Starting phenix.real_space_refine on Mon Sep 23 19:30:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/09_2024/8gtn_34258.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/09_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/09_2024/8gtn_34258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/09_2024/8gtn_34258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/09_2024/8gtn_34258.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/09_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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.39, per 1000 atoms: 0.22 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: 8.96 Conformation dependent library (CDL) restraints added in 4.8 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: 3.76 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: 12.45 Time building geometry restraints manager: 10.76 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.050 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: 1.580 Check model and map are aligned: 0.300 Set scattering table: 0.390 Process input model: 67.730 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.280 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.250 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 81 poor density : 872 time to evaluate : 4.683 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: 0.4750 time to fit residues: 757.8894 Evaluate side-chains 531 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 496 time to evaluate : 4.580 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 68 poor density : 621 time to evaluate : 4.613 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: 0.4364 time to fit residues: 522.1677 Evaluate side-chains 539 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 493 time to evaluate : 5.515 ------------------------------------------------------------------------------- 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: 4.9990 chunk 428 optimal weight: 20.0000 chunk 350 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 515 optimal weight: 0.9980 chunk 557 optimal weight: 5.9990 chunk 459 optimal weight: 1.9990 chunk 511 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 413 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 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 L 175 GLN ** 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 186 HIS 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 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 175 GLN ** S 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 194 GLN ** 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 Z 111 GLN Z 175 GLN ** 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: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 49221 Z= 0.397 Angle : 0.715 14.223 66042 Z= 0.362 Chirality : 0.047 0.155 7290 Planarity : 0.005 0.031 8397 Dihedral : 5.625 47.204 6466 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.74 % Allowed : 16.22 % Favored : 81.04 % 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: -2.21 (0.11), residues: 5751 helix: -0.74 (0.20), residues: 621 sheet: -2.04 (0.10), residues: 2430 loop : -0.84 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP G 179 HIS 0.006 0.002 HIS C 115 PHE 0.023 0.002 PHE G 178 TYR 0.021 0.003 TYR M 52 ARG 0.004 0.000 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 641 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 493 time to evaluate : 4.570 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. 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: symmetry clash REVERT: A 111 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: D 129 TYR cc_start: 0.7587 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: E 96 LEU cc_start: 0.7345 (mp) cc_final: 0.7077 (tt) REVERT: E 179 TRP cc_start: 0.6959 (p90) cc_final: 0.6743 (p-90) REVERT: F 16 MET cc_start: 0.8387 (mmp) cc_final: 0.8151 (mmp) REVERT: F 136 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.6025 (mtp180) REVERT: G 96 LEU cc_start: 0.7346 (mp) cc_final: 0.6880 (tt) REVERT: H 16 MET cc_start: 0.8223 (mmp) cc_final: 0.7552 (mmt) REVERT: I 16 MET cc_start: 0.8516 (mmp) cc_final: 0.7725 (mmp) REVERT: I 111 GLN cc_start: 0.7074 (OUTLIER) cc_final: 0.6231 (pp30) REVERT: L 16 MET cc_start: 0.8399 (mmp) cc_final: 0.7538 (mmp) REVERT: L 217 LYS cc_start: 0.8872 (mttt) cc_final: 0.8503 (mmtt) REVERT: M 16 MET cc_start: 0.8383 (mmp) cc_final: 0.7876 (mmt) REVERT: N 16 MET cc_start: 0.7888 (mmp) cc_final: 0.7308 (mmt) REVERT: N 129 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6731 (m-80) REVERT: P 60 ASP cc_start: 0.6856 (m-30) cc_final: 0.6610 (m-30) REVERT: P 168 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7302 (mm-30) REVERT: Q 60 ASP cc_start: 0.6498 (m-30) cc_final: 0.6270 (m-30) REVERT: Q 171 LYS cc_start: 0.8596 (mtpt) cc_final: 0.8321 (mptt) REVERT: R 179 TRP cc_start: 0.6884 (p90) cc_final: 0.6565 (p-90) REVERT: S 11 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7677 (mp) REVERT: S 16 MET cc_start: 0.8211 (mmp) cc_final: 0.7832 (mmt) REVERT: T 8 ILE cc_start: 0.8694 (tp) cc_final: 0.8490 (tp) REVERT: T 16 MET cc_start: 0.8342 (mmp) cc_final: 0.7453 (mmt) REVERT: W 11 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7772 (mp) REVERT: W 16 MET cc_start: 0.8200 (mmp) cc_final: 0.7620 (mmp) REVERT: X 16 MET cc_start: 0.8268 (mmp) cc_final: 0.7565 (mmt) REVERT: Y 11 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7734 (mp) REVERT: Y 96 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7815 (tt) REVERT: AA 16 MET cc_start: 0.8171 (mmt) cc_final: 0.7712 (mmt) REVERT: AA 129 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: BA 8 ILE cc_start: 0.8914 (tp) cc_final: 0.8687 (tp) REVERT: BA 16 MET cc_start: 0.8333 (mmp) cc_final: 0.7770 (mmt) outliers start: 148 outliers final: 66 residues processed: 626 average time/residue: 0.4238 time to fit residues: 466.4450 Evaluate side-chains 520 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 444 time to evaluate : 4.534 ------------------------------------------------------------------------------- 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 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 120 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 114 HIS Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 120 ILE 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 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 56 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 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 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 129 TYR 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 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 205 LEU Chi-restraints excluded: chain Z residue 120 ILE 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 BA residue 87 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: 0.9980 chunk 387 optimal weight: 9.9990 chunk 267 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 346 optimal weight: 0.9990 chunk 517 optimal weight: 5.9990 chunk 548 optimal weight: 2.9990 chunk 270 optimal weight: 0.5980 chunk 490 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 HIS ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 