Starting phenix.real_space_refine on Fri Sep 27 04:41:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/09_2024/7khw_22881_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/09_2024/7khw_22881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/09_2024/7khw_22881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/09_2024/7khw_22881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/09_2024/7khw_22881_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7khw_22881/09_2024/7khw_22881_neut.cif" } resolution = 3.4 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= 0.008 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 400 5.16 5 C 40400 2.51 5 N 11050 2.21 5 O 13700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 250 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 65550 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1311 Classifications: {'peptide': 174} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 170} Restraints were copied for chains: 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, o, n, q, p, s, r, u, t, w, v, x Time building chain proxies: 10.10, per 1000 atoms: 0.15 Number of scatterers: 65550 At special positions: 0 Unit cell: (128.52, 128.52, 320.76, 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 400 16.00 O 13700 8.00 N 11050 7.00 C 40400 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: 12.49 Conformation dependent library (CDL) restraints added in 6.6 seconds 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16700 Finding SS restraints... Secondary structure from input PDB file: 400 helices and 0 sheets defined 69.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 89 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP A 117 " --> pdb=" O PRO A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 89 Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP B 117 " --> pdb=" O PRO B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 114 through 117' Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 89 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP C 117 " --> pdb=" O PRO C 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 114 through 117' Processing helix chain 'C' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 186 removed outlier: 3.508A pdb=" N GLN C 161 " --> pdb=" O GLN C 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 89 Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP D 117 " --> pdb=" O PRO D 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 114 through 117' Processing helix chain 'D' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 186 removed outlier: 3.508A pdb=" N GLN D 161 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE D 185 " --> pdb=" O GLN D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 89 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER E 109 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP E 117 " --> pdb=" O PRO E 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 114 through 117' Processing helix chain 'E' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL E 138 " --> pdb=" O ASP E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN E 155 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE E 185 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 89 Processing helix chain 'F' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER F 109 " --> pdb=" O ASP F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP F 117 " --> pdb=" O PRO F 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 114 through 117' Processing helix chain 'F' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL F 138 " --> pdb=" O ASP F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN F 155 " --> pdb=" O THR F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN F 161 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN F 162 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 185 " --> pdb=" O GLN F 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 89 Processing helix chain 'G' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER G 109 " --> pdb=" O ASP G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP G 117 " --> pdb=" O PRO G 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 114 through 117' Processing helix chain 'G' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL G 138 " --> pdb=" O ASP G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN G 155 " --> pdb=" O THR G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN G 161 " --> pdb=" O GLN G 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN G 162 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA G 173 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE G 185 " --> pdb=" O GLN G 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 89 Processing helix chain 'H' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER H 109 " --> pdb=" O ASP H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP H 117 " --> pdb=" O PRO H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 114 through 117' Processing helix chain 'H' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL H 138 " --> pdb=" O ASP H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN H 155 " --> pdb=" O THR H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN H 161 " --> pdb=" O GLN H 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN H 162 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA H 173 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE H 185 " --> pdb=" O GLN H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP I 34 " --> pdb=" O ASP I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 89 Processing helix chain 'I' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER I 109 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP I 117 " --> pdb=" O PRO I 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 114 through 117' Processing helix chain 'I' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL I 138 " --> pdb=" O ASP I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN I 155 " --> pdb=" O THR I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN I 161 " --> pdb=" O GLN I 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN I 162 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 89 Processing helix chain 'J' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER J 109 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP J 117 " --> pdb=" O PRO J 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'J' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL J 138 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN J 161 " --> pdb=" O GLN J 157 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN J 162 " --> pdb=" O LEU J 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA J 173 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP J 176 " --> pdb=" O SER J 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET J 177 " --> pdb=" O ALA J 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE J 185 " --> pdb=" O GLN J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP K 34 " --> pdb=" O ASP K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 89 Processing helix chain 'K' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER K 109 " --> pdb=" O ASP K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP K 117 " --> pdb=" O PRO K 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 114 through 117' Processing helix chain 'K' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN K 155 " --> pdb=" O THR K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN K 161 " --> pdb=" O GLN K 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN K 162 " --> pdb=" O LEU K 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA K 173 " --> pdb=" O LEU K 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET K 177 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE K 185 " --> pdb=" O GLN K 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP L 34 " --> pdb=" O ASP L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 89 Processing helix chain 'L' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER L 109 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP L 117 " --> pdb=" O PRO L 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 114 through 117' Processing helix chain 'L' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL L 138 " --> pdb=" O ASP L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN L 155 " --> pdb=" O THR L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN L 161 " --> pdb=" O GLN L 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN L 162 " --> pdb=" O LEU L 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP L 176 " --> pdb=" O SER L 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 185 " --> pdb=" O GLN L 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP M 34 " --> pdb=" O ASP M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA M 45 " --> pdb=" O VAL M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 89 Processing helix chain 'M' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER M 109 " --> pdb=" O ASP M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP M 117 " --> pdb=" O PRO M 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 114 through 117' Processing helix chain 'M' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL M 138 " --> pdb=" O ASP M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN M 155 " --> pdb=" O THR M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN M 161 " --> pdb=" O GLN M 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA M 173 " --> pdb=" O LEU M 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP M 176 " --> pdb=" O SER M 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET M 177 " --> pdb=" O ALA M 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE M 185 " --> pdb=" O GLN M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP N 34 " --> pdb=" O ASP N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA N 45 " --> pdb=" O VAL N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 89 Processing helix chain 'N' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER N 109 " --> pdb=" O ASP N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP N 117 " --> pdb=" O PRO N 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 114 through 117' Processing helix chain 'N' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL N 138 " --> pdb=" O ASP N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN N 155 " --> pdb=" O THR N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN N 161 " --> pdb=" O GLN N 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN N 162 " --> pdb=" O LEU N 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA N 173 " --> pdb=" O LEU N 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP N 176 " --> pdb=" O SER N 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE N 185 " --> pdb=" O GLN N 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP O 34 " --> pdb=" O ASP O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA O 45 " --> pdb=" O VAL O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 89 Processing helix chain 'O' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER O 109 " --> pdb=" O ASP O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 117 removed outlier: 3.971A pdb=" N ASP O 117 " --> pdb=" O PRO O 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 114 through 117' Processing helix chain 'O' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL O 138 " --> pdb=" O ASP O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN O 155 " --> pdb=" O THR O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN O 161 " --> pdb=" O GLN O 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN O 162 " --> pdb=" O LEU O 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA O 173 " --> pdb=" O LEU O 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP O 176 " --> pdb=" O SER O 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE O 185 " --> pdb=" O GLN O 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP P 34 " --> pdb=" O ASP P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA P 45 " --> pdb=" O VAL P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 89 Processing helix chain 'P' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER P 109 " --> pdb=" O ASP P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP P 117 " --> pdb=" O PRO P 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 114 through 117' Processing helix chain 'P' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL P 138 " --> pdb=" O ASP P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN P 155 