Starting phenix.real_space_refine on Sat Jun 14 06:27:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tuq_10594/06_2025/6tuq_10594.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tuq_10594/06_2025/6tuq_10594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tuq_10594/06_2025/6tuq_10594.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tuq_10594/06_2025/6tuq_10594.map" model { file = "/net/cci-nas-00/data/ceres_data/6tuq_10594/06_2025/6tuq_10594.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tuq_10594/06_2025/6tuq_10594.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 10250 2.51 5 N 2600 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16100 Number of models: 1 Model: "" Number of chains: 1 Chain: "1" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Restraints were copied for chains: 0, 3, 2, 5, 4, 7, 6, 9, 8, A, C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, e, d, g, f, i, h, k, j, m, l, n Time building chain proxies: 4.96, per 1000 atoms: 0.31 Number of scatterers: 16100 At special positions: 0 Unit cell: (73.14, 73.14, 245.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3150 8.00 N 2600 7.00 C 10250 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: 3.86 Conformation dependent library (CDL) restraints added in 2.3 seconds 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 91.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 29 " --> pdb=" O TYR A 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 27 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 29 " --> pdb=" O TYR B 25 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE B 32 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 43 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 46 removed outlier: 4.077A pdb=" N GLU C 9 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS C 20 " --> pdb=" O GLN C 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 26 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA C 29 " --> pdb=" O TYR C 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 43 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS D 20 " --> pdb=" O GLN D 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA D 21 " --> pdb=" O GLY D 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 26 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 27 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 29 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE D 32 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 10 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS E 20 " --> pdb=" O GLN E 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA E 21 " --> pdb=" O GLY E 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 27 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA E 29 " --> pdb=" O TYR E 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE E 32 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU E 33 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 43 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU F 9 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER F 10 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP F 14 " --> pdb=" O SER F 10 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS F 20 " --> pdb=" O GLN F 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA F 21 " --> pdb=" O GLY F 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE F 26 " --> pdb=" O ILE F 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 27 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE F 32 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 38 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER F 41 " --> pdb=" O GLY F 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F 43 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER G 10 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP G 14 " --> pdb=" O SER G 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS G 20 " --> pdb=" O GLN G 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA G 21 " --> pdb=" O GLY G 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE G 26 " --> pdb=" O ILE G 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL G 27 " --> pdb=" O GLY G 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY G 28 " --> pdb=" O GLY G 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA G 29 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU G 43 " --> pdb=" O ILE G 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU H 9 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER H 10 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP H 14 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS H 20 " --> pdb=" O GLN H 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA H 21 " --> pdb=" O GLY H 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE H 26 " --> pdb=" O ILE H 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL H 27 " --> pdb=" O GLY H 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE H 32 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR H 40 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU I 9 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER I 10 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP I 14 " --> pdb=" O SER I 10 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS I 20 " --> pdb=" O GLN I 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA I 21 " --> pdb=" O GLY I 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE I 26 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL I 27 " --> pdb=" O GLY I 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA I 29 " --> pdb=" O TYR I 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE I 32 " --> pdb=" O GLY I 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU I 33 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU I 38 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER I 41 " --> pdb=" O GLY I 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU I 43 " --> pdb=" O ILE I 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU J 9 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER J 10 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP J 14 " --> pdb=" O SER J 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS J 20 " --> pdb=" O GLN J 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA J 21 " --> pdb=" O GLY J 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE J 26 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL J 27 " --> pdb=" O GLY J 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY J 28 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA J 29 " --> pdb=" O TYR J 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE J 32 " --> pdb=" O GLY J 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU J 43 " --> pdb=" O ILE J 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU K 9 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER K 10 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS K 20 " --> pdb=" O GLN K 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE K 26 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA K 29 " --> pdb=" O TYR K 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE K 32 " --> pdb=" O GLY K 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU K 33 " --> pdb=" O ALA K 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR K 40 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU K 43 " --> pdb=" O ILE K 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU L 9 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 10 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP L 14 " --> pdb=" O SER L 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS L 20 " --> pdb=" O GLN L 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE L 26 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL L 27 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA L 29 " --> pdb=" O TYR L 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE L 32 " --> pdb=" O GLY L 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU L 38 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR L 40 " --> pdb=" O ALA L 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU L 43 " --> pdb=" O ILE L 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU M 9 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER M 10 " --> pdb=" O SER M 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP M 14 " --> pdb=" O SER M 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS M 20 " --> pdb=" O GLN M 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE M 26 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL M 27 " --> pdb=" O GLY M 23 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA M 29 " --> pdb=" O TYR M 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE M 32 " --> pdb=" O GLY M 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER M 41 " --> pdb=" O GLY M 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU M 43 " --> pdb=" O ILE M 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU N 9 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER N 10 " --> pdb=" O SER N 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP N 14 " --> pdb=" O SER N 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS N 20 " --> pdb=" O GLN N 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE N 26 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL N 27 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY N 28 " --> pdb=" O GLY N 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA N 29 " --> pdb=" O TYR N 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE N 32 " --> pdb=" O GLY N 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU N 33 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU N 38 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR N 40 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER N 41 " --> pdb=" O GLY N 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU N 43 " --> pdb=" O ILE N 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU O 9 " --> pdb=" O THR O 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER O 10 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP O 14 " --> pdb=" O SER O 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS O 20 " --> pdb=" O GLN O 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE O 26 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL O 27 " --> pdb=" O