21 (0.19), residues: 594 sheet: -1.74 (0.10), residues: 2430 loop : -0.50 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 179 HIS 0.016 0.001 HIS W 114 PHE 0.018 0.001 PHE J 178 TYR 0.008 0.001 TYR J 176 ARG 0.003 0.000 ARG S 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 524 time to evaluate : 4.575 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 61 ILE cc_start: 0.6711 (OUTLIER) cc_final: 0.6222 (mm) REVERT: A 96 LEU cc_start: 0.7505 (mp) cc_final: 0.7102 (tt) REVERT: B 61 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6305 (mm) REVERT: C 96 LEU cc_start: 0.7498 (mp) cc_final: 0.7218 (tt) REVERT: D 16 MET cc_start: 0.8289 (mmp) cc_final: 0.8019 (mmp) REVERT: D 61 ILE cc_start: 0.6753 (OUTLIER) cc_final: 0.6385 (mm) REVERT: D 96 LEU cc_start: 0.7656 (mp) cc_final: 0.7335 (tt) REVERT: D 190 LYS cc_start: 0.9036 (mttt) cc_final: 0.8821 (mmtt) REVERT: E 11 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7655 (mp) REVERT: E 46 PHE cc_start: 0.4928 (m-10) cc_final: 0.4424 (m-10) REVERT: E 61 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6407 (mm) REVERT: E 62 LEU cc_start: 0.6613 (tp) cc_final: 0.6348 (tp) REVERT: E 96 LEU cc_start: 0.7502 (mp) cc_final: 0.7207 (tt) REVERT: F 16 MET cc_start: 0.8318 (mmp) cc_final: 0.7770 (mmt) REVERT: F 61 ILE cc_start: 0.6648 (OUTLIER) cc_final: 0.6273 (mm) REVERT: F 120 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8079 (pt) REVERT: F 231 PHE cc_start: 0.6147 (m-10) cc_final: 0.5907 (m-10) REVERT: G 22 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8097 (mtt) REVERT: G 96 LEU cc_start: 0.7593 (mp) cc_final: 0.7249 (tt) REVERT: H 16 MET cc_start: 0.8026 (mmp) cc_final: 0.7457 (mmt) REVERT: H 61 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6788 (mm) REVERT: I 16 MET cc_start: 0.8437 (mmp) cc_final: 0.7739 (mmp) REVERT: I 61 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6434 (mm) REVERT: J 16 MET cc_start: 0.7858 (mmp) cc_final: 0.7348 (mmt) REVERT: L 11 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7738 (mp) REVERT: L 16 MET cc_start: 0.8204 (mmp) cc_final: 0.7818 (mmt) REVERT: L 46 PHE cc_start: 0.4825 (m-10) cc_final: 0.4552 (m-10) REVERT: L 217 LYS cc_start: 0.8863 (mttt) cc_final: 0.8518 (mmtt) REVERT: M 16 MET cc_start: 0.8246 (mmp) cc_final: 0.7776 (mmt) REVERT: M 96 LEU cc_start: 0.7594 (mp) cc_final: 0.7215 (tt) REVERT: N 16 MET cc_start: 0.7862 (mmp) cc_final: 0.7230 (mmt) REVERT: N 61 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.6256 (mm) REVERT: N 96 LEU cc_start: 0.7432 (mp) cc_final: 0.7067 (tt) REVERT: N 178 PHE cc_start: 0.7684 (p90) cc_final: 0.7300 (p90) REVERT: O 11 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7892 (mp) REVERT: O 96 LEU cc_start: 0.7580 (mp) cc_final: 0.7196 (tt) REVERT: P 16 MET cc_start: 0.8165 (mmp) cc_final: 0.7531 (mmp) REVERT: P 60 ASP cc_start: 0.6625 (m-30) cc_final: 0.6372 (m-30) REVERT: P 168 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6795 (mm-30) REVERT: Q 11 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7654 (mp) REVERT: Q 16 MET cc_start: 0.8355 (mmp) cc_final: 0.7751 (mmt) REVERT: Q 171 LYS cc_start: 0.8566 (mtpt) cc_final: 0.8284 (mptt) REVERT: R 61 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.6130 (mm) REVERT: R 89 ASN cc_start: 0.7795 (t0) cc_final: 0.7567 (t0) REVERT: R 96 LEU cc_start: 0.7534 (mp) cc_final: 0.7171 (tt) REVERT: S 11 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7761 (mp) REVERT: S 16 MET cc_start: 0.8206 (mmp) cc_final: 0.7764 (mmt) REVERT: T 16 MET cc_start: 0.8296 (mmp) cc_final: 0.7305 (mmt) REVERT: T 96 LEU cc_start: 0.7565 (mp) cc_final: 0.7198 (tt) REVERT: V 16 MET cc_start: 0.7993 (mmp) cc_final: 0.7211 (mmp) REVERT: