Starting phenix.real_space_refine on Fri Sep 27 03:22:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/09_2024/6ncv_0438.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/09_2024/6ncv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/09_2024/6ncv_0438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/09_2024/6ncv_0438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/09_2024/6ncv_0438.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/09_2024/6ncv_0438.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T, V Time building chain proxies: 3.78, per 1000 atoms: 0.24 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: 3.39 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.41 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: 3.38 Time building geometry restraints manager: 3.97 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: 0.00 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 27.030 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- 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= 0.511 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.003 TRP K 53 HIS 0.002 0.001 HIS N 39 PHE 0.004 0.001 PHE K 37 TYR 0.004 0.001 TYR P 72 ARG 0.011 0.001 ARG L 58 *********************** 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 fitting. rotamer outliers: 42 poor density : 570 time to evaluate : 1.820 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: 0.8855 (tttp) REVERT: C 40 LYS cc_start: 0.9081 (tppt) cc_final: 0.8849 (mmtt) REVERT: C 63 ASP cc_start: 0.8725 (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: 0.8673 (m-30) cc_final: 0.8348 (m-30) REVERT: E 35 LYS cc_start: 0.9382 (tttt) cc_final: 0.9111 (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: 0.9173 (tttt) cc_final: 0.8840 (tttm) REVERT: F 83 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8924 (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: 0.8791 (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: 0.8581 (tp30) cc_final: 0.8133 (mt-10) REVERT: I 32 GLU cc_start: 0.8879 (tp30) cc_final: 0.8475 (tp30) REVERT: I 86 LYS cc_start: 0.8899 (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: 0.8911 (tm-30) cc_final: 0.7567 (tm-30) REVERT: M 31 GLN cc_start: 0.8795 (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: 0.8564 (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: 0.9198 (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: 0.8642 (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: 0.9277 (tppt) cc_final: 0.9011 (mttm) REVERT: V 57 GLU cc_start: 0.7907 (tt0) cc_final: 0.7617 (tt0) REVERT: V 58 ARG cc_start: 0.8360 (mtm110) cc_final: 0.7858 (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: 0.3160 time to fit residues: 263.0034 Evaluate side-chains 436 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 418 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 159 optimal weight: 0.6980 chunk 143 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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 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 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 96 GLN 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15645 Z= 0.255 Angle : 0.605 8.258 21021 Z= 0.312 Chirality : 0.039 0.145 2289 Planarity : 0.005 0.034 2835 Dihedral : 5.410 56.454 2227 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.61 % Allowed : 17.35 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.93 (0.15), residues: 1869 helix: -3.38 (0.10), residues: 1239 sheet: None (None), residues: 0 loop : -2.58 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 53 HIS 0.003 0.001 HIS Q 39 PHE 0.008 0.001 PHE H 37 TYR 0.005 0.001 TYR P 72 ARG 0.007 0.001 ARG E 58 *********************** 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 498 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 458 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8683 (tm-30) REVERT: A 66 GLU cc_start: 0.8443 (tp30) cc_final: 0.7885 (tm-30) REVERT: A 98 GLN cc_start: 0.9230 (mm-40) cc_final: 0.9010 (mm-40) REVERT: B 30 SER cc_start: 0.8345 (t) cc_final: 0.7701 (p) REVERT: B 31 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8544 (tm-30) REVERT: B 32 GLU cc_start: 0.8811 (tp30) cc_final: 0.8402 (tp30) REVERT: B 66 GLU cc_start: 0.8615 (tp30) cc_final: 0.8098 (tm-30) REVERT: B 83 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8015 (mmtt) REVERT: B 96 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8896 (tm-30) REVERT: D 31 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8407 (tm-30) REVERT: D 35 LYS cc_start: 0.9314 (tttp) cc_final: 0.9080 (tttp) REVERT: D 39 HIS cc_start: 0.7338 (t-90) cc_final: 0.6353 (t-90) REVERT: D 99 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: E 20 GLU cc_start: 0.8688 (tp30) cc_final: 0.8408 (tm-30) REVERT: E 32 GLU cc_start: 0.8479 (tp30) cc_final: 0.7901 (tp30) REVERT: F 28 GLU cc_start: 0.8945 (tp30) cc_final: 0.8726 (tp30) REVERT: F 32 GLU cc_start: 0.8640 (tp30) cc_final: 0.8418 (tp30) REVERT: F 35 LYS cc_start: 0.9337 (tttt) cc_final: 0.9129 (tttp) REVERT: G 58 ARG cc_start: 0.8368 (mtm110) cc_final: 0.7932 (mtt-85) REVERT: G 96 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8470 (tm-30) REVERT: H 30 SER cc_start: 0.8351 (t) cc_final: 0.7723 (p) REVERT: H 31 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8469 (tm-30) REVERT: H 32 GLU cc_start: 0.8778 (tp30) cc_final: 0.8519 (tp30) REVERT: H 66 GLU cc_start: 0.8584 (tp30) cc_final: 0.8148 (tp30) REVERT: I 66 GLU cc_start: 0.7826 (tt0) cc_final: 0.6953 (mt-10) REVERT: I 86 LYS cc_start: 0.9046 (mttt) cc_final: 0.8841 (mtpp) REVERT: J 21 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8956 (mp) REVERT: J 39 HIS cc_start: 0.8326 (t70) cc_final: 0.8020 (t70) REVERT: K 31 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8334 (tm-30) REVERT: L 20 GLU cc_start: 0.8551 (tp30) cc_final: 0.8248 (tm-30) REVERT: L 31 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8583 (tm-30) REVERT: L 32 GLU cc_start: 0.8614 (tp30) cc_final: 0.8064 (tp30) REVERT: L 89 ASP cc_start: 0.7809 (m-30) cc_final: 0.7499 (m-30) REVERT: L 99 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: M 35 LYS cc_start: 0.9337 (tttt) cc_final: 0.9117 (tttm) REVERT: N 20 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7900 (mm-30) REVERT: N 31 GLN cc_start: 0.8532 (tt0) cc_final: 0.8243 (pt0) REVERT: N 58 ARG cc_start: 0.8172 (mtm110) cc_final: 0.7970 (mtt-85) REVERT: N 96 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8421 (tm-30) REVERT: O 30 SER cc_start: 0.8434 (t) cc_final: 0.7566 (p) REVERT: O 31 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8358 (tm-30) REVERT: O 32 GLU cc_start: 0.8642 (tp30) cc_final: 0.8349 (tp30) REVERT: O 33 GLN cc_start: 0.9033 (mt0) cc_final: 0.8378 (mt0) REVERT: O 66 GLU cc_start: 0.8366 (tp30) cc_final: 0.7822 (tm-30) REVERT: P 20 GLU cc_start: 0.8519 (tt0) cc_final: 0.8294 (tt0) REVERT: P 31 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8631 (tm-30) REVERT: P 66 GLU cc_start: 0.8306 (tp30) cc_final: 0.8010 (tm-30) REVERT: P 79 GLU cc_start: 0.8616 (tp30) cc_final: 0.8366 (tp30) REVERT: P 98 GLN cc_start: 0.9273 (mm-40) cc_final: 0.9044 (mm-40) REVERT: Q 79 GLU cc_start: 