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN P 161 " --> pdb=" O GLN P 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN P 162 " --> pdb=" O LEU P 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA P 173 " --> pdb=" O LEU P 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP P 176 " --> pdb=" O SER P 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET P 177 " --> pdb=" O ALA P 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE P 185 " --> pdb=" O GLN P 181 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP Q 34 " --> pdb=" O ASP Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA Q 45 " --> pdb=" O VAL Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 89 Processing helix chain 'Q' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER Q 109 " --> pdb=" O ASP Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP Q 117 " --> pdb=" O PRO Q 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 114 through 117' Processing helix chain 'Q' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL Q 138 " --> pdb=" O ASP Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN Q 155 " --> pdb=" O THR Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN Q 161 " --> pdb=" O GLN Q 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN Q 162 " --> pdb=" O LEU Q 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA Q 173 " --> pdb=" O LEU Q 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP Q 176 " --> pdb=" O SER Q 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET Q 177 " --> pdb=" O ALA Q 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE Q 185 " --> pdb=" O GLN Q 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP R 34 " --> pdb=" O ASP R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA R 45 " --> pdb=" O VAL R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 89 Processing helix chain 'R' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER R 109 " --> pdb=" O ASP R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP R 117 " --> pdb=" O PRO R 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 114 through 117' Processing helix chain 'R' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL R 138 " --> pdb=" O ASP R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN R 155 " --> pdb=" O THR R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN R 161 " --> pdb=" O GLN R 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET R 177 " --> pdb=" O ALA R 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE R 185 " --> pdb=" O GLN R 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP S 34 " --> pdb=" O ASP S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA S 45 " --> pdb=" O VAL S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 89 Processing helix chain 'S' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER S 109 " --> pdb=" O ASP S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP S 117 " --> pdb=" O PRO S 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 114 through 117' Processing helix chain 'S' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL S 138 " --> pdb=" O ASP S 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN S 155 " --> pdb=" O THR S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN S 161 " --> pdb=" O GLN S 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN S 162 " --> pdb=" O LEU S 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA S 173 " --> pdb=" O LEU S 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP S 176 " --> pdb=" O SER S 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET S 177 " --> pdb=" O ALA S 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE S 185 " --> pdb=" O GLN S 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP T 34 " --> pdb=" O ASP T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA T 45 " --> pdb=" O VAL T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 89 Processing helix chain 'T' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER T 109 " --> pdb=" O ASP T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP T 117 " --> pdb=" O PRO T 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 114 through 117' Processing helix chain 'T' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL T 138 " --> pdb=" O ASP T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN T 155 " --> pdb=" O THR T 151 " (cutoff:3.500A) Processing helix chain 'T' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN T 161 " --> pdb=" O GLN T 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN T 162 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA T 173 " --> pdb=" O LEU T 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP T 176 " --> pdb=" O SER T 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET T 177 " --> pdb=" O ALA T 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE T 185 " --> pdb=" O GLN T 181 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP U 34 " --> pdb=" O ASP U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA U 45 " --> pdb=" O VAL U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 89 Processing helix chain 'U' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER U 109 " --> pdb=" O ASP U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP U 117 " --> pdb=" O PRO U 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 114 through 117' Processing helix chain 'U' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL U 138 " --> pdb=" O ASP U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN U 155 " --> pdb=" O THR U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN U 161 " --> pdb=" O GLN U 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN U 162 " --> pdb=" O LEU U 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA U 173 " --> pdb=" O LEU U 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP U 176 " --> pdb=" O SER U 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET U 177 " --> pdb=" O ALA U 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE U 185 " --> pdb=" O GLN U 181 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP V 34 " --> pdb=" O ASP V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA V 45 " --> pdb=" O VAL V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 89 Processing helix chain 'V' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER V 109 " --> pdb=" O ASP V 