V 61 ILE cc_start: 0.6678 (OUTLIER) cc_final: 0.6473 (mm) REVERT: V 96 LEU cc_start: 0.8251 (pp) cc_final: 0.8050 (tt) REVERT: W 11 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7712 (mp) REVERT: W 16 MET cc_start: 0.8119 (mmp) cc_final: 0.7656 (mmp) REVERT: W 61 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6452 (mm) REVERT: X 11 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7967 (mp) REVERT: X 16 MET cc_start: 0.8089 (mmp) cc_final: 0.7665 (mmt) REVERT: Y 11 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7639 (mp) REVERT: Y 16 MET cc_start: 0.8309 (mmp) cc_final: 0.7586 (mmt) REVERT: Y 96 LEU cc_start: 0.7723 (mp) cc_final: 0.7310 (tt) REVERT: Z 16 MET cc_start: 0.7928 (mmp) cc_final: 0.7552 (mmt) REVERT: Z 61 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6549 (mm) REVERT: Z 96 LEU cc_start: 0.7429 (mp) cc_final: 0.7187 (tt) REVERT: AA 16 MET cc_start: 0.8101 (mmt) cc_final: 0.7699 (mmt) REVERT: AA 22 MET cc_start: 0.8518 (mtt) cc_final: 0.8226 (ttt) REVERT: AA 61 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.6258 (mm) REVERT: AA 146 PHE cc_start: 0.6948 (t80) cc_final: 0.6449 (t80) REVERT: BA 16 MET cc_start: 0.8275 (mmp) cc_final: 0.7771 (mmt) REVERT: BA 61 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6472 (mm) outliers start: 96 outliers final: 37 residues processed: 605 average time/residue: 0.3907 time to fit residues: 426.6666 Evaluate side-chains 541 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 480 time to evaluate : 4.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 114 HIS Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 22 MET Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 61 ILE Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 56 LEU Chi-restraints excluded: chain AA residue 61 ILE Chi-restraints excluded: chain BA residue 22 MET Chi-restraints excluded: chain BA residue 56 LEU Chi-restraints excluded: chain BA residue 61 ILE Chi-restraints excluded: chain BA residue 120 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 338 optimal weight: 2.9990 chunk 218 optimal weight: 20.0000 chunk 326 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 347 optimal weight: 0.7980 chunk 372 optimal weight: 0.9990 chunk 270 optimal weight: 0.9990 chunk 50 optimal weight: 0.0270 chunk 429 optimal weight: 7.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 HIS ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS V 114 HIS ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 186 HIS X 114 HIS ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 HIS ** Y 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 49221 Z= 0.159 Angle : 0.564 9.239 66042 Z= 0.281 Chirality : 0.042 0.181 7290 Planarity : 0.003 0.033 8397 Dihedral : 3.971 14.221 6426 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.70 % Allowed : 24.06 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.11), residues: 5751 helix: -0.11 (0.19), residues: 594 sheet: -1.62 (0.10), residues: 2430 loop : -0.43 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 179 HIS 0.007 0.001 HIS R 114 PHE 0.018 0.001 PHE H 178 TYR 0.007 0.001 TYR A 176 ARG 0.003 0.000 ARGBA 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 522 time to evaluate : 4.706 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 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 F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 61 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6361 (mm) REVERT: A 96 LEU cc_start: 0.7601 (mp) cc_final: 0.7358 (tt) REVERT: B 61 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6357 (mm) REVERT: C 96 LEU cc_start: 0.7501 (mp) cc_final: 0.7232 (tt) REVERT: D 16 MET cc_start: 0.8298 (mmp) cc_final: 0.8022 (mmp) REVERT: D 96 LEU cc_start: 0.7645 (mp) cc_final: 0.7187 (tt) REVERT: D 190 LYS cc_start: 0.9101 (mttt) cc_final: 0.8848 (mmtt) REVERT: E 11 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7653 (mp) REVERT: E 46 PHE cc_start: 0.5086 (m-10) cc_final: 0.4615 (m-10) REVERT: E 61 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6383 (mm) REVERT: E 62 LEU cc_start: 0.6465 (tp) cc_final: 0.6178 (tp) REVERT: E 96 LEU cc_start: 0.7529 (mp) cc_final: 0.7234 (tt) REVERT: F 16 MET cc_start: 0.8313 (mmp) cc_final: 0.7771 (mmt) REVERT: F 61 ILE cc_start: 0.6612 (OUTLIER) cc_final: 0.6301 (mm) REVERT: F 96 LEU cc_start: 0.7530 (mp) cc_final: 0.7137 (tt) REVERT: F 120 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8016 (pt) REVERT: F 231 PHE cc_start: 0.6159 (m-10) cc_final: 0.5934 (m-10) REVERT: G 16 MET cc_start: 0.7964 (mmt) cc_final: 0.7345 (mmt) REVERT: G 22 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8058 (mtt) REVERT: G 96 LEU cc_start: 0.7682 (mp) cc_final: 0.7311 (tt) REVERT: G 194 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7549 (tm-30) REVERT: H 16 MET cc_start: 0.8039 (mmp) cc_final: 0.7468 (mmt) REVERT: H 61 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6833 (mm) REVERT: I 16 MET cc_start: 0.8418 (mmp) cc_final: 0.7732 (mmp) REVERT: I 61 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6371 (mm) REVERT: I 96 LEU cc_start: 0.7620 (mp) cc_final: 0.7142 (tt) REVERT: I 111 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6901 (pp30) REVERT: J 16 MET cc_start: 0.7899 (mmp) cc_final: 0.7350 (mmt) REVERT: K 96 LEU cc_start: 0.7450 (mp) cc_final: 0.7056 (tt) REVERT: K 217 LYS cc_start: 0.8855 (mttt) cc_final: 0.8528 (mmtt) REVERT: L 11 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7738 (mp) REVERT: L 16 MET cc_start: 0.8205 (mmp) cc_final: 0.7822 (mmt) REVERT: L 46 PHE cc_start: 0.4532 (m-10) cc_final: 0.4240 (m-10) REVERT: L 217 LYS cc_start: 0.8809 (mttt) cc_final: 0.8562 (mmtt) REVERT: M 16 MET cc_start: 0.8242 (mmp) cc_final: 0.7740 (mmt) REVERT: M 96 LEU cc_start: 0.7510 (mp) cc_final: 0.7197 (tt) REVERT: N 16 MET cc_start: 0.7853 (mmp) cc_final: 0.7218 (mmt) REVERT: N 61 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6439 (mt) REVERT: N 96 LEU cc_start: 0.7691 (mp) cc_final: 0.7317 (tt) REVERT: N 178 PHE cc_start: 0.7685 (p90) cc_final: 0.7314 (p90) REVERT: O 11 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7907 (mp) REVERT: O 16 MET cc_start: 0.7735 (tpp) cc_final: 0.7336 (mmt) REVERT: O 96 LEU cc_start: 0.7715 (mp) cc_final: 0.7324 (tt) REVERT: P 16 MET cc_start: 0.8160 (mmp) cc_final: 0.7522 (mmp) REVERT: P 60 ASP cc_start: 0.6662 (m-30) cc_final: 0.6418 (m-30) REVERT: P 168 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6780 (mm-30) REVERT: Q 11 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7645 (mp) REVERT: Q 16 MET cc_start: 0.8365 (mmp) cc_final: 0.7755 (mmt) REVERT: Q 171 LYS cc_start: 0.8560 (mtpt) cc_final: 0.8279 (mptt) REVERT: R 61 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6112 (mm) REVERT: R 89 ASN cc_start: 0.7782 (t0) cc_final: 0.7557 (t0) REVERT: R 96 LEU cc_start: 0.7542 (mp) cc_final: 0.7021 (tt) REVERT: S 11 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7766 (mp) REVERT: S 16 MET cc_start: 0.8203 (mmp) cc_final: 0.7767 (mmt) REVERT: S 96 LEU cc_start: 0.7400 (mp) cc_final: 0.6986 (tt) REVERT: T 16 MET cc_start: 0.8303 (mmp) cc_final: 0.7365 (mmt) REVERT: T 96 LEU cc_start: 0.7735 (mp) cc_final: 0.7365 (tt) REVERT: V 16 MET cc_start: 0.7975 (mmp) cc_final: 0.7195 (mmp) REVERT: W 11 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7702 (mp) REVERT: W 16 MET cc_start: 0.8123 (mmp) cc_final: 0.7662 (mmp) REVERT: W 61 ILE cc_start: 0.6719 (OUTLIER) cc_final: 0.6376 (mm) REVERT: X 11 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7959 (mp) REVERT: X 16 MET cc_start: 0.8104 (mmp) cc_final: 0.7666 (mmt) REVERT: Y 11 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7640 (mp) REVERT: Y 16 MET cc_start: 0.8347 (mmp) cc_final: 0.7639 (mmt) REVERT: Y 96 LEU cc_start: 0.7726 (mp) cc_final: 0.7122 (tt) REVERT: Z 16 MET cc_start: 0.7928 (mmp) cc_final: 0.7546 (mmt) REVERT: Z 61 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6553 (mm) REVERT: AA 16 MET cc_start: 0.8108 (mmt) cc_final: 0.7698 (mmt) REVERT: AA 22 MET cc_start: 0.8494 (mtt) cc_final: 0.8191 (ttt) REVERT: AA 60 ASP cc_start: 0.6183 (m-30) cc_final: 0.5891 (m-30) REVERT: AA 61 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.5989 (mm) REVERT: AA 146 PHE cc_start: 0.6875 (t80) cc_final: 0.6399 (t80) REVERT: BA 16 MET cc_start: 0.8253 (mmp) cc_final: 0.7614 (mmt) REVERT: BA 61 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6495 (mm) outliers start: 92 outliers final: 40 residues processed: 597 average time/residue: 0.3920 time to fit residues: 421.6850 Evaluate side-chains 561 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 498 time to evaluate : 4.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 22 MET Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 106 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain V residue 106 ILE Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 61 ILE Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 53 THR Chi-restraints excluded: chain AA residue 56 LEU Chi-restraints excluded: chain AA residue 61 ILE Chi-restraints excluded: chain BA residue 22 MET Chi-restraints excluded: chain BA residue 56 LEU Chi-restraints excluded: chain BA residue 61 ILE Chi-restraints excluded: chain BA residue 120 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 497 optimal weight: 3.9990 chunk 523 optimal weight: 4.9990 chunk 477 optimal weight: 3.9990 chunk 509 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 221 optimal weight: 0.0770 chunk 399 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 460 optimal weight: 1.9990 chunk 481 optimal weight: 0.7980 chunk 507 optimal weight: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 HIS ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 HIS ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 HIS ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS V 114 HIS ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS ** X 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 HIS ** Y 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 49221 Z= 0.186 Angle : 0.581 8.867 66042 Z= 0.290 Chirality : 0.043 0.175 7290 Planarity : 0.003 0.033 8397 Dihedral : 4.045 15.409 6426 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.83 % Allowed : 24.20 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.11), residues: 5751 helix: -0.11 (0.19), residues: 594 sheet: -1.57 (0.10), residues: 2430 loop : -0.44 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 179 HIS 0.009 0.001 HIS R 114 PHE 0.019 0.001 PHE I 178 TYR 0.010 0.001 TYRAA 52 ARG 0.003 0.000 ARGBA 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 511 time to evaluate : 4.564 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET D 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 F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 61 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6341 (mm) REVERT: B 61 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6281 (mm) REVERT: B 96 LEU cc_start: 0.7603 (mp) cc_final: 0.7276 (tt) REVERT: C 96 LEU cc_start: 0.7499 (mp) cc_final: 0.7247 (tt) REVERT: D 16 