HIS L 186 HIS ** L 194 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 ** S 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 HIS V 186 HIS V 194 GLN ** 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 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 49221 Z= 0.222 Angle : 0.603 9.344 66042 Z= 0.301 Chirality : 0.043 0.143 7290 Planarity : 0.004 0.031 8397 Dihedral : 4.664 45.404 6438 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.72 % Allowed : 20.48 % 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: -1.95 (0.11), residues: 5751 helix: -0.42 (0.19), residues: 594 sheet: -1.92 (0.10), residues: 2430 loop : -0.66 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 179 HIS 0.010 0.001 HIS J 114 PHE 0.021 0.002 PHEBA 178 TYR 0.012 0.001 TYR S 176 ARG 0.004 0.000 ARG C 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 606 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 513 time to evaluate : 4.658 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: symmetry clash REVERT: A 96 LEU cc_start: 0.7499 (mp) cc_final: 0.7115 (tt) REVERT: C 11 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7909 (mp) REVERT: C 96 LEU cc_start: 0.7439 (mp) cc_final: 0.7110 (tt) REVERT: C 146 PHE cc_start: 0.6528 (t80) cc_final: 0.6308 (t80) REVERT: D 16 MET cc_start: 0.8246 (mmp) cc_final: 0.7938 (mmp) REVERT: D 217 LYS cc_start: 0.8889 (mttt) cc_final: 0.8534 (mmtt) REVERT: E 96 LEU cc_start: 0.7482 (mp) cc_final: 0.7144 (tt) REVERT: E 217 LYS cc_start: 0.8873 (mttt) cc_final: 0.8610 (mmtt) REVERT: F 16 MET cc_start: 0.8333 (mmp) cc_final: 0.7989 (mmt) REVERT: G 96 LEU cc_start: 0.7546 (mp) cc_final: 0.7131 (tt) REVERT: H 16 MET cc_start: 0.8222 (mmp) cc_final: 0.7597 (mmt) REVERT: I 16 MET cc_start: 0.8597 (mmp) cc_final: 0.7756 (mmp) REVERT: J 16 MET cc_start: 0.7816 (mmp) cc_final: 0.7469 (mmt) REVERT: J 120 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8152 (pt) REVERT: L 16 MET cc_start: 0.8283 (mmp) cc_final: 0.7530 (mmp) REVERT: L 146 PHE cc_start: 0.6818 (t80) cc_final: 0.6554 (t80) REVERT: L 217 LYS cc_start: 0.8851 (mttt) cc_final: 0.8520 (mmtt) REVERT: M 16 MET cc_start: 0.8399 (mmp) cc_final: 0.7833 (mmt) REVERT: N 16 MET cc_start: 0.7864 (mmp) cc_final: 0.7192 (mmt) REVERT: P 16 MET cc_start: 0.8204 (mmp) cc_final: 0.7536 (mmp) REVERT: P 60 ASP cc_start: 0.6838 (m-30) cc_final: 0.6541 (m-30) REVERT: Q 11 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7678 (mp) REVERT: Q 16 MET cc_start: 0.8431 (mmp) cc_final: 0.7955 (mmt) REVERT: Q 60 ASP cc_start: 0.6545 (m-30) cc_final: 0.6270 (m-30) REVERT: Q 171 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8359 (mptt) REVERT: R 96 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7942 (tt) REVERT: R 179 TRP cc_start: 0.6906 (p90) cc_final: 0.6587 (p-90) REVERT: R 217 LYS cc_start: 0.8843 (mttt) cc_final: 0.8571 (mmtt) REVERT: S 16 MET cc_start: 0.8324 (mmp) cc_final: 0.7744 (mmt) REVERT: T 16 MET cc_start: 0.8346 (mmp) cc_final: 0.7352 (mmt) REVERT: T 110 PHE cc_start: 0.6843 (m-80) cc_final: 0.6582 (m-80) REVERT: W 16 MET cc_start: 0.8147 (mmp) cc_final: 0.7629 (mmp) REVERT: W 217 LYS cc_start: 0.8751 (mttt) cc_final: 0.8523 (mmtt) REVERT: X 11 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7966 (mp) REVERT: X 16 MET cc_start: 0.8126 (mmp) cc_final: 0.7605 (mmt) REVERT: Y 16 MET cc_start: 0.8301 (mmp) cc_final: 0.7576 (mmt) REVERT: Z 16 MET cc_start: 0.7975 (mmp) cc_final: 0.7516 (mmt) REVERT: AA 16 MET cc_start: 0.8152 (mmt) cc_final: 0.7661 (mmt) REVERT: AA 22 MET cc_start: 0.8514 (mtt) cc_final: 0.8198 (ttt) REVERT: AA 129 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: AA 146 PHE cc_start: 0.6850 (t80) cc_final: 0.6407 (t80) REVERT: AA 217 LYS cc_start: 0.8867 (mttt) cc_final: 0.8488 (mmtt) REVERT: BA 8 ILE cc_start: 0.8855 (tp) cc_final: 0.8614 (tp) REVERT: BA 16 MET cc_start: 0.8338 (mmp) cc_final: 0.7759 (mmt) REVERT: BA 118 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8475 (mm) outliers start: 93 outliers final: 42 residues processed: 587 average time/residue: 0.4035 time to fit residues: 423.0798 Evaluate side-chains 534 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 485 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain C residue 11 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 120 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain I residue 56 LEU 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 87 LEU 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 120 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 R residue 96 LEU 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 V residue 22 MET 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 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 56 LEU Chi-restraints excluded: chain BA residue 118 ILE Chi-restraints excluded: chain BA residue 120 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 456 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 408 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 467 optimal weight: 1.9990 chunk 378 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 279 optimal weight: 0.0970 chunk 491 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 HIS ** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 HIS ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 116 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 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS V 114 HIS ** V 116 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 49221 Z= 0.373 Angle : 0.706 12.245 66042 Z= 0.355 Chirality : 0.046 0.154 7290 Planarity : 0.004 0.032 8397 Dihedral : 4.925 43.670 6428 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.22 % Allowed : 21.76 % Favored : 76.02 % 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: -2.32 (0.11), residues: 5751 helix: -0.50 (0.20), residues: 594 sheet: -2.15 (0.10), residues: 2430 loop : -0.96 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 179 HIS 0.015 0.002 HIS L 114 PHE 0.022 0.002 PHEAA 178 TYR 0.021 0.002 TYR M 52 ARG 0.004 0.000 ARG N 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 586 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 466 time to evaluate : 4.557 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: 0.6657 (OUTLIER) cc_final: 0.6016 (mm) REVERT: A 96 LEU cc_start: 0.7556 (mp) cc_final: 0.7184 (tt) REVERT: A 111 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7054 (pp30) REVERT: B 16 MET cc_start: 0.8053 (mmp) cc_final: 0.7748 (mmt) REVERT: C 96 LEU cc_start: 0.7465 (mp) cc_final: 0.7178 (tt) REVERT: D 16 MET cc_start: 0.8359 (mmp) cc_final: 0.7968 (mmt) REVERT: D 59 MET cc_start: 0.7828 (mpp) cc_final: 0.7546 (mpp) REVERT: D 190 LYS cc_start: 0.9045 (mttt) cc_final: 0.8823 (mmtt) REVERT: E 96 LEU cc_start: 0.7498 (mp) cc_final: 0.7252 (tt) REVERT: F 16 MET cc_start: 0.8384 (mmp) cc_final: 0.8146 (mmp) REVERT: F 136 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.6111 (mtp180) REVERT: F 231 PHE cc_start: 0.6367 (m-10) cc_final: 0.6129 (m-10) REVERT: G 96 LEU cc_start: 0.7606 (mp) cc_final: 0.7214 (tt) REVERT: H 16 MET cc_start: 0.8198 (mmp) cc_final: 0.7587 (mmt) REVERT: I 16 MET cc_start: 0.8543 (mmp) cc_final: 0.7768 (mmp) REVERT: I 61 