0.8914 (tp30) cc_final: 0.8696 (tp30) REVERT: R 31 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8288 (tm-30) REVERT: R 32 GLU cc_start: 0.8679 (tp30) cc_final: 0.8002 (tp30) REVERT: R 35 LYS cc_start: 0.9270 (tttm) cc_final: 0.9011 (tttp) REVERT: R 57 GLU cc_start: 0.8085 (tt0) cc_final: 0.7784 (tt0) REVERT: R 79 GLU cc_start: 0.8499 (tp30) cc_final: 0.8150 (tp30) REVERT: R 83 LYS cc_start: 0.9072 (mtpt) cc_final: 0.8794 (mtpp) REVERT: R 99 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: S 28 GLU cc_start: 0.8627 (tp30) cc_final: 0.8425 (tp30) REVERT: S 32 GLU cc_start: 0.8485 (tp30) cc_final: 0.7868 (tp30) REVERT: S 83 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8786 (mmtt) REVERT: S 99 GLU cc_start: 0.8546 (pt0) cc_final: 0.7994 (tm-30) REVERT: T 79 GLU cc_start: 0.8524 (tp30) cc_final: 0.8224 (tp30) REVERT: T 83 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8803 (mtpp) REVERT: V 20 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7975 (mm-30) REVERT: V 58 ARG cc_start: 0.8458 (mtm110) cc_final: 0.7988 (mtt-85) REVERT: V 89 ASP cc_start: 0.8261 (m-30) cc_final: 0.7922 (m-30) REVERT: V 96 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8241 (tm-30) outliers start: 40 outliers final: 16 residues processed: 476 average time/residue: 0.2748 time to fit residues: 188.0293 Evaluate side-chains 427 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 407 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN 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 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 95 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 142 optimal weight: 0.0050 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.0076 ------------------------------------------------------------------------------- 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 33 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN F 39 HIS F 96 GLN H 33 GLN I 39 HIS I 96 GLN J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS L 96 GLN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 HIS P 96 GLN Q 39 HIS T 33 GLN T 39 HIS T 96 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3689 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= 0.168 Angle : 0.520 8.001 21021 Z= 0.273 Chirality : 0.036 0.127 2289 Planarity : 0.004 0.031 2835 Dihedral : 4.331 49.883 2210 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.94 % Allowed : 18.92 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.16), residues: 1869 helix: -2.57 (0.12), residues: 1281 sheet: None (None), residues: 0 loop : -2.68 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 53 HIS 0.013 0.001 HIS F 39 PHE 0.004 0.001 PHE N 37 TYR 0.004 0.001 TYR T 72 ARG 0.004 0.000 ARG E 58 *********************** 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 474 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 429 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8557 (tm-30) REVERT: A 66 GLU cc_start: 0.8287 (tp30) cc_final: 0.7767 (tm-30) REVERT: B 30 SER cc_start: 0.8373 (t) cc_final: 0.7584 (p) REVERT: B 31 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8363 (tm-30) REVERT: B 32 GLU cc_start: 0.8669 (tp30) cc_final: 0.8405 (tp30) REVERT: B 33 GLN cc_start: 0.9134 (mt0) cc_final: 0.8714 (mt0) REVERT: C 63 ASP cc_start: 0.8622 (m-30) cc_final: 0.8339 (m-30) REVERT: D 31 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8307 (tm-30) REVERT: D 32 GLU cc_start: 0.8642 (tp30) cc_final: 0.8141 (tp30) REVERT: D 99 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: E 20 GLU cc_start: 0.8672 (tp30) cc_final: 0.8321 (tm-30) REVERT: E 32 GLU cc_start: 0.8404 (tp30) cc_final: 0.7739 (tp30) REVERT: E 63 ASP cc_start: 0.8899 (m-30) cc_final: 0.8633 (m-30) REVERT: E 66 GLU cc_start: 0.8320 (tp30) cc_final: 0.8099 (tp30) REVERT: E 79 GLU cc_start: 0.8710 (tp30) cc_final: 0.8315 (tp30) REVERT: E 99 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: F 32 GLU cc_start: 0.8526 (tp30) cc_final: 0.8190 (tp30) REVERT: F 35 LYS cc_start: 0.9244 (tttt) cc_final: 0.9031 (tttp) REVERT: G 31 GLN cc_start: 0.8593 (tt0) cc_final: 0.8269 (pt0) REVERT: G 58 ARG cc_start: 0.8353 (mtm110) cc_final: 0.7944 (mtt-85) REVERT: G 96 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8035 (tm-30) REVERT: H 30 SER cc_start: 0.8209 (t) cc_final: 0.7562 (p) REVERT: H 31 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8323 (tm-30) REVERT: H 32 GLU cc_start: 0.8655 (tp30) cc_final: 0.8326 (tp30) REVERT: H 66 GLU cc_start: 0.8471 (tp30) cc_final: 0.7982 (tp30) REVERT: I 79 GLU cc_start: 0.8564 (tp30) cc_final: 0.8363 (tp30) REVERT: I 83 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8577 (mtpp) REVERT: I 86 LYS cc_start: 0.9074 (mttt) cc_final: 0.8802 (mtpp) REVERT: K 31 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8263 (tm-30) REVERT: K 32 GLU cc_start: 0.8562 (tp30) cc_final: 0.8355 (tp30) REVERT: L 20 GLU cc_start: 0.8584 (tp30) cc_final: 0.8247 (tm-30) REVERT: L 31 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8546 (tm-30) REVERT: L 32 GLU cc_start: 0.8553 (tp30) cc_final: 0.7966 (tp30) REVERT: L 89 ASP cc_start: 0.7706 (m-30) cc_final: 0.7363 (m-30) REVERT: L 99 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: N 20 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7929 (mm-30) REVERT: N 31 GLN cc_start: 0.8450 (tt0) cc_final: 0.8236 (pt0) REVERT: N 96 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8320 (tm-30) REVERT: O 30 SER cc_start: 0.8427 (t) cc_final: 0.7606 (p) REVERT: O 31 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8363 (tm-30) REVERT: O 32 GLU cc_start: 0.8497 (tp30) cc_final: 0.8224 (tp30) REVERT: O 33 GLN cc_start: 0.8982 (mt0) cc_final: 0.8324 (mt0) REVERT: O 66 GLU cc_start: 0.8249 (tp30) cc_final: 0.7745 (tm-30) REVERT: P 31 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8578 (tm-30) REVERT: P 66 GLU cc_start: 0.8248 (tp30) cc_final: 0.7905 (tm-30) REVERT: P 79 GLU cc_start: 0.8640 (tp30) cc_final: 0.8346 (tp30) REVERT: Q 66 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7284 (mm-30) REVERT: R 31 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8205 (tm-30) REVERT: R 32 GLU cc_start: 0.8546 (tp30) cc_final: 0.7814 (tp30) REVERT: R 39 HIS cc_start: 0.7166 (t-90) cc_final: 0.6626 (t-90) REVERT: R 79 GLU cc_start: 0.8404 (tp30) cc_final: 0.7891 (tp30) REVERT: R 99 GLU cc_start: 0.8690 (pt0) cc_final: 0.8200 (tm-30) REVERT: S 32 GLU cc_start: 0.8461 (tp30) cc_final: 0.7735 (tp30) REVERT: S 63 ASP cc_start: 0.8956 (m-30) cc_final: 0.8484 (m-30) REVERT: S 99 GLU cc_start: 0.8556 (pt0) cc_final: 0.8048 (tm-30) REVERT: T 33 GLN cc_start: 0.8399 (mt0) cc_final: 0.7878 (mt0) REVERT: T 35 LYS cc_start: 0.9281 (tttm) cc_final: 0.8787 (tttp) REVERT: T 79 GLU cc_start: 0.8426 (tp30) cc_final: 0.8073 (tp30) REVERT: T 83 LYS cc_start: 0.9019 (mtpt) cc_final: 0.8721 (mtpp) REVERT: V 20 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7985 (mm-30) REVERT: V 32 GLU cc_start: 0.8495 (tp30) cc_final: 0.8207 (tp30) REVERT: V 58 ARG cc_start: 0.8454 (mtm110) cc_final: 0.7993 (mtt-85) REVERT: V 89 ASP cc_start: 0.8194 (m-30) cc_final: 0.7814 (m-30) REVERT: V 96 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8250 (tm-30) outliers