MET cc_start: 0.8338 (mmp) cc_final: 0.8022 (mmp) REVERT: D 96 LEU cc_start: 0.7548 (mp) cc_final: 0.7242 (tt) REVERT: D 190 LYS cc_start: 0.9114 (mttt) cc_final: 0.8870 (mmtt) REVERT: D 217 LYS cc_start: 0.8848 (mttt) cc_final: 0.8571 (mmtt) REVERT: E 11 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7641 (mp) REVERT: E 46 PHE cc_start: 0.4951 (m-10) cc_final: 0.4512 (m-10) REVERT: E 61 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6333 (mm) REVERT: E 62 LEU cc_start: 0.6576 (tp) cc_final: 0.6280 (tp) REVERT: E 96 LEU cc_start: 0.7582 (mp) cc_final: 0.7259 (tt) REVERT: F 16 MET cc_start: 0.8248 (mmp) cc_final: 0.7807 (mmt) REVERT: F 61 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6280 (mm) REVERT: F 96 LEU cc_start: 0.7586 (mp) cc_final: 0.7014 (tt) REVERT: F 120 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8074 (pt) REVERT: F 231 PHE cc_start: 0.6182 (m-10) cc_final: 0.5956 (m-10) REVERT: G 16 MET cc_start: 0.8059 (mmt) cc_final: 0.7417 (mmt) REVERT: G 22 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8088 (mtt) REVERT: G 96 LEU cc_start: 0.7681 (mp) cc_final: 0.7296 (tt) REVERT: G 194 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7470 (tm-30) REVERT: H 16 MET cc_start: 0.8092 (mmp) cc_final: 0.7471 (mmt) REVERT: H 61 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6860 (mm) REVERT: I 16 MET cc_start: 0.8454 (mmp) cc_final: 0.7770 (mmp) REVERT: I 61 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6362 (mm) REVERT: I 96 LEU cc_start: 0.7659 (mp) cc_final: 0.7254 (tt) REVERT: I 111 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6915 (pp30) REVERT: J 16 MET cc_start: 0.7946 (mmp) cc_final: 0.7356 (mmt) REVERT: J 96 LEU cc_start: 0.7575 (mp) cc_final: 0.7308 (tt) REVERT: K 96 LEU cc_start: 0.7464 (mp) cc_final: 0.7075 (tt) REVERT: K 217 LYS cc_start: 0.8878 (mttt) cc_final: 0.8549 (mmtt) REVERT: L 16 MET cc_start: 0.8253 (mmp) cc_final: 0.7857 (mmp) REVERT: L 46 PHE cc_start: 0.4635 (m-10) cc_final: 0.4282 (m-10) REVERT: M 16 MET cc_start: 0.8279 (mmp) cc_final: 0.7804 (mmt) REVERT: N 15 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7461 (mm-30) REVERT: N 61 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6431 (mt) REVERT: N 96 LEU cc_start: 0.7689 (mp) cc_final: 0.7323 (tt) REVERT: N 178 PHE cc_start: 0.7696 (p90) cc_final: 0.7343 (p90) REVERT: O 11 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7876 (mp) REVERT: O 96 LEU cc_start: 0.7737 (mp) cc_final: 0.7349 (tt) REVERT: P 16 MET cc_start: 0.8204 (mmp) cc_final: 0.7543 (mmp) REVERT: P 60 ASP cc_start: 0.6613 (m-30) cc_final: 0.6379 (m-30) REVERT: P 96 LEU cc_start: 0.7665 (mp) cc_final: 0.7031 (tt) REVERT: P 168 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6791 (mm-30) REVERT: P 217 LYS cc_start: 0.8886 (mttt) cc_final: 0.8668 (mmtt) REVERT: Q 11 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7664 (mp) REVERT: Q 16 MET cc_start: 0.8418 (mmp) cc_final: 0.7764 (mmt) REVERT: R 16 MET cc_start: 0.8044 (mmp) cc_final: 0.7812 (mmt) REVERT: R 61 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6081 (mm) REVERT: R 96 LEU cc_start: 0.7398 (mp) cc_final: 0.7047 (tt) REVERT: S 11 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7744 (mp) REVERT: S 16 MET cc_start: 0.8123 (mmp) cc_final: 0.7782 (mmt) REVERT: S 96 LEU cc_start: 0.7524 (mp) cc_final: 0.7205 (tt) REVERT: T 16 MET cc_start: 0.8253 (mmp) cc_final: 0.7282 (mmt) REVERT: T 96 LEU cc_start: 0.7780 (mp) cc_final: 0.7210 (tt) REVERT: V 16 MET cc_start: 0.7975 (mmp) cc_final: 0.7189 (mmp) REVERT: W 11 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7708 (mp) REVERT: W 16 MET cc_start: 0.8175 (mmp) cc_final: 0.7668 (mmp) REVERT: X 11 