GLY O 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY O 28 " --> pdb=" O GLY O 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA O 29 " --> pdb=" O TYR O 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE O 32 " --> pdb=" O GLY O 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU O 33 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU O 38 " --> pdb=" O ALA O 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR O 40 " --> pdb=" O ALA O 36 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER O 41 " --> pdb=" O GLY O 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU O 43 " --> pdb=" O ILE O 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU P 9 " --> pdb=" O THR P 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER P 10 " --> pdb=" O SER P 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP P 14 " --> pdb=" O SER P 10 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS P 20 " --> pdb=" O GLN P 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE P 26 " --> pdb=" O ILE P 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY P 28 " --> pdb=" O GLY P 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA P 29 " --> pdb=" O TYR P 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE P 32 " --> pdb=" O GLY P 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU P 33 " --> pdb=" O ALA P 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU P 38 " --> pdb=" O ALA P 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR P 40 " --> pdb=" O ALA P 36 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER P 41 " --> pdb=" O GLY P 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU P 43 " --> pdb=" O ILE P 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU Q 9 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER Q 10 " --> pdb=" O SER Q 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP Q 14 " --> pdb=" O SER Q 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS Q 20 " --> pdb=" O GLN Q 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE Q 26 " --> pdb=" O ILE Q 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL Q 27 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY Q 28 " --> pdb=" O GLY Q 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA Q 29 " --> pdb=" O TYR Q 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU Q 33 " --> pdb=" O ALA Q 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR Q 40 " --> pdb=" O ALA Q 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER Q 41 " --> pdb=" O GLY Q 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU Q 43 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU R 9 " --> pdb=" O THR R 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER R 10 " --> pdb=" O SER R 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP R 14 " --> pdb=" O SER R 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS R 20 " --> pdb=" O GLN R 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE R 26 " --> pdb=" O ILE R 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL R 27 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY R 28 " --> pdb=" O GLY R 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA R 29 " --> pdb=" O TYR R 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE R 32 " --> pdb=" O GLY R 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU R 33 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU R 38 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR R 40 " --> pdb=" O ALA R 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU R 43 " --> pdb=" O ILE R 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU S 9 " --> pdb=" O THR S 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER S 10 " --> pdb=" O SER S 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP S 14 " --> pdb=" O SER S 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS S 20 " --> pdb=" O GLN S 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA S 21 " --> pdb=" O GLY S 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE S 26 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL S 27 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY S 28 " --> pdb=" O GLY S 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA S 29 " --> pdb=" O TYR S 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE S 32 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU S 33 " --> pdb=" O ALA S 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU S 38 " --> pdb=" O ALA S 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR S 40 " --> pdb=" O ALA S 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER S 41 " --> pdb=" O GLY S 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU S 43 " --> pdb=" O ILE S 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU T 9 " --> pdb=" O THR T 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER T 10 " --> pdb=" O SER T 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP T 14 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS T 20 " --> pdb=" O GLN T 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA T 21 " --> pdb=" O GLY T 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE T 26 " --> pdb=" O ILE T 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL T 27 " --> pdb=" O GLY T 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY T 28 " --> pdb=" O GLY T 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA T 29 " --> pdb=" O TYR T 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE T 32 " --> pdb=" O GLY T 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU T 38 " --> pdb=" O ALA T 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR T 40 " --> pdb=" O ALA T 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER T 41 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU T 43 " --> pdb=" O ILE T 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU U 9 " --> pdb=" O THR U 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER U 10 " --> pdb=" O SER U 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP U 14 " --> pdb=" O SER U 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS U 20 " --> pdb=" O GLN U 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA U 21 " --> pdb=" O GLY U 17 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE U 26 " --> pdb=" O ILE U 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL U 27 " --> pdb=" O GLY U 23 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY U 28 " --> pdb=" O GLY U 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA U 29 " --> pdb=" O TYR U 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE U 32 " --> pdb=" O GLY U 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU U 38 " --> pdb=" O ALA U 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER U 41 " --> pdb=" O GLY U 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU U 43 " --> pdb=" O ILE U 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU V 9 " --> pdb=" O THR V 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER V 10 " --> pdb=" O SER V 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP V 14 " --> pdb=" O SER V 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS V 20 " --> pdb=" O GLN V 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA V 21 " --> pdb=" O GLY V 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE V 26 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL V 27 " --> pdb=" O GLY V 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY V 28 " --> pdb=" O GLY V 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA V 29 " --> pdb=" O TYR V 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE V 32 " --> pdb=" O GLY V 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU V 33 " --> pdb=" O ALA V 29 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU V 38 " --> pdb=" O ALA V 34 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR V 40 " --> pdb=" O ALA V 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER V 41 " --> pdb=" O GLY V 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU V 43 " --> pdb=" O ILE V 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER W 10 " --> pdb=" O SER W 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP W 14 " --> pdb=" O SER W 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS W 20 " --> pdb=" O GLN W 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA W 21 " --> pdb=" O GLY W 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE W 26 " --> pdb=" O ILE W 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL W 27 " --> pdb=" O GLY W 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY W 28 " --> pdb=" O GLY W 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA W 29 " --> pdb=" O TYR W 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE W 32 " --> pdb=" O GLY W 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU W 33 " --> pdb=" O ALA W 29 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR W 40 " --> pdb=" O ALA W 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER W 41 " --> pdb=" O GLY W 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU W 43 " --> pdb=" O ILE W 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU X 9 " --> pdb=" O THR X 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER X 10 " --> pdb=" O SER X 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP X 14 " --> pdb=" O SER X 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS X 20 " --> pdb=" O GLN X 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA X 21 " --> pdb=" O GLY X 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE X 26 " --> pdb=" O ILE X 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL X 27 " --> pdb=" O GLY X 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY X 28 " --> pdb=" O GLY X 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA X 29 " --> pdb=" O TYR X 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE X 32 " --> pdb=" O GLY X 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU X 33 " --> pdb=" O ALA X 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU X 38 " --> pdb=" O ALA X 34 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR X 40 " --> pdb=" O ALA X 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER X 41 " --> pdb=" O GLY X 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU X 43 " --> pdb=" O ILE X 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU Y 9 " --> pdb=" O THR Y 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER Y 10 " --> pdb=" O SER Y 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS Y 20 " --> pdb=" O GLN Y 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA Y 21 " --> pdb=" O GLY Y 17 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE Y 26 " --> pdb=" O ILE Y 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL Y 27 " --> pdb=" O GLY Y 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY Y 28 " --> pdb=" O GLY Y 24 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA Y 29 " --> pdb=" O TYR Y 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE Y 32 " --> pdb=" O GLY Y 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU Y 33 " --> pdb=" O ALA Y 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU Y 38 " --> pdb=" O ALA Y 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR Y 40 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER Y 41 " --> pdb=" O GLY Y 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU Y 43 " --> pdb=" O ILE Y 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU Z 9 " --> pdb=" O THR Z 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER Z 10 " --> pdb=" O SER Z 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP Z 14 " --> pdb=" O SER Z 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS Z 20 " --> pdb=" O GLN Z 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA Z 21 " --> pdb=" O GLY Z 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE Z 26 " --> pdb=" O ILE Z 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL Z 27 " --> pdb=" O GLY Z 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY Z 28 " --> pdb=" O GLY Z 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA Z 29 " --> pdb=" O TYR Z 25 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE Z 32 " --> pdb=" O GLY Z 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU Z 33 " --> pdb=" O ALA Z 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU Z 38 " --> pdb=" O ALA Z 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR Z 40 " --> pdb=" O ALA Z 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER Z 41 " --> pdb=" O GLY Z 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU Z 43 " --> pdb=" O ILE Z 39 " (cutoff:3.500A) Processing helix chain '0' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU 0 9 " --> pdb=" O THR 0 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER 0 10 " --> pdb=" O SER 0 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP 0 14 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS 0 20 " --> pdb=" O GLN 0 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA 0 21 " --> pdb=" O GLY 0 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 0 26 " --> pdb=" O ILE 0 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL 0 27 " --> pdb=" O GLY 0 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY 0 28 " --> pdb=" O GLY 0 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA 0 29 " --> pdb=" O TYR 0 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE 0 32 " --> pdb=" O GLY 0 28 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU 0 33 " --> pdb=" O ALA 0 29 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU 0 38 " --> pdb=" O ALA 0 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR 0 40 " --> pdb=" O ALA 0 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 0 41 " --> pdb=" O GLY 0 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 0 43 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) Processing helix chain '1' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU 1 9 " --> pdb=" O THR 1 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER 1 10 " --> pdb=" O SER 1 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP 1 14 " --> pdb=" O SER 1 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS 1 20 " --> pdb=" O GLN 1 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 1 26 " --> pdb=" O ILE 1 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL 1 27 " --> pdb=" O GLY 1 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY 1 28 " --> pdb=" O GLY 1 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA 1 29 " --> pdb=" O TYR 1 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE 1 32 " --> pdb=" O GLY 1 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU 1 33 " --> pdb=" O ALA 1 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU 1 38 " --> pdb=" O ALA 1 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR 1 40 " --> pdb=" O ALA 1 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 1 41 " --> pdb=" O GLY 1 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU 1 43 " --> pdb=" O ILE 1 39 " (cutoff:3.500A) Processing helix chain '2' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU 2 9 " --> pdb=" O THR 2 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER 2 10 " --> pdb=" O SER 2 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP 2 14 " --> pdb=" O SER 2 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS 2 20 " --> pdb=" O GLN 2 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 2 26 " --> pdb=" O ILE 2 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL 2 27 " --> pdb=" O GLY 2 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY 2 28 " --> pdb=" O GLY 2 24 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA 2 29 " --> pdb=" O TYR 2 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE 2 32 " --> pdb=" O GLY 2 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU 2 33 " --> pdb=" O ALA 2 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR 2 40 " --> pdb=" O ALA 2 36 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER 2 41 " --> pdb=" O GLY 2 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 2 43 " --> pdb=" O ILE 2 39 " (cutoff:3.500A) Processing helix chain '3' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU 3 9 " --> pdb=" O THR 3 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER 3 10 " --> pdb=" O SER 3 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP 3 14 " --> pdb=" O SER 3 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS 3 20 " --> pdb=" O GLN 3 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA 3 21 " --> pdb=" O GLY 3 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 3 26 " --> pdb=" O ILE 3 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL 3 27 " --> pdb=" O GLY 3 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY 3 28 " --> pdb=" O GLY 3 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA 3 29 " --> pdb=" O TYR 3 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE 3 32 " --> pdb=" O GLY 3 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU 3 33 " --> pdb=" O ALA 3 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU 3 38 " --> pdb=" O ALA 3 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR 3 40 " --> pdb=" O ALA 3 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 3 41 " --> pdb=" O GLY 3 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU 3 43 " --> pdb=" O ILE 3 39 " (cutoff:3.500A) Processing helix chain '4' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU 4 9 " --> pdb=" O THR 4 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER 4 10 " --> pdb=" O SER 4 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP 4 14 " --> pdb=" O SER 4 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS 4 20 " --> pdb=" O GLN 4 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA 4 21 " --> pdb=" O GLY 4 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 4 26 " --> pdb=" O ILE 4 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL 4 27 " --> pdb=" O GLY 4 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY 4 28 " --> pdb=" O GLY 4 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA 4 29 " --> pdb=" O TYR 4 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE 4 32 " --> pdb=" O GLY 4 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU 4 33 " --> pdb=" O ALA 4 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU 4 38 " --> pdb=" O ALA 4 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR 4 40 " --> pdb=" O ALA 4 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 4 41 " --> pdb=" O GLY 4 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 4 43 " --> pdb=" O ILE 4 39 " (cutoff:3.500A) Processing helix chain '5' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU 5 9 " --> pdb=" O THR 5 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER 5 10 " --> pdb=" O SER 5 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP 5 14 " --> pdb=" O SER 5 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS 5 20 " --> pdb=" O GLN 5 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 5 26 " --> pdb=" O ILE 5 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL 5 27 " --> pdb=" O GLY 5 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY 5 28 " --> pdb=" O GLY 5 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA 5 29 " --> pdb=" O TYR 5 25 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE 5 32 " --> pdb=" O GLY 5 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU 5 33 " --> pdb=" O ALA 5 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU 5 38 " --> pdb=" O ALA 5 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR 5 40 " --> pdb=" O ALA 5 36 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER 5 41 " --> pdb=" O GLY 5 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 5 43 " --> pdb=" O ILE 5 39 " (cutoff:3.500A) Processing helix chain '6' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU 6 9 " --> pdb=" O THR 6 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER 6 10 " --> pdb=" O SER 6 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP 6 14 " --> pdb=" O SER 6 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS 6 20 " --> pdb=" O GLN 6 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 6 26 " --> pdb=" O ILE 6 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL 6 27 " --> pdb=" O GLY 6 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY 6 28 " --> pdb=" O GLY 6 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA 6 29 " --> pdb=" O TYR 6 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE 6 32 " --> pdb=" O GLY 6 28 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU 6 33 " --> pdb=" O ALA 6 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU 6 38 " --> pdb=" O ALA 6 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR 6 40 " --> pdb=" O ALA 6 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 