start: 45 outliers final: 19 residues processed: 446 average time/residue: 0.2632 time to fit residues: 171.3144 Evaluate side-chains 411 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 389 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 99 GLU 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 H residue 92 ASP Chi-restraints excluded: chain I residue 39 HIS Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 99 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 S residue 30 SER 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 169 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 C 31 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 GLN I 39 HIS I 98 GLN J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 GLN O 96 GLN P 39 HIS S 96 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4021 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= 0.206 Angle : 0.514 6.813 21021 Z= 0.270 Chirality : 0.037 0.124 2289 Planarity : 0.003 0.030 2835 Dihedral : 4.099 53.961 2209 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.59 % Allowed : 20.09 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.18), residues: 1869 helix: -1.84 (0.13), residues: 1281 sheet: None (None), residues: 0 loop : -2.21 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 53 HIS 0.007 0.001 HIS I 39 PHE 0.006 0.001 PHE H 37 TYR 0.005 0.001 TYR T 72 ARG 0.003 0.000 ARG L 100 *********************** 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 465 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 410 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 66 GLU cc_start: 0.8302 (tp30) cc_final: 0.7852 (tm-30) REVERT: A 75 GLU cc_start: 0.9010 (tp30) cc_final: 0.8740 (tp30) REVERT: A 98 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8943 (mm-40) REVERT: B 30 SER cc_start: 0.8175 (t) cc_final: 0.7399 (p) REVERT: B 31 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8392 (tm-30) REVERT: B 32 GLU cc_start: 0.8642 (tp30) cc_final: 0.8389 (tp30) REVERT: B 33 GLN cc_start: 0.9078 (mt0) cc_final: 0.8699 (mt0) REVERT: B 66 GLU cc_start: 0.8468 (tp30) cc_final: 0.7990 (tm-30) REVERT: C 31 GLN cc_start: 0.8272 (tt0) cc_final: 0.7941 (tt0) REVERT: D 31 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8410 (tm-30) REVERT: D 32 GLU cc_start: 0.8636 (tp30) cc_final: 0.8132 (tp30) REVERT: E 20 GLU cc_start: 0.8741 (tp30) cc_final: 0.8320 (tm-30) REVERT: E 32 GLU cc_start: 0.8404 (tp30) cc_final: 0.7709 (tp30) REVERT: E 63 ASP cc_start: 0.8949 (m-30) cc_final: 0.8640 (m-30) REVERT: E 66 GLU cc_start: 0.8301 (tp30) cc_final: 0.8083 (tp30) REVERT: E 79 GLU cc_start: 0.8715 (tp30) cc_final: 0.8329 (tp30) REVERT: F 32 GLU cc_start: 0.8640 (tp30) cc_final: 0.8324 (tp30) REVERT: F 57 GLU cc_start: 0.8687 (tt0) cc_final: 0.8156 (tt0) REVERT: G 58 ARG cc_start: 0.8371 (mtm110) cc_final: 0.7932 (mtt-85) REVERT: G 89 ASP cc_start: 0.8306 (m-30) cc_final: 0.8102 (m-30) REVERT: G 96 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8019 (tm-30) REVERT: H 30 SER cc_start: 0.8324 (t) cc_final: 0.7687 (p) REVERT: H 31 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8352 (tm-30) REVERT: H 32 GLU cc_start: 0.8655 (tp30) cc_final: 0.8321 (tp30) REVERT: H 66 GLU cc_start: 0.8522 (tp30) cc_final: 0.8089 (tp30) REVERT: I 83 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8542 (mtpp) REVERT: I 86 LYS cc_start: 0.9110 (mttt) cc_final: 0.8847 (mtpp) REVERT: J 66 GLU cc_start: 0.7772 (tp30) cc_final: 0.6902 (tp30) REVERT: K 31 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8222 (tm-30) REVERT: K 32 GLU cc_start: 0.8624 (tp30) cc_final: 0.8309 (tp30) REVERT: L 20 GLU cc_start: 0.8537 (tp30) cc_final: 0.8284 (tm-30) REVERT: L 32 GLU cc_start: 0.8551 (tp30) cc_final: 0.7980 (tp30) REVERT: L 63 ASP cc_start: 0.8977 (m-30) cc_final: 0.8762 (m-30) REVERT: L 89 ASP cc_start: 0.7651 (m-30) cc_final: 0.7227 (m-30) REVERT: L 99 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: N 31 GLN cc_start: 0.8516 (tt0) cc_final: 0.8220 (pt0) REVERT: N 96 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8245 (tm-30) REVERT: O 30 SER cc_start: 0.8464 (t) cc_final: 0.7856 (p) REVERT: O 31 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8382 (tm-30) REVERT: O 32 GLU cc_start: 0.8495 (tp30) cc_final: 0.8211 (tp30) REVERT: O 66 GLU cc_start: 0.8340 (tp30) cc_final: 0.7823 (tm-30) REVERT: P 31 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8605 (tm-30) REVERT: P 66 GLU cc_start: 0.8290 (tp30) cc_final: 0.7948 (tm-30) REVERT: P 79 GLU cc_start: 0.8679 (tp30) cc_final: 0.8428 (tp30) REVERT: P 98 GLN cc_start: 0.9251 (mm-40) cc_final: 0.8937 (mm-40) REVERT: Q 63 ASP cc_start: 0.8686 (m-30) cc_final: 0.8451 (m-30) REVERT: R 31 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8303 (tm-30) REVERT: R 32 GLU cc_start: 0.8559 (tp30) cc_final: 0.7825 (tp30) REVERT: R 79 GLU cc_start: 0.8418 (tp30) cc_final: 0.8003 (tp30) REVERT: R 83 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8749 (ttpp) REVERT: R 99 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: S 32 GLU cc_start: 0.8450 (tp30) cc_final: 0.7783 (tp30) REVERT: S 99 GLU cc_start: 0.8614 (pt0) cc_final: 0.8241 (tm-30) REVERT: T 35 LYS cc_start: 0.9317 (tttm) cc_final: 0.9002 (tttm) REVERT: T 79 GLU cc_start: 0.8388 (tp30) cc_final: 0.7957 (tp30) REVERT: T 83 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8654 (mtpp) REVERT: V 20 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7966 (mm-30) REVERT: V 30 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7965 (t) REVERT: V 40 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8921 (ttmm) REVERT: V 58 ARG cc_start: 0.8514 (mtm110) cc_final: 0.8080 (mtt-85) REVERT: V 89 ASP cc_start: 0.8229 (m-30) cc_final: 0.7877 (m-30) REVERT: V 96 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8242 (tm-30) outliers start: 55 outliers final: 23 residues processed: 433 average time/residue: 0.2588 time to fit residues: 164.3250 Evaluate side-chains 415 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 388 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN 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 99 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 99 GLU 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 60 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 63 ASP 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 R residue 99 GLU Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain V residue 30 SER Chi-restraints excluded: chain V residue 40 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 30.0000 chunk 155 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 96 GLN B 96 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN F 98 GLN G 67 GLN I 96 GLN J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS K 98 GLN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 HIS T 98 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 67 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15645 Z= 0.328 Angle : 0.587 5.619 21021 Z= 0.305 Chirality : 0.040 0.141 2289 Planarity : 0.004 0.032 2835 Dihedral : 4.201 59.131 2207 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.07 % Allowed : 21.79 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.19), residues: 