Starting phenix.real_space_refine on Wed Mar 4 16:24:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ncv_0438/03_2026/6ncv_0438.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ncv_0438/03_2026/6ncv_0438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ncv_0438/03_2026/6ncv_0438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ncv_0438/03_2026/6ncv_0438.map" model { file = "/net/cci-nas-00/data/ceres_data/6ncv_0438/03_2026/6ncv_0438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ncv_0438/03_2026/6ncv_0438.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.020 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: 3 Type Number sf(0) Gaussians C 9597 2.51 5 N 3087 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 231 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15456 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V Time building chain proxies: 1.47, per 1000 atoms: 0.10 Number of scatterers: 15456 At special positions: 0 Unit cell: (98.58, 95.4, 122.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2772 8.00 N 3087 7.00 C 9597 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: 1.15 Conformation dependent library (CDL) restraints added in 542.8 milliseconds 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 0 sheets defined 69.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.778A pdb=" N LEU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 removed outlier: 3.874A pdb=" N THR B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG C 55 " --> pdb=" O PRO C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS D 39 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.842A pdb=" N ALA D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS E 35 " --> pdb=" O GLN E 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 removed outlier: 3.746A pdb=" N ARG E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.844A pdb=" N ALA E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS F 35 " --> pdb=" O GLN F 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS F 39 " --> pdb=" O LYS F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG F 55 " --> pdb=" O PRO F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.844A pdb=" N ALA F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU F 99 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS G 35 " --> pdb=" O GLN G 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG G 55 " --> pdb=" O PRO G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU G 99 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG G 100 " --> pdb=" O GLN G 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG H 55 " --> pdb=" O PRO H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR H 84 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.842A pdb=" N ALA H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG H 100 " --> pdb=" O GLN H 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 102 " --> pdb=" O GLN H 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS I 39 " --> pdb=" O LYS I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG I 55 " --> pdb=" O PRO I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA I 69 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR I 84 " --> pdb=" O VAL I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG I 100 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU I 102 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU J 22 " --> pdb=" O ALA J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS J 35 " --> pdb=" O GLN J 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS J 39 " --> pdb=" O LYS J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG J 55 " --> pdb=" O PRO J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA J 69 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR J 84 " --> pdb=" O VAL J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU J 99 " --> pdb=" O ALA J 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG J 100 " --> pdb=" O GLN J 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU J 102 " --> pdb=" O GLN J 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU K 22 " --> pdb=" O ALA K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS K 35 " --> pdb=" O GLN K 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS K 39 " --> pdb=" O LYS K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG K 55 " --> pdb=" O PRO K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA K 69 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR K 84 " --> pdb=" O VAL K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA K 94 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU K 99 " --> pdb=" O ALA K 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG K 100 " --> pdb=" O GLN K 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU K 102 " --> pdb=" O GLN K 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU L 22 " --> pdb=" O ALA L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS L 35 " --> pdb=" O GLN L 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS L 39 " --> pdb=" O LYS L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG L 55 " --> pdb=" O PRO L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA L 69 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR L 72 " --> pdb=" O LEU L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR L 84 " --> pdb=" O VAL L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU L 99 " --> pdb=" O ALA L 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG L 100 " --> pdb=" O GLN L 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU L 102 " --> pdb=" O GLN L 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS M 35 " --> pdb=" O GLN M 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS M 39 " --> pdb=" O LYS M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG M 55 " --> pdb=" O PRO M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA M 69 " --> pdb=" O ALA M 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR M 84 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU M 99 " --> pdb=" O ALA M 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU M 102 " --> pdb=" O GLN M 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS N 35 " --> pdb=" O GLN N 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS N 39 " --> pdb=" O LYS N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG N 55 " --> pdb=" O PRO N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA N 69 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 102 removed outlier: 3.844A pdb=" N ALA N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU N 99 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG N 100 " --> pdb=" O GLN N 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU N 102 " --> pdb=" O GLN N 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS O 35 " --> pdb=" O GLN O 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS O 39 " --> pdb=" O LYS O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG O 55 " --> pdb=" O PRO O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR O 72 " --> pdb=" O LEU O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA O 94 " --> pdb=" O ALA O 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU O 99 " --> pdb=" O ALA O 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG O 100 " --> pdb=" O GLN O 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU O 102 " --> pdb=" O GLN O 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU P 22 " --> pdb=" O ALA P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS P 35 " --> pdb=" O GLN P 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS P 39 " --> pdb=" O LYS P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG P 55 " --> pdb=" O PRO P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA P 69 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR P 72 " --> pdb=" O LEU P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR P 84 " --> pdb=" O VAL P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA P 94 " --> pdb=" O ALA P 90 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU P 99 " --> pdb=" O ALA P 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG P 100 " --> pdb=" O GLN P 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU P 102 " --> pdb=" O GLN P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU Q 22 " --> pdb=" O ALA Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS Q 35 " --> pdb=" O GLN Q 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS Q 39 " --> pdb=" O LYS Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG Q 55 " --> pdb=" O PRO Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA Q 69 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR Q 72 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR Q 84 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG Q 100 " --> pdb=" O GLN Q 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU Q 102 " --> pdb=" O GLN Q 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU R 22 " --> pdb=" O ALA R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS R 35 " --> pdb=" O GLN R 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS R 39 " --> pdb=" O LYS R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG R 55 " --> pdb=" O PRO R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA R 69 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 86 removed outlier: 3.874A pdb=" N THR R 84 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU R 99 " --> pdb=" O ALA R 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG R 100 " --> pdb=" O GLN R 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU R 102 " --> pdb=" O GLN R 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU S 22 " --> pdb=" O ALA S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS S 35 " --> pdb=" O GLN S 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS S 39 " --> pdb=" O LYS S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG S 55 " --> pdb=" O PRO S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR S 72 " --> pdb=" O LEU S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR S 84 " --> pdb=" O VAL S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA S 94 " --> pdb=" O ALA S 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU S 99 " --> pdb=" O ALA S 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG S 100 " --> pdb=" O GLN S 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU S 102 " --> pdb=" O GLN S 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU T 22 " --> pdb=" O ALA T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS T 35 " --> pdb=" O GLN T 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS T 39 " --> pdb=" O LYS T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG T 55 " --> pdb=" O PRO T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA T 69 " --> pdb=" O ALA T 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR T 72 " --> pdb=" O LEU T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR T 84 " --> pdb=" O VAL T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 102 removed outlier: 3.844A pdb=" N ALA T 94 " --> pdb=" O ALA T 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU T 99 " --> pdb=" O ALA T 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG T 100 " --> pdb=" O GLN T 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU T 102 " --> pdb=" O GLN T 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU V 22 " --> pdb=" O ALA V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS V 35 " --> pdb=" O GLN V 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS V 39 " --> pdb=" O LYS V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG V 55 " --> pdb=" O PRO V 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA V 69 " --> pdb=" O ALA V 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR V 72 " --> pdb=" O LEU V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 86 removed outlier: 3.872A pdb=" N THR V 84 " --> pdb=" O VAL V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA V 94 " --> pdb=" O ALA V 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU V 99 " --> pdb=" O ALA V 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG V 100 " --> pdb=" O GLN V 96 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU V 102 " --> pdb=" O GLN V 98 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 2688 1.29 - 1.35: 3003 1.35 - 1.42: 651 1.42 - 1.49: 2548 1.49 - 1.55: 6755 Bond restraints: 15645 Sorted by residual: bond pdb=" CB TRP G 53 " pdb=" CG TRP G 53 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.65e+00 bond pdb=" CB TRP B 53 " pdb=" CG TRP B 53 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.61e+00 bond pdb=" CB TRP M 53 " pdb=" CG TRP M 53 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.59e+00 bond pdb=" CB TRP Q 53 " pdb=" CG TRP Q 53 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.57e+00 bond pdb=" CB TRP K 53 " pdb=" CG TRP K 53 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.56e+00 ... (remaining 15640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 19494 1.57 - 3.14: 1157 3.14 - 4.72: 303 4.72 - 6.29: 25 6.29 - 7.86: 42 Bond angle restraints: 21021 Sorted by residual: angle pdb=" CB ARG J 58 " pdb=" CG ARG J 58 " pdb=" CD ARG J 58 " ideal model delta sigma weight residual 111.30 119.16 -7.86 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CB ARG S 58 " pdb=" CG ARG S 58 " pdb=" CD ARG S 58 " ideal model delta sigma weight residual 111.30 119.16 -7.86 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CB ARG R 58 " pdb=" CG ARG R 58 " pdb=" CD ARG R 58 " ideal model delta sigma weight residual 111.30 119.15 -7.85 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CB ARG N 58 " pdb=" CG ARG N 58 " pdb=" CD ARG N 58 " ideal model delta sigma weight residual 111.30 119.14 -7.84 2.30e+00 1.89e-01 1.16e+01 angle pdb=" CB ARG C 58 " pdb=" CG ARG C 58 " pdb=" CD ARG C 58 " ideal model delta sigma weight residual 111.30 119.13 -7.83 2.30e+00 1.89e-01 1.16e+01 ... (remaining 21016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.91: 7938 13.91 - 27.82: 1281 27.82 - 41.72: 504 41.72 - 55.63: 105 55.63 - 69.54: 105 Dihedral angle restraints: 9933 sinusoidal: 4368 harmonic: 5565 Sorted by residual: dihedral pdb=" CA GLU K 27 " pdb=" C GLU K 27 " pdb=" N GLU K 28 " pdb=" CA GLU K 28 " ideal model delta harmonic sigma weight residual 180.00 162.73 17.27 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLU C 27 " pdb=" C GLU C 27 " pdb=" N GLU C 28 " pdb=" CA GLU C 28 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLU N 27 " pdb=" C GLU N 27 " pdb=" N GLU N 28 " pdb=" CA GLU N 28 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 9930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1023 0.026 - 0.052: 622 0.052 - 0.078: 409 0.078 - 0.104: 189 0.104 - 0.130: 46 Chirality restraints: 2289 Sorted by residual: chirality pdb=" CB VAL I 93 " pdb=" CA VAL I 93 " pdb=" CG1 VAL I 93 " pdb=" CG2 VAL I 93 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CB VAL S 93 " pdb=" CA VAL S 93 " pdb=" CG1 VAL S 93 " pdb=" CG2 VAL S 93 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CB VAL P 93 " pdb=" CA VAL P 93 " pdb=" CG1 VAL P 93 " pdb=" CG2 VAL P 93 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2286 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 75 " 0.026 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO C 76 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU O 75 " -0.026 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO O 76 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO O 76 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO O 76 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 75 " -0.026 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO E 76 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 76 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 76 " -0.022 5.00e-02 4.00e+02 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 5434 2.90 - 3.40: 14511 3.40 - 3.90: 23366 3.90 - 4.40: 27137 4.40 - 4.90: 45253 Nonbonded interactions: 115701 Sorted by model distance: nonbonded pdb=" OG SER M 30 " pdb=" N GLN M 31 " model vdw 2.398 3.120 nonbonded pdb=" OG SER H 30 " pdb=" N GLN H 31 " model vdw 2.398 3.120 nonbonded pdb=" OG SER J 30 " pdb=" N GLN J 31 " model vdw 2.398 3.120 nonbonded pdb=" OG SER K 30 " pdb=" N GLN K 31 " model vdw 2.398 3.120 nonbonded pdb=" OG SER B 30 " pdb=" N GLN B 31 " model vdw 2.398 3.120 ... (remaining 115696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.970 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.008 0.066 15645 Z= 0.341 Angle : 0.941 7.862 21021 Z= 0.527 Chirality : 0.047 0.130 2289 Planarity : 0.005 0.038 2835 Dihedral : 17.275 69.540 6279 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.74 % Allowed : 12.33 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.46 (0.10), residues: 1869 helix: -4.69 (0.06), residues: 1155 sheet: None (None), residues: 0 loop : -3.24 (0.16), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 58 TYR 0.004 0.001 TYR P 72 PHE 0.004 0.001 PHE K 37 TRP 0.010 0.003 TRP K 53 HIS 0.002 0.001 HIS N 39 Details of bonding type rmsd covalent geometry : bond 0.00782 (15645) covalent geometry : angle 0.94085 (21021) hydrogen bonds : bond 0.32710 ( 610) hydrogen bonds : angle 9.60915 ( 1767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 570 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.9143 (tttt) cc_final: 0.8856 (tttm) REVERT: A 40 LYS cc_start: 0.9010 (tppt) cc_final: 0.8766 (mttm) REVERT: A 57 GLU cc_start: 0.8070 (tt0) cc_final: 0.7740 (tt0) REVERT: A 66 GLU cc_start: 0.8099 (tp30) cc_final: 0.7786 (tm-30) REVERT: A 86 LYS cc_start: 0.9040 (mttt) cc_final: 0.8643 (mtpp) REVERT: A 96 GLN cc_start: 0.9339 (tm-30) cc_final: 0.8993 (tm-30) REVERT: B 30 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8296 (p) REVERT: B 31 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8651 (tm-30) REVERT: B 32 GLU cc_start: 0.9000 (tp30) cc_final: 0.8768 (tp30) REVERT: B 35 LYS cc_start: 0.9470 (tttt) cc_final: 0.9160 (ttmm) REVERT: B 60 ASP cc_start: 0.8429 (t70) cc_final: 0.8221 (t70) REVERT: C 35 LYS cc_start: 0.9132 (tttt) cc_final: 0.8856 (tttp) REVERT: C 40 LYS cc_start: 0.9081 (tppt) cc_final: 0.8849 (mmtt) REVERT: C 63 ASP cc_start: 0.8726 (m-30) cc_final: 0.8494 (m-30) REVERT: D 31 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8659 (tm-30) REVERT: D 63 ASP cc_start: 0.8672 (m-30) cc_final: 0.8348 (m-30) REVERT: E 35 LYS cc_start: 0.9382 (tttt) cc_final: 0.9112 (tttt) REVERT: E 83 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8783 (mmtm) REVERT: E 96 GLN cc_start: 0.8905 (tm-30) cc_final: 0.7867 (tm-30) REVERT: F 33 GLN cc_start: 0.8373 (mt0) cc_final: 0.8057 (mt0) REVERT: F 35 LYS cc_start: 0.9172 (tttt) cc_final: 0.8840 (tttm) REVERT: F 83 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8925 (mtpp) REVERT: G 15 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8658 (tp) REVERT: G 40 LYS cc_start: 0.9243 (tppt) cc_final: 0.8998 (mttm) REVERT: G 58 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7853 (mtt90) REVERT: G 86 LYS cc_start: 0.9156 (mttt) cc_final: 0.8914 (mttm) REVERT: G 89 ASP cc_start: 0.8367 (m-30) cc_final: 0.8130 (m-30) REVERT: G 96 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8279 (tm-30) REVERT: H 30 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8375 (p) REVERT: H 31 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8612 (tm-30) REVERT: H 32 GLU cc_start: 0.9039 (tp30) cc_final: 0.8650 (tp30) REVERT: H 60 ASP cc_start: 0.8419 (t70) cc_final: 0.8146 (t0) REVERT: H 66 GLU cc_start: 0.8580 (tp30) cc_final: 0.8133 (mt-10) REVERT: I 32 GLU cc_start: 0.8879 (tp30) cc_final: 0.8474 (tp30) REVERT: I 86 LYS cc_start: 0.8900 (mttt) cc_final: 0.8573 (mtpp) REVERT: I 96 GLN cc_start: 0.9258 (tm-30) cc_final: 0.8762 (tm-30) REVERT: J 15 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8982 (tp) REVERT: K 31 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8605 (tm-30) REVERT: K 63 ASP cc_start: 0.8713 (m-30) cc_final: 0.8465 (m-30) REVERT: L 30 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8595 (t) REVERT: L 83 LYS cc_start: 0.9106 (mtpt) cc_final: 0.8829 (mmtt) REVERT: L 96 GLN cc_start: 0.8912 (tm-30) cc_final: 0.7567 (tm-30) REVERT: M 31 