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP V 117 " --> pdb=" O PRO V 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 114 through 117' Processing helix chain 'V' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL V 138 " --> pdb=" O ASP V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN V 155 " --> pdb=" O THR V 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN V 161 " --> pdb=" O GLN V 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN V 162 " --> pdb=" O LEU V 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA V 173 " --> pdb=" O LEU V 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP V 176 " --> pdb=" O SER V 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET V 177 " --> pdb=" O ALA V 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE V 185 " --> pdb=" O GLN V 181 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP W 34 " --> pdb=" O ASP W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA W 45 " --> pdb=" O VAL W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 89 Processing helix chain 'W' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER W 109 " --> pdb=" O ASP W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP W 117 " --> pdb=" O PRO W 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 114 through 117' Processing helix chain 'W' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL W 138 " --> pdb=" O ASP W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN W 161 " --> pdb=" O GLN W 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN W 162 " --> pdb=" O LEU W 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP W 176 " --> pdb=" O SER W 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET W 177 " --> pdb=" O ALA W 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE W 185 " --> pdb=" O GLN W 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP X 34 " --> pdb=" O ASP X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA X 45 " --> pdb=" O VAL X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 67 through 89 Processing helix chain 'X' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER X 109 " --> pdb=" O ASP X 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP X 117 " --> pdb=" O PRO X 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 114 through 117' Processing helix chain 'X' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL X 138 " --> pdb=" O ASP X 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN X 155 " --> pdb=" O THR X 151 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN X 161 " --> pdb=" O GLN X 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN X 162 " --> pdb=" O LEU X 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA X 173 " --> pdb=" O LEU X 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP X 176 " --> pdb=" O SER X 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET X 177 " --> pdb=" O ALA X 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE X 185 " --> pdb=" O GLN X 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP Y 34 " --> pdb=" O ASP Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA Y 45 " --> pdb=" O VAL Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 89 Processing helix chain 'Y' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER Y 109 " --> pdb=" O ASP Y 105 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP Y 117 " --> pdb=" O PRO Y 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 114 through 117' Processing helix chain 'Y' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL Y 138 " --> pdb=" O ASP Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN Y 155 " --> pdb=" O THR Y 151 " (cutoff:3.500A) Processing helix chain 'Y' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN Y 161 " --> pdb=" O GLN Y 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN Y 162 " --> pdb=" O LEU Y 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA Y 173 " --> pdb=" O LEU Y 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP Y 176 " --> pdb=" O SER Y 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET Y 177 " --> pdb=" O ALA Y 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE Y 185 " --> pdb=" O GLN Y 181 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP Z 34 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA Z 45 " --> pdb=" O VAL Z 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 67 through 89 Processing helix chain 'Z' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER Z 109 " --> pdb=" O ASP Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP Z 117 " --> pdb=" O PRO Z 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 114 through 117' Processing helix chain 'Z' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL Z 138 " --> pdb=" O ASP Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN Z 155 " --> pdb=" O THR Z 151 " (cutoff:3.500A) Processing helix chain 'Z' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN Z 161 " --> pdb=" O GLN Z 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN Z 162 " --> pdb=" O LEU Z 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA Z 173 " --> pdb=" O LEU Z 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP Z 176 " --> pdb=" O SER Z 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET Z 177 " --> pdb=" O ALA Z 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE Z 185 " --> pdb=" O GLN Z 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP a 34 " --> pdb=" O ASP a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA a 45 " --> pdb=" O VAL a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 67 through 89 Processing helix chain 'a' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER a 109 " --> pdb=" O ASP a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP a 117 " --> pdb=" O PRO a 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 114 through 117' Processing helix chain 'a' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL a 138 " --> pdb=" O ASP a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN a 155 " --> pdb=" O THR a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN a 161 " --> pdb=" O GLN a 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN a 162 " --> pdb=" O LEU a 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA a 173 " --> pdb=" O LEU a 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP a 176 " --> pdb=" O SER a 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET a 177 " --> pdb=" O ALA a 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE a 185 " --> pdb=" O GLN a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP b 34 " --> pdb=" O ASP b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA b 45 " --> pdb=" O VAL b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 89 Processing helix chain 'b' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER b 109 " --> pdb=" O ASP b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 114 through 117 removed outlier: 3.971A pdb=" N ASP b 117 " --> pdb=" O PRO b 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 114 through 117' Processing helix chain 'b' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL b 138 " --> pdb=" O ASP b 134 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN b 155 " --> pdb=" O THR b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN b 161 " --> pdb=" O GLN b 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN b 162 " --> pdb=" O LEU b 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA b 173 " --> pdb=" O LEU b 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP b 176 " --> pdb=" O SER b 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET b 177 " --> pdb=" O ALA b 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE b 185 " --> pdb=" O GLN b 181 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP c 34 " --> pdb=" O ASP c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA c 45 " --> pdb=" O VAL c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 89 Processing helix chain 'c' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER c 109 " --> pdb=" O ASP c 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP c 117 " --> pdb=" O PRO c 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 114 through 117' Processing helix chain 'c' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL c 138 " --> pdb=" O ASP c 134 " (cutoff:3.500A) Processing helix chain 'c' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN c 155 " --> pdb=" O THR c 151 " (cutoff:3.500A) Processing helix chain 'c' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN c 161 " --> pdb=" O GLN c 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN c 162 " --> pdb=" O LEU c 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA c 173 " --> pdb=" O LEU c 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP c 176 " --> pdb=" O SER c 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET c 177 " --> pdb=" O ALA c 173 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE c 185 " --> pdb=" O GLN c 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP d 34 " --> pdb=" O ASP d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA d 45 " --> pdb=" O VAL d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 89 Processing helix chain 'd' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER d 109 " --> pdb=" O ASP d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP d 117 " --> pdb=" O PRO d 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 114 through 117' Processing helix chain 'd' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL d 138 " --> pdb=" O ASP d 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN d 155 " --> pdb=" O THR d 151 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN d 161 " --> pdb=" O GLN d 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA d 173 " --> pdb=" O LEU d 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP d 176 " --> pdb=" O SER d 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET d 177 " --> pdb=" O ALA d 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE d 185 " --> pdb=" O GLN d 181 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP e 34 " --> pdb=" O ASP e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA e 45 " --> pdb=" O VAL e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 67 through 89 Processing helix chain 'e' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER e 109 " --> pdb=" O ASP e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP e 117 " --> pdb=" O PRO e 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 114 through 117' Processing helix chain 'e' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL e 138 " --> pdb=" O ASP e 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN e 155 " --> pdb=" O THR e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN e 161 " --> pdb=" O GLN e 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN e 162 " --> pdb=" O LEU e 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA e 173 " --> pdb=" O LEU e 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP e 176 " --> pdb=" O SER e 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET e 177 " --> pdb=" O ALA e 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE e 185 " --> pdb=" O GLN e 181 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP f 34 " --> pdb=" O ASP f 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA f 45 " --> pdb=" O VAL f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 89 Processing helix chain 'f' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER f 109 " --> pdb=" O ASP f 105 " (cutoff:3.500A) Processing helix chain 'f' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP f 117 " --> pdb=" O PRO f 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 114 through 117' Processing helix chain 'f' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL f 138 " --> pdb=" O ASP f 134 " (cutoff:3.500A) Processing helix chain 'f' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN f 155 " --> pdb=" O THR f 151 " (cutoff:3.500A) Processing helix chain 'f' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN f 161 " --> pdb=" O GLN f 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN f 162 " --> pdb=" O LEU f 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP f 176 " --> pdb=" O SER f 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET f 177 " --> pdb=" O ALA f 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE f 185 " --> pdb=" O GLN f 181 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP g 34 " --> pdb=" O ASP g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA g 45 " --> pdb=" O VAL g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 67 through 89 Processing