1869 helix: -1.45 (0.13), residues: 1281 sheet: None (None), residues: 0 loop : -1.65 (0.30), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 53 HIS 0.005 0.001 HIS I 39 PHE 0.011 0.002 PHE H 37 TYR 0.007 0.001 TYR T 72 ARG 0.003 0.000 ARG P 55 *********************** 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 454 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 407 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8554 (tm-30) REVERT: A 66 GLU cc_start: 0.8320 (tp30) cc_final: 0.7822 (tm-30) REVERT: A 75 GLU cc_start: 0.9034 (tp30) cc_final: 0.8744 (tp30) REVERT: B 31 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 32 GLU cc_start: 0.8717 (tp30) cc_final: 0.8441 (tp30) REVERT: B 66 GLU cc_start: 0.8647 (tp30) cc_final: 0.8194 (tm-30) REVERT: C 31 GLN cc_start: 0.8378 (tt0) cc_final: 0.7733 (tt0) REVERT: D 31 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8447 (tm-30) REVERT: D 32 GLU cc_start: 0.8680 (tp30) cc_final: 0.8146 (tp30) REVERT: D 66 GLU cc_start: 0.8627 (tp30) cc_final: 0.8417 (tp30) REVERT: D 99 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8393 (tm-30) REVERT: E 20 GLU cc_start: 0.8731 (tp30) cc_final: 0.8385 (tm-30) REVERT: E 31 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8739 (tm-30) REVERT: E 32 GLU cc_start: 0.8528 (tp30) cc_final: 0.7825 (tp30) REVERT: E 57 GLU cc_start: 0.7685 (tt0) cc_final: 0.7477 (tt0) REVERT: E 66 GLU cc_start: 0.8249 (tp30) cc_final: 0.8043 (tp30) REVERT: E 79 GLU cc_start: 0.8784 (tp30) cc_final: 0.8264 (tp30) REVERT: F 32 GLU cc_start: 0.8727 (tp30) cc_final: 0.8490 (tp30) REVERT: G 58 ARG cc_start: 0.8384 (mtm110) cc_final: 0.7903 (mtt-85) REVERT: G 89 ASP cc_start: 0.8320 (m-30) cc_final: 0.8073 (m-30) REVERT: G 96 GLN cc_start: 0.8621 (tm-30) cc_final: 0.7963 (tm-30) REVERT: H 31 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8450 (tm-30) REVERT: H 32 GLU cc_start: 0.8664 (tp30) cc_final: 0.8347 (tp30) REVERT: H 66 GLU cc_start: 0.8618 (tp30) cc_final: 0.8258 (tp30) REVERT: I 35 LYS cc_start: 0.9125 (tptm) cc_final: 0.8914 (tttm) REVERT: I 58 ARG cc_start: 0.7951 (ptp90) cc_final: 0.7674 (ptp-110) REVERT: I 86 LYS cc_start: 0.9080 (mttt) cc_final: 0.8844 (mtpp) REVERT: J 31 GLN cc_start: 0.8893 (tp40) cc_final: 0.8561 (tp40) REVERT: K 31 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8253 (tm-30) REVERT: K 32 GLU cc_start: 0.8678 (tp30) cc_final: 0.8387 (tp30) REVERT: K 66 GLU cc_start: 0.8370 (tp30) cc_final: 0.7873 (tm-30) REVERT: K 99 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8196 (tm-30) REVERT: L 32 GLU cc_start: 0.8658 (tp30) cc_final: 0.8152 (tp30) REVERT: L 89 ASP cc_start: 0.7718 (m-30) cc_final: 0.7294 (m-30) REVERT: L 99 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: N 31 GLN cc_start: 0.8521 (tt0) cc_final: 0.8173 (pt0) REVERT: N 92 ASP cc_start: 0.8561 (p0) cc_final: 0.7777 (p0) REVERT: N 96 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8172 (tm-30) REVERT: O 30 SER cc_start: 0.8392 (t) cc_final: 0.7355 (p) REVERT: O 31 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8323 (tm-30) REVERT: O 32 GLU cc_start: 0.8603 (tp30) cc_final: 0.8290 (tp30) REVERT: O 33 GLN cc_start: 0.9046 (mt0) cc_final: 0.8382 (mt0) REVERT: O 66 GLU cc_start: 0.8400 (tp30) cc_final: 0.8089 (tm-30) REVERT: O 83 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7998 (mmtt) REVERT: O 96 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8969 (tp40) REVERT: P 31 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8467 (tm-30) REVERT: P 39 HIS cc_start: 0.8566 (OUTLIER) cc_final: 0.8160 (t70) REVERT: P 66 GLU cc_start: 0.8387 (tp30) cc_final: 0.8037 (tm-30) REVERT: P 79 GLU cc_start: 0.8699 (tp30) cc_final: 0.8441 (tp30) REVERT: R 31 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8377 (tm-30) REVERT: R 32 GLU cc_start: 0.8656 (tp30) cc_final: 0.8048 (tp30) REVERT: R 83 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8792 (mtpp) REVERT: R 99 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8252 (tm-30) REVERT: S 32 GLU cc_start: 0.8483 (tp30) cc_final: 0.7878 (tp30) REVERT: S 70 GLN cc_start: 0.8689 (tp40) cc_final: 0.8098 (tp40) REVERT: S 99 GLU cc_start: 0.8625 (pt0) cc_final: 0.8261 (tm-30) REVERT: T 31 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8448 (tm-30) REVERT: T 35 LYS cc_start: 0.9357 (tttm) cc_final: 0.9121 (tttm) REVERT: T 79 GLU cc_start: 0.8337 (tp30) cc_final: 0.7847 (tp30) REVERT: T 83 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8560 (mtpp) REVERT: V 20 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8083 (mm-30) REVERT: V 32 GLU cc_start: 0.8541 (tp30) cc_final: 0.8290 (tp30) REVERT: V 58 ARG cc_start: 0.8560 (mtm110) cc_final: 0.8111 (mtt-85) REVERT: V 89 ASP cc_start: 0.8369 (m-30) cc_final: 0.8163 (m-30) REVERT: V 96 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8212 (tm-30) outliers start: 47 outliers final: 29 residues processed: 423 average time/residue: 0.2812 time to fit residues: 173.7967 Evaluate side-chains 416 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 384 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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 96 GLN 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 99 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 99 GLU 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 60 ASP Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 63 ASP Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain P residue 39 HIS Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain T residue 99 GLU Chi-restraints excluded: chain V residue 40 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 0.0370 chunk 15 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 96 GLN B 96 GLN C 96 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS L 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 GLN P 39 HIS R 70 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 67 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15645 Z= 0.166 Angle : 0.521 9.258 21021 Z= 0.276 Chirality : 0.035 0.125 2289 Planarity : 0.003 0.030 2835 Dihedral : 3.666 28.761 2207 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.94 % Allowed : 23.03 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.20), residues: 1869 helix: -0.72 (0.14), residues: 1281 sheet: None (None), residues: 0 loop : -1.68 (0.29), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP K 53 HIS 0.007 0.001 HIS P 39 PHE 0.005 0.001 PHE L 37 TYR 0.004 0.001 TYR D 72 ARG 0.003 0.000 ARG K 58 *********************** 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 452 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 407 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8467 (tm-30) REVERT: A 66 GLU cc_start: 0.8314 (tp30) cc_final: 0.7845 (tm-30) REVERT: A 75 GLU cc_start: 0.8970 (tp30) cc_final: 0.8575 (mm-30) REVERT: A 98 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8832 (mm-40) REVERT: B 31 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8439 (tm-30) REVERT: B 32 GLU cc_start: 0.8581 (tp30) cc_final: 0.8304 (tp30) REVERT: C 66 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8216 (tm-30) REVERT: D 31 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8286 (tm-30) REVERT: D 32 GLU cc_start: 0.8573 (tp30) cc_final: 0.8025 (tp30) REVERT: D 63 ASP cc_start: 0.8531 (m-30) cc_final: 0.8230 (m-30) REVERT: D 79 GLU cc_start: 0.8107 (tp30) cc_final: 0.7476 (tp30) REVERT: D 99 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8399 (tm-30) REVERT: E 20 GLU cc_start: 0.8716 (tp30) cc_final: 0.8350 (tm-30) REVERT: E 32 GLU cc_start: 0.8406 (tp30) cc_final: 0.7758 (tp30) REVERT: E 79 GLU cc_start: 0.8693 (tp30) cc_final: 0.8227 (tp30) REVERT: E 99 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: F 32 GLU cc_start: 0.8746 (tp30) cc_final: 0.8463 (tp30) REVERT: G 55 ARG cc_start: 0.8471 (ptp90) cc_final: 0.8250 (mtp180) REVERT: G 58 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7897 (mtt-85) REVERT: G 96 GLN cc_start: 0.8588 (tm-30) cc_final: 0.7947 (tm-30) REVERT: H 31 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8415 (tm-30) REVERT: H 32 GLU cc_start: 0.8614 (tp30) cc_final: 0.8283 (tp30) REVERT: H 66 GLU cc_start: 0.8400 (tp30) cc_final: 0.8042 (tm-30) REVERT: I 31 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8441 (tm-30) REVERT: I 75 GLU cc_start: 0.9028 (tp30) cc_final: 0.8521 (mm-30) REVERT: I 83 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8472 (mtpp) REVERT: J 33 GLN cc_start: 0.8467 (mt0) cc_final: 0.8225 (mt0) REVERT: K 31 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8188 (tm-30) REVERT: K 32 GLU cc_start: 0.8571 (tp30) cc_final: 0.8188 (tp30) REVERT: K 99 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8198 (tm-30) REVERT: L 32 GLU cc_start: 0.8482 (tp30) cc_final: 0.7860 (tp30) REVERT: L 99 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: N 31 GLN cc_start: 0.8496 (tt0) cc_final: 0.8161 (pt0) REVERT: N 92 ASP cc_start: 0.8553 (p0) cc_final: 0.8274 (p0) REVERT: O 30 SER cc_start: 0.8362 (t) cc_final: 0.7362 (p) REVERT: O 31 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8283 (tm-30) REVERT: O 32 GLU cc_start: 0.8488 (tp30) cc_final: 0.8166 (tp30) REVERT: O 33 GLN cc_start: 0.9027 (mt0) cc_final: 0.8361 (mt0) REVERT: O 66 GLU cc_start: 0.8319 (tp30) cc_final: 0.7980 (tm-30) REVERT: O 83 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7944 (mmtt) REVERT: P 31 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8393 (tm-30) REVERT: P 39 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8175 (t70) REVERT: P 57 GLU cc_start: 0.8022 (tt0) cc_final: 0.7798 (tt0) REVERT: P 66 GLU cc_start: 0.8307 (tp30) cc_final: 0.7941 (tm-30) REVERT: P 79 GLU cc_start: 0.8644 (tp30) cc_final: 0.8397 (tp30) REVERT: P 98 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8897 (mm-40) REVERT: R 31 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8313 (tm-30) REVERT: R 32 GLU cc_start: 0.8464 (tp30) cc_final: 0.7706 (tp30) REVERT: R 79 GLU cc_start: 0.8353 (tp30) cc_final: 0.8042 (tp30) REVERT: R 83 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8518 (mtpp) REVERT: R 99 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: S 32 GLU cc_start: 0.8484 (tp30) cc_final: 0.7757 (tp30) REVERT: S 99 GLU cc_start: 0.8625 (pt0) cc_final: 0.8263 (tm-30) REVERT: T 35 LYS cc_start: 0.9246 (tttm) cc_final: 0.8882 (tttp) REVERT: T 79 GLU cc_start: 0.8327 (tp30) cc_final: 0.7875 (tp30) REVERT: T 83 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8529 (mtpp) REVERT: V 32 GLU cc_start: 0.8524 (tp30) cc_final: 0.8254 (tp30) REVERT: V 55 ARG cc_start: 0.8955 (ptp90) cc_final: 0.8647 (mtp180) REVERT: V 58 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8109 (mtt-85) REVERT: V 89 ASP cc_start: 0.8208 (m-30) cc_final: 0.7873 (m-30) REVERT: V 96 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8411 (tm-30) outliers start: 45 outliers final: 22 residues processed: 424 average time/residue: 0.2767 time to fit residues: 170.0604 Evaluate side-chains 410 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 384 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 70 GLN 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 B residue 96 GLN Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 93 VAL 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 O residue 63 ASP 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 R residue 99 GLU Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain T residue 99 GLU Chi-restraints excluded: chain V residue 40 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 102 optimal weight: 0.0980 chunk 182 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 96 GLN B 96 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN J 96 GLN K 39 HIS L 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 GLN O 96 GLN P 39 HIS ** S 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4494 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= 0.239 Angle : 0.554 7.788 21021 Z= 0.291 Chirality : 0.038 0.128 2289 Planarity : 0.003 0.032 2835 Dihedral : 3.593 13.873 2205 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.80 % Allowed : 23.81 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1869 helix: -0.50 (0.14), residues: 1281 sheet: None (None), residues: 0 loop : -1.41 (0.31), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 53 HIS 0.008 0.001 HIS P 39 PHE 0.007 0.001 PHE O 37 TYR 0.005 0.001 TYR T 72 ARG 0.003 0.000 ARG K 58 *********************** 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 436 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 393 time to evaluate : 1.938 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8492 (tm-30) REVERT: A 66 GLU cc_start: 0.8367 (tp30) cc_final: 0.7899 (tm-30) REVERT: A 75 GLU cc_start: 0.8997 (tp30) cc_final: 0.8776 (tp30) REVERT: B 31 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8489 (tm-30) REVERT: B 32 GLU cc_start: 0.8667 (tp30) cc_final: 0.8374 (tp30) REVERT: B 33 GLN cc_start: 0.8727 (mt0) cc_final: 0.8245 (mp10) REVERT: B 35 LYS cc_start: 0.9362 (ttmt) cc_final: 0.9104 (ttmm) REVERT: D 31 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8306 (tm-30) REVERT: D 32 GLU cc_start: 0.8651 (tp30) cc_final: 0.8180 (tp30) REVERT: D 99 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8337 (tm-30) REVERT: E 20 GLU cc_start: 0.8738 (tp30) cc_final: 0.8398 (tm-30) REVERT: E 32 GLU cc_start: 0.8479 (tp30) cc_final: 0.7796 (tp30) REVERT: E 79 GLU cc_start: 0.8724 (tp30) cc_final: 0.8269 (tp30) REVERT: F 32 GLU cc_start: 0.8727 (tp30) cc_final: 0.8508 (tp30) REVERT: G 58 ARG cc_start: 0.8369 (mtm110) cc_final: 0.8037 (mtt-85) REVERT: G 96 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8209 (tm-30) REVERT: H 31 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8455 (tm-30) REVERT: H 32 GLU cc_start: 0.8709 (tp30) cc_final: 0.8397 (tp30) REVERT: H 33 GLN cc_start: 0.8746 (mt0) cc_final: 0.8302 (mp10) REVERT: H 66 GLU cc_start: 0.8452 (tp30) cc_final: 0.8140 (tm-30) REVERT: I 31 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8553 (tm-30) REVERT: K 31 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8249 (tm-30) REVERT: K 32 GLU cc_start: 0.8635 (tp30) cc_final: 0.8274 (tp30) REVERT: K 99 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8209 (tm-30) REVERT: L 32 GLU cc_start: 0.8544 (tp30) cc_final: 0.7966 (tp30) REVERT: L 66 GLU cc_start: 0.8145 (tp30) cc_final: 0.7853 (tp30) REVERT: L 89 ASP cc_start: 0.7702 (m-30) cc_final: 0.7281 (m-30) REVERT: L 99 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: N 31 GLN cc_start: 0.8515 (tt0) cc_final: 0.8180 (pt0) REVERT: O 30 SER cc_start: 0.7925 (t) cc_final: 0.6917 (p) REVERT: O 31 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8236 (tm-30) REVERT: O 32 GLU cc_start: 0.8529 (tp30) cc_final: 0.8178 (tp30) REVERT: O 33 GLN cc_start: 0.9106 (mt0) cc_final: 0.8427 (mt0) REVERT: O 66 GLU cc_start: 0.8407 (tp30) cc_final: 0.8119 (tm-30) REVERT: O 83 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7942 (mmtt) REVERT: P 31 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8452 (tm-30) REVERT: P 66 GLU cc_start: 0.8313 (tp30) cc_final: 0.7926 (tm-30) REVERT: P 79 GLU cc_start: 0.8693 (tp30) cc_final: 0.8440 (tp30) REVERT: Q 67 GLN cc_start: 0.8465 (mt0) cc_final: 0.8230 (mt0) REVERT: R 31 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8381 (tm-30) REVERT: R 32 GLU cc_start: 0.8533 (tp30) cc_final: 0.7787 (tp30) REVERT: R 83 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8681 (mtpp) REVERT: R 99 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: S 32 GLU cc_start: 0.8486 (tp30) cc_final: 0.7805 (tp30) REVERT: S 99 GLU cc_start: 0.8602 (pt0) cc_final: 0.8215 (tm-30) REVERT: T 31 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8379 (tm-30) REVERT: T 35 LYS cc_start: 0.9285 (tttm) cc_final: 0.8902 (tttp) REVERT: T 67 GLN cc_start: 0.7724 (mt0) cc_final: 0.7395 (mp10) REVERT: T 79 GLU cc_start: 0.8288 (tp30) cc_final: 0.7910 (tp30) REVERT: T 83 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8642 (mtpp) REVERT: V 32 GLU cc_start: 0.8549 (tp30) cc_final: 0.8318 (tp30) REVERT: V 58 ARG cc_start: 0.8548 (mtm110) cc_final: 0.8216 (mtt-85) REVERT: V 89 ASP cc_start: 0.8260 (m-30) cc_final: 0.7952 (m-30) REVERT: V 96 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8176 (tm-30) outliers start: 43 outliers final: 27 residues processed: 403 average time/residue: 0.2325 time to fit residues: 138.8893 Evaluate side-chains 407 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 378 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 96 GLN Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain F residue 20 GLU 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 J residue 99 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain N residue 30 SER 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 O residue 96 GLN Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain R residue 99 GLU 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 40 LYS 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 112 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 HIS ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN F 39 HIS ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS L 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 70 GLN ** S 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 39 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15645 Z= 0.273 Angle : 0.577 7.460 21021 Z= 0.304 Chirality : 0.039 0.132 2289 Planarity : 0.003 0.034 2835 Dihedral : 3.675 14.532 2205 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.94 % Allowed : 24.20 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1869 helix: -0.41 (0.14), residues: 1281 sheet: None (None), residues: 0 loop : -1.30 (0.32), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 53 HIS 0.005 0.001 HIS K 39 PHE 0.008 0.001 PHE B 37 TYR 0.005 0.001 TYR T 72 ARG 0.004 0.000 ARG I 55 *********************** 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 435 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 390 time to evaluate : 1.779 Fit side-chains REVERT: A 31 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 66 GLU cc_start: 0.8347 (tp30) cc_final: 0.7869 (tm-30) REVERT: A 98 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8799 (mm-40) REVERT: B 31 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8421 (tm-30) REVERT: B 32 GLU cc_start: 0.8689 (tp30) cc_final: 0.8356 (tp30) REVERT: B 33 GLN cc_start: 0.8747 (mt0) cc_final: 0.8259 (mp10) REVERT: B 35 LYS cc_start: 0.9374 (ttmt) cc_final: 0.9108 (ttmm) REVERT: B 66 GLU cc_start: 0.8657 (tp30) cc_final: 0.8368 (tm-30) REVERT: D 31 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8354 (tm-30) REVERT: D 32 GLU cc_start: 0.8725 (tp30) cc_final: 0.8215 (tp30) REVERT: D 99 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8359 (tm-30) REVERT: E 20 GLU cc_start: 0.8731 (tp30) cc_final: 0.8434 (tm-30) REVERT: E 32 GLU cc_start: 0.8531 (tp30) cc_final: 0.7978 (tp30) REVERT: E 79 GLU cc_start: 0.8748 (tp30) cc_final: 0.8285 (tp30) REVERT: F 79 GLU cc_start: 0.8222 (tp30) cc_final: 0.8008 (tp30) REVERT: G 58 ARG cc_start: 0.8462 (mtm110) cc_final: 0.8173 (mtt-85) REVERT: G 96 GLN cc_start: 0.8581 (tm-30) cc_final: 0.7888 (tm-30) REVERT: H 27 GLU cc_start: 0.8113 (pt0) cc_final: 0.7857 (pt0) REVERT: H 31 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8425 (tm-30) REVERT: H 32 GLU cc_start: 0.8708 (tp30) cc_final: 0.8380 (tp30) REVERT: H 33 GLN cc_start: 0.8754 (mt0) cc_final: 0.8313 (mp10) REVERT: H 66 GLU cc_start: 0.8504 (tp30) cc_final: 0.8158 (tm-30) REVERT: H 83 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7871 (mmtt) REVERT: I 31 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8584 (tm-30) REVERT: K 31 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8318 (tm-30) REVERT: K 32 GLU cc_start: 0.8675 (tp30) cc_final: 0.8312 (tp30) REVERT: K 66 GLU cc_start: 0.8314 (tp30) cc_final: 0.7634 (tm-30) REVERT: K 98 GLN cc_start: 0.9007 (tp40) cc_final: 0.8743 (tp-100) REVERT: K 99 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8288 (tm-30) REVERT: L 32 GLU cc_start: 0.8583 (tp30) cc_final: 0.8031 (tp30) REVERT: L 66 GLU cc_start: 0.8174 (tp30) cc_final: 0.7903 (tp30) REVERT: L 89 ASP cc_start: 0.7683 (m-30) cc_final: 0.7246 (m-30) REVERT: L 99 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: M 66 GLU cc_start: 0.8195 (tt0) cc_final: 0.7708 (mt-10) REVERT: N 31 GLN cc_start: 0.8462 (tt0) cc_final: 0.8121 (pt0) REVERT: O 31 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8384 (tm-30) REVERT: O 32 GLU cc_start: 0.8529 (tp30) cc_final: 0.8185 (tp30) REVERT: O 75 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8108 (tt0) REVERT: O 83 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7891 (mmtt) REVERT: P 31 GLN cc_start: 0.8992 (tm-30) cc_final: 0.8484 (tm-30) REVERT: P 66 GLU cc_start: 0.8343 (tp30) cc_final: 0.7962 (tm-30) REVERT: P 79 GLU cc_start: 0.8701 (tp30) cc_final: 0.8447 (tp30) REVERT: P 98 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8877 (mm-40) REVERT: Q 57 GLU cc_start: 0.8026 (tt0) cc_final: 0.7752 (tt0) REVERT: Q 67 GLN cc_start: 0.8496 (mt0) cc_final: 0.8270 (mt0) REVERT: R 31 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8401 (tm-30) REVERT: R 32 GLU cc_start: 0.8585 (tp30) cc_final: 0.7837 (tp30) REVERT: R 66 GLU cc_start: 0.8370 (tp30) cc_final: 0.7930 (tm-30) REVERT: R 99 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: S 32 GLU cc_start: 0.8485 (tp30) cc_final: 0.7830 (tp30) REVERT: S 99 GLU cc_start: 0.8612 (pt0) cc_final: 0.8232 (tm-30) REVERT: T 31 