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8583 (tm-30) REVERT: M 33 GLN cc_start: 0.8359 (mt0) cc_final: 0.7920 (mt0) REVERT: M 57 GLU cc_start: 0.8665 (tt0) cc_final: 0.8184 (tt0) REVERT: M 83 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8920 (mtpp) REVERT: N 15 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8454 (tp) REVERT: N 40 LYS cc_start: 0.9169 (tppt) cc_final: 0.8937 (mttm) REVERT: N 58 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7850 (mtt180) REVERT: N 86 LYS cc_start: 0.9247 (mttt) cc_final: 0.8978 (mttp) REVERT: N 89 ASP cc_start: 0.8293 (m-30) cc_final: 0.8015 (m-30) REVERT: N 96 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8213 (tm-30) REVERT: O 30 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8183 (p) REVERT: O 31 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8568 (tm-30) REVERT: O 32 GLU cc_start: 0.8946 (tp30) cc_final: 0.8686 (tp30) REVERT: O 66 GLU cc_start: 0.8287 (tp30) cc_final: 0.7786 (mt-10) REVERT: P 31 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8722 (tm-30) REVERT: P 35 LYS cc_start: 0.9056 (tttt) cc_final: 0.8829 (tptm) REVERT: P 66 GLU cc_start: 0.8309 (tp30) cc_final: 0.8081 (tm-30) REVERT: P 86 LYS cc_start: 0.8869 (mttt) cc_final: 0.8536 (mtpp) REVERT: P 96 GLN cc_start: 0.9311 (tm-30) cc_final: 0.8742 (tm-30) REVERT: Q 31 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8294 (tm-30) REVERT: Q 35 LYS cc_start: 0.9295 (tttt) cc_final: 0.9005 (tttp) REVERT: Q 63 ASP cc_start: 0.8693 (m-30) cc_final: 0.8492 (m-30) REVERT: R 31 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8600 (tm-30) REVERT: R 32 GLU cc_start: 0.8848 (tp30) cc_final: 0.8623 (tp30) REVERT: R 57 GLU cc_start: 0.8076 (tt0) cc_final: 0.7689 (tt0) REVERT: R 83 LYS cc_start: 0.9197 (mtpt) cc_final: 0.8912 (mtpp) REVERT: R 89 ASP cc_start: 0.8241 (m-30) cc_final: 0.8033 (m-30) REVERT: S 63 ASP cc_start: 0.8885 (m-30) cc_final: 0.8608 (m-30) REVERT: S 83 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8872 (mmtt) REVERT: T 31 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8643 (tm-30) REVERT: T 33 GLN cc_start: 0.8288 (mt0) cc_final: 0.7737 (mt0) REVERT: T 35 LYS cc_start: 0.9169 (tttt) cc_final: 0.8898 (tttm) REVERT: T 57 GLU cc_start: 0.8675 (tt0) cc_final: 0.8215 (tt0) REVERT: T 79 GLU cc_start: 0.8233 (tp30) cc_final: 0.7812 (tp30) REVERT: T 83 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8769 (mtpp) REVERT: V 40 LYS cc_start: 0.9276 (tppt) cc_final: 0.9011 (mttm) REVERT: V 57 GLU cc_start: 0.7907 (tt0) cc_final: 0.7616 (tt0) REVERT: V 58 ARG cc_start: 0.8360 (mtm110) cc_final: 0.7857 (mtt180) REVERT: V 86 LYS cc_start: 0.9196 (mttt) cc_final: 0.8923 (mttm) REVERT: V 89 ASP cc_start: 0.8205 (m-30) cc_final: 0.7971 (m-30) REVERT: V 96 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8445 (tm-30) outliers start: 42 outliers final: 11 residues processed: 599 average time/residue: 0.1427 time to fit residues: 119.8640 Evaluate side-chains 436 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 418 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain T residue 30 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN C 33 GLN C 39 HIS C 70 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 HIS ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS F 103 GLN I 39 HIS J 33 GLN J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN M 39 HIS O 70 GLN O 96 GLN Q 39 HIS R 39 HIS ** R 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 GLN S 96 GLN ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.091474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.077599 restraints weight = 34901.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.080302 restraints weight = 18095.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.082162 restraints weight = 11308.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.083425 restraints weight = 8010.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.084289 restraints weight = 6198.440| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15645 Z= 0.138 Angle : 0.576 8.055 21021 Z= 0.298 Chirality : 0.038 0.155 2289 Planarity : 0.005 0.033 2835 Dihedral : 5.305 55.526 2227 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.41 % Allowed : 16.96 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.96 (0.14), residues: 1869 helix: -3.36 (0.10), residues: 1239 sheet: None (None), residues: 0 loop : -2.69 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 58 TYR 0.005 0.001 TYR P 72 PHE 0.005 0.001 PHE H 37 TRP 0.008 0.001 TRP G 53 HIS 0.005 0.001 HIS R 39 Details of bonding type rmsd covalent geometry : bond 0.00315 (15645) covalent geometry : angle 0.57648 (21021) hydrogen bonds : bond 0.04300 ( 610) hydrogen bonds : angle 4.72731 ( 1767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 462 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8546 (tm-30) REVERT: A 66 GLU cc_start: 0.8361 (tp30) cc_final: 0.7845 (tm-30) REVERT: B 30 SER cc_start: 0.8400 (t) cc_final: 0.7823 (p) REVERT: B 31 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8525 (tm-30) REVERT: B 32 GLU cc_start: 0.8752 (tp30) cc_final: 0.8338 (tp30) REVERT: B 83 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8015 (mmtt) REVERT: B 96 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8905 (tm-30) REVERT: C 32 GLU cc_start: 0.8420 (tp30) cc_final: 0.8119 (tp30) REVERT: D 31 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8376 (tm-30) REVERT: D 35 LYS cc_start: 0.9327 (tttp) cc_final: 0.9099 (tttp) REVERT: D 39 HIS cc_start: 0.7142 (t-90) cc_final: 0.6201 (t-90) REVERT: D 57 GLU cc_start: 0.7740 (tt0) cc_final: 0.7514 (tt0) REVERT: D 99 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8062 (tm-30) REVERT: E 20 GLU cc_start: 0.8674 (tp30) cc_final: 0.8375 (tm-30) REVERT: E 32 GLU cc_start: 0.8372 (tp30) cc_final: 0.7845 (tp30) REVERT: F 32 GLU cc_start: 0.8570 (tp30) cc_final: 0.8349 (tp30) REVERT: G 58 ARG cc_start: 0.8399 (mtm110) cc_final: 0.7941 (mtt-85) REVERT: G 89 ASP cc_start: 0.8307 (m-30) cc_final: 0.8052 (m-30) REVERT: G 96 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8473 (tm-30) REVERT: H 30 SER cc_start: 0.8555 (t) cc_final: 0.7942 (p) REVERT: H 31 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8314 (tm-30) REVERT: H 32 GLU cc_start: 0.8743 (tp30) cc_final: 0.8412 (tp30) REVERT: H 66 GLU cc_start: 0.8499 (tp30) cc_final: 0.8018 (tp30) REVERT: I 66 GLU cc_start: 0.7880 (tt0) cc_final: 0.7067 (mt-10) REVERT: J 21 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8976 (mp) REVERT: J 39 HIS cc_start: 0.8265 (t70) cc_final: 0.8001 (t70) REVERT: J 79 GLU cc_start: 0.8934 (tp30) cc_final: 0.8731 (tp30) REVERT: K 31 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8293 (tm-30) REVERT: L 31 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8495 (tm-30) REVERT: L 32 GLU cc_start: 0.8539 (tp30) cc_final: 0.7978 (tp30) REVERT: L 89 ASP cc_start: 0.7720 (m-30) cc_final: 0.7436 (m-30) REVERT: L 99 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: N 20 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8045 (mm-30) REVERT: N 31 GLN cc_start: 0.8508 (tt0) cc_final: 0.8227 (pt0) REVERT: O 30 SER cc_start: 0.8504 (t) cc_final: 0.7586 (p) REVERT: O 31 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8327 (tm-30) REVERT: O 32 GLU cc_start: 0.8611 (tp30) cc_final: 0.8312 (tp30) REVERT: O 33 GLN cc_start: 0.9015 (mt0) cc_final: 0.8331 (mt0) REVERT: O 66 GLU cc_start: 0.8300 (tp30) cc_final: 0.7717 (tm-30) REVERT: P 20 GLU cc_start: 0.8411 (tt0) cc_final: 0.8188 (tt0) REVERT: P 66 GLU cc_start: 0.8207 (tp30) cc_final: 0.7941 (tm-30) REVERT: P 79 GLU cc_start: 0.8579 (tp30) cc_final: 0.8337 (tp30) REVERT: Q 79 GLU cc_start: 0.8898 (tp30) cc_final: 0.8623 (tp30) REVERT: R 31 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8211 (tm-30) REVERT: R 32 GLU cc_start: 0.8596 (tp30) cc_final: 0.7869 (tp30) REVERT: R 35 LYS cc_start: 0.9280 (tttm) cc_final: 0.9044 (tttp) REVERT: R 39 HIS cc_start: 0.7325 (t-90) cc_final: 0.7059 (t-90) REVERT: R 79 GLU cc_start: 0.8369 (tp30) cc_final: 0.7570 (tp30) REVERT: R 83 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8344 (ttmm) REVERT: R 99 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: S 32 GLU cc_start: 0.8403 (tp30) cc_final: 0.7783 (tp30) REVERT: S 83 LYS cc_start: 0.9034 (mtpt) cc_final: 0.8829 (mmtm) REVERT: S 99 GLU cc_start: 0.8428 (pt0) cc_final: 0.7985 (tm-30) REVERT: T 83 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8848 (mtpp) REVERT: V 20 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7978 (mm-30) REVERT: V 58 ARG cc_start: 0.8469 (mtm110) cc_final: 0.7967 (mtt-85) REVERT: V 89 ASP cc_start: 0.8243 (m-30) cc_final: 0.7863 (m-30) REVERT: V 96 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8245 (tm-30) outliers start: 37 outliers final: 18 residues processed: 478 average time/residue: 0.1275 time to fit residues: 89.0811 Evaluate side-chains 427 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 405 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 39 HIS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain Q residue 39 HIS Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 96 GLN Chi-restraints excluded: chain T residue 39 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 72 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 96 optimal weight: 0.0670 chunk 105 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 33 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 HIS ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN F 39 HIS F 96 GLN I 39 HIS I 96 GLN J 96 GLN L 96 GLN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 GLN P 39 HIS P 96 GLN Q 39 HIS S 96 GLN T 39 HIS ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.090248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.076161 restraints weight = 35107.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078860 restraints weight = 18220.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.080756 restraints weight = 11452.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.082024 restraints weight = 8097.