6 41 " --> pdb=" O GLY 6 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 6 43 " --> pdb=" O ILE 6 39 " (cutoff:3.500A) Processing helix chain '7' and resid 5 through 46 removed outlier: 4.077A pdb=" N GLU 7 9 " --> pdb=" O THR 7 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER 7 10 " --> pdb=" O SER 7 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP 7 14 " --> pdb=" O SER 7 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS 7 20 " --> pdb=" O GLN 7 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE 7 26 " --> pdb=" O ILE 7 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL 7 27 " --> pdb=" O GLY 7 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY 7 28 " --> pdb=" O GLY 7 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA 7 29 " --> pdb=" O TYR 7 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE 7 32 " --> pdb=" O GLY 7 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU 7 33 " --> pdb=" O ALA 7 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU 7 38 " --> pdb=" O ALA 7 34 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR 7 40 " --> pdb=" O ALA 7 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 7 41 " --> pdb=" O GLY 7 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 7 43 " --> pdb=" O ILE 7 39 " (cutoff:3.500A) Processing helix chain '8' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU 8 9 " --> pdb=" O THR 8 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER 8 10 " --> pdb=" O SER 8 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP 8 14 " --> pdb=" O SER 8 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS 8 20 " --> pdb=" O GLN 8 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA 8 21 " --> pdb=" O GLY 8 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE 8 26 " --> pdb=" O ILE 8 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL 8 27 " --> pdb=" O GLY 8 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY 8 28 " --> pdb=" O GLY 8 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA 8 29 " --> pdb=" O TYR 8 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE 8 32 " --> pdb=" O GLY 8 28 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU 8 33 " --> pdb=" O ALA 8 29 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU 8 38 " --> pdb=" O ALA 8 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR 8 40 " --> pdb=" O ALA 8 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 8 41 " --> pdb=" O GLY 8 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 8 43 " --> pdb=" O ILE 8 39 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU 9 9 " --> pdb=" O THR 9 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER 9 10 " --> pdb=" O SER 9 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP 9 14 " --> pdb=" O SER 9 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS 9 20 " --> pdb=" O GLN 9 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA 9 21 " --> pdb=" O GLY 9 17 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE 9 26 " --> pdb=" O ILE 9 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL 9 27 " --> pdb=" O GLY 9 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY 9 28 " --> pdb=" O GLY 9 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA 9 29 " --> pdb=" O TYR 9 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE 9 32 " --> pdb=" O GLY 9 28 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU 9 33 " --> pdb=" O ALA 9 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU 9 38 " --> pdb=" O ALA 9 34 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR 9 40 " --> pdb=" O ALA 9 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER 9 41 " --> pdb=" O GLY 9 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 9 43 " --> pdb=" O ILE 9 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU a 9 " --> pdb=" O THR a 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER a 10 " --> pdb=" O SER a 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP a 14 " --> pdb=" O SER a 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS a 20 " --> pdb=" O GLN a 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA a 21 " --> pdb=" O GLY a 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE a 26 " --> pdb=" O ILE a 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL a 27 " --> pdb=" O GLY a 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY a 28 " --> pdb=" O GLY a 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA a 29 " --> pdb=" O TYR a 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE a 32 " --> pdb=" O GLY a 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU a 33 " --> pdb=" O ALA a 29 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU a 38 " --> pdb=" O ALA a 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR a 40 " --> pdb=" O ALA a 36 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER a 41 " --> pdb=" O GLY a 37 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU a 43 " --> pdb=" O ILE a 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU b 9 " --> pdb=" O THR b 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER b 10 " --> pdb=" O SER b 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP b 14 " --> pdb=" O SER b 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS b 20 " --> pdb=" O GLN b 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA b 21 " --> pdb=" O GLY b 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE b 26 " --> pdb=" O ILE b 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL b 27 " --> pdb=" O GLY b 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY b 28 " --> pdb=" O GLY b 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA b 29 " --> pdb=" O TYR b 25 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE b 32 " --> pdb=" O GLY b 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU b 33 " --> pdb=" O ALA b 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU b 38 " --> pdb=" O ALA b 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR b 40 " --> pdb=" O ALA b 36 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU b 43 " --> pdb=" O ILE b 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU c 9 " --> pdb=" O THR c 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER c 10 " --> pdb=" O SER c 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP c 14 " --> pdb=" O SER c 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS c 20 " --> pdb=" O GLN c 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA c 21 " --> pdb=" O GLY c 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE c 26 " --> pdb=" O ILE c 22 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL c 27 " --> pdb=" O GLY c 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY c 28 " --> pdb=" O GLY c 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA c 29 " --> pdb=" O TYR c 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE c 32 " --> pdb=" O GLY c 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU c 38 " --> pdb=" O ALA c 34 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR c 40 " --> pdb=" O ALA c 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER c 41 " --> pdb=" O GLY c 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU c 43 " --> pdb=" O ILE c 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU d 9 " --> pdb=" O THR d 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER d 10 " --> pdb=" O SER d 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP d 14 " --> pdb=" O SER d 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS d 20 " --> pdb=" O GLN d 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA d 21 " --> pdb=" O GLY d 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE d 26 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL d 27 " --> pdb=" O GLY d 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY d 28 " --> pdb=" O GLY d 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA d 29 " --> pdb=" O TYR d 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE d 32 " --> pdb=" O GLY d 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU d 33 " --> pdb=" O ALA d 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU d 38 " --> pdb=" O ALA d 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER d 41 " --> pdb=" O GLY d 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU d 43 " --> pdb=" O ILE d 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU e 9 " --> pdb=" O THR e 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER e 10 " --> pdb=" O SER e 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP e 14 " --> pdb=" O SER e 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS e 20 " --> pdb=" O GLN e 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA e 21 " --> pdb=" O GLY e 17 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE e 26 " --> pdb=" O ILE e 22 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL e 27 " --> pdb=" O GLY e 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY e 28 " --> pdb=" O GLY e 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA e 29 " --> pdb=" O TYR e 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE e 32 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU e 33 " --> pdb=" O ALA e 29 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU e 38 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER e 41 " --> pdb=" O GLY e 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU e 43 " --> pdb=" O ILE e 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU f 9 " --> pdb=" O THR f 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER f 10 " --> pdb=" O SER f 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP f 14 " --> pdb=" O SER f 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS f 20 " --> pdb=" O GLN f 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA f 21 " --> pdb=" O GLY f 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE f 26 " --> pdb=" O ILE f 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL f 27 " --> pdb=" O GLY f 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY f 28 " --> pdb=" O GLY f 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE f 32 " --> pdb=" O GLY f 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU f 33 " --> pdb=" O ALA f 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU f 38 " --> pdb=" O ALA f 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR f 40 " --> pdb=" O ALA f 