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8405 (tm-30) REVERT: T 35 LYS cc_start: 0.9235 (tttm) cc_final: 0.8854 (tttp) REVERT: T 63 ASP cc_start: 0.8430 (t70) cc_final: 0.7939 (t70) REVERT: T 79 GLU cc_start: 0.8277 (tp30) cc_final: 0.7944 (tp30) REVERT: T 83 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8643 (mtpp) REVERT: V 32 GLU cc_start: 0.8559 (tp30) cc_final: 0.8354 (tp30) REVERT: V 40 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8919 (ttmm) REVERT: V 58 ARG cc_start: 0.8580 (mtm110) cc_final: 0.8219 (mtt-85) REVERT: V 89 ASP cc_start: 0.8322 (m-30) cc_final: 0.8071 (m-30) REVERT: V 96 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8175 (tm-30) outliers start: 45 outliers final: 30 residues processed: 404 average time/residue: 0.2702 time to fit residues: 160.3128 Evaluate side-chains 413 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 379 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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 96 GLN Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 99 GLU 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 83 LYS Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N 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 27 GLU Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain R residue 96 GLN Chi-restraints excluded: chain R residue 99 GLU 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 40 LYS 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 174 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 GLN P 33 GLN P 39 HIS ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 HIS ** S 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15645 Z= 0.264 Angle : 0.583 7.291 21021 Z= 0.307 Chirality : 0.038 0.133 2289 Planarity : 0.003 0.032 2835 Dihedral : 3.673 14.623 2205 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.74 % Allowed : 24.40 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1869 helix: -0.34 (0.14), residues: 1281 sheet: None (None), residues: 0 loop : -1.24 (0.32), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 53 HIS 0.004 0.001 HIS K 39 PHE 0.008 0.001 PHE N 37 TYR 0.005 0.001 TYR D 72 ARG 0.003 0.000 ARG I 58 *********************** 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 432 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 390 time to evaluate : 2.063 Fit side-chains REVERT: A 31 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8572 (tm-30) REVERT: A 66 GLU cc_start: 0.8355 (tp30) cc_final: 0.7890 (tm-30) REVERT: A 98 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8819 (mm-40) REVERT: B 31 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8332 (tm-30) REVERT: B 32 GLU cc_start: 0.8684 (tp30) cc_final: 0.8333 (tp30) REVERT: B 33 GLN cc_start: 0.8748 (mt0) cc_final: 0.8468 (mt0) REVERT: B 35 LYS cc_start: 0.9376 (ttmt) cc_final: 0.9118 (ttmm) REVERT: B 66 GLU cc_start: 0.8656 (tp30) cc_final: 0.8350 (tm-30) REVERT: D 31 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8372 (tm-30) REVERT: D 32 GLU cc_start: 0.8744 (tp30) cc_final: 0.8227 (tp30) REVERT: D 99 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8376 (tm-30) REVERT: E 20 GLU cc_start: 0.8705 (tp30) cc_final: 0.8413 (tm-30) REVERT: E 32 GLU cc_start: 0.8572 (tp30) cc_final: 0.7996 (tp30) REVERT: E 79 GLU cc_start: 0.8733 (tp30) cc_final: 0.8301 (tp30) REVERT: F 20 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: F 66 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7995 (tm-30) REVERT: F 79 GLU cc_start: 0.8241 (tp30) cc_final: 0.8012 (tp30) REVERT: G 58 ARG cc_start: 0.8513 (mtm110) cc_final: 0.8198 (mtt-85) REVERT: G 96 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8132 (tm-30) REVERT: H 31 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8340 (tm-30) REVERT: H 32 GLU cc_start: 0.8731 (tp30) cc_final: 0.8338 (tp30) REVERT: H 66 GLU cc_start: 0.8536 (tp30) cc_final: 0.8142 (tm-30) REVERT: H 83 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7779 (mmtt) REVERT: I 31 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8595 (tm-30) REVERT: K 31 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8322 (tm-30) REVERT: K 32 GLU cc_start: 0.8628 (tp30) cc_final: 0.8287 (tp30) REVERT: K 66 GLU cc_start: 0.8308 (tp30) cc_final: 0.7950 (tm-30) REVERT: K 98 GLN cc_start: 0.8996 (tp40) cc_final: 0.8709 (tp-100) REVERT: K 99 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8306 (tm-30) REVERT: L 32 GLU cc_start: 0.8587 (tp30) cc_final: 0.8049 (tp30) REVERT: L 66 GLU cc_start: 0.8191 (tp30) cc_final: 0.7980 (tp30) REVERT: L 89 ASP cc_start: 0.7646 (m-30) cc_final: 0.7206 (m-30) REVERT: L 99 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: M 66 GLU cc_start: 0.8232 (tt0) cc_final: 0.7283 (mt-10) REVERT: N 31 GLN cc_start: 0.8481 (tt0) cc_final: 0.8132 (pt0) REVERT: N 39 HIS cc_start: 0.7625 (t-90) cc_final: 0.7213 (m-70) REVERT: N 96 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8187 (tm-30) REVERT: O 31 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8338 (tm-30) REVERT: O 32 GLU cc_start: 0.8607 (tp30) cc_final: 0.8313 (tp30) REVERT: O 83 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7897 (mmtt) REVERT: P 31 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8501 (tm-30) REVERT: P 66 GLU cc_start: 0.8371 (tp30) cc_final: 0.7979 (tm-30) REVERT: P 79 GLU cc_start: 0.8707 (tp30) cc_final: 0.8458 (tp30) REVERT: P 98 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8860 (mm-40) REVERT: Q 57 GLU cc_start: 0.8018 (tt0) cc_final: 0.7777 (tt0) REVERT: Q 67 GLN cc_start: 0.8517 (mt0) cc_final: 0.8299 (mt0) REVERT: R 31 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8255 (tm-30) REVERT: R 32 GLU cc_start: 0.8574 (tp30) cc_final: 0.7807 (tp30) REVERT: R 66 GLU cc_start: 0.8380 (tp30) cc_final: 0.7900 (tm-30) REVERT: S 32 GLU cc_start: 0.8469 (tp30) cc_final: 0.7810 (tp30) REVERT: S 99 GLU cc_start: 0.8610 (pt0) cc_final: 0.8238 (tm-30) REVERT: T 31 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8403 (tm-30) REVERT: T 35 LYS cc_start: 0.9290 (tttm) cc_final: 0.8904 (tttp) REVERT: T 63 ASP cc_start: 0.8302 (t70) cc_final: 0.7359 (t70) REVERT: T 66 GLU cc_start: 0.8399 (tt0) cc_final: 0.8096 (mt-10) REVERT: T 67 GLN cc_start: 0.7802 (mp10) cc_final: 0.6853 (mp10) REVERT: T 79 GLU cc_start: 0.8280 (tp30) cc_final: 0.7945 (tp30) REVERT: T 83 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8638 (mtpp) REVERT: V 40 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8893 (ttmm) REVERT: V 58 ARG cc_start: 0.8584 (mtm110) cc_final: 0.8213 (mtt-85) REVERT: V 89 ASP cc_start: 0.8316 (m-30) cc_final: 0.8051 (m-30) REVERT: V 96 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8169 (tm-30) outliers start: 42 outliers final: 27 residues processed: 403 average time/residue: 0.2658 time to fit residues: 158.3406 Evaluate side-chains 414 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 383 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER 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 99 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 99 GLU 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 83 LYS Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 30 SER 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 27 