helix chain 'g' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER g 109 " --> pdb=" O ASP g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP g 117 " --> pdb=" O PRO g 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 114 through 117' Processing helix chain 'g' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL g 138 " --> pdb=" O ASP g 134 " (cutoff:3.500A) Processing helix chain 'g' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN g 155 " --> pdb=" O THR g 151 " (cutoff:3.500A) Processing helix chain 'g' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN g 161 " --> pdb=" O GLN g 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN g 162 " --> pdb=" O LEU g 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA g 173 " --> pdb=" O LEU g 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP g 176 " --> pdb=" O SER g 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET g 177 " --> pdb=" O ALA g 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE g 185 " --> pdb=" O GLN g 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP h 34 " --> pdb=" O ASP h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA h 45 " --> pdb=" O VAL h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 89 Processing helix chain 'h' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER h 109 " --> pdb=" O ASP h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP h 117 " --> pdb=" O PRO h 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 114 through 117' Processing helix chain 'h' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL h 138 " --> pdb=" O ASP h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN h 155 " --> pdb=" O THR h 151 " (cutoff:3.500A) Processing helix chain 'h' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN h 161 " --> pdb=" O GLN h 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN h 162 " --> pdb=" O LEU h 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA h 173 " --> pdb=" O LEU h 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP h 176 " --> pdb=" O SER h 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET h 177 " --> pdb=" O ALA h 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE h 185 " --> pdb=" O GLN h 181 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP i 34 " --> pdb=" O ASP i 30 " (cutoff:3.500A) Processing helix chain 'i' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA i 45 " --> pdb=" O VAL i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 89 Processing helix chain 'i' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER i 109 " --> pdb=" O ASP i 105 " (cutoff:3.500A) Processing helix chain 'i' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP i 117 " --> pdb=" O PRO i 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 114 through 117' Processing helix chain 'i' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL i 138 " --> pdb=" O ASP i 134 " (cutoff:3.500A) Processing helix chain 'i' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN i 155 " --> pdb=" O THR i 151 " (cutoff:3.500A) Processing helix chain 'i' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN i 161 " --> pdb=" O GLN i 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN i 162 " --> pdb=" O LEU i 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA i 173 " --> pdb=" O LEU i 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP i 176 " --> pdb=" O SER i 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET i 177 " --> pdb=" O ALA i 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE i 185 " --> pdb=" O GLN i 181 " (cutoff:3.500A) Processing helix chain 'j' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP j 34 " --> pdb=" O ASP j 30 " (cutoff:3.500A) Processing helix chain 'j' and resid 41 through 65 removed outlier: 3.563A pdb=" N ALA j 45 " --> pdb=" O VAL j 41 " (cutoff:3.500A) Processing helix chain 'j' and resid 67 through 89 Processing helix chain 'j' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER j 109 " --> pdb=" O ASP j 105 " (cutoff:3.500A) Processing helix chain 'j' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP j 117 " --> pdb=" O PRO j 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 114 through 117' Processing helix chain 'j' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL j 138 " --> pdb=" O ASP j 134 " (cutoff:3.500A) Processing helix chain 'j' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN j 155 " --> pdb=" O THR j 151 " (cutoff:3.500A) Processing helix chain 'j' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN j 161 " --> pdb=" O GLN j 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN j 162 " --> pdb=" O LEU j 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA j 173 " --> pdb=" O LEU j 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP j 176 " --> pdb=" O SER j 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET j 177 " --> pdb=" O ALA j 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE j 185 " --> pdb=" O GLN j 181 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP k 34 " --> pdb=" O ASP k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA k 45 " --> pdb=" O VAL k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 89 Processing helix chain 'k' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER k 109 " --> pdb=" O ASP k 105 " (cutoff:3.500A) Processing helix chain 'k' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP k 117 " --> pdb=" O PRO k 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 114 through 117' Processing helix chain 'k' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL k 138 " --> pdb=" O ASP k 134 " (cutoff:3.500A) Processing helix chain 'k' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN k 155 " --> pdb=" O THR k 151 " (cutoff:3.500A) Processing helix chain 'k' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN k 161 " --> pdb=" O GLN k 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN k 162 " --> pdb=" O LEU k 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA k 173 " --> pdb=" O LEU k 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP k 176 " --> pdb=" O SER k 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE k 185 " --> pdb=" O GLN k 181 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP l 34 " --> pdb=" O ASP l 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA l 45 " --> pdb=" O VAL l 41 " (cutoff:3.500A) Processing helix chain 'l' and resid 67 through 89 Processing helix chain 'l' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER l 109 " --> pdb=" O ASP l 105 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP l 117 " --> pdb=" O PRO l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 114 through 117' Processing helix chain 'l' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL l 138 " --> pdb=" O ASP l 134 " (cutoff:3.500A) Processing helix chain 'l' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN l 155 " --> pdb=" O THR l 151 " (cutoff:3.500A) Processing helix chain 'l' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN l 161 " --> pdb=" O GLN l 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN l 162 " --> pdb=" O LEU l 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA l 173 " --> pdb=" O LEU l 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP l 176 " --> pdb=" O SER l 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET l 177 " --> pdb=" O ALA l 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE l 185 " --> pdb=" O GLN l 181 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP m 34 " --> pdb=" O ASP m 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA m 45 " --> pdb=" O VAL m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 89 Processing helix chain 'm' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER m 109 " --> pdb=" O ASP m 105 " (cutoff:3.500A) Processing helix chain 'm' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP m 117 " --> pdb=" O PRO m 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 114 through 117' Processing helix chain 'm' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL m 138 " --> pdb=" O ASP m 134 " (cutoff:3.500A) Processing helix chain 'm' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN m 155 " --> pdb=" O THR m 151 " (cutoff:3.500A) Processing helix chain 'm' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN m 161 " --> pdb=" O GLN m 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN m 162 " --> pdb=" O LEU m 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA m 173 " --> pdb=" O LEU m 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP m 176 " --> pdb=" O SER m 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET m 177 " --> pdb=" O ALA m 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE m 185 " --> pdb=" O GLN m 181 " (cutoff:3.500A) Processing helix chain 'n' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP n 34 " --> pdb=" O ASP n 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA n 45 " --> pdb=" O VAL n 41 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 89 Processing helix chain 'n' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER n 109 " --> pdb=" O ASP n 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP n 117 " --> pdb=" O PRO n 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 114 through 117' Processing helix chain 'n' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL n 138 " --> pdb=" O ASP n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN n 155 " --> pdb=" O THR n 151 " (cutoff:3.500A) Processing helix chain 'n' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN n 161 " --> pdb=" O GLN n 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN n 162 " --> pdb=" O LEU n 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA n 173 " --> pdb=" O LEU n 169 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP n 176 " --> pdb=" O SER n 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET n 177 " --> pdb=" O ALA n 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE n 185 " --> pdb=" O GLN n 181 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP o 34 " --> pdb=" O ASP o 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA o 45 " --> pdb=" O VAL o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 89 Processing helix chain 'o' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER o 109 " --> pdb=" O ASP o 105 " (cutoff:3.500A) Processing helix chain 'o' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP o 117 " --> pdb=" O PRO o 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 114 through 117' Processing helix chain 'o' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL o 138 " --> pdb=" O ASP o 134 " (cutoff:3.500A) Processing helix chain 'o' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN o 155 " --> pdb=" O THR o 151 " (cutoff:3.500A) Processing helix chain 'o' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN o 161 " --> pdb=" O GLN o 157 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN o 162 " --> pdb=" O LEU o 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA o 173 " --> pdb=" O LEU o 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP o 176 " --> pdb=" O SER o 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET o 177 " --> pdb=" O ALA o 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE o 185 " --> pdb=" O GLN o 181 " (cutoff:3.500A) Processing helix chain 'p' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP p 34 " --> pdb=" O ASP p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA p 45 " --> pdb=" O VAL p 41 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 89 Processing helix chain 'p' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER p 109 " --> pdb=" O ASP p 105 " (cutoff:3.500A) Processing helix chain 'p' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP p 117 " --> pdb=" O PRO p 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 114 through 117' Processing helix chain 'p' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL p 138 " --> pdb=" O ASP p 134 " (cutoff:3.500A) Processing helix chain 'p' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN p 155 " --> pdb=" O THR p 151 " (cutoff:3.500A) Processing helix chain 'p' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN p 161 " --> pdb=" O GLN p 157 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN p 162 " --> pdb=" O LEU p 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA p 173 " --> pdb=" O LEU p 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP p 176 " --> pdb=" O SER p 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET p 177 " --> pdb=" O ALA p 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE p 185 " --> pdb=" O GLN p 181 