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER f 41 " --> pdb=" O GLY f 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU f 43 " --> pdb=" O ILE f 39 " (cutoff:3.500A) Processing helix chain 'g' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU g 9 " --> pdb=" O THR g 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER g 10 " --> pdb=" O SER g 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP g 14 " --> pdb=" O SER g 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS g 20 " --> pdb=" O GLN g 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA g 21 " --> pdb=" O GLY g 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE g 26 " --> pdb=" O ILE g 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL g 27 " --> pdb=" O GLY g 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY g 28 " --> pdb=" O GLY g 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA g 29 " --> pdb=" O TYR g 25 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE g 32 " --> pdb=" O GLY g 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU g 33 " --> pdb=" O ALA g 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU g 38 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR g 40 " --> pdb=" O ALA g 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER g 41 " --> pdb=" O GLY g 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU g 43 " --> pdb=" O ILE g 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU h 9 " --> pdb=" O THR h 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER h 10 " --> pdb=" O SER h 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP h 14 " --> pdb=" O SER h 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS h 20 " --> pdb=" O GLN h 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA h 21 " --> pdb=" O GLY h 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE h 26 " --> pdb=" O ILE h 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL h 27 " --> pdb=" O GLY h 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY h 28 " --> pdb=" O GLY h 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA h 29 " --> pdb=" O TYR h 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE h 32 " --> pdb=" O GLY h 28 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR h 40 " --> pdb=" O ALA h 36 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER h 41 " --> pdb=" O GLY h 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU h 43 " --> pdb=" O ILE h 39 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU i 9 " --> pdb=" O THR i 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER i 10 " --> pdb=" O SER i 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP i 14 " --> pdb=" O SER i 10 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS i 20 " --> pdb=" O GLN i 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA i 21 " --> pdb=" O GLY i 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE i 26 " --> pdb=" O ILE i 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL i 27 " --> pdb=" O GLY i 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY i 28 " --> pdb=" O GLY i 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA i 29 " --> pdb=" O TYR i 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE i 32 " --> pdb=" O GLY i 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU i 33 " --> pdb=" O ALA i 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU i 38 " --> pdb=" O ALA i 34 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR i 40 " --> pdb=" O ALA i 36 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER i 41 " --> pdb=" O GLY i 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU i 43 " --> pdb=" O ILE i 39 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 46 removed outlier: 4.077A pdb=" N GLU j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP j 14 " --> pdb=" O SER j 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS j 20 " --> pdb=" O GLN j 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA j 21 " --> pdb=" O GLY j 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE j 26 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL j 27 " --> pdb=" O GLY j 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY j 28 " --> pdb=" O GLY j 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA j 29 " --> pdb=" O TYR j 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE j 32 " --> pdb=" O GLY j 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU j 38 " --> pdb=" O ALA j 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR j 40 " --> pdb=" O ALA j 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER j 41 " --> pdb=" O GLY j 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU j 43 " --> pdb=" O ILE j 39 " (cutoff:3.500A) Processing helix chain 'k' and resid 5 through 46 removed outlier: 4.079A pdb=" N GLU k 9 " --> pdb=" O THR k 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER k 10 " --> pdb=" O SER k 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP k 14 " --> pdb=" O SER k 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS k 20 " --> pdb=" O GLN k 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA k 21 " --> pdb=" O GLY k 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE k 26 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL k 27 " --> pdb=" O GLY k 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY k 28 " --> pdb=" O GLY k 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA k 29 " --> pdb=" O TYR k 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE k 32 " --> pdb=" O GLY k 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU k 33 " --> pdb=" O ALA k 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU k 38 " --> pdb=" O ALA k 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR k 40 " --> pdb=" O ALA k 36 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU k 43 " --> pdb=" O ILE k 39 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU l 9 " --> pdb=" O THR l 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER l 10 " --> pdb=" O SER l 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP l 14 " --> pdb=" O SER l 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS l 20 " --> pdb=" O GLN l 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA l 21 " --> pdb=" O GLY l 17 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE l 26 " --> pdb=" O ILE l 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL l 27 " --> pdb=" O GLY l 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY l 28 " --> pdb=" O GLY l 24 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA l 29 " --> pdb=" O TYR l 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE l 32 " --> pdb=" O GLY l 28 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU l 33 " --> pdb=" O ALA l 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU l 38 " --> pdb=" O ALA l 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR l 40 " --> pdb=" O ALA l 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER l 41 " --> pdb=" O GLY l 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU l 43 " --> pdb=" O ILE l 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU m 9 " --> pdb=" O THR m 5 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER m 10 " --> pdb=" O SER m 6 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP m 14 " --> pdb=" O SER m 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS m 20 " --> pdb=" O GLN m 16 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA m 21 " --> pdb=" O GLY m 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE m 26 " --> pdb=" O ILE m 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL m 27 " --> pdb=" O GLY m 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY m 28 " --> pdb=" O GLY m 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA m 29 " --> pdb=" O TYR m 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE m 32 " --> pdb=" O GLY m 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU m 33 " --> pdb=" O ALA m 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU m 38 " --> pdb=" O ALA m 34 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR m 40 " --> pdb=" O ALA m 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER m 41 " --> pdb=" O GLY m 37 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU m 43 " --> pdb=" O ILE m 39 " (cutoff:3.500A) Processing helix chain 'n' and resid 5 through 46 removed outlier: 4.078A pdb=" N GLU n 9 " --> pdb=" O THR n 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER n 10 " --> pdb=" O SER n 6 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP n 14 " --> pdb=" O SER n 10 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS n 20 " --> pdb=" O GLN n 16 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA n 21 " --> pdb=" O GLY n 17 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE n 26 " --> pdb=" O ILE n 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL n 27 " --> pdb=" O GLY n 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY n 28 " --> pdb=" O GLY n 24 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA n 29 " --> pdb=" O TYR n 25 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE n 32 " --> pdb=" O GLY n 28 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU n 33 " --> pdb=" O ALA n 29 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU n 38 " --> pdb=" O ALA n 34 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR n 40 " --> pdb=" O ALA n 36 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER n 41 " --> pdb=" O GLY n 37 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU n 43 " --> pdb=" O ILE n 39 " (cutoff:3.500A) 1150 hydrogen bonds defined for protein. 