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6348 (mm) REVERT: I 111 GLN cc_start: 0.7174 (OUTLIER) cc_final: 0.6370 (pp30) REVERT: J 16 MET cc_start: 0.7906 (mmp) cc_final: 0.7541 (mmt) REVERT: J 120 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8204 (pt) REVERT: K 16 MET cc_start: 0.8321 (mmp) cc_final: 0.8057 (mmp) REVERT: K 59 MET cc_start: 0.7615 (mpp) cc_final: 0.7404 (mpp) REVERT: L 11 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7662 (mp) REVERT: L 217 LYS cc_start: 0.8865 (mttt) cc_final: 0.8516 (mmtt) REVERT: M 16 MET cc_start: 0.8374 (mmp) cc_final: 0.7859 (mmt) REVERT: M 22 MET cc_start: 0.8521 (mtt) cc_final: 0.8119 (ttm) REVERT: N 96 LEU cc_start: 0.7540 (mp) cc_final: 0.7090 (tt) REVERT: O 11 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7916 (mp) REVERT: P 46 PHE cc_start: 0.4735 (m-10) cc_final: 0.4398 (m-80) REVERT: P 60 ASP cc_start: 0.6752 (m-30) cc_final: 0.6464 (m-30) REVERT: Q 11 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7705 (mp) REVERT: Q 16 MET cc_start: 0.8520 (mmp) cc_final: 0.7871 (mmt) REVERT: Q 60 ASP cc_start: 0.6628 (m-30) cc_final: 0.6363 (m-30) REVERT: R 96 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7967 (tt) REVERT: R 179 TRP cc_start: 0.6976 (p90) cc_final: 0.6584 (p-90) REVERT: S 11 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7667 (mp) REVERT: S 16 MET cc_start: 0.8166 (mmp) cc_final: 0.7788 (mmt) REVERT: T 16 MET cc_start: 0.8280 (mmp) cc_final: 0.7341 (mmt) REVERT: T 96 LEU cc_start: 0.7546 (mp) cc_final: 0.7101 (tt) REVERT: T 110 PHE cc_start: 0.6940 (m-80) cc_final: 0.6725 (m-80) REVERT: W 11 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7736 (mp) REVERT: W 16 MET cc_start: 0.8227 (mmp) cc_final: 0.7700 (mmp) REVERT: X 11 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8012 (mp) REVERT: X 16 MET cc_start: 0.8220 (mmp) cc_final: 0.7614 (mmt) REVERT: Y 11 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7670 (mp) REVERT: Y 111 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6713 (pp30) REVERT: Z 61 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6522 (mm) REVERT: Z 96 LEU cc_start: 0.7501 (mp) cc_final: 0.7218 (tt) REVERT: Z 192 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8908 (tttp) REVERT: AA 16 MET cc_start: 0.8128 (mmt) cc_final: 0.7722 (mmt) REVERT: BA 8 ILE cc_start: 0.8955 (tp) cc_final: 0.8595 (tp) REVERT: BA 16 MET cc_start: 0.8306 (mmp) cc_final: 0.7605 (mmt) outliers start: 120 outliers final: 78 residues processed: 570 average time/residue: 0.3969 time to fit residues: 406.5221 Evaluate side-chains 547 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 452 time to evaluate : 4.589 ------------------------------------------------------------------------------- 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 111 GLN Chi-restraints excluded: chain A residue 120 ILE 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 120 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 158 VAL 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 E residue 158 VAL 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 136 ARG Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain G residue 114 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain J residue 84 PHE 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 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 N residue 56 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 114 HIS Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 120 ILE 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 11 ILE 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 11 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 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 S residue 158 VAL 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 84 PHE 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 11 ILE 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 111 GLN Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 158 VAL Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 192 LYS Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 87 LEU Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain BA residue 22 MET Chi-restraints excluded: chain BA residue 87 LEU Chi-restraints excluded: chain BA residue 96 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: 10.0000 chunk 493 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 321 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 548 optimal weight: 1.9990 chunk 455 optimal weight: 2.9990 chunk 253 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 GLN E 186 HIS F 114 HIS ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 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** R 114 HIS ** S 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 GLN T 114 HIS ** T 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 HIS W 114 HIS ** X 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 49221 Z= 0.225 Angle : 0.601 9.206 66042 Z= 0.302 Chirality : 0.043 0.157 7290 Planarity : 0.004 0.035 8397 Dihedral : 4.422 15.361 6426 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.28 % Allowed : 22.50 % Favored : 75.22 % 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: -2.11 (0.11), residues: 5751 helix: -0.44 (0.19), residues: 594 sheet: -2.06 (0.10), residues: 2430 loop : -0.75 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 179 HIS 0.012 0.001 HIS V 114 PHE 0.027 0.002 PHE G 47 TYR 0.012 0.001 TYR N 176 ARG 0.003 0.000 ARG C 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 628 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 505 time to evaluate : 4.718 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 96 LEU cc_start: 0.7569 (mp) cc_final: 0.7253 (tt) REVERT: B 16 MET cc_start: 0.7975 (mmp) cc_final: 0.7693 (mmp) REVERT: B 61 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6322 (mm) REVERT: C 96 LEU cc_start: 0.7603 (mp) cc_final: 0.7155 (tt) REVERT: D 16 MET cc_start: 0.8371 (mmp) cc_final: 0.8009 (mmp) REVERT: D 61 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6380 (mm) REVERT: D 96 LEU cc_start: 0.7529 (mp) cc_final: 0.7034 (tt) REVERT: D 190 LYS cc_start: 0.9064 (mttt) cc_final: 0.8809 (mmtt) REVERT: E 11 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7662 (mp) REVERT: E 61 ILE cc_start: 0.6660 (OUTLIER) cc_final: 0.6288 (mm) REVERT: E 96 LEU cc_start: 0.7546 (mp) cc_final: 0.7209 (tt) REVERT: F 16 MET cc_start: 0.8227 (mmp) cc_final: 0.7782 (mmt) REVERT: F 61 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6255 (mm) REVERT: F 96 LEU cc_start: 0.7475 (mp) cc_final: 0.7067 (tt) REVERT: F 231 PHE cc_start: 0.6226 (m-10) cc_final: 0.6009 (m-10) REVERT: G 96 LEU cc_start: 0.7646 (mp) cc_final: 0.7263 (tt) REVERT: H 16 MET cc_start: 0.8109 (mmp) cc_final: 0.7498 (mmt) REVERT: H 61 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6805 (mm) REVERT: I 16 MET cc_start: 0.8518 (mmp) cc_final: 0.7747 (mmp) REVERT: J 16 MET cc_start: 0.7907 (mmp) cc_final: 0.7351 (mmt) REVERT: J 61 ILE cc_start: 0.6684 (OUTLIER) cc_final: 0.6426 (mm) REVERT: L 11 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7738 (mp) REVERT: L 16 MET cc_start: 0.8193 (mmp) cc_final: 0.7812 (mmt) REVERT: L 46 PHE cc_start: 0.4871 (m-10) cc_final: 0.4584 (m-10) REVERT: L 61 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.6261 (mm) REVERT: L 217 LYS cc_start: 0.8844 (mttt) cc_final: 0.8501 (mmtt) REVERT: M 16 MET cc_start: 0.8375 (mmp) cc_final: 0.7784 (mmt) REVERT: M 61 ILE cc_start: 0.6861 (OUTLIER) cc_final: 0.6459 (mm) REVERT: N 96 LEU cc_start: 0.7443 (mp) cc_final: 0.7044 (tt) REVERT: O 11 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7900 (mp) REVERT: O 96 LEU cc_start: 0.7553 (mp) cc_final: 0.7162 (tt) REVERT: P 16 MET cc_start: 0.8196 (mmp) cc_final: 0.7519 (mmp) REVERT: P 46 PHE cc_start: 0.4608 (m-10) cc_final: 0.4323 (m-80) REVERT: P 60 ASP cc_start: 0.6754 (m-30) cc_final: 0.6315 (m-30) REVERT: P 114 HIS cc_start: 0.6917 (OUTLIER) cc_final: 0.6656 (m-70) REVERT: P 194 GLN cc_start: 0.7333 (tm130) cc_final: 0.7070 (tm-30) REVERT: Q 11 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7695 (mp) REVERT: Q 16 MET cc_start: 0.8478 (mmp) cc_final: 0.7833 (mmt) REVERT: Q 60 ASP cc_start: 0.6616 (m-30) cc_final: 0.6158 (m-30) REVERT: Q 96 LEU cc_start: 0.8176 (pp) cc_final: 0.7951 (tt) REVERT: R 61 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6148 (mm) REVERT: R 179 TRP cc_start: 0.6842 (OUTLIER) cc_final: 0.6541 (p-90) REVERT: S 11 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7711 (mp) REVERT: S 16 MET cc_start: 0.8189 (mmp) cc_final: 0.7827 (mmt) REVERT: T 16 MET cc_start: 0.8327 (mmp) cc_final: 0.7232 (mmt) REVERT: T 96 LEU cc_start: 0.7520 (mp) cc_final: 0.7136 (tt) REVERT: V 61 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6618 (mm) REVERT: W 11 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7715 (mp) REVERT: W 16 MET cc_start: 0.8209 (mmp) cc_final: 0.7653 (mmp) REVERT: X 11 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7972 (mp) REVERT: X 16 MET cc_start: 0.8165 (mmp) cc_final: 0.7693 (mmt) REVERT: Y 11 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7715 (mp) REVERT: Y 16 MET cc_start: 0.8368 (mmp) cc_final: 0.7628 (mmt) REVERT: Y 96 LEU cc_start: 0.7541 (mp) cc_final: 0.7188 (tt) REVERT: Z 96 LEU cc_start: 0.7535 (mp) cc_final: 0.7232 (tt) REVERT: AA 16 MET cc_start: 0.8119 (mmt) cc_final: 0.7593 (mmt) REVERT: AA 22 MET cc_start: 0.8539 (mtt) cc_final: 0.8237 (ttt) REVERT: AA 61 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6356 (mm) REVERT: AA 146 PHE cc_start: 0.6949 (t80) cc_final: 0.6552 (t80) REVERT: BA 8 ILE cc_start: 0.8824 (tp) cc_final: 0.8619 (tp) REVERT: BA 16 MET cc_start: 0.8365 (mmp) cc_final: 0.7768 (mmt) REVERT: BA 61 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6438 (mm) outliers start: 123 outliers final: 54 residues processed: 606 average time/residue: 0.3946 time to fit residues: 431.5203 Evaluate side-chains 540 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 464 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 61 ILE 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 11 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 87 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 61 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 61 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 114 HIS 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 56 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 179 TRP 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 T residue 53 THR Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain V residue 61 ILE 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 13 VAL Chi-restraints excluded: chain Y residue 114 HIS 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 61 ILE Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain BA residue 22 MET 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: 0.9990 chunk 61 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 400 optimal weight: 0.7980 chunk 310 optimal weight: 10.0000 chunk 461 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 546 optimal weight: 0.9980 chunk 342 optimal weight: 4.9990 chunk 333 optimal weight: 0.3980 chunk 252 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 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 194 GLN 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** ** S 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS ** T 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 49221 Z= 0.169 Angle : 0.565 9.167 66042 Z= 0.283 Chirality : 0.042 0.190 7290 Planarity : 0.003 0.035 8397 Dihedral : 4.096 14.515 6426 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.78 % Allowed : 23.35 % Favored : 74.87 % 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: -1.81 (0.11), residues: 5751 helix: -0.20 (0.19), residues: 594 sheet: -1.87 (0.10), residues: 2430 loop : -0.55 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 179 HIS 0.012 0.001 HIS A 114 PHE 0.027 0.001 PHE Y 47 TYR 0.008 0.001 TYR X 176 ARG 0.003 0.000 ARG C 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 640 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 544 time to evaluate : 4.642 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. 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: 0.6747 (OUTLIER) cc_final: 0.6218 (mm) REVERT: A 96 LEU cc_start: 0.7545 (mp) cc_final: 0.7256 (tt) REVERT: A 194 GLN cc_start: 0.7670 (tm130) cc_final: 0.7294 (tm-30) REVERT: B 16 MET cc_start: 0.8081 (mmp) cc_final: 0.7772 (mmt) REVERT: B 61 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.6301 (mm) REVERT: B 96 LEU cc_start: 0.8070 (pp) cc_final: 0.7861 (tt) REVERT: C 16 MET cc_start: 0.8188 (mmp) cc_final: 0.7705 (mmt) REVERT: C 96 LEU cc_start: 0.7542 (mp) cc_final: 0.7193 (tt) REVERT: D 16 MET cc_start: 0.8301 (mmp) cc_final: 0.8031 (mmp) REVERT: D 61 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6455 (mm) REVERT: D 96 LEU cc_start: 0.7490 (mp) cc_final: 0.7186 (tt) REVERT: D 190 LYS cc_start: 0.9070 (mttt) cc_final: 0.8817 (mmtt) REVERT: E 11 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7664 (mp) REVERT: E 46 PHE cc_start: 0.4983 (m-10) cc_final: 0.4484 (m-10) REVERT: E 61 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6333 (mm) REVERT: E 62 LEU cc_start: 0.6753 (tp) cc_final: 0.6477 (tp) REVERT: E 96 LEU cc_start: 0.7716 (mp) cc_final: 0.7372 (tt) REVERT: E 217 LYS cc_start: 0.8900 (mttt) cc_final: 0.8695 (mmtt) REVERT: F 16 MET cc_start: 0.8284 (mmp) cc_final: 0.7768 (mmt) REVERT: F 61 ILE cc_start: 0.6660 (OUTLIER) cc_final: 0.6296 (mm) REVERT: F 96 LEU cc_start: 0.7490 (mp) cc_final: 0.7085 (tt) REVERT: F 231 PHE cc_start: 0.6132 (m-10) cc_final: 0.5892 (m-10) REVERT: G 96 LEU cc_start: 0.7596 (mp) cc_final: 0.7226 (tt) REVERT: H 16 MET cc_start: 0.8014 (mmp) cc_final: 0.7468 (mmt) REVERT: H 61 ILE cc_start: 0.7122 (OUTLIER) cc_final: 0.6835 (mm) REVERT: I 16 MET cc_start: 0.8449 (mmp) cc_final: 0.7725 (mmp) REVERT: I 61 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6430 (mm) REVERT: J 16 MET cc_start: 0.7855 (mmp) cc_final: 0.7356 (mmt) REVERT: J 120 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8113 (pt) REVERT: K 217 LYS cc_start: 0.8875 (mttt) cc_final: 0.8547 (mmtt) REVERT: L 11 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7735 (mp) REVERT: L 16 MET cc_start: 0.8154 (mmp) cc_final: 0.7870 (mmt) REVERT: L 46 PHE cc_start: 0.4582 (m-10) cc_final: 0.4211 (m-10) REVERT: L 61 ILE cc_start: 0.6614 (OUTLIER) cc_final: 0.6401 (mm) REVERT: L 217 LYS cc_start: 0.8862 (mttt) cc_final: 0.8542 (mmtt) REVERT: M 16 MET cc_start: 0.8276 (mmp) cc_final: 0.7771 (mmt) REVERT: N 61 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6302 (mm) REVERT: N 96 LEU cc_start: 0.7414 (mp) cc_final: 0.7074 (tt) REVERT: N 178 PHE cc_start: 0.7708 (p90) cc_final: 0.7176 (p90) REVERT: O 11 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7936 (mp) REVERT: O 96 LEU cc_start: 0.7679 (mp) cc_final: 0.7275 (tt) REVERT: P 16 MET cc_start: 0.8146 (mmp) cc_final: 0.7550 (mmp) REVERT: P 46 PHE cc_start: 0.4583 (m-10) cc_final: 0.4322 (m-80) REVERT: P 60 ASP cc_start: 0.6621 (m-30) cc_final: 0.6354 (m-30) REVERT: P 187 LEU cc_start: 0.8655 (mm) cc_final: 0.8410 (mm) REVERT: P 194 GLN cc_start: 0.7337 (tm130) cc_final: 0.7070 (tm-30) REVERT: Q 11 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7661 (mp) REVERT: Q 16 MET cc_start: 0.8406 (mmp) cc_final: 0.7800 (mmt) REVERT: Q 171 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8355 (mptt) REVERT: R 61 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6142 (mm) REVERT: R 179 TRP cc_start: 0.6866 (OUTLIER) cc_final: 0.6647 (p-90) REVERT: R 217 LYS cc_start: 0.8844 (mttt) cc_final: 0.8584 (mmtt) REVERT: S 11 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7769 (mp) REVERT: S 16 MET cc_start: 0.8220 (mmp) cc_final: 0.7766 (mmt) REVERT: T 16 MET cc_start: 0.8310 (mmp) cc_final: 0.7340 (mmt) REVERT: T 96 LEU cc_start: 0.7668 (mp) cc_final: 0.7342 (tt) REVERT: V 16 MET cc_start: 0.7964 (mmp) cc_final: 0.7649 (mmp) REVERT: W 11 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7712 (mp) REVERT: W 16 MET cc_start: 0.8134 (mmp) cc_final: 0.7658 (mmp) REVERT: W 61 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6453 (mm) REVERT: X 11 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7975 (mp) REVERT: X 16 MET cc_start: 0.8145 (mmp) cc_final: 0.7712 (mmt) REVERT: Y 11 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7649 (mp) REVERT: Y 16 MET cc_start: 0.8275 (mmp) cc_final: 0.7611 (mmt) REVERT: Y 96 LEU cc_start: 0.7623 (mp) cc_final: 0.7306 (tt) REVERT: Z 16 MET cc_start: 0.7944 (mmp) cc_final: 0.7549 (mmt) REVERT: Z 61 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6526 (mm) REVERT: Z 96 LEU cc_start: 0.7511 (mp) cc_final: 0.7093 (tt) REVERT: AA 16 MET cc_start: 0.8043 (mmt) cc_final: 0.7620 (mmt) REVERT: AA 22 MET cc_start: 0.8517 (mtt) cc_final: 0.8210 (ttt) REVERT: AA 61 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6238 (mm) REVERT: AA 146 PHE cc_start: 0.6868 (t80) cc_final: 0.6412 (t80) REVERT: BA 8 ILE cc_start: 0.8798 (tp) cc_final: 0.8592 (tp) REVERT: BA 16 MET cc_start: 0.8235 (mmp) cc_final: 0.7738 (mmt) REVERT: BA 61 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6452 (mm) outliers start: 96 outliers final: 36 residues processed: 623 average time/residue: 0.4028 time to fit residues: 453.4387 Evaluate side-chains 536 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 476 time to evaluate : 4.557 ------------------------------------------------------------------------------- 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 87 LEU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain D residue 22 MET 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 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 56 LEU 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 L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 61 ILE 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 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 53 THR 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 56 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 56 LEU 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 22 MET 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 61 ILE Chi-restraints excluded: chain BA residue 22 MET 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: 0.6980 chunk 218 optimal weight: 0.9990 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: 0.9990 chunk 372 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 429 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** 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 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS ** 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** 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 114 HIS P 186 HIS ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS ** T 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 HIS ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 114 HIS ** W 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 194 GLN ** 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** Z 186 HIS ** AA 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 194 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 49221 Z= 0.176 Angle : 0.578 9.803 66042 Z= 0.287 Chirality : 0.043 0.182 7290 Planarity : 0.003 0.033 8397 Dihedral : 4.078 15.694 6426 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.85 % Allowed : 24.02 % Favored : 74.13 % 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: -1.71 (0.11), residues: 5751 helix: -0.11 (0.19), residues: 594 sheet: -1.77 (0.10), residues: 2430 loop : -0.52 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 179 HIS 0.006 0.001 HIS N 114 PHE 0.025 0.001 PHE Y 47 TYR 0.010 0.001 TYRAA 52 ARG 0.003 0.000 ARG C 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 613 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 513 time to evaluate : 4.597 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. 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: 0.6704 (OUTLIER) cc_final: 0.6325 (mm) REVERT: A 96 LEU cc_start: 0.7686 (mp) cc_final: 0.7378 (tt) REVERT: A 194 GLN cc_start: 0.7666 (tm130) cc_final: 0.7282 (tm-30) REVERT: B 16 MET cc_start: 0.8110 (mmp) cc_final: 0.7777 (mmt) REVERT: B 61 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6304 (mm) REVERT: C 16 MET cc_start: 0.8188 (mmp) cc_final: 0.7717 (mmt) REVERT: C 96 LEU cc_start: 0.7442 (mp) cc_final: 0.7200 (tt) REVERT: D 16 MET cc_start: 0.8330 (mmp) cc_final: 0.8049 (mmp) REVERT: D 61 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6401 (mm) REVERT: D 96 LEU cc_start: 0.7484 (mp) cc_final: 0.7186 (tt) REVERT: D 190 LYS cc_start: 0.9090 (mttt) cc_final: 0.8846 (mmtt) REVERT: E 11 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7664 (mp) REVERT: E 46 PHE cc_start: 0.4970 (m-10) cc_final: 0.4521 (m-10) REVERT: E 61 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6250 (mm) REVERT: E 62 LEU cc_start: 0.6637 (tp) cc_final: 0.6353 (tp) REVERT: E 96 LEU cc_start: 0.7648 (mp) cc_final: 0.7331 (tt) REVERT: F 16 MET cc_start: 0.8267 (mmp) cc_final: 0.7708 (mmt) REVERT: F 96 LEU cc_start: 0.7523 (mp) cc_final: 0.7068 (tt) REVERT: F 231 PHE cc_start: 0.6134 (m-10) cc_final: 0.5890 (m-10) REVERT: G 96 LEU cc_start: 0.7625 (mp) cc_final: 0.7266 (tt) REVERT: H 16 MET cc_start: 0.8029 (mmp) cc_final: 0.7502 (mmt) REVERT: H 61 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6815 (mm) REVERT: I 16 MET cc_start: 0.8442 (mmp) cc_final: 0.7598 (mmt) REVERT: I 61 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6386 (mm) REVERT: I 96 LEU cc_start: 0.7662 (mp) cc_final: 0.7204 (tt) REVERT: I 111 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6938 (pp30) REVERT: J 16 MET cc_start: 0.7869 (mmp) cc_final: 0.7357 (mmt) REVERT: J 120 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8070 (pt) REVERT: K 96 LEU cc_start: 0.7487 (mp) cc_final: 0.7086 (tt) REVERT: K 217 LYS cc_start: 0.8879 (mttt) cc_final: 0.8547 (mmtt) REVERT: L 11 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7740 (mp) REVERT: L 16 MET cc_start: 0.8170 (mmp) cc_final: 0.7841 (mmt) REVERT: L 46 PHE cc_start: 0.4410 (m-10) cc_final: 0.4044 (m-10) REVERT: L 61 ILE cc_start: 0.6574 (OUTLIER) cc_final: 0.6312 (mm) REVERT: L 217 LYS cc_start: 0.8866 (mttt) cc_final: 0.8506 (mmtt) REVERT: M 16 MET cc_start: 0.8254 (mmp) cc_final: 0.7697 (mmt) REVERT: N 61 ILE cc_start: 0.6655 (OUTLIER) cc_final: 0.6331 (mm) REVERT: N 96 LEU cc_start: 0.7704 (mp) cc_final: 0.7305 (tt) REVERT: N 178 PHE cc_start: 0.7662 (p90) cc_final: 0.7205 (p90) REVERT: O 11 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7881 (mp) REVERT: O 96 LEU cc_start: 0.7724 (mp) cc_final: 0.7341 (tt) REVERT: P 16 MET cc_start: 0.8158 (mmp) cc_final: 0.7550 (mmp) REVERT: P 60 ASP cc_start: 0.6600 (m-30) cc_final: 0.6343 (m-30) REVERT: P 96 LEU cc_start: 0.7564 (mp) cc_final: 0.7101 (tt) REVERT: Q 11 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7659 (mp) REVERT: Q 16 MET cc_start: 0.8404 (mmp) cc_final: 0.7804 (mmt) REVERT: R 61 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.6123 (mm) REVERT: R 96 LEU cc_start: 0.7432 (mp) cc_final: 0.7106 (tt) REVERT: R 179 TRP cc_start: 0.6882 (OUTLIER) cc_final: 0.6619 (p-90) REVERT: R 217 LYS cc_start: 0.8848 (mttt) cc_final: 0.8589 (mmtt) REVERT: S 11 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7747 (mp) REVERT: S 16 MET cc_start: 0.8219 (mmp) cc_final: 0.7774 (mmt) REVERT: S 96 LEU cc_start: 0.7399 (mp) cc_final: 0.7009 (tt) REVERT: T 16 MET cc_start: 0.8293 (mmp) cc_final: 0.7339 (mmt) REVERT: T 96 LEU cc_start: 0.7735 (mp) cc_final: 0.7389 (tt) REVERT: T 110 PHE cc_start: 0.6766 (m-80) cc_final: 0.6473 (m-80) REVERT: V 96 LEU cc_start: 0.8441 (tt) cc_final: 0.8096 (mp) REVERT: W 11 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7707 (mp) REVERT: W 16 MET cc_start: 0.8154 (mmp) cc_final: 0.7664 (mmp) REVERT: X 11 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7972 (mp) REVERT: X 16 MET cc_start: 0.8126 (mmp) cc_final: 0.7680 (mmt) REVERT: Y 11 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7642 (mp) REVERT: Y 16 MET cc_start: 0.8286 (mmp) cc_final: 0.7617 (mmt) REVERT: Y 96 LEU cc_start: 0.7625 (mp) cc_final: 0.7158 (tt) REVERT: Z 16 MET cc_start: 0.7957 (mmp) cc_final: 0.7597 (mmt) REVERT: Z 61 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6523 (mm) REVERT: Z 96 LEU cc_start: 0.7452 (mp) cc_final: 0.7227 (tt) REVERT: AA 16 MET cc_start: 0.8050 (mmt) cc_final: 0.7581 (mmt) REVERT: AA 22 MET cc_start: 0.8512 (mtt) cc_final: 0.8192 (ttt) REVERT: AA 60 ASP cc_start: 0.6166 (m-30) cc_final: 0.5875 (m-30) REVERT: AA 61 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.6112 (mm) REVERT: AA 146 PHE cc_start: 0.6932 (t80) cc_final: 0.6493 (t80) REVERT: BA 8 ILE cc_start: 0.8790 (tp) cc_final: 0.8577 (tp) REVERT: BA 16 MET cc_start: 0.8264 (mmp) cc_final: 0.7757 (mmt) REVERT: BA 61 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6447 (mm) outliers start: 100 outliers final: 49 residues processed: 594 average time/residue: 0.3994 time to fit residues: 428.8468 Evaluate side-chains 563 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 491 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 13 VAL 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 56 LEU 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 120 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 53 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 61 ILE 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 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 53 THR Chi-restraints excluded: chain O residue 114 HIS 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 56 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 179 TRP 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 22 MET Chi-restraints excluded: chain V residue 106 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 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 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 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: 1.9990 chunk 477 optimal weight: 6.9990 chunk 509 optimal weight: 0.9990 chunk 306 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 399 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 460 optimal weight: 3.9990 chunk 481 optimal weight: 0.5980 chunk 507 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** 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 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 HIS ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 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** ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 HIS ** S 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS ** T 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 HIS ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 114 HIS ** W 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3694 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= 0.194 Angle : 0.593 8.977 66042 Z= 0.295 Chirality : 0.043 0.182 7290 Planarity : 0.003 0.033 8397 Dihedral : 4.138 14.939 6426 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.91 % Allowed : 24.52 % Favored : 73.57 % 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: -1.68 (0.11), residues: 5751 helix: -0.11 (0.19), residues: 594 sheet: -1.72 (0.10), residues: 2430 loop : -0.52 (0.12), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 179 HIS 0.013 0.001 HIS O 114 PHE 0.024 0.001 PHE Y 47 TYR 0.011 0.001 TYR M 52 ARG 0.003 0.000 ARG C 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 608 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 505 time to evaluate : 4.617 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. 