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.082851 restraints weight = 6309.715| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15645 Z= 0.149 Angle : 0.543 5.710 21021 Z= 0.285 Chirality : 0.038 0.132 2289 Planarity : 0.004 0.033 2835 Dihedral : 4.357 55.106 2210 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.20 % Allowed : 19.05 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.16), residues: 1869 helix: -2.48 (0.12), residues: 1239 sheet: None (None), residues: 0 loop : -2.18 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 58 TYR 0.005 0.001 TYR T 72 PHE 0.007 0.001 PHE H 37 TRP 0.003 0.001 TRP E 53 HIS 0.015 0.002 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00352 (15645) covalent geometry : angle 0.54278 (21021) hydrogen bonds : bond 0.03763 ( 610) hydrogen bonds : angle 4.24769 ( 1767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 421 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8595 (tm-30) REVERT: A 66 GLU cc_start: 0.8269 (tp30) cc_final: 0.7810 (tm-30) REVERT: A 98 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8969 (mm-40) REVERT: B 30 SER cc_start: 0.8460 (t) cc_final: 0.7684 (p) REVERT: B 31 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8377 (tm-30) REVERT: B 32 GLU cc_start: 0.8698 (tp30) cc_final: 0.8263 (tp30) REVERT: B 33 GLN cc_start: 0.9092 (mt0) cc_final: 0.8683 (mt0) REVERT: B 83 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8128 (mmtt) REVERT: C 21 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8969 (mp) REVERT: D 31 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8369 (tm-30) REVERT: D 32 GLU cc_start: 0.8647 (tp30) cc_final: 0.8179 (tp30) REVERT: E 20 GLU cc_start: 0.8704 (tp30) cc_final: 0.8332 (tm-30) REVERT: E 32 GLU cc_start: 0.8414 (tp30) cc_final: 0.7804 (tp30) REVERT: E 79 GLU cc_start: 0.8649 (tp30) cc_final: 0.8294 (tp30) REVERT: E 96 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: E 100 ARG cc_start: 0.8486 (mtm180) cc_final: 0.8279 (mtm180) REVERT: F 32 GLU cc_start: 0.8581 (tp30) cc_final: 0.8244 (tp30) REVERT: G 58 ARG cc_start: 0.8446 (mtm110) cc_final: 0.8006 (mtt-85) REVERT: G 96 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8017 (tm-30) REVERT: H 30 SER cc_start: 0.8247 (t) cc_final: 0.7558 (p) REVERT: H 31 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8357 (tm-30) REVERT: H 32 GLU cc_start: 0.8733 (tp30) cc_final: 0.8382 (tp30) REVERT: H 66 GLU cc_start: 0.8505 (tp30) cc_final: 0.8038 (tp30) REVERT: I 83 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8599 (mtpp) REVERT: J 21 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8969 (mp) REVERT: K 31 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8266 (tm-30) REVERT: L 20 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8182 (tm-30) REVERT: L 32 GLU cc_start: 0.8548 (tp30) cc_final: 0.8020 (tp30) REVERT: L 89 ASP cc_start: 0.7740 (m-30) cc_final: 0.7415 (m-30) REVERT: L 99 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: M 66 GLU cc_start: 0.7889 (tt0) cc_final: 0.7337 (tt0) REVERT: N 20 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7973 (mm-30) REVERT: N 31 GLN cc_start: 0.8479 (tt0) cc_final: 0.8231 (pt0) REVERT: O 30 SER cc_start: 0.8407 (t) cc_final: 0.7595 (p) REVERT: O 31 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8403 (tm-30) REVERT: O 32 GLU cc_start: 0.8556 (tp30) cc_final: 0.8251 (tp30) REVERT: O 33 GLN cc_start: 0.9001 (mt0) cc_final: 0.8344 (mt0) REVERT: O 66 GLU cc_start: 0.8326 (tp30) cc_final: 0.7788 (tm-30) REVERT: P 35 LYS cc_start: 0.9292 (tptm) cc_final: 0.9005 (tttm) REVERT: P 66 GLU cc_start: 0.8253 (tp30) cc_final: 0.7973 (tm-30) REVERT: P 79 GLU cc_start: 0.8653 (tp30) cc_final: 0.8419 (tp30) REVERT: P 98 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8932 (mm-40) REVERT: R 31 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8159 (tm-30) REVERT: R 32 GLU cc_start: 0.8566 (tp30) cc_final: 0.7843 (tp30) REVERT: R 79 GLU cc_start: 0.8297 (tp30) cc_final: 0.7481 (tp30) REVERT: R 83 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8286 (ttmm) REVERT: R 99 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: S 32 GLU cc_start: 0.8372 (tp30) cc_final: 0.7721 (tp30) REVERT: S 99 GLU cc_start: 0.8453 (pt0) cc_final: 0.8021 (tm-30) REVERT: T 35 LYS cc_start: 0.9268 (tttm) cc_final: 0.8963 (tttm) REVERT: T 79 GLU cc_start: 0.8360 (tp30) cc_final: 0.8149 (tp30) REVERT: T 83 LYS cc_start: 0.9017 (mtpt) cc_final: 0.8746 (mtpp) REVERT: V 20 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7960 (mm-30) REVERT: V 32 GLU cc_start: 0.8482 (tp30) cc_final: 0.8214 (tp30) REVERT: V 58 ARG cc_start: 0.8565 (mtm110) cc_final: 0.8115 (mtt-85) REVERT: V 89 ASP cc_start: 0.8261 (m-30) cc_final: 0.7908 (m-30) REVERT: V 92 ASP cc_start: 0.8552 (p0) cc_final: 0.8115 (t0) REVERT: V 96 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8275 (tm-30) outliers start: 49 outliers final: 25 residues processed: 440 average time/residue: 0.1093 time to fit residues: 71.5750 Evaluate side-chains 424 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 394 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 39 HIS Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain P residue 39 HIS Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain Q residue 39 HIS Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain V residue 70 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 171 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 37 optimal weight: 0.0970 chunk 80 optimal weight: 8.9990 chunk 162 optimal weight: 0.0470 chunk 173 optimal weight: 0.9980 chunk 8 optimal weight: 0.0370 chunk 111 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 0.0670 chunk 119 optimal weight: 0.9980 overall best weight: 0.2492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 39 HIS A 96 GLN B 96 GLN C 96 GLN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN I 39 HIS I 98 GLN J 33 GLN L 96 GLN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 GLN O 33 GLN O 96 GLN P 39 HIS Q 39 HIS S 96 GLN T 96 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS V 67 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.078950 restraints weight = 34363.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.081742 restraints weight = 17629.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.083643 restraints weight = 11011.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.084935 restraints weight = 7850.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085811 restraints weight = 6111.721| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15645 Z= 0.098 Angle : 0.510 9.162 21021 Z= 0.268 Chirality : 0.034 0.113 2289 Planarity : 0.003 0.032 2835 Dihedral : 3.947 50.598 2208 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.87 % Allowed : 21.46 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.17), residues: 1869 helix: -1.76 (0.13), residues: 1281 sheet: None (None), residues: 0 loop : -2.41 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 58 TYR 0.003 0.001 TYR T 72 PHE 0.004 0.001 PHE E 37 TRP 0.005 0.001 TRP F 53 HIS 0.008 0.001 HIS Q 39 Details of bonding type rmsd covalent geometry : bond 0.00233 (15645) covalent geometry : angle 0.51027 (21021) hydrogen bonds : bond 0.03118 ( 610) hydrogen bonds : angle 3.77020 ( 1767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 428 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8302 (tm-30) REVERT: A 66 GLU cc_start: 0.8206 (tp30) cc_final: 0.7795 (tm-30) REVERT: A 75 GLU cc_start: 0.8843 (tp30) cc_final: 0.8609 (tp30) REVERT: B 30 SER cc_start: 0.8214 (t) cc_final: 0.7466 (p) REVERT: B 31 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8416 (tm-30) REVERT: B 32 GLU cc_start: 0.8546 (tp30) cc_final: 0.8302 (tp30) REVERT: B 33 GLN cc_start: 0.9002 (mt0) cc_final: 0.8582 (mt0) REVERT: B 66 GLU cc_start: 0.8272 (tp30) cc_final: 0.7943 (tm-30) REVERT: B 83 LYS cc_start: 0.8290 (mmtt) cc_final: 0.8060 (mmtt) REVERT: C 21 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8941 (mp) REVERT: D 31 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8324 (tm-30) REVERT: D 32 GLU cc_start: 0.8543 (tp30) cc_final: 0.8018 (tp30) REVERT: D 79 GLU cc_start: 0.8059 (tp30) cc_final: 0.7428 (tp30) REVERT: E 20 GLU cc_start: 0.8704 (tp30) cc_final: 0.8326 (tm-30) REVERT: E 32 GLU cc_start: 0.8320 (tp30) cc_final: 0.7641 (tp30) REVERT: E 75 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8481 (mm-30) REVERT: E 79 GLU cc_start: 0.8541 (tp30) cc_final: 0.8235 (tp30) REVERT: F 32 GLU cc_start: 0.8589 (tp30) cc_final: 0.8214 (tp30) REVERT: F 57 GLU cc_start: 0.8592 (tt0) cc_final: 0.8226 (tt0) REVERT: G 31 GLN cc_start: 0.8419 (tt0) cc_final: 0.8126 (pt0) REVERT: G 58 ARG cc_start: 0.8420 (mtm110) cc_final: 0.7984 (mtt-85) REVERT: G 75 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8187 (mm-30) REVERT: G 96 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8034 (tm-30) REVERT: H 30 SER cc_start: 0.8313 (t) cc_final: 0.7690 (p) REVERT: H 31 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8337 (tm-30) REVERT: H 32 GLU cc_start: 0.8585 (tp30) cc_final: 0.8270 (tp30) REVERT: H 57 GLU cc_start: 0.8140 (tt0) cc_final: 0.7896 (mt-10) REVERT: H 66 GLU cc_start: 0.8374 (tp30) cc_final: 0.7853 (tm-30) REVERT: I 39 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.7923 (t70) REVERT: I 75 GLU cc_start: 0.8896 (tp30) cc_final: 0.8428 (mm-30) REVERT: I 83 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8486 (mtpp) REVERT: J 21 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8990 (mp) REVERT: J 66 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8187 (tm-30) REVERT: K 31 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8203 (tm-30) REVERT: L 20 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8201 (tm-30) REVERT: L 31 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8505 (tm-30) REVERT: L 32 GLU cc_start: 0.8426 (tp30) cc_final: 0.7733 (tp30) REVERT: L 63 ASP cc_start: 0.8871 (m-30) cc_final: 0.8612 (m-30) REVERT: L 66 GLU cc_start: 0.7835 (tp30) cc_final: 0.7626 (tp30) REVERT: L 99 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: N 31 GLN