3450 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: 4.69 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5250 1.34 - 1.45: 1987 1.45 - 1.57: 8713 1.57 - 1.68: 0 1.68 - 1.79: 200 Bond restraints: 16150 Sorted by residual: bond pdb=" CG1 ILE j 12 " pdb=" CD1 ILE j 12 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" CG1 ILE a 12 " pdb=" CD1 ILE a 12 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" CG1 ILE O 12 " pdb=" CD1 ILE O 12 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" CG1 ILE 0 12 " pdb=" CD1 ILE 0 12 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" CG1 ILE S 12 " pdb=" CD1 ILE S 12 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.84e+00 ... (remaining 16145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 19367 1.47 - 2.94: 2041 2.94 - 4.41: 192 4.41 - 5.89: 150 5.89 - 7.36: 50 Bond angle restraints: 21800 Sorted by residual: angle pdb=" N ASP G 4 " pdb=" CA ASP G 4 " pdb=" C ASP G 4 " ideal model delta sigma weight residual 108.63 113.30 -4.67 1.60e+00 3.91e-01 8.52e+00 angle pdb=" N ASP l 4 " pdb=" CA ASP l 4 " pdb=" C ASP l 4 " ideal model delta sigma weight residual 108.63 113.29 -4.66 1.60e+00 3.91e-01 8.49e+00 angle pdb=" N ASP D 4 " pdb=" CA ASP D 4 " pdb=" C ASP D 4 " ideal model delta sigma weight residual 108.63 113.28 -4.65 1.60e+00 3.91e-01 8.44e+00 angle pdb=" N ASP T 4 " pdb=" CA ASP T 4 " pdb=" C ASP T 4 " ideal model delta sigma weight residual 108.63 113.28 -4.65 1.60e+00 3.91e-01 8.43e+00 angle pdb=" N ASP d 4 " pdb=" CA ASP d 4 " pdb=" C ASP d 4 " ideal model delta sigma weight residual 108.63 113.28 -4.65 1.60e+00 3.91e-01 8.43e+00 ... (remaining 21795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.79: 7743 7.79 - 15.59: 1007 15.59 - 23.38: 300 23.38 - 31.18: 400 31.18 - 38.97: 100 Dihedral angle restraints: 9550 sinusoidal: 3300 harmonic: 6250 Sorted by residual: dihedral pdb=" CA ILE l 39 " pdb=" C ILE l 39 " pdb=" N TYR l 40 " pdb=" CA TYR l 40 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ILE D 39 " pdb=" C ILE D 39 " pdb=" N TYR D 40 " pdb=" CA TYR D 40 " ideal model delta harmonic sigma weight residual 180.00 160.94 19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ILE f 39 " pdb=" C ILE f 39 " pdb=" N TYR f 40 " pdb=" CA TYR f 40 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 9547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 881 0.026 - 0.052: 1120 0.052 - 0.078: 410 0.078 - 0.104: 319 0.104 - 0.130: 70 Chirality restraints: 2800 Sorted by residual: chirality pdb=" CB ILE 1 3 " pdb=" CA ILE 1 3 " pdb=" CG1 ILE 1 3 " pdb=" CG2 ILE 1 3 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CB ILE O 3 " pdb=" CA ILE O 3 " pdb=" CG1 ILE O 3 " pdb=" CG2 ILE O 3 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CB ILE U 3 " pdb=" CA ILE U 3 " pdb=" CG1 ILE U 3 " pdb=" CG2 ILE U 3 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2797 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL 8 27 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C VAL 8 27 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL 8 27 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY 8 28 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL n 27 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C VAL n 27 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL n 27 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY n 28 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL m 27 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.86e+00 pdb=" C VAL m 27 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL m 27 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY m 28 " -0.008 2.00e-02 2.50e+03 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1533 2.73 - 3.27: 17855 3.27 - 3.82: 25214 3.82 - 4.36: 31701 4.36 - 4.90: 49124 Nonbonded interactions: 125427 Sorted by model distance: nonbonded pdb=" OD2 ASP I 14 " pdb=" N GLY S 1 " model vdw 2.191 3.120 nonbonded pdb=" OD2 ASP 5 14 " pdb=" N GLY 6 1 " model vdw 2.238 3.120 nonbonded pdb=" OD1 ASP l 18 " pdb=" OG1 THR m 5 " model vdw 2.463 3.040 nonbonded pdb=" N ASP 5 4 " pdb=" OD1 ASP 5 4 " model vdw 2.479 3.120 nonbonded pdb=" N ASP c 4 " pdb=" OD1 ASP c 4 " model vdw 2.480 3.120 ... (remaining 125422 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: 0.19 Found NCS groups: ncs_group { reference = chain '1' selection = chain '0' selection = chain '3' selection = chain '2' selection = chain '5' selection = chain '4' selection = chain '7' selection = chain '6' selection = chain '9' selection = chain '8' selection = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' selection = chain 'i' selection = chain 'h' selection = chain 'k' selection = chain 'j' selection = chain 'm' selection = chain 'l' selection = chain 'n' } 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.790 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 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 : 0.009 0.066 16150 Z= 0.391 Angle : 1.009 7.356 21800 Z= 0.532 Chirality : 0.050 0.130 2800 Planarity : 0.004 0.014 2700 Dihedral : 11.218 38.974 5650 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.12 % Allowed : 12.50 % Favored : 84.38 % 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: -6.69 (0.09), residues: 2200 helix: -4.48 (0.05), residues: 1850 sheet: None (None), residues: 0 loop : -1.86 (0.27), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.004 TYR F 25 ARG 0.001 0.000 ARG e 44 Details of bonding type rmsd hydrogen bonds : bond 0.27146 ( 1150) hydrogen bonds : angle 11.25551 ( 3450) covalent geometry : bond 0.00911 (16150) covalent geometry : angle 1.00859 (21800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 1.767 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 MET cc_start: 0.9083 (mtp) cc_final: 0.8559 (tpt) REVERT: E 19 MET cc_start: 0.9390 (mtp) cc_final: 0.8619 (tpt) REVERT: H 19 MET cc_start: 0.9481 (mtp) cc_final: 0.9006 (tpt) REVERT: J 19 MET cc_start: 0.9573 (mtp) cc_final: 0.8893 (ppp) REVERT: M 19 MET cc_start: 0.9376 (mtp) cc_final: 0.8491 (ppp) REVERT: N 19 MET cc_start: 0.9483 (mtp) cc_final: 0.8711 (tpt) REVERT: Q 19 MET cc_start: 0.9333 (mtp) cc_final: 0.8044 (tpt) REVERT: T 42 MET cc_start: 0.8551 (tpp) cc_final: 0.8316 (tpt) REVERT: U 19 MET cc_start: 0.9317 (mtp) cc_final: 0.8458 (tpt) REVERT: W 44 ARG cc_start: 0.8621 (mtt-85) cc_final: 0.8373 (mtm-85) REVERT: 0 4 ASP cc_start: 0.9142 (p0) cc_final: 0.8937 (p0) REVERT: 9 44 ARG cc_start: 0.8602 (mtt-85) cc_final: 0.8082 (ptp-110) REVERT: a 19 MET cc_start: 0.9168 (mtp) cc_final: 0.8918 (mtp) REVERT: a 44 ARG cc_start: 0.8716 (mtt-85) cc_final: 0.8191 (mtm-85) REVERT: b 44 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.8221 (mtm-85) REVERT: g 44 ARG cc_start: 0.9003 (mtt-85) cc_final: 0.8575 (ptp-110) outliers start: 50 outliers final: 0 residues processed: 236 average time/residue: 0.4208 time to fit residues: 130.8020 Evaluate side-chains 125 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.0040 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 116 optimal weight: 0.0570 chunk 181 optimal weight: 3.9990 overall best weight: 0.8512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN F 16 GLN G 16 GLN I 16 GLN J 16 GLN K 16 GLN L 16 GLN M 16 GLN N 16 GLN O 16 GLN P 16 GLN R 16 GLN S 16 GLN T 16 GLN V 16 GLN 0 16 GLN 1 16 GLN 2 16 GLN 3 16 GLN 4 16 GLN 5 16 GLN 6 16 GLN 8 16 GLN h 16 GLN i 16 GLN j 16 GLN k 16 GLN l 16 GLN m 16 GLN n 16 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.026779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.022558 restraints weight = 162154.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.023496 restraints weight = 82243.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.024168 restraints weight = 48890.524| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16150 Z= 0.126 Angle : 0.582 8.103 21800 Z= 0.318 Chirality : 0.040 0.148 2800 Planarity : 0.003 0.023 2700 Dihedral : 4.870 14.787 2450 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.69 % Allowed : 17.25 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.68 (0.12), residues: 2200 helix: -2.89 (0.07), residues: 1950 sheet: None (None), residues: 0 loop : -2.14 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR H 40 ARG 0.008 0.001 ARG f 44 Details of bonding type rmsd hydrogen bonds : bond 0.04768 ( 1150) hydrogen bonds : angle 4.13933 ( 3450) covalent geometry : bond 0.00254 (16150) covalent geometry : angle 0.58194 (21800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 MET cc_start: 0.9246 (mtp) cc_final: 0.8892 (tpt) REVERT: H 42 MET cc_start: 0.8959 (tpp) cc_final: 0.8695 (tpp) REVERT: J 19 MET cc_start: 0.9334 (mtp) cc_final: 0.8878 (ttt) REVERT: M 19 MET cc_start: 0.9270 (mtp) cc_final: 0.9044 (tpt) REVERT: N 19 MET cc_start: 0.9272 (mtp) cc_final: 0.8614 (tpt) REVERT: N 44 ARG cc_start: 0.8863 (mtt-85) cc_final: 0.8650 (mtm-85) REVERT: T 42 MET cc_start: 0.8894 (tpp) cc_final: 0.8355 (tpp) REVERT: T 44 ARG cc_start: 0.9033 (mtt-85) cc_final: 0.8815 (ttm110) REVERT: V 19 MET cc_start: 0.8901 (mmp) cc_final: 0.8637 (tmm) REVERT: 3 44 ARG cc_start: 0.9105 (mtt-85) cc_final: 0.8800 (ttm110) REVERT: 5 19 MET cc_start: 0.9395 (mmm) cc_final: 0.9146 (mmt) REVERT: 8 44 ARG cc_start: 0.8963 (mtt-85) cc_final: 0.8700 (ttm110) REVERT: 9 42 MET cc_start: 0.8948 (ttm) cc_final: 0.8621 (tpp) REVERT: f 42 MET cc_start: 0.8663 (tpp) cc_final: 0.8376 (tpt) REVERT: n 44 ARG cc_start: 0.9041 (mtt-85) cc_final: 0.8571 (ttm110) outliers start: 11 outliers final: 0 residues processed: 170 average time/residue: 0.4148 time to fit residues: 94.4986 Evaluate side-chains 112 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 195 optimal weight: 0.7980 chunk 180 optimal weight: 0.0170 chunk 165 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 114 optimal weight: 0.0000 chunk 62 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN 9 16 GLN f 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.027222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.023016 restraints weight = 157647.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.023992 restraints weight = 78578.