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: 0.6730 (OUTLIER) cc_final: 0.6310 (mm) REVERT: A 96 LEU cc_start: 0.7687 (mp) cc_final: 0.7404 (tt) REVERT: A 194 GLN cc_start: 0.7676 (tm130) cc_final: 0.7288 (tm-30) REVERT: B 16 MET cc_start: 0.8157 (mmp) cc_final: 0.7789 (mmt) REVERT: B 61 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6204 (mm) REVERT: C 16 MET cc_start: 0.8155 (mmp) cc_final: 0.7627 (mmt) REVERT: C 96 LEU cc_start: 0.7501 (mp) cc_final: 0.7267 (tt) REVERT: D 16 MET cc_start: 0.8361 (mmp) cc_final: 0.8044 (mmp) REVERT: D 96 LEU cc_start: 0.7454 (mp) cc_final: 0.7183 (tt) REVERT: E 11 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7652 (mp) REVERT: E 46 PHE cc_start: 0.4959 (m-10) cc_final: 0.4517 (m-10) REVERT: E 61 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6297 (mm) REVERT: E 62 LEU cc_start: 0.6640 (tp) cc_final: 0.6356 (tp) REVERT: E 96 LEU cc_start: 0.7715 (mp) cc_final: 0.7402 (tt) REVERT: F 16 MET cc_start: 0.8268 (mmp) cc_final: 0.7678 (mmt) REVERT: F 96 LEU cc_start: 0.7538 (mp) cc_final: 0.7078 (tt) REVERT: F 231 PHE cc_start: 0.6157 (m-10) cc_final: 0.5912 (m-10) REVERT: G 96 LEU cc_start: 0.7696 (mp) cc_final: 0.7305 (tt) REVERT: G 194 GLN cc_start: 0.8007 (tm-30) cc_final: 0.7491 (tm-30) REVERT: H 16 MET cc_start: 0.8064 (mmp) cc_final: 0.7473 (mmt) REVERT: H 61 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6859 (mm) REVERT: I 16 MET cc_start: 0.8454 (mmp) cc_final: 0.7759 (mmp) REVERT: I 61 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6292 (mm) REVERT: I 96 LEU cc_start: 0.7658 (mp) cc_final: 0.7254 (tt) REVERT: I 111 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6936 (pp30) REVERT: J 16 MET cc_start: 0.7920 (mmp) cc_final: 0.7356 (mmt) REVERT: J 120 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8101 (pt) REVERT: K 96 LEU cc_start: 0.7496 (mp) cc_final: 0.7136 (tt) REVERT: K 217 LYS cc_start: 0.8877 (mttt) cc_final: 0.8632 (mmtt) REVERT: L 11 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7746 (mp) REVERT: L 16 MET cc_start: 0.8213 (mmp) cc_final: 0.7851 (mmt) REVERT: L 46 PHE cc_start: 0.4518 (m-10) cc_final: 0.4164 (m-10) REVERT: L 61 ILE cc_start: 0.6666 (OUTLIER) cc_final: 0.6450 (mm) REVERT: L 217 LYS cc_start: 0.8808 (mttt) cc_final: 0.8518 (mmtt) REVERT: M 16 MET cc_start: 0.8275 (mmp) cc_final: 0.7811 (mmt) REVERT: M 96 LEU cc_start: 0.7575 (mp) cc_final: 0.7353 (tt) REVERT: N 61 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6307 (mm) REVERT: N 96 LEU cc_start: 0.7712 (mp) cc_final: 0.7347 (tt) REVERT: N 178 PHE cc_start: 0.7675 (p90) cc_final: 0.7232 (p90) REVERT: O 11 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7887 (mp) REVERT: O 96 LEU cc_start: 0.7747 (mp) cc_final: 0.7376 (tt) REVERT: P 16 MET cc_start: 0.8149 (mmp) cc_final: 0.7542 (mmp) REVERT: P 96 LEU cc_start: 0.7634 (mp) cc_final: 0.7170 (tt) REVERT: Q 11 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7665 (mp) REVERT: Q 16 MET cc_start: 0.8433 (mmp) cc_final: 0.7658 (mmt) REVERT: Q 171 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8340 (mptt) REVERT: R 61 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.6143 (mm) REVERT: R 96 LEU cc_start: 0.7445 (mp) cc_final: 0.7104 (tt) REVERT: R 179 TRP cc_start: 0.6914 (OUTLIER) cc_final: 0.6621 (p-90) REVERT: S 11 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7752 (mp) REVERT: S 16 MET cc_start: 0.8093 (mmp) cc_final: 0.7776 (mmt) REVERT: S 96 LEU cc_start: 0.7403 (mp) cc_final: 0.7042 (tt) REVERT: T 16 MET cc_start: 0.8260 (mmp) cc_final: 0.7280 (mmt) REVERT: T 96 LEU cc_start: 0.7804 (mp) cc_final: 0.7444 (tt) REVERT: V 16 MET cc_start: 0.8062 (mmp) cc_final: 0.7598 (mmt) REVERT: W 11 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7718 (mp) REVERT: W 16 MET cc_start: 0.8109 (mmp) cc_final: 0.7547 (mmt) REVERT: X 11 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7966 (mp) REVERT: X 16 MET cc_start: 0.8175 (mmp) cc_final: 0.7708 (mmt) REVERT: Y 11 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7683 (mp) REVERT: Y 96 LEU cc_start: 0.7553 (mp) cc_final: 0.7256 (tt) REVERT: Z 16 MET cc_start: 0.7979 (mmp) cc_final: 0.7606 (mmt) REVERT: Z 61 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6646 (mt) REVERT: Z 96 LEU cc_start: 0.7455 (mp) cc_final: 0.7247 (tt) REVERT: Z 194 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7328 (tm-30) REVERT: AA 16 MET cc_start: 0.8064 (mmt) cc_final: 0.7604 (mmt) REVERT: AA 22 MET cc_start: 0.8508 (mtt) cc_final: 0.8182 (ttt) REVERT: AA 60 ASP cc_start: 0.6250 (m-30) cc_final: 0.5920 (m-30) REVERT: AA 61 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6085 (mm) REVERT: AA 146 PHE cc_start: 0.6838 (t80) cc_final: 0.6490 (t80) REVERT: BA 8 ILE cc_start: 0.8826 (tp) cc_final: 0.8604 (tp) REVERT: BA 16 MET cc_start: 0.8282 (mmp) cc_final: 0.7765 (mmt) REVERT: BA 61 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6758 (mt) outliers start: 103 outliers final: 63 residues processed: 588 average time/residue: 0.4021 time to fit residues: 425.2799 Evaluate side-chains 581 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 496 time to evaluate : 4.553 ------------------------------------------------------------------------------- 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 87 LEU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 114 HIS 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 53 THR Chi-restraints excluded: chain I residue 56 LEU 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 120 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 53 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 61 ILE 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 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 13 VAL 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 53 THR Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 179 TRP 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 22 MET 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 Y residue 114 HIS Chi-restraints excluded: chain Z 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 61 ILE Chi-restraints excluded: chain AA residue 120 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 120 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 334 optimal weight: 0.0070 chunk 538 optimal weight: 6.9990 chunk 328 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 374 optimal weight: 5.9990 chunk 564 optimal weight: 0.9980 chunk 519 optimal weight: 3.9990 chunk 449 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 347 optimal weight: 0.0870 chunk 275 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** 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 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** F 194 GLN ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN ** H 211 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** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 HIS ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 HIS ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS ** T 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 HIS ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 114 HIS W 186 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 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 49221 Z= 0.148 Angle : 0.567 10.147 66042 Z= 0.283 Chirality : 0.042 0.180 7290 Planarity : 0.003 0.033 8397 Dihedral : 3.919 17.117 6426 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.48 % Allowed : 25.13 % Favored : 73.39 % 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: -1.39 (0.11), residues: 5751 helix: 0.02 (0.19), residues: 594 sheet: -1.57 (0.11), residues: 2538 loop : -0.18 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 179 HIS 0.010 0.001 HIS N 114 PHE 0.023 0.001 PHE Y 47 TYR 0.006 0.001 TYR P 189 ARG 0.005 0.000 ARG C 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 632 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 552 time to evaluate : 4.518 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. 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. 