cc_start: 0.8497 (tt0) cc_final: 0.8263 (pt0) REVERT: N 96 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: O 30 SER cc_start: 0.8446 (t) cc_final: 0.7536 (p) REVERT: O 31 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8366 (tm-30) REVERT: O 32 GLU cc_start: 0.8423 (tp30) cc_final: 0.8129 (tp30) REVERT: O 33 GLN cc_start: 0.8959 (mt0) cc_final: 0.8227 (mt0) REVERT: O 99 GLU cc_start: 0.8569 (pt0) cc_final: 0.8275 (pt0) REVERT: P 35 LYS cc_start: 0.9292 (tptm) cc_final: 0.8997 (tttm) REVERT: P 66 GLU cc_start: 0.8226 (tp30) cc_final: 0.7893 (tm-30) REVERT: P 79 GLU cc_start: 0.8599 (tp30) cc_final: 0.8273 (tp30) REVERT: R 31 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8247 (tm-30) REVERT: R 32 GLU cc_start: 0.8391 (tp30) cc_final: 0.7690 (tp30) REVERT: R 79 GLU cc_start: 0.8269 (tp30) cc_final: 0.7444 (tp30) REVERT: R 83 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8194 (ttmm) REVERT: R 99 GLU cc_start: 0.8472 (pt0) cc_final: 0.8208 (tm-30) REVERT: S 32 GLU cc_start: 0.8302 (tp30) cc_final: 0.7598 (tp30) REVERT: S 63 ASP cc_start: 0.8879 (m-30) cc_final: 0.8514 (m-30) REVERT: S 89 ASP cc_start: 0.7639 (m-30) cc_final: 0.7390 (t0) REVERT: S 99 GLU cc_start: 0.8433 (pt0) cc_final: 0.8173 (tm-30) REVERT: T 35 LYS cc_start: 0.9205 (tttm) cc_final: 0.8804 (tttp) REVERT: T 79 GLU cc_start: 0.8280 (tp30) cc_final: 0.8057 (tp30) REVERT: T 83 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8711 (mtpp) REVERT: V 20 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7976 (mm-30) REVERT: V 58 ARG cc_start: 0.8505 (mtm110) cc_final: 0.8010 (mtt-85) REVERT: V 89 ASP cc_start: 0.8217 (m-30) cc_final: 0.7773 (m-30) REVERT: V 96 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8237 (tm-30) outliers start: 44 outliers final: 19 residues processed: 444 average time/residue: 0.1153 time to fit residues: 77.4279 Evaluate side-chains 409 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 385 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 39 HIS Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 39 HIS Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain Q residue 39 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 74 optimal weight: 1.9990 chunk 172 optimal weight: 0.0040 chunk 129 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 96 GLN B 96 GLN D 39 HIS ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN ** G 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 HIS G 67 GLN I 39 HIS I 96 GLN J 67 GLN J 96 GLN L 96 GLN M 67 GLN ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 HIS Q 39 HIS S 96 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS V 67 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.091225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.077201 restraints weight = 34441.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.079913 restraints weight = 17474.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.081738 restraints weight = 10877.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.082983 restraints weight = 7744.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083846 restraints weight = 6042.902| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15645 Z= 0.130 Angle : 0.514 5.367 21021 Z= 0.271 Chirality : 0.036 0.120 2289 Planarity : 0.003 0.031 2835 Dihedral : 3.801 53.629 2207 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.87 % Allowed : 21.79 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.19), residues: 1869 helix: -1.11 (0.14), residues: 1281 sheet: None (None), residues: 0 loop : -2.00 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 100 TYR 0.005 0.001 TYR T 72 PHE 0.006 0.001 PHE H 37 TRP 0.003 0.001 TRP E 53 HIS 0.008 0.001 HIS Q 39 Details of bonding type rmsd covalent geometry : bond 0.00311 (15645) covalent geometry : angle 0.51354 (21021) hydrogen bonds : bond 0.03184 ( 610) hydrogen bonds : angle 3.72183 ( 1767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 403 time to evaluate : 0.589 Fit side-chains REVERT: A 31 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8450 (tm-30) REVERT: A 66 GLU cc_start: 0.8222 (tp30) cc_final: 0.7819 (tm-30) REVERT: A 75 GLU cc_start: 0.8895 (tp30) cc_final: 0.8560 (mm-30) REVERT: B 30 SER cc_start: 0.8146 (t) cc_final: 0.7392 (p) REVERT: B 31 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8406 (tm-30) REVERT: B 32 GLU cc_start: 0.8533 (tp30) cc_final: 0.8273 (tp30) REVERT: B 33 GLN cc_start: 0.9027 (mt0) cc_final: 0.8711 (mt0) REVERT: B 66 GLU cc_start: 0.8418 (tp30) cc_final: 0.8047 (tm-30) REVERT: C 21 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8987 (mp) REVERT: D 31 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8267 (tm-30) REVERT: D 32 GLU cc_start: 0.8532 (tp30) cc_final: 0.8100 (tp30) REVERT: E 20 GLU cc_start: 0.8726 (tp30) cc_final: 0.8356 (tm-30) REVERT: E 32 GLU cc_start: 0.8402 (tp30) cc_final: 0.7711 (tp30) REVERT: E 75 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8493 (mm-30) REVERT: E 79 GLU cc_start: 0.8533 (tp30) cc_final: 0.8051 (tp30) REVERT: E 96 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8681 (tm-30) REVERT: F 32 GLU cc_start: 0.8627 (tp30) cc_final: 0.8309 (tp30) REVERT: F 66 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7664 (mm-30) REVERT: G 31 GLN cc_start: 0.8463 (tt0) cc_final: 0.8198 (pt0) REVERT: G 58 ARG cc_start: 0.8433 (mtm110) cc_final: 0.7980 (mtt-85) REVERT: G 75 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8131 (mm-30) REVERT: G 96 GLN cc_start: 0.8613 (tm-30) cc_final: 0.7972 (tm-30) REVERT: H 31 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8481 (tm-30) REVERT: H 32 GLU cc_start: 0.8557 (tp30) cc_final: 0.8247 (tp30) REVERT: H 66 GLU cc_start: 0.8457 (tp30) cc_final: 0.7959 (tm-30) REVERT: I 31 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8321 (tm-30) REVERT: I 75 GLU cc_start: 0.8896 (tp30) cc_final: 0.8493 (mm-30) REVERT: I 83 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8520 (mtpp) REVERT: J 21 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8986 (mp) REVERT: J 33 GLN cc_start: 0.8432 (mt0) cc_final: 0.7986 (mt0) REVERT: K 31 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8234 (tm-30) REVERT: K 32 GLU cc_start: 0.8363 (tp30) cc_final: 0.8157 (tp30) REVERT: K 99 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8101 (tm-30) REVERT: L 20 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8282 (tm-30) REVERT: L 32 GLU cc_start: 0.8510 (tp30) cc_final: 0.7876 (tp30) REVERT: L 66 GLU cc_start: 0.7922 (tp30) cc_final: 0.7599 (tp30) REVERT: L 99 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: M 66 GLU cc_start: 0.8155 (tt0) cc_final: 0.7871 (tt0) REVERT: N 31 GLN cc_start: 0.8498 (tt0) cc_final: 0.8257 (pt0) REVERT: N 55 ARG cc_start: 0.8419 (ptp90) cc_final: 0.8098 (ptt180) REVERT: O 30 SER cc_start: 0.8409 (t) cc_final: 0.7458 (p) REVERT: O 31 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8347 (tm-30) REVERT: O 32 GLU cc_start: 0.8444 (tp30) cc_final: 0.8144 (tp30) REVERT: O 33 GLN cc_start: 0.9020 (mt0) cc_final: 0.8333 (mt0) REVERT: O 99 GLU cc_start: 0.8634 (pt0) cc_final: 0.8365 (pt0) REVERT: P 31 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8439 (tm-30) REVERT: P 35 LYS cc_start: 0.9288 (tptm) cc_final: 0.8973 (tttm) REVERT: P 66 GLU cc_start: 0.8241 (tp30) cc_final: 0.7870 (tm-30) REVERT: P 75 GLU cc_start: 0.8862 (tp30) cc_final: 0.8529 (mm-30) REVERT: P 79 GLU cc_start: 0.8622 (tp30) cc_final: 0.8380 (tp30) REVERT: R 31 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8314 (tm-30) REVERT: R 32 GLU cc_start: 0.8422 (tp30) cc_final: 0.7710 (tp30) REVERT: R 79 GLU cc_start: 0.8264 (tp30) cc_final: 0.7943 (tp30) REVERT: R 83 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8672 (mtpp) REVERT: R 99 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8239 (tm-30) REVERT: S 32 GLU cc_start: 0.8313 (tp30) cc_final: 0.7611 (tp30) REVERT: S 99 GLU cc_start: 0.8481 (pt0) cc_final: 0.8194 (tm-30) REVERT: T 35 LYS cc_start: 0.9238 (tttm) cc_final: 0.8824 (tttp) REVERT: T 79 GLU cc_start: 0.8261 (tp30) cc_final: 0.7847 (tp30) REVERT: T 83 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8603 (mtpp) REVERT: V 20 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8044 (mm-30) REVERT: V 32 GLU cc_start: 0.8353 (tp30) cc_final: 0.8066 (tp30) REVERT: V 58 ARG cc_start: 0.8598 (mtm110) cc_final: 0.8132 (mtt-85) REVERT: V 89 ASP cc_start: 0.8237 (m-30) cc_final: 0.7817 (m-30) REVERT: V 96 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8255 (tm-30) outliers start: 44 outliers final: 25 residues processed: 420 average time/residue: 0.1157 time to fit residues: 73.4357 Evaluate side-chains 411 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 382 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain T residue 33 GLN Chi-restraints excluded: chain T residue 99 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 92 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 159 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 158 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN C 33 GLN D 39 HIS ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN G 39 HIS G 67 GLN I 70 GLN K 39 HIS K 96 GLN L 96 GLN N 39 HIS N 67 GLN N 96 GLN O 96 GLN P 39 HIS Q 39 HIS R 70 GLN S 96 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078081 restraints weight = 34444.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.080842 restraints weight = 17843.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082684 restraints weight = 11256.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.083883 restraints weight = 8101.