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.024682 restraints weight = 45543.804| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16150 Z= 0.094 Angle : 0.525 6.603 21800 Z= 0.268 Chirality : 0.039 0.135 2800 Planarity : 0.003 0.031 2700 Dihedral : 3.951 14.043 2450 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.62 % Allowed : 20.25 % Favored : 78.12 % 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: -2.76 (0.15), residues: 2200 helix: -1.58 (0.10), residues: 1950 sheet: None (None), residues: 0 loop : -1.84 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.000 TYR E 40 ARG 0.006 0.001 ARG X 44 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1150) hydrogen bonds : angle 3.31510 ( 3450) covalent geometry : bond 0.00195 (16150) covalent geometry : angle 0.52509 (21800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 MET cc_start: 0.9172 (mtp) cc_final: 0.8873 (tpt) REVERT: J 19 MET cc_start: 0.9205 (mtp) cc_final: 0.8826 (ttt) REVERT: M 19 MET cc_start: 0.9190 (mtp) cc_final: 0.8666 (tmm) REVERT: M 44 ARG cc_start: 0.8876 (mtt-85) cc_final: 0.8581 (ttm110) REVERT: N 19 MET cc_start: 0.9216 (mtp) cc_final: 0.8705 (tpt) REVERT: T 42 MET cc_start: 0.8966 (tpp) cc_final: 0.8497 (tpp) REVERT: X 42 MET cc_start: 0.8694 (tpp) cc_final: 0.8463 (tpp) REVERT: 3 44 ARG cc_start: 0.8966 (mtt-85) cc_final: 0.8722 (ttm110) REVERT: 4 44 ARG cc_start: 0.9030 (mtt-85) cc_final: 0.8800 (ttm110) REVERT: 8 44 ARG cc_start: 0.8948 (mtt-85) cc_final: 0.8699 (ttm110) REVERT: 9 42 MET cc_start: 0.8852 (ttm) cc_final: 0.8515 (tpp) REVERT: c 42 MET cc_start: 0.8884 (tpp) cc_final: 0.8627 (tpp) outliers start: 26 outliers final: 10 residues processed: 140 average time/residue: 0.3154 time to fit residues: 63.8865 Evaluate side-chains 119 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain O residue 42 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain 5 residue 39 ILE Chi-restraints excluded: chain i residue 2 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 173 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 95 optimal weight: 0.0010 chunk 137 optimal weight: 0.9990 chunk 198 optimal weight: 0.0060 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN 9 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.027845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.023532 restraints weight = 152193.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.024566 restraints weight = 76634.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.025273 restraints weight = 44253.264| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16150 Z= 0.084 Angle : 0.503 7.058 21800 Z= 0.250 Chirality : 0.039 0.127 2800 Planarity : 0.002 0.021 2700 Dihedral : 3.698 14.417 2450 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.31 % Allowed : 22.00 % Favored : 76.69 % 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: -1.74 (0.17), residues: 2200 helix: -0.93 (0.11), residues: 1950 sheet: None (None), residues: 0 loop : -1.29 (0.44), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR j 25 ARG 0.005 0.001 ARG b 44 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 1150) hydrogen bonds : angle 3.04565 ( 3450) covalent geometry : bond 0.00174 (16150) covalent geometry : angle 0.50325 (21800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 MET cc_start: 0.9181 (mtp) cc_final: 0.8871 (tpt) REVERT: J 19 MET cc_start: 0.9160 (mtp) cc_final: 0.8742 (ttt) REVERT: L 44 ARG cc_start: 0.9099 (mtt-85) cc_final: 0.8824 (ttm110) REVERT: M 19 MET cc_start: 0.9191 (mtp) cc_final: 0.8656 (tmm) REVERT: M 44 ARG cc_start: 0.8823 (mtt-85) cc_final: 0.8586 (ttm110) REVERT: N 19 MET cc_start: 0.9248 (mtp) cc_final: 0.8719 (tpt) REVERT: X 19 MET cc_start: 0.8863 (mmm) cc_final: 0.8647 (mmm) REVERT: X 33 LEU cc_start: 0.8673 (pp) cc_final: 0.8417 (mp) REVERT: Y 42 MET cc_start: 0.9164 (tpp) cc_final: 0.8563 (tpp) REVERT: 1 19 MET cc_start: 0.8958 (mtt) cc_final: 0.8551 (tpt) REVERT: 4 44 ARG cc_start: 0.9062 (mtt-85) cc_final: 0.8847 (ttm110) REVERT: 8 44 ARG cc_start: 0.8951 (mtt-85) cc_final: 0.8700 (ttm110) REVERT: 9 42 MET cc_start: 0.8786 (ttm) cc_final: 0.8507 (tpp) REVERT: c 42 MET cc_start: 0.8862 (tpp) cc_final: 0.8518 (tpp) outliers start: 21 outliers final: 6 residues processed: 131 average time/residue: 0.2963 time to fit residues: 57.9169 Evaluate side-chains 117 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain 5 residue 39 ILE Chi-restraints excluded: chain l residue 39 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 163 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 16 GLN g 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.026480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.022311 restraints weight = 161019.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.023287 restraints weight = 79781.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.023978 restraints weight = 46139.041| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16150 Z= 0.104 Angle : 0.529 12.846 21800 Z= 0.267 Chirality : 0.039 0.143 2800 Planarity : 0.002 0.018 2700 Dihedral : 3.631 13.682 2450 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.94 % Allowed : 22.31 % Favored : 75.75 % 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: -1.15 (0.17), residues: 2200 helix: -0.57 (0.11), residues: 1950 sheet: None (None), residues: 0 loop : -0.86 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.000 TYR F 25 ARG 0.003 0.000 ARG T 44 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 1150) hydrogen bonds : angle 3.18793 ( 3450) covalent geometry : bond 0.00230 (16150) covalent geometry : angle 0.52892 (21800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 MET cc_start: 0.9151 (mtp) cc_final: 0.8896 (tpt) REVERT: H 19 MET cc_start: 0.7973 (mmt) cc_final: 0.7108 (tpt) REVERT: H 42 MET cc_start: 0.8620 (tpp) cc_final: 0.8091 (tpp) REVERT: J 19 MET cc_start: 0.9222 (mtp) cc_final: 0.8788 (ttt) REVERT: L 44 ARG cc_start: 0.9139 (mtt-85) cc_final: 0.8849 (ttm110) REVERT: M 19 MET cc_start: 0.9214 (mtp) cc_final: 0.8632 (tmm) REVERT: N 19 MET cc_start: 0.9219 (mtp) cc_final: 0.8641 (tpt) REVERT: X 33 LEU cc_start: 0.8652 (pp) cc_final: 0.8401 (mp) REVERT: 7 42 MET cc_start: 0.9156 (tpp) cc_final: 0.8917 (tpp) REVERT: 9 42 MET cc_start: 0.8860 (ttm) cc_final: 0.8567 (tpp) REVERT: c 42 MET cc_start: 0.8815 (tpp) cc_final: 0.8389 (tpp) outliers start: 31 outliers final: 8 residues processed: 135 average time/residue: 0.2436 time to fit residues: 51.5639 Evaluate side-chains 112 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain O residue 42 MET Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain 5 residue 39 ILE Chi-restraints excluded: chain i residue 39 ILE Chi-restraints excluded: chain l residue 39 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 69 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 196 optimal weight: 0.0170 chunk 183 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 199 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.027197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.022969 restraints weight = 157128.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.023981 restraints weight = 78738.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.024699 restraints weight = 45506.793| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16150 Z= 0.087 Angle : 0.528 9.968 21800 Z= 0.251 Chirality : 0.038 0.130 2800 Planarity : 0.002 0.013 2700 Dihedral : 3.577 14.181 2450 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 1.44 % Allowed : 22.19 % Favored : 76.38 % 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: -0.77 (0.17), residues: 2200 helix: -0.31 (0.11), residues: 1950 sheet: None (None), residues: 0 loop : -0.79 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.000 TYR l 25 ARG 0.004 0.000 ARG N 44 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 1150) hydrogen bonds : angle 2.96772 ( 3450) covalent geometry : bond 0.00198 (16150) covalent geometry : angle 0.52758 (21800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 MET cc_start: 0.9175 (mtp) cc_final: 0.8897 (tpt) REVERT: B 42 MET cc_start: 0.9008 (tpp) cc_final: 0.8700 (tmm) REVERT: F 19 MET cc_start: 0.9413 (mmm) cc_final: 0.8745 (mpp) REVERT: H 42 MET cc_start: 0.8621 (tpp) cc_final: 0.8294 (tpp) REVERT: J 19 MET cc_start: 0.9187 (mtp) cc_final: 0.8720 (ttt) REVERT: L 44 ARG cc_start: 0.9078 (mtt-85) cc_final: 0.8774 (ttm110) REVERT: M 19 MET cc_start: 0.9259 (mtp) cc_final: 0.8657 (tmm) REVERT: V 19 MET cc_start: 0.8695 (mmt) cc_final: 0.8042 (ttt) REVERT: X 33 LEU cc_start: 0.8604 (pp) cc_final: 0.8383 (mp) REVERT: Y 42 MET cc_start: 0.9082 (tpp) cc_final: 0.8727 (tmm) REVERT: 2 42 MET cc_start: 0.8717 (tpp) cc_final: 0.8267 (tmm) REVERT: 8 44 ARG cc_start: 0.9016 (mtt-85) cc_final: 0.8748 (ttm110) REVERT: 9 42 MET cc_start: 0.8912 (ttm) cc_final: 0.8628 (tpp) REVERT: c 42 MET cc_start: 0.8826 (tpp) cc_final: 0.8568 (tpp) REVERT: f 19 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8804 (mtm) outliers start: 23 outliers final: 6 residues processed: 125 average time/residue: 0.2475 time to fit residues: 48.6783 Evaluate side-chains 112 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain O residue 42 MET Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 5 residue 39 ILE Chi-restraints excluded: chain f residue 19 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 188 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 132 optimal weight: 0.0170 chunk 192 optimal weight: 0.0040 chunk 101 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 186 optimal weight: 0.5980 overall best weight: 0.4630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.027797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.023563 restraints weight = 154131.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.024587 restraints weight = 77024.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.025317 restraints weight = 44597.787| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16150 Z= 0.083 Angle : 0.530 10.680 21800 Z= 0.248 Chirality : 0.038 0.126 2800 Planarity : 0.002 0.016 2700 Dihedral : 3.455 14.081 2450 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.12 % Allowed : 22.19 % Favored : 76.69 % 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: -0.49 (0.18), residues: 2200 helix: -0.13 (0.11), residues: 1950 sheet: None (None), residues: 0 loop : -0.63 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.000 TYR C 25 ARG 0.003 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.02808 ( 1150) hydrogen bonds : angle 2.84698 ( 3450) covalent geometry : bond 0.00186 (16150) covalent geometry : angle 0.53014 (21800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.896 Fit side-chains revert: symmetry clash REVERT: B 19 MET cc_start: 0.9192 (mtp) cc_final: 0.8900 (tpt) REVERT: B 39 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8754 (tp) REVERT: B 42 MET cc_start: 0.9042 (tpp) cc_final: 0.8756 (tmm) REVERT: C 39 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8699 (tp) REVERT: H 19 MET cc_start: 0.7840 (mmt) cc_final: 0.6946 (tpt) REVERT: H 42 MET cc_start: 0.8621 (tpp) cc_final: 0.8417 (tpp) REVERT: J 19 MET cc_start: 0.9201 (mtp) cc_final: 0.8752 (tmm) REVERT: K 39 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.9020 (tp) REVERT: L 44 ARG cc_start: 0.9011 (mtt-85) cc_final: 0.8792 (ttm110) REVERT: M 19 MET cc_start: 0.9273 (mtp) cc_final: 0.8610 (tmm) REVERT: R 42 MET cc_start: 0.8798 (tpp) cc_final: 0.8563 (tpp) REVERT: T 42 MET cc_start: 0.9003 (tpp) cc_final: 0.8644 (tpp) REVERT: V 19 MET cc_start: 0.8643 (mmt) cc_final: 0.8173 (ttt) REVERT: W 39 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8368 (tp) REVERT: Y 19 MET cc_start: 0.9377 (mmm) cc_final: 0.8998 (mmp) REVERT: Y 42 MET cc_start: 0.9097 (tpp) cc_final: 0.8692 (tmm) REVERT: 2 42 MET cc_start: 0.8813 (tpp) cc_final: 0.8375 (tmm) REVERT: 4 19 MET cc_start: 0.8891 (mmt) cc_final: 0.8189 (mmp) REVERT: 9 42 MET cc_start: 0.8839 (ttm) cc_final: 0.8575 (tpp) REVERT: c 42 MET cc_start: 0.8740 (tpp) cc_final: 0.8469 (tpp) REVERT: f 19 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8741 (mtm) outliers start: 18 outliers final: 3 residues processed: 119 average time/residue: 0.2496 time to fit residues: 47.1254 Evaluate side-chains 111 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 5 residue 39 ILE Chi-restraints excluded: chain f residue 19 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 97 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 164 optimal weight: 0.0470 chunk 71 optimal weight: 1.9990 chunk 156 optimal weight: 0.0270 chunk 150 optimal weight: 4.