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: 0.6919 (OUTLIER) cc_final: 0.6585 (mm) REVERT: A 96 LEU cc_start: 0.7651 (mp) cc_final: 0.7444 (tt) REVERT: B 16 MET cc_start: 0.8005 (mmp) cc_final: 0.7724 (mmt) REVERT: B 61 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6219 (mm) REVERT: C 110 PHE cc_start: 0.7191 (m-80) cc_final: 0.6951 (m-80) REVERT: D 16 MET cc_start: 0.8241 (mmp) cc_final: 0.7976 (mmp) REVERT: D 96 LEU cc_start: 0.7572 (mp) cc_final: 0.7288 (tt) REVERT: E 11 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7640 (mp) REVERT: E 46 PHE cc_start: 0.4972 (m-10) cc_final: 0.4534 (m-10) REVERT: E 61 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6333 (mm) REVERT: E 62 LEU cc_start: 0.6648 (tp) cc_final: 0.6430 (tp) REVERT: E 96 LEU cc_start: 0.7766 (mp) cc_final: 0.7476 (tt) REVERT: F 16 MET cc_start: 0.8255 (mmp) cc_final: 0.7661 (mmt) REVERT: F 96 LEU cc_start: 0.7507 (mp) cc_final: 0.7092 (tt) REVERT: F 231 PHE cc_start: 0.6159 (m-10) cc_final: 0.5910 (m-10) REVERT: G 96 LEU cc_start: 0.7657 (mp) cc_final: 0.7293 (tt) REVERT: G 194 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7549 (tm-30) REVERT: H 16 MET cc_start: 0.8012 (mmp) cc_final: 0.7469 (mmt) REVERT: H 61 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6742 (mm) REVERT: I 16 MET cc_start: 0.8370 (mmp) cc_final: 0.7576 (mmt) REVERT: I 61 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6320 (mm) REVERT: I 96 LEU cc_start: 0.7746 (mp) cc_final: 0.7476 (tt) REVERT: J 16 MET cc_start: 0.7859 (mmp) cc_final: 0.7337 (mmt) REVERT: J 120 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8025 (pt) REVERT: K 96 LEU cc_start: 0.7685 (mp) cc_final: 0.7420 (tt) REVERT: K 217 LYS cc_start: 0.8884 (mttt) cc_final: 0.8539 (mmtt) REVERT: L 11 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7736 (mp) REVERT: L 16 MET cc_start: 0.8130 (mmp) cc_final: 0.7862 (mmt) REVERT: L 46 PHE cc_start: 0.4376 (m-10) cc_final: 0.4024 (m-10) REVERT: L 62 LEU cc_start: 0.6227 (tp) cc_final: 0.6006 (tp) REVERT: L 96 LEU cc_start: 0.7681 (mp) cc_final: 0.7263 (tt) REVERT: L 217 LYS cc_start: 0.8798 (mttt) cc_final: 0.8516 (mmtt) REVERT: M 16 MET cc_start: 0.8249 (mmp) cc_final: 0.7675 (mmt) REVERT: M 96 LEU cc_start: 0.7533 (mp) cc_final: 0.7267 (tt) REVERT: N 61 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6290 (mm) REVERT: N 96 LEU cc_start: 0.7783 (mp) cc_final: 0.7388 (tt) REVERT: N 178 PHE cc_start: 0.7732 (p90) cc_final: 0.7258 (p90) REVERT: O 11 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7943 (mp) REVERT: O 96 LEU cc_start: 0.7750 (mp) cc_final: 0.7234 (tt) REVERT: P 16 MET cc_start: 0.8172 (mmp) cc_final: 0.7533 (mmp) REVERT: P 22 MET cc_start: 0.8443 (mtt) cc_final: 0.7896 (ttt) REVERT: P 96 LEU cc_start: 0.7651 (mp) cc_final: 0.7064 (tt) REVERT: Q 11 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7630 (mp) REVERT: Q 16 MET cc_start: 0.8354 (mmp) cc_final: 0.7770 (mmt) REVERT: Q 96 LEU cc_start: 0.7672 (mp) cc_final: 0.7390 (tt) REVERT: R 61 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6121 (mm) REVERT: R 96 LEU cc_start: 0.7436 (mp) cc_final: 0.7114 (tt) REVERT: R 179 TRP cc_start: 0.6869 (OUTLIER) cc_final: 0.6604 (p-90) REVERT: S 11 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7765 (mp) REVERT: S 16 MET cc_start: 0.8149 (mmp) cc_final: 0.7816 (mmt) REVERT: S 96 LEU cc_start: 0.7502 (mp) cc_final: 0.7107 (tt) REVERT: T 16 MET cc_start: 0.8313 (mmp) cc_final: 0.7309 (mmt) REVERT: T 96 LEU cc_start: 0.7835 (mp) cc_final: 0.7512 (tt) REVERT: V 16 MET cc_start: 0.7975 (mmp) cc_final: 0.7562 (mmt) REVERT: V 217 LYS cc_start: 0.8853 (mttt) cc_final: 0.8637 (mmtt) REVERT: W 11 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7760 (mp) REVERT: W 16 MET cc_start: 0.8038 (mmp) cc_final: 0.7508 (mmt) REVERT: X 11 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8025 (mt) REVERT: X 16 MET cc_start: 0.8083 (mmp) cc_final: 0.7693 (mmt) REVERT: X 111 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: Y 16 MET cc_start: 0.8261 (mmp) cc_final: 0.7574 (mmt) REVERT: Y 96 LEU cc_start: 0.7594 (mp) cc_final: 0.7327 (tt) REVERT: Z 16 MET cc_start: 0.7915 (mmp) cc_final: 0.7538 (mmt) REVERT: Z 96 LEU cc_start: 0.7456 (mp) cc_final: 0.7237 (tt) REVERT: AA 16 MET cc_start: 0.8036 (mmt) cc_final: 0.7544 (mmt) REVERT: AA 22 MET cc_start: 0.8474 (mtt) cc_final: 0.8181 (ttt) REVERT: AA 60 ASP cc_start: 0.6120 (m-30) cc_final: 0.5767 (m-30) REVERT: AA 61 ILE cc_start: 0.6610 (OUTLIER) cc_final: 0.6045 (mm) REVERT: AA 146 PHE cc_start: 0.6740 (t80) cc_final: 0.6333 (t80) REVERT: BA 8 ILE cc_start: 0.8758 (tp) cc_final: 0.8552 (tp) REVERT: BA 16 MET cc_start: 0.8233 (mmp) cc_final: 0.7741 (mmt) outliers start: 80 outliers final: 40 residues processed: 618 average time/residue: 0.4079 time to fit residues: 448.8923 Evaluate side-chains 575 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 517 time to evaluate : 4.527 ------------------------------------------------------------------------------- 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 111 GLN Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 106 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 53 THR 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 56 LEU Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N 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 53 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain O residue 114 HIS Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 179 TRP 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 T residue 53 THR Chi-restraints excluded: chain V residue 114 HIS Chi-restraints excluded: chain W residue 11 ILE 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 Z residue 13 VAL 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 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 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: 3.9990 chunk 137 optimal weight: 0.9980 chunk 414 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 125 optimal weight: 0.3980 chunk 450 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 462 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** 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** N 114 HIS ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 HIS ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 114 HIS ** T 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 HIS ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 114 HIS ** W 116 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.134263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.099204 restraints weight = 89238.218| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.75 r_work: 0.3749 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3863 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= 0.265 Angle : 0.648 9.843 66042 Z= 0.323 Chirality : 0.044 0.169 7290 Planarity : 0.004 0.034 8397 Dihedral : 4.374 15.399 6426 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.78 % Allowed : 25.44 % Favored : 72.78 % 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: -1.61 (0.11), residues: 5751 helix: -0.13 (0.20), residues: 594 sheet: -1.72 (0.10), residues: 2619 loop : -0.27 (0.13), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 179 HIS 0.021 0.001 HIS V 114 PHE 0.023 0.002 PHE Y 47 TYR 0.018 0.002 TYR C 52 ARG 0.004 0.000 ARG O 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10050.21 seconds wall clock time: 175 minutes 40.75 seconds (10540.75 seconds total)