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.084792 restraints weight = 6416.612| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15645 Z= 0.107 Angle : 0.509 4.920 21021 Z= 0.270 Chirality : 0.035 0.115 2289 Planarity : 0.003 0.031 2835 Dihedral : 3.442 16.573 2206 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.39 % Allowed : 22.31 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.20), residues: 1869 helix: -0.48 (0.14), residues: 1281 sheet: None (None), residues: 0 loop : -1.84 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 58 TYR 0.005 0.001 TYR O 72 PHE 0.005 0.001 PHE N 37 TRP 0.006 0.001 TRP H 53 HIS 0.004 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00262 (15645) covalent geometry : angle 0.50870 (21021) hydrogen bonds : bond 0.02917 ( 610) hydrogen bonds : angle 3.51942 ( 1767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 404 time to evaluate : 0.676 Fit side-chains REVERT: A 31 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8296 (tm-30) REVERT: A 66 GLU cc_start: 0.8194 (tp30) cc_final: 0.7801 (tm-30) REVERT: A 75 GLU cc_start: 0.8840 (tp30) cc_final: 0.8491 (mm-30) REVERT: B 30 SER cc_start: 0.8161 (t) cc_final: 0.7425 (p) REVERT: B 31 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8374 (tm-30) REVERT: B 32 GLU cc_start: 0.8488 (tp30) cc_final: 0.8211 (tp30) REVERT: B 33 GLN cc_start: 0.9025 (mt0) cc_final: 0.8711 (mt0) REVERT: B 35 LYS cc_start: 0.9309 (tttt) cc_final: 0.9059 (ttmm) REVERT: C 21 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8979 (mp) REVERT: C 66 GLU cc_start: 0.7780 (tp30) cc_final: 0.7228 (mm-30) REVERT: D 31 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8276 (tm-30) REVERT: D 32 GLU cc_start: 0.8529 (tp30) cc_final: 0.8100 (tp30) REVERT: E 20 GLU cc_start: 0.8762 (tp30) cc_final: 0.8362 (tm-30) REVERT: E 32 GLU cc_start: 0.8322 (tp30) cc_final: 0.7580 (tp30) REVERT: E 75 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8489 (mm-30) REVERT: E 79 GLU cc_start: 0.8554 (tp30) cc_final: 0.8136 (tp30) REVERT: F 31 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8071 (tm-30) REVERT: F 32 GLU cc_start: 0.8641 (tp30) cc_final: 0.8358 (tp30) REVERT: F 66 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7751 (mm-30) REVERT: G 31 GLN cc_start: 0.8415 (tt0) cc_final: 0.8091 (pt0) REVERT: G 58 ARG cc_start: 0.8446 (mtm110) cc_final: 0.7964 (mtt-85) REVERT: G 96 GLN cc_start: 0.8589 (tm-30) cc_final: 0.7988 (tm-30) REVERT: H 31 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8456 (tm-30) REVERT: H 32 GLU cc_start: 0.8589 (tp30) cc_final: 0.8251 (tp30) REVERT: H 66 GLU cc_start: 0.8364 (tp30) cc_final: 0.7995 (tm-30) REVERT: I 30 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8430 (p) REVERT: I 31 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8278 (tm-30) REVERT: I 75 GLU cc_start: 0.8886 (tp30) cc_final: 0.8495 (mm-30) REVERT: I 83 LYS cc_start: 0.8756 (mtpp) cc_final: 0.8462 (mtpp) REVERT: J 21 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9003 (mp) REVERT: K 31 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8262 (tm-30) REVERT: K 32 GLU cc_start: 0.8473 (tp30) cc_final: 0.8240 (tp30) REVERT: K 99 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8146 (tm-30) REVERT: L 20 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8300 (tm-30) REVERT: L 31 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8404 (tm-30) REVERT: L 32 GLU cc_start: 0.8403 (tp30) cc_final: 0.7691 (tp30) REVERT: L 66 GLU cc_start: 0.8008 (tp30) cc_final: 0.7752 (tp30) REVERT: L 99 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: M 66 GLU cc_start: 0.8104 (tt0) cc_final: 0.7877 (tt0) REVERT: N 31 GLN cc_start: 0.8429 (tt0) cc_final: 0.8133 (pt0) REVERT: N 96 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: O 30 SER cc_start: 0.8344 (t) cc_final: 0.7378 (p) REVERT: O 31 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8334 (tm-30) REVERT: O 32 GLU cc_start: 0.8420 (tp30) cc_final: 0.8123 (tp30) REVERT: O 33 GLN cc_start: 0.9056 (mt0) cc_final: 0.8315 (mt0) REVERT: O 99 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: P 31 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8436 (tm-30) REVERT: P 35 LYS cc_start: 0.9243 (tptm) cc_final: 0.8977 (tttm) REVERT: P 66 GLU cc_start: 0.8233 (tp30) cc_final: 0.7909 (tm-30) REVERT: P 75 GLU cc_start: 0.8867 (tp30) cc_final: 0.8537 (mm-30) REVERT: P 79 GLU cc_start: 0.8610 (tp30) cc_final: 0.8353 (tp30) REVERT: R 31 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8337 (tm-30) REVERT: R 32 GLU cc_start: 0.8372 (tp30) cc_final: 0.7999 (tp30) REVERT: R 99 GLU cc_start: 0.8469 (pt0) cc_final: 0.8179 (tm-30) REVERT: S 32 GLU cc_start: 0.8303 (tp30) cc_final: 0.7622 (tp30) REVERT: S 63 ASP cc_start: 0.8980 (m-30) cc_final: 0.8525 (m-30) REVERT: S 99 GLU cc_start: 0.8502 (pt0) cc_final: 0.8185 (tm-30) REVERT: T 35 LYS cc_start: 0.9129 (tttm) cc_final: 0.8823 (tttp) REVERT: T 79 GLU cc_start: 0.8245 (tp30) cc_final: 0.7876 (tp30) REVERT: T 83 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8653 (mtpp) REVERT: V 20 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8021 (mm-30) REVERT: V 32 GLU cc_start: 0.8493 (tp30) cc_final: 0.8111 (tp30) REVERT: V 55 ARG cc_start: 0.8886 (ptp90) cc_final: 0.8541 (mtp180) REVERT: V 58 ARG cc_start: 0.8616 (mtm110) cc_final: 0.8110 (mtt-85) REVERT: V 89 ASP cc_start: 0.8217 (m-30) cc_final: 0.7789 (m-30) REVERT: V 96 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8462 (tm-30) outliers start: 52 outliers final: 27 residues processed: 419 average time/residue: 0.1198 time to fit residues: 75.4241 Evaluate side-chains 411 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 378 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain K residue 39 HIS Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain T residue 99 GLU Chi-restraints excluded: chain V residue 60 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN D 39 HIS D 98 GLN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN F 98 GLN G 39 HIS G 67 GLN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 98 GLN ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN M 98 GLN N 39 HIS P 33 GLN P 39 HIS R 39 HIS R 70 GLN R 103 GLN S 96 GLN T 39 HIS T 98 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.089332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.075089 restraints weight = 34506.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.077653 restraints weight = 18264.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079407 restraints weight = 11699.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.080598 restraints weight = 8496.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081373 restraints weight = 6724.753| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15645 Z= 0.201 Angle : 0.582 5.307 21021 Z= 0.303 Chirality : 0.040 0.131 2289 Planarity : 0.004 0.033 2835 Dihedral : 3.678 14.350 2205 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.52 % Allowed : 22.31 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.20), residues: 1869 helix: -0.62 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : -1.15 (0.33), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 100 TYR 0.007 0.001 TYR G 72 PHE 0.011 0.002 PHE H 37 TRP 0.006 0.001 TRP F 53 HIS 0.007 0.001 HIS K 39 Details of bonding type rmsd covalent geometry : bond 0.00472 (15645) covalent geometry : angle 0.58163 (21021) hydrogen bonds : bond 0.03579 ( 610) hydrogen bonds : angle 3.92232 ( 1767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 396 time to evaluate : 0.643 Fit side-chains REVERT: A 31 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8417 (tm-30) REVERT: A 66 GLU cc_start: 0.8243 (tp30) cc_final: 0.7810 (tm-30) REVERT: A 75 GLU cc_start: 0.8902 (tp30) cc_final: 0.8649 (tp30) REVERT: B 31 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8449 (tm-30) REVERT: B 32 GLU cc_start: 0.8580 (tp30) cc_final: 0.8250 (tp30) REVERT: B 35 LYS cc_start: 0.9396 (tttt) cc_final: 0.9161 (ttmm) REVERT: C 21 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9071 (mp) REVERT: D 31 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8356 (tm-30) REVERT: D 32 GLU cc_start: 0.8621 (tp30) cc_final: 0.8107 (tp30) REVERT: D 66 GLU cc_start: 0.8609 (tp30) cc_final: 0.8331 (tp30) REVERT: E 20 GLU cc_start: 0.8747 (tp30) cc_final: 0.8401 (tm-30) REVERT: E 32 GLU cc_start: 0.8430 (tp30) cc_final: 0.7745 (tp30) REVERT: E 79 GLU cc_start: 0.8624 (tp30) cc_final: 0.8223 (tp30) REVERT: F 20 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: F 31 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8199 (tm-30) REVERT: F 32 GLU cc_start: 0.8697 (tp30) cc_final: 0.8451 (tp30) REVERT: G 58 ARG cc_start: 0.8409 (mtm110) cc_final: 0.8051 (mtt-85) REVERT: G 75 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7858 (mm-30) REVERT: G 96 GLN cc_start: 0.8586 (tm-30) cc_final: 0.7956 (tm-30) REVERT: H 31 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8464 (tm-30) REVERT: H 32 GLU cc_start: 0.8709 (tp30) cc_final: 0.8350 (tp30) REVERT: H 33 GLN cc_start: 0.8683 (mt0) cc_final: 0.8309 (mp10) REVERT: H 66 GLU cc_start: 0.8533 (tp30) cc_final: 0.8195 (tm-30) REVERT: I 31 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8594 (tm-30) REVERT: J 21 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9085 (mp) REVERT: K 31 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8323 (tm-30) REVERT: K 32 GLU cc_start: 0.8566 (tp30) cc_final: 0.8302 (tp30) REVERT: K 99 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8141 (tm-30) REVERT: L 20 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8264 (tm-30) REVERT: L 32 GLU cc_start: 0.8561 (tp30) cc_final: 0.8010 (tp30) REVERT: L 70 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8337 (tp40) REVERT: L 89 ASP cc_start: 0.7614 (m-30) cc_final: 0.7235 (m-30) REVERT: L 99 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: N 31 GLN cc_start: 0.8501 (tt0) cc_final: 0.8259 (pt0) REVERT: O 31 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8422 (tm-30) REVERT: O 32 GLU cc_start: 0.8509 (tp30) cc_final: 0.8194 (tp30) REVERT: O 66 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8120 (tm-30) REVERT: P 31 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8539 (tm-30) REVERT: P 35 LYS cc_start: 0.9265 (tptm) cc_final: 0.8975 (tttm) REVERT: P 66 GLU cc_start: 0.8297 (tp30) cc_final: 0.7987 (tm-30) REVERT: R 31 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8390 (tm-30) REVERT: R 32 GLU cc_start: 0.8482 (tp30) cc_final: 0.7801 (tp30) REVERT: R 66 GLU cc_start: 0.8379 (tp30) cc_final: 0.8146 (tp30) REVERT: R 99 