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.027155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.023060 restraints weight = 155208.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.024043 restraints weight = 76734.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.024738 restraints weight = 43948.437| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16150 Z= 0.087 Angle : 0.557 13.283 21800 Z= 0.257 Chirality : 0.038 0.152 2800 Planarity : 0.002 0.012 2700 Dihedral : 3.431 13.984 2450 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.88 % Allowed : 22.31 % Favored : 76.81 % 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: -0.35 (0.18), residues: 2200 helix: -0.04 (0.11), residues: 1950 sheet: None (None), residues: 0 loop : -0.57 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.000 TYR 5 25 ARG 0.003 0.000 ARG N 44 Details of bonding type rmsd hydrogen bonds : bond 0.02899 ( 1150) hydrogen bonds : angle 2.88003 ( 3450) covalent geometry : bond 0.00201 (16150) covalent geometry : angle 0.55712 (21800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 MET cc_start: 0.9167 (mtp) cc_final: 0.8901 (tpt) REVERT: B 39 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8757 (tp) REVERT: B 42 MET cc_start: 0.9034 (tpp) cc_final: 0.8768 (tmm) REVERT: C 39 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8505 (tp) REVERT: C 42 MET cc_start: 0.8987 (tpp) cc_final: 0.8327 (tmm) REVERT: F 19 MET cc_start: 0.9358 (mmm) cc_final: 0.8836 (mpp) REVERT: H 19 MET cc_start: 0.7837 (mmt) cc_final: 0.6940 (tpt) REVERT: H 42 MET cc_start: 0.8652 (tpp) cc_final: 0.8391 (ttm) REVERT: J 19 MET cc_start: 0.9127 (mtp) cc_final: 0.8663 (tmm) REVERT: L 44 ARG cc_start: 0.8999 (mtt-85) cc_final: 0.8782 (ttm110) REVERT: M 19 MET cc_start: 0.9286 (mtp) cc_final: 0.8573 (tmm) REVERT: R 42 MET cc_start: 0.8816 (tpp) cc_final: 0.8422 (tpp) REVERT: T 39 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8759 (tp) REVERT: X 19 MET cc_start: 0.8610 (mmm) cc_final: 0.8302 (mpp) REVERT: Y 19 MET cc_start: 0.9147 (mmm) cc_final: 0.8851 (mmp) REVERT: Y 42 MET cc_start: 0.9122 (tpp) cc_final: 0.8719 (tmm) REVERT: Z 19 MET cc_start: 0.8883 (mtt) cc_final: 0.8412 (tpt) REVERT: 2 42 MET cc_start: 0.8750 (tpp) cc_final: 0.8326 (tmm) REVERT: 9 42 MET cc_start: 0.8842 (ttm) cc_final: 0.8517 (tpp) REVERT: c 42 MET cc_start: 0.8749 (tpp) cc_final: 0.8493 (tpp) REVERT: f 19 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8808 (mtm) outliers start: 14 outliers final: 4 residues processed: 115 average time/residue: 0.2441 time to fit residues: 44.5530 Evaluate side-chains 111 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain f residue 19 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 75 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 164 optimal weight: 0.0470 chunk 167 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.027215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.023090 restraints weight = 155745.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.024084 restraints weight = 76299.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.024793 restraints weight = 43619.901| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16150 Z= 0.087 Angle : 0.570 13.243 21800 Z= 0.260 Chirality : 0.038 0.126 2800 Planarity : 0.002 0.013 2700 Dihedral : 3.423 13.895 2450 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.62 % Allowed : 22.38 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2200 helix: 0.04 (0.12), residues: 1950 sheet: None (None), residues: 0 loop : -0.50 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.000 TYR 4 25 ARG 0.002 0.000 ARG N 44 Details of bonding type rmsd hydrogen bonds : bond 0.02879 ( 1150) hydrogen bonds : angle 2.86330 ( 3450) covalent geometry : bond 0.00202 (16150) covalent geometry : angle 0.57033 (21800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 MET cc_start: 0.9173 (mtp) cc_final: 0.8886 (tpt) REVERT: B 42 MET cc_start: 0.9000 (tpp) cc_final: 0.8730 (tmm) REVERT: C 39 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8675 (tp) REVERT: C 42 MET cc_start: 0.8904 (tpp) cc_final: 0.8226 (tpp) REVERT: F 19 MET cc_start: 0.9398 (mmm) cc_final: 0.8842 (mpp) REVERT: H 19 MET cc_start: 0.7831 (mmt) cc_final: 0.6948 (tpt) REVERT: J 19 MET cc_start: 0.9110 (mtp) cc_final: 0.8592 (tmm) REVERT: L 44 ARG cc_start: 0.9019 (mtt-85) cc_final: 0.8782 (ttm110) REVERT: M 19 MET cc_start: 0.9316 (mtp) cc_final: 0.8628 (tmm) REVERT: R 42 MET cc_start: 0.8781 (tpp) cc_final: 0.8451 (tpp) REVERT: V 19 MET cc_start: 0.8758 (mmt) cc_final: 0.8346 (ttt) REVERT: X 19 MET cc_start: 0.8629 (mmm) cc_final: 0.8390 (mpp) REVERT: Y 19 MET cc_start: 0.9187 (mmm) cc_final: 0.8700 (mmp) REVERT: Y 42 MET cc_start: 0.9066 (tpp) cc_final: 0.8675 (tmm) REVERT: 2 42 MET cc_start: 0.8741 (tpp) cc_final: 0.8320 (tmm) REVERT: 9 42 MET cc_start: 0.8850 (ttm) cc_final: 0.8515 (tpp) REVERT: f 19 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8862 (mtm) outliers start: 10 outliers final: 3 residues processed: 112 average time/residue: 0.2626 time to fit residues: 47.3173 Evaluate side-chains 107 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain f residue 19 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 121 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 175 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.027047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.022924 restraints weight = 157422.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.023906 restraints weight = 78213.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.024598 restraints weight = 45281.670| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16150 Z= 0.095 Angle : 0.593 12.785 21800 Z= 0.269 Chirality : 0.038 0.137 2800 Planarity : 0.002 0.012 2700 Dihedral : 3.434 14.708 2450 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.44 % Allowed : 22.69 % Favored : 76.88 % 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: -0.19 (0.18), residues: 2200 helix: 0.06 (0.12), residues: 1950 sheet: None (None), residues: 0 loop : -0.44 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR 5 25 ARG 0.002 0.000 ARG N 44 Details of bonding type rmsd hydrogen bonds : bond 0.03007 ( 1150) hydrogen bonds : angle 2.91973 ( 3450) covalent geometry : bond 0.00225 (16150) covalent geometry : angle 0.59309 (21800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 MET cc_start: 0.9090 (mtp) cc_final: 0.8754 (tpt) REVERT: B 42 MET cc_start: 0.8989 (tpp) cc_final: 0.8736 (tmm) REVERT: C 39 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8746 (tp) REVERT: C 42 MET cc_start: 0.8952 (tpp) cc_final: 0.8351 (tpp) REVERT: F 19 MET cc_start: 0.9382 (mmm) cc_final: 0.8815 (mpp) REVERT: H 19 MET cc_start: 0.7832 (mmt) cc_final: 0.6951 (tpt) REVERT: J 19 MET cc_start: 0.9060 (mtp) cc_final: 0.8544 (tmm) REVERT: L 44 ARG cc_start: 0.8984 (mtt-85) cc_final: 0.8758 (ttm110) REVERT: M 19 MET cc_start: 0.9315 (mtp) cc_final: 0.8635 (tmm) REVERT: R 42 MET cc_start: 0.8813 (tpp) cc_final: 0.8481 (tpp) REVERT: X 19 MET cc_start: 0.8678 (mmm) cc_final: 0.8410 (mpp) REVERT: Y 19 MET cc_start: 0.9285 (mmm) cc_final: 0.8938 (mmp) REVERT: Y 42 MET cc_start: 0.9085 (tpp) cc_final: 0.8734 (tmm) REVERT: 0 42 MET cc_start: 0.8779 (tpp) cc_final: 0.8554 (tpp) REVERT: 2 42 MET cc_start: 0.8764 (tpp) cc_final: 0.8335 (tmm) REVERT: 4 19 MET cc_start: 0.8556 (mmt) cc_final: 0.7837 (mmp) REVERT: 9 42 MET cc_start: 0.8722 (ttm) cc_final: 0.8402 (tpp) REVERT: f 19 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8668 (mtm) outliers start: 7 outliers final: 3 residues processed: 108 average time/residue: 0.2544 time to fit residues: 43.4884 Evaluate side-chains 107 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain W residue 39 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain f residue 19 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 196 optimal weight: 0.0370 chunk 153 optimal weight: 1.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.026932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.022853 restraints weight = 158190.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.023837 restraints weight = 77430.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.024530 restraints weight = 44221.517| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16150 Z= 0.092 Angle : 0.585 13.047 21800 Z= 0.265 Chirality : 0.038 0.140 2800 Planarity : 0.002 0.011 2700 Dihedral : 3.448 14.385 2450 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.50 % Allowed : 22.50 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2200 helix: 0.12 (0.12), residues: 1950 sheet: None (None), residues: 0 loop : -0.41 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.000 TYR 5 25 ARG 0.002 0.000 ARG N 44 Details of bonding type rmsd hydrogen bonds : bond 0.02957 ( 1150) hydrogen bonds : angle 2.89389 ( 3450) covalent geometry : bond 0.00217 (16150) covalent geometry : angle 0.58471 (21800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3934.29 seconds wall clock time: 69 minutes 56.65 seconds (4196.65 seconds total)