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7946 (mp) REVERT: X 16 MET cc_start: 0.8125 (mmp) cc_final: 0.7658 (mmt) REVERT: Y 11 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7701 (mp) REVERT: Y 16 MET cc_start: 0.8332 (mmp) cc_final: 0.7588 (mmt) REVERT: Y 96 LEU cc_start: 0.7550 (mp) cc_final: 0.7265 (tt) REVERT: Z 16 MET cc_start: 0.7959 (mmp) cc_final: 0.7596 (mmt) REVERT: Z 61 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6562 (mm) REVERT: AA 16 MET cc_start: 0.8114 (mmt) cc_final: 0.7728 (mmt) REVERT: AA 22 MET cc_start: 0.8493 (mtt) cc_final: 0.8177 (ttt) REVERT: AA 60 ASP cc_start: 0.6203 (m-30) cc_final: 0.5869 (m-30) REVERT: AA 61 ILE cc_start: 0.6721 (OUTLIER) cc_final: 0.6190 (mm) REVERT: BA 16 MET cc_start: 0.8280 (mmp) cc_final: 0.7776 (mmt) REVERT: BA 61 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6489 (mm) outliers start: 99 outliers final: 53 residues processed: 594 average time/residue: 0.3935 time to fit residues: 419.6214 Evaluate side-chains 567 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 493 time to evaluate : 4.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 114 HIS Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 114 HIS Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 22 MET Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 56 LEU Chi-restraints excluded: chain S residue 106 ILE Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain V residue 106 ILE Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain V residue 222 ILE Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 53 THR Chi-restraints excluded: chain AA residue 56 LEU Chi-restraints excluded: chain AA residue 61 ILE Chi-restraints excluded: chain BA residue 22 MET Chi-restraints excluded: chain BA residue 56 LEU Chi-restraints excluded: chain BA residue 61 ILE Chi-restraints excluded: chain BA residue 106 ILE Chi-restraints excluded: chain BA residue 120 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 334 optimal weight: 0.9990 chunk 538 optimal weight: 0.5980 chunk 328 optimal weight: 4.9990 chunk 255 optimal weight: 0.0970 chunk 374 optimal weight: 6.9990 chunk 564 optimal weight: 2.9990 chunk 519 optimal weight: 5.9990 chunk 449 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 347 optimal weight: 0.7980 chunk 275 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS F 114 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 HIS ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS V 114 HIS ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 HIS ** Y 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 49221 Z= 0.160 Angle : 0.572 9.076 66042 Z= 0.285 Chirality : 0.042 0.172 7290 Planarity : 0.003 0.033 8397 Dihedral : 3.940 15.207 6426 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.72 % Allowed : 24.85 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.11), residues: 5751 helix: -0.05 (0.19), residues: 594 sheet: -1.49 (0.10), residues: 2619 loop : -0.13 (0.13), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 179 HIS 0.013 0.001 HIS R 114 PHE 0.021 0.001 PHEBA 146 TYR 0.007 0.001 TYR H 176 ARG 0.003 0.000 ARG M 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 525 time to evaluate : 4.469 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 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 F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 61 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6427 (mm) REVERT: B 61 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6230 (mm) REVERT: B 96 LEU cc_start: 0.7601 (mp) cc_final: 0.7294 (tt) REVERT: C 96 LEU cc_start: 0.7477 (mp) cc_final: 0.7247 (tt) REVERT: D 16 MET cc_start: 0.8305 (mmp) cc_final: 0.8034 (mmp) REVERT: D 96 LEU cc_start: 0.7528 (mp) cc_final: 0.7257 (tt) REVERT: D 190 LYS cc_start: 0.9121 (mttt) cc_final: 0.8888 (mmtt) REVERT: E 11 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7642 (mp) REVERT: E 46 PHE cc_start: 0.4940 (m-10) cc_final: 0.4506 (m-10) REVERT: E 61 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6301 (mm) REVERT: E 62 LEU cc_start: 0.6582 (tp) cc_final: 0.6297 (tp) REVERT: E 96 LEU cc_start: 0.7752 (mp) cc_final: 0.7434 (tt) REVERT: F 16 MET cc_start: 0.8321 (mmp) cc_final: 0.7768 (mmt) REVERT: F 61 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6276 (mm) REVERT: F 96 LEU cc_start: 0.7471 (mp) cc_final: 0.7122 (tt) REVERT: F 120 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8048 (pt) REVERT: F 231 PHE cc_start: 0.6168 (m-10) cc_final: 0.5952 (m-10) REVERT: G 16 MET cc_start: 0.8002 (mmt) cc_final: 0.7375 (mmt) REVERT: G 22 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8016 (mtt) REVERT: G 96 LEU cc_start: 0.7673 (mp) cc_final: 0.7259 (tt) REVERT: G 194 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7548 (tm-30) REVERT: H 16 MET cc_start: 0.8105 (mmp) cc_final: 0.7516 (mmt) REVERT: H 61 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6902 (mm) REVERT: I 16 MET cc_start: 0.8426 (mmp) cc_final: 0.7738 (mmp) REVERT: I 61 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6409 (mm) REVERT: I 96 LEU cc_start: 0.7701 (mp) cc_final: 0.7313 (tt) REVERT: J 16 MET cc_start: 0.7930 (mmp) cc_final: 0.7330 (mmt) REVERT: J 96 LEU cc_start: 0.7622 (mp) cc_final: 0.7324 (tt) REVERT: J 120 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8011 (pt) REVERT: K 96 LEU cc_start: 0.7452 (mp) cc_final: 0.7060 (tt) REVERT: K 217 LYS cc_start: 0.8868 (mttt) cc_final: 0.8597 (mmtt) REVERT: L 16 MET cc_start: 0.8224 (mmp) cc_final: 0.7826 (mmt) REVERT: L 46 PHE cc_start: 0.4433 (m-10) cc_final: 0.4067 (m-10) REVERT: L 96 LEU cc_start: 0.7594 (mp) cc_final: 0.7189 (tt) REVERT: M 16 MET cc_start: 0.8253 (mmp) cc_final: 0.7707 (mmt) REVERT: M 217 LYS cc_start: 0.8855 (mttt) cc_final: 0.8486 (mmtt) REVERT: N 16 MET cc_start: 0.7855 (mmp) cc_final: 0.7208 (mmt) REVERT: N 61 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.6447 (mt) REVERT: N 96 LEU cc_start: 0.7832 (mp) cc_final: 0.7445 (tt) REVERT: N 178 PHE cc_start: 0.7686 (p90) cc_final: 0.7334 (p90) REVERT: O 11 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7964 (mp) REVERT: O 16 MET cc_start: 0.7621 (tpp) cc_final: 0.6956 (mmm) REVERT: O 96 LEU cc_start: 0.7739 (mp) cc_final: 0.7212 (tt) REVERT: P 16 MET cc_start: 0.8164 (mmp) cc_final: 0.7517 (mmp) REVERT: P 60 ASP cc_start: 0.6657 (m-30) cc_final: 0.6431 (m-30) REVERT: P 96 LEU cc_start: 0.7543 (mp) cc_final: 0.7093 (tt) REVERT: Q 11 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7655 (mp) REVERT: Q 16 MET cc_start: 0.8393 (mmp) cc_final: 0.7736 (mmt) REVERT: Q 96 LEU cc_start: 0.7480 (mp) cc_final: 0.7193 (tt) REVERT: Q 171 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8287 (mptt) REVERT: R 16 MET cc_start: 0.8059 (mmp) cc_final: 0.7853 (mmt) REVERT: R 61 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.6137 (mm) REVERT: R 96 LEU cc_start: 0.7434 (mp) cc_final: 0.7101 (tt) REVERT: S 11 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7766 (mp) REVERT: S 16 MET cc_start: 0.8230 (mmp) cc_final: 0.7785 (mmt) REVERT: S 96 LEU cc_start: 0.7521 (mp) cc_final: 0.7237 (tt) REVERT: T 16 MET cc_start: 0.8270 (mmp) cc_final: 0.7303 (mmt) REVERT: T 96 LEU cc_start: 0.7791 (mp) cc_final: 0.7470 (tt) REVERT: V 16 MET cc_start: 0.8024 (mmp) cc_final: 0.7257 (mmp) REVERT: V 217 LYS cc_start: 0.8830 (mttt) cc_final: 0.8560 (mmtt) REVERT: W 11 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7703 (mp) REVERT: W 16 MET cc_start: 0.8155 (mmp) cc_final: 0.7517 (mmt) REVERT: X 11 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7999 (mt) REVERT: X 16 MET cc_start: 0.8098 (mmp) cc_final: 0.7665 (mmt) REVERT: Y 11 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7643 (mp) REVERT: Y 16 MET cc_start: 0.8356 (mmp) cc_final: 0.7656 (mmt) REVERT: Y 96 LEU cc_start: 0.7570 (mp) cc_final: 0.7283 (tt) REVERT: Z 16 MET cc_start: 0.7938 (mmp) cc_final: 0.7540 (mmt) REVERT: Z 61 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6557 (mm) REVERT: Z 96 LEU cc_start: 0.7606 (mp) cc_final: 0.7353 (tt) REVERT: AA 16 MET cc_start: 0.8111 (mmt) cc_final: 0.7688 (mmt) REVERT: AA 22 MET cc_start: 0.8464 (mtt) cc_final: 0.8187 (ttt) REVERT: AA 60 ASP cc_start: 0.6165 (m-30) cc_final: 0.5810 (m-30) REVERT: AA 61 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6109 (mm) REVERT: BA 16 MET cc_start: 0.8260 (mmp) cc_final: 0.7605 (mmt) REVERT: BA 61 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.6598 (mm) outliers start: 93 outliers final: 53 residues processed: 604 average time/residue: 0.3923 time to fit residues: 424.2411 Evaluate side-chains 585 residues out of total 5427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 511 time to evaluate : 5.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 114 HIS Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 114 HIS Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 22 MET Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 106 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain V residue 222 ILE Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 106 ILE Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 53 THR Chi-restraints excluded: chain AA residue 56 LEU Chi-restraints excluded: chain AA residue 61 ILE Chi-restraints excluded: chain BA residue 22 MET Chi-restraints excluded: chain BA residue 53 THR Chi-restraints excluded: chain BA residue 56 LEU Chi-restraints excluded: chain BA residue 61 ILE Chi-restraints excluded: chain BA residue 106 ILE Chi-restraints excluded: chain BA residue 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 357 optimal weight: 3.9990 chunk 479 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 414 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 450 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 462 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 HIS ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 223 HIS ** L 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 223 HIS ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS T 223 HIS V 114 HIS ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 HIS ** X 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 HIS ** Y 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.132193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.096901 restraints weight = 90071.236| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.72 r_work: 0.3698 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 49221 Z= 0.396 Angle : 0.735 12.619 66042 Z= 0.368 Chirality : 0.047 0.182 7290 Planarity : 0.004 0.031 8397 Dihedral : 4.806 16.623 6426 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.93 % Allowed : 24.85 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.11), residues: 5751 helix: -0.47 (0.20), residues: 594 sheet: -1.86 (0.10), residues: 2619 loop : -0.54 (0.13), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 179 HIS 0.014 0.002 HIS V 114 PHE 0.023 0.002 PHE Q 178 TYR 0.026 0.003 TYR M 52 ARG 0.005 0.000 ARG D 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9748.00 seconds wall clock time: 172 minutes 41.23 seconds (10361.23 seconds total)