GLU Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain R residue 96 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 40 LYS 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 109 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 124 optimal weight: 0.0970 chunk 188 optimal weight: 0.0470 chunk 173 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 67 GLN O 96 GLN P 33 GLN P 39 HIS ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4811 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= 0.187 Angle : 0.560 7.515 21021 Z= 0.298 Chirality : 0.036 0.125 2289 Planarity : 0.003 0.031 2835 Dihedral : 3.504 15.250 2205 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.02 % Allowed : 25.38 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1869 helix: -0.02 (0.15), residues: 1281 sheet: None (None), residues: 0 loop : -1.36 (0.32), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 53 HIS 0.003 0.001 HIS P 39 PHE 0.006 0.001 PHE N 37 TYR 0.004 0.001 TYR K 72 ARG 0.004 0.000 ARG K 58 ********************** 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 422 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 391 time to evaluate : 1.904 Fit side-chains REVERT: A 31 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8573 (tm-30) REVERT: A 66 GLU cc_start: 0.8342 (tp30) cc_final: 0.7880 (tm-30) REVERT: A 98 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8759 (mm-40) REVERT: B 31 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8249 (tm-30) REVERT: B 32 GLU cc_start: 0.8613 (tp30) cc_final: 0.8229 (tp30) REVERT: B 35 LYS cc_start: 0.9341 (ttmt) cc_final: 0.9083 (ttmm) REVERT: B 66 GLU cc_start: 0.8535 (tp30) cc_final: 0.8241 (tm-30) REVERT: D 31 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8368 (tm-30) REVERT: D 32 GLU cc_start: 0.8662 (tp30) cc_final: 0.8112 (tp30) REVERT: D 99 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8354 (tm-30) REVERT: E 20 GLU cc_start: 0.8720 (tp30) cc_final: 0.8409 (tm-30) REVERT: E 32 GLU cc_start: 0.8503 (tp30) cc_final: 0.7923 (tp30) REVERT: E 79 GLU cc_start: 0.8682 (tp30) cc_final: 0.8294 (tp30) REVERT: F 31 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8261 (tm-30) REVERT: F 66 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7969 (tm-30) REVERT: F 79 GLU cc_start: 0.8191 (tp30) cc_final: 0.7982 (tp30) REVERT: G 58 ARG cc_start: 0.8479 (mtm110) cc_final: 0.8161 (mtt-85) REVERT: G 96 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8029 (tm-30) REVERT: H 31 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8236 (tm-30) REVERT: H 32 GLU cc_start: 0.8722 (tp30) cc_final: 0.8356 (tp30) REVERT: H 33 GLN cc_start: 0.8738 (mt0) cc_final: 0.8446 (mp10) REVERT: H 66 GLU cc_start: 0.8386 (tp30) cc_final: 0.8057 (tm-30) REVERT: H 83 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7861 (mmtt) REVERT: I 31 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8555 (tm-30) REVERT: I 75 GLU cc_start: 0.9060 (tp30) cc_final: 0.8590 (mm-30) REVERT: K 31 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8349 (tm-30) REVERT: K 32 GLU cc_start: 0.8589 (tp30) cc_final: 0.8182 (tp30) REVERT: K 98 GLN cc_start: 0.8948 (tp40) cc_final: 0.8716 (tp-100) REVERT: K 99 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8276 (tm-30) REVERT: L 32 GLU cc_start: 0.8464 (tp30) cc_final: 0.7891 (tp30) REVERT: L 66 GLU cc_start: 0.8035 (tp30) cc_final: 0.7830 (tp30) REVERT: L 89 ASP cc_start: 0.7639 (m-30) cc_final: 0.7199 (m-30) REVERT: L 99 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: M 66 GLU cc_start: 0.8287 (tt0) cc_final: 0.8078 (mt-10) REVERT: N 31 GLN cc_start: 0.8483 (tt0) cc_final: 0.8156 (pt0) REVERT: O 31 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8265 (tm-30) REVERT: O 32 GLU cc_start: 0.8635 (tp30) cc_final: 0.8314 (tp30) REVERT: O 83 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7933 (mmtt) REVERT: P 31 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8447 (tm-30) REVERT: P 57 GLU cc_start: 0.8005 (tt0) cc_final: 0.7800 (tt0) REVERT: P 66 GLU cc_start: 0.8320 (tp30) cc_final: 0.7902 (tm-30) REVERT: P 79 GLU cc_start: 0.8689 (tp30) cc_final: 0.8444 (tp30) REVERT: P 98 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8866 (mm-40) REVERT: Q 57 GLU cc_start: 0.7938 (tt0) cc_final: 0.7706 (tt0) REVERT: Q 67 GLN cc_start: 0.8498 (mt0) cc_final: 0.8292 (mt0) REVERT: R 31 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8376 (tm-30) REVERT: R 32 GLU cc_start: 0.8459 (tp30) cc_final: 0.8249 (tp30) REVERT: R 99 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8226 (tm-30) REVERT: S 32 GLU cc_start: 0.8448 (tp30) cc_final: 0.7742 (tp30) REVERT: S 63 ASP cc_start: 0.9034 (m-30) cc_final: 0.8537 (m-30) REVERT: S 96 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8374 (tm130) REVERT: S 99 GLU cc_start: 0.8603 (pt0) cc_final: 0.8187 (tm-30) REVERT: T 31 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8346 (tm-30) REVERT: T 35 LYS cc_start: 0.9193 (tttm) cc_final: 0.8813 (tttp) REVERT: T 79 GLU cc_start: 0.8263 (tp30) cc_final: 0.7969 (tp30) REVERT: T 83 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8636 (mtpp) REVERT: V 58 ARG cc_start: 0.8562 (mtm110) cc_final: 0.8198 (mtt-85) REVERT: V 89 ASP cc_start: 0.8218 (m-30) cc_final: 0.7862 (m-30) REVERT: V 96 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8090 (tm-30) outliers start: 31 outliers final: 19 residues processed: 400 average time/residue: 0.2604 time to fit residues: 153.7232 Evaluate side-chains 393 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 371 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER 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 E residue 60 ASP Chi-restraints excluded: chain E residue 99 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 83 LYS Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 96 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 45 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** C 67 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** F 39 HIS ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 HIS ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 GLN P 39 HIS ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 70 GLN ** S 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.076759 restraints weight = 34476.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.079356 restraints weight = 17830.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.081147 restraints weight = 11288.009| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4825 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= 0.229 Angle : 0.588 6.893 21021 Z= 0.311 Chirality : 0.037 0.128 2289 Planarity : 0.003 0.030 2835 Dihedral : 3.503 14.895 2205 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.15 % Allowed : 25.38 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1869 helix: 0.06 (0.15), residues: 1281 sheet: None (None), residues: 0 loop : -1.31 (0.32), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 53 HIS 0.004 0.001 HIS P 39 PHE 0.007 0.001 PHE N 37 TYR 0.005 0.001 TYR K 72 ARG 0.008 0.000 ARG O 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3403.09 seconds wall clock time: 61 minutes 24.51 seconds (3684.51 seconds total)