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: S 32 GLU cc_start: 0.8382 (tp30) cc_final: 0.7789 (tp30) REVERT: S 99 GLU cc_start: 0.8507 (pt0) cc_final: 0.8212 (tm-30) REVERT: T 35 LYS cc_start: 0.9305 (tttm) cc_final: 0.8940 (tttp) REVERT: T 79 GLU cc_start: 0.8265 (tp30) cc_final: 0.7820 (tp30) REVERT: T 83 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8643 (mtpp) REVERT: V 32 GLU cc_start: 0.8488 (tp30) cc_final: 0.8242 (tp30) REVERT: V 58 ARG cc_start: 0.8538 (mtm110) cc_final: 0.8200 (mtt-85) REVERT: V 89 ASP cc_start: 0.8321 (m-30) cc_final: 0.8049 (m-30) REVERT: V 96 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8211 (tm-30) outliers start: 54 outliers final: 30 residues processed: 413 average time/residue: 0.1168 time to fit residues: 73.5785 Evaluate side-chains 419 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 383 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 39 HIS Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 70 GLN Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain R residue 39 HIS Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain S residue 70 GLN Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain T residue 33 GLN Chi-restraints excluded: chain T residue 99 GLU Chi-restraints excluded: chain V residue 39 HIS Chi-restraints excluded: chain V residue 60 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 84 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN G 39 HIS I 67 GLN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 HIS O 96 GLN Q 67 GLN R 39 HIS S 96 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.075553 restraints weight = 34618.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.078177 restraints weight = 18104.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.079970 restraints weight = 11504.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.081130 restraints weight = 8302.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.082020 restraints weight = 6577.111| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15645 Z= 0.174 Angle : 0.572 5.550 21021 Z= 0.302 Chirality : 0.038 0.129 2289 Planarity : 0.003 0.035 2835 Dihedral : 3.672 14.220 2205 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.94 % Allowed : 24.01 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.21), residues: 1869 helix: -0.49 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 38 TYR 0.006 0.001 TYR G 72 PHE 0.009 0.001 PHE H 37 TRP 0.004 0.001 TRP R 53 HIS 0.004 0.001 HIS I 39 Details of bonding type rmsd covalent geometry : bond 0.00415 (15645) covalent geometry : angle 0.57248 (21021) hydrogen bonds : bond 0.03461 ( 610) hydrogen bonds : angle 3.88898 ( 1767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 387 time to evaluate : 0.662 Fit side-chains REVERT: A 31 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8386 (tm-30) REVERT: A 66 GLU cc_start: 0.8217 (tp30) cc_final: 0.7782 (tm-30) REVERT: A 75 GLU cc_start: 0.8900 (tp30) cc_final: 0.8650 (tp30) REVERT: B 31 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8428 (tm-30) REVERT: B 32 GLU cc_start: 0.8569 (tp30) cc_final: 0.8242 (tp30) REVERT: B 35 LYS cc_start: 0.9392 (tttt) cc_final: 0.9156 (ttmm) REVERT: C 21 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9051 (mp) REVERT: C 98 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8813 (mm-40) REVERT: D 31 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8382 (tm-30) REVERT: D 32 GLU cc_start: 0.8605 (tp30) cc_final: 0.8078 (tp30) REVERT: D 99 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8330 (tm-30) REVERT: E 20 GLU cc_start: 0.8715 (tp30) cc_final: 0.8387 (tm-30) REVERT: E 32 GLU cc_start: 0.8442 (tp30) cc_final: 0.7733 (tp30) REVERT: E 79 GLU cc_start: 0.8580 (tp30) cc_final: 0.8189 (tp30) REVERT: F 20 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: F 32 GLU cc_start: 0.8685 (tp30) cc_final: 0.8470 (tp30) REVERT: G 58 ARG cc_start: 0.8508 (mtm110) cc_final: 0.8182 (mtt-85) REVERT: G 96 GLN cc_start: 0.8597 (tm-30) cc_final: 0.7890 (tm-30) REVERT: H 31 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8427 (tm-30) REVERT: H 32 GLU cc_start: 0.8710 (tp30) cc_final: 0.8322 (tp30) REVERT: H 33 GLN cc_start: 0.8679 (mt0) cc_final: 0.8317 (mp10) REVERT: H 66 GLU cc_start: 0.8504 (tp30) cc_final: 0.8153 (tm-30) REVERT: I 31 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8609 (tm-30) REVERT: J 21 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9051 (mp) REVERT: K 31 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8369 (tm-30) REVERT: K 32 GLU cc_start: 0.8599 (tp30) cc_final: 0.8335 (tp30) REVERT: K 99 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8144 (tm-30) REVERT: L 20 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8244 (tm-30) REVERT: L 32 GLU cc_start: 0.8585 (tp30) cc_final: 0.7966 (tp30) REVERT: L 70 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8352 (tp40) REVERT: L 89 ASP cc_start: 0.7556 (m-30) cc_final: 0.7171 (m-30) REVERT: L 99 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: N 31 GLN cc_start: 0.8481 (tt0) cc_final: 0.8271 (pt0) REVERT: O 31 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8411 (tm-30) REVERT: O 32 GLU cc_start: 0.8570 (tp30) cc_final: 0.8273 (tp30) REVERT: O 66 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8133 (tm-30) REVERT: P 31 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8746 (tm-30) REVERT: P 35 LYS cc_start: 0.9272 (tptm) cc_final: 0.9009 (tttm) REVERT: P 66 GLU cc_start: 0.8284 (tp30) cc_final: 0.7974 (tm-30) REVERT: R 31 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8339 (tm-30) REVERT: R 32 GLU cc_start: 0.8454 (tp30) cc_final: 0.7804 (tp30) REVERT: R 66 GLU cc_start: 0.8420 (tp30) cc_final: 0.8062 (tm-30) REVERT: S 32 GLU cc_start: 0.8392 (tp30) cc_final: 0.7777 (tp30) REVERT: S 99 GLU cc_start: 0.8475 (pt0) cc_final: 0.8197 (tm-30) REVERT: T 32 GLU cc_start: 0.8380 (tp30) cc_final: 0.8151 (tp30) REVERT: T 35 LYS cc_start: 0.9263 (tttm) cc_final: 0.8849 (tttp) REVERT: T 79 GLU cc_start: 0.8265 (tp30) cc_final: 0.7980 (tp30) REVERT: T 83 LYS cc_start: 0.8880 (mtpt) cc_final: 0.8657 (mtpp) REVERT: V 32 GLU cc_start: 0.8472 (tp30) cc_final: 0.8211 (tp30) REVERT: V 58 ARG cc_start: 0.8572 (mtm110) cc_final: 0.8225 (mtt-85) REVERT: V 89 ASP cc_start: 0.8327 (m-30) cc_final: 0.8058 (m-30) REVERT: V 96 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8160 (tm-30) outliers start: 45 outliers final: 31 residues processed: 402 average time/residue: 0.1151 time to fit residues: 70.1278 Evaluate side-chains 412 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 376 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 70 GLN Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain Q residue 67 GLN Chi-restraints excluded: chain R residue 39 HIS Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 70 GLN Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain T residue 33 GLN Chi-restraints excluded: chain T residue 99 GLU Chi-restraints excluded: chain V residue 39 HIS Chi-restraints excluded: chain V residue 60 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 HIS O 96 GLN Q 67 GLN R 39 HIS S 96 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.076335 restraints weight = 34207.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.078998 restraints weight = 17815.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080768 restraints weight = 11289.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082014 restraints weight = 8135.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082813 restraints weight = 6408.726| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15645 Z= 0.144 Angle : 0.569 5.598 21021 Z= 0.302 Chirality : 0.037 0.124 2289 Planarity : 0.003 0.033 2835 Dihedral : 3.608 14.276 2205 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.80 % Allowed : 24.85 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.21), residues: 1869 helix: -0.30 (0.14), residues: 1323 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 38 TYR 0.006 0.001 TYR G 72 PHE 0.007 0.001 PHE V 37 TRP 0.007 0.001 TRP O 53 HIS 0.005 0.001 HIS R 39 Details of bonding type rmsd covalent geometry : bond 0.00350 (15645) covalent geometry : angle 0.56852 (21021) hydrogen bonds : bond 0.03320 ( 610) hydrogen bonds : angle 3.80379 ( 1767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 384 time to evaluate : 0.693 Fit side-chains REVERT: A 31 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 66 GLU cc_start: 0.8219 (tp30) cc_final: 0.7792 (tm-30) REVERT: A 75 GLU cc_start: 0.8888 (tp30) cc_final: 0.8649 (tp30) REVERT: B 31 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8389 (tm-30) REVERT: B 32 GLU cc_start: 0.8579 (tp30) cc_final: 0.8247 (tp30) REVERT: B 33 GLN cc_start: 0.8670 (mt0) cc_final: 0.8427 (mt0) REVERT: B 35 LYS cc_start: 0.9375 (tttt) cc_final: 0.9134 (ttmm) REVERT: C 21 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9045 (mp) REVERT: C 67 GLN cc_start: 0.8434 (mt0) cc_final: 0.8201 (mt0) REVERT: D 31 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8365 (tm-30) REVERT: D 32 GLU cc_start: 0.8573 (tp30) cc_final: 0.8035 (tp30) REVERT: D 99 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8341 (tm-30) REVERT: E 20 GLU cc_start: 0.8708 (tp30) cc_final: 0.8376 (tm-30) REVERT: E 32 GLU cc_start: 0.8418 (tp30) cc_final: 0.7852 (tp30) REVERT: E 79 GLU cc_start: 0.8569 (tp30) cc_final: 0.8143 (tp30) REVERT: F 20 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7717 (tm-30) REVERT: F 31 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8252 (tm-30) REVERT: F 32 GLU cc_start: 0.8671 (tp30) cc_final: 0.8408 (tp30) REVERT: F 79 GLU cc_start: 0.8262 (tp30) cc_final: 0.7984 (tp30) REVERT: G 58 ARG cc_start: 0.8507 (mtm110) cc_final: 0.8178 (mtt-85) REVERT: G 75 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8112 (mm-30) REVERT: G 96 GLN cc_start: 0.8598 (tm-30) cc_final: 0.7908 (tm-30) REVERT: H 31 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8395 (tm-30) REVERT: H 32 GLU cc_start: 0.8697 (tp30) cc_final: 0.8294 (tp30) REVERT: H 33 GLN cc_start: 0.8666 (mt0) cc_final: 0.8287 (mp10) REVERT: H 66 GLU cc_start: 0.8440 (tp30) cc_final: 0.8109 (tm-30) REVERT: I 31 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8589 (tm-30) REVERT: J 21 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9035 (mp) REVERT: K 31 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8348 (tm-30) REVERT: K 32 GLU cc_start: 0.8551 (tp30) cc_final: 0.8291 (tp30) REVERT: K 99 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8154 (tm-30) REVERT: L 20 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8216 (tm-30) REVERT: L 31 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8508 (tm-30) REVERT: L 32 GLU cc_start: 0.8550 (tp30) cc_final: 0.7926 (tp30) REVERT: L 70 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8166 (tp40) REVERT: L 89 ASP cc_start: 0.7588 (m-30) cc_final: 0.7188 (m-30) REVERT: L 99 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: N 31 GLN cc_start: 0.8472 (tt0) cc_final: 0.8246 (pt0) REVERT: O 31 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8348 (tm-30) REVERT: O 32 GLU cc_start: 0.8612 (tp30) cc_final: 0.8336 (tp30) REVERT: O 33 GLN cc_start: 0.8607 (mt0) cc_final: 0.8286 (mp10) REVERT: O 66 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8133 (tm-30) REVERT: O 96 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.9025 (tp40) REVERT: O 98 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8661 (mm-40) REVERT: P 31 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8724 (tm-30) REVERT: P 35 LYS cc_start: 0.9280 (tptm) cc_final: 0.8973 (tttm) REVERT: P 66 GLU cc_start: 0.8280 (tp30) cc_final: 0.7971 (tm-30) REVERT: R 31 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8246 (tm-30) REVERT: R 32 GLU cc_start: 0.8494 (tp30) cc_final: 0.7819 (tp30) REVERT: R 66 GLU cc_start: 0.8377 (tp30) cc_final: 0.8157 (tp30) REVERT: S 32 GLU cc_start: 0.8350 (tp30) cc_final: 0.7735 (tp30) REVERT: S 99 GLU cc_start: 0.8453 (pt0) cc_final: 0.8203 (tm-30) REVERT: T 35 LYS cc_start: 0.9239 (tttm) cc_final: 0.8875 (tttp) REVERT: T 79 GLU cc_start: 0.8239 (tp30) cc_final: 0.7968 (tp30) REVERT: T 83 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8648 (mtpp) REVERT: V 32 GLU cc_start: 0.8489 (tp30) cc_final: 0.8181 (tp30) REVERT: V 58 ARG cc_start: 0.8564 (mtm110) cc_final: 0.8238 (mtt-85) REVERT: V 89 ASP cc_start: 0.8302 (m-30) cc_final: 0.7997 (m-30) REVERT: V 96 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8139 (tm-30) outliers start: 43 outliers final: 25 residues processed: 397 average time/residue: 0.1126 time to fit residues: 68.6267 Evaluate side-chains 406 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 375 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 70 GLN Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain Q residue 67 GLN Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain T residue 33 GLN Chi-restraints excluded: chain T residue 99 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 151 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.0370 chunk 160 optimal weight: 0.0070 chunk 155 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 HIS O 96 GLN Q 67 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.091423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.077068 restraints weight = 34201.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.079738 restraints weight = 17832.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081553 restraints weight = 11290.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082789 restraints weight = 8131.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.083635 restraints weight = 6390.610| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15645 Z= 0.132 Angle : 0.566 7.410 21021 Z= 0.301 Chirality : 0.037 0.123 2289 Planarity : 0.003 0.033 2835 Dihedral : 3.549 14.151 2205 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.54 % Allowed : 24.66 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1869 helix: 0.00 (0.15), residues: 1281 sheet: None (None), residues: 0 loop : -1.31 (0.32), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 58 TYR 0.006 0.001 TYR G 72 PHE 0.007 0.001 PHE N 37 TRP 0.005 0.001 TRP P 53 HIS 0.003 0.001 HIS I 39 Details of bonding type rmsd covalent geometry : bond 0.00324 (15645) covalent geometry : angle 0.56568 (21021) hydrogen bonds : bond 0.03254 ( 610) hydrogen bonds : angle 3.74332 ( 1767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 380 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 66 GLU cc_start: 0.8235 (tp30) cc_final: 0.7796 (tm-30) REVERT: A 75 GLU cc_start: 0.8880 (tp30) cc_final: 0.8670 (tp30) REVERT: B 31 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8336 (tm-30) REVERT: B 32 GLU cc_start: 0.8547 (tp30) cc_final: 0.8219 (tp30) REVERT: B 33 GLN cc_start: 0.8672 (mt0) cc_final: 0.8450 (mt0) REVERT: B 35 LYS cc_start: 0.9361 (tttt) cc_final: 0.9134 (ttmm) REVERT: C 21 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9022 (mp) REVERT: D 31 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8357 (tm-30) REVERT: D 32 GLU cc_start: 0.8546 (tp30) cc_final: 0.7993 (tp30) REVERT: D 99 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8243 (tm-30) REVERT: E 20 GLU cc_start: 0.8715 (tp30) cc_final: 0.8381 (tm-30) REVERT: E 32 GLU cc_start: 0.8367 (tp30) cc_final: 0.7679 (tp30) REVERT: E 79 GLU cc_start: 0.8578 (tp30) cc_final: 0.8198 (tp30) REVERT: F 20 GLU cc_start: 0.8250 (tt0) cc_final: 0.7700 (tm-30) REVERT: F 31 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8254 (tm-30) REVERT: F 32 GLU cc_start: 0.8671 (tp30) cc_final: 0.8410 (tp30) REVERT: F 79 GLU cc_start: 0.8232 (tp30) cc_final: 0.7934 (tp30) REVERT: G 31 GLN cc_start: 0.8476 (tt0) cc_final: 0.8235 (pt0) REVERT: G 58 ARG cc_start: 0.8511 (mtm110) cc_final: 0.8167 (mtt-85) REVERT: G 75 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8050 (mm-30) REVERT: G 96 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8109 (tm-30) REVERT: H 31 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8316 (tm-30) REVERT: H 32 GLU cc_start: 0.8654 (tp30) cc_final: 0.8266 (tp30) REVERT: H 66 GLU cc_start: 0.8391 (tp30) cc_final: 0.8083 (tm-30) REVERT: I 31 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8589 (tm-30) REVERT: I 75 GLU cc_start: 0.8981 (tp30) cc_final: 0.8515 (mm-30) REVERT: J 21 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9011 (mp) REVERT: K 31 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8353 (tm-30) REVERT: K 32 GLU cc_start: 0.8552 (tp30) cc_final: 0.8253 (tp30) REVERT: K 99 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8143 (tm-30) REVERT: L 20 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8221 (tm-30) REVERT: L 32 GLU cc_start: 0.8493 (tp30) cc_final: 0.7896 (tp30) REVERT: L 70 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8232 (tp40) REVERT: L 89 ASP cc_start: 0.7567 (m-30) cc_final: 0.7161 (m-30) REVERT: L 99 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: O 31 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8435 (tm-30) REVERT: O 66 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8105 (tm-30) REVERT: P 31 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8695 (tm-30) REVERT: P 35 LYS cc_start: 0.9227 (tptm) cc_final: 0.8958 (tttm) REVERT: P 66 GLU cc_start: 0.8290 (tp30) cc_final: 0.7964 (tm-30) REVERT: R 31 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8282 (tm-30) REVERT: R 32 GLU cc_start: 0.8458 (tp30) cc_final: 0.8199 (tp30) REVERT: R 66 GLU cc_start: 0.8361 (tp30) cc_final: 0.8155 (tp30) REVERT: S 32 GLU cc_start: 0.8353 (tp30) cc_final: 0.7707 (tp30) REVERT: S 99 GLU cc_start: 0.8457 (pt0) cc_final: 0.8174 (tm-30) REVERT: T 31 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8173 (tm-30) REVERT: T 35 LYS cc_start: 0.9205 (tttm) cc_final: 0.8817 (tttp) REVERT: T 79 GLU cc_start: 0.8228 (tp30) cc_final: 0.7824 (tp30) REVERT: T 83 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8586 (mtpp) REVERT: V 32 GLU cc_start: 0.8448 (tp30) cc_final: 0.8213 (tp30) REVERT: V 58 ARG cc_start: 0.8562 (mtm110) cc_final: 0.8224 (mtt-85) REVERT: V 89 ASP cc_start: 0.8230 (m-30) cc_final: 0.7835 (m-30) REVERT: V 96 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8131 (tm-30) outliers start: 39 outliers final: 27 residues processed: 393 average time/residue: 0.1134 time to fit residues: 68.3067 Evaluate side-chains 406 residues out of total 1533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 375 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 63 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 70 GLN Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain T residue 99 GLU Chi-restraints excluded: chain V residue 39 HIS Chi-restraints excluded: chain V residue 60 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 183 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.076759 restraints weight = 34096.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.079418 restraints weight = 17458.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.081217 restraints weight = 10947.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082446 restraints weight = 7821.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083277 restraints weight = 6114.362| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 15645 Z= 0.236 Angle : 0.903 59.190 21021 Z= 0.546 Chirality : 0.038 0.296 2289 Planarity : 0.005 0.203 2835 Dihedral : 3.557 14.463 2205 Min Nonbonded Distance : 1.482 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.35 % Allowed : 24.92 % Favored : 72.73 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.21), residues: 1869 helix: -0.02 (0.15), residues: 1281 sheet: None (None), residues: 0 loop : -1.33 (0.32), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 58 TYR 0.006 0.001 TYR G 72 PHE 0.007 0.001 PHE N 37 TRP 0.017 0.001 TRP O 53 HIS 0.336 0.010 HIS V 39 Details of bonding type rmsd covalent geometry : bond 0.00456 (15645) covalent geometry : angle 0.90277 (21021) hydrogen bonds : bond 0.03338 ( 610) hydrogen bonds : angle 3.75115 ( 1767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.01 seconds wall clock time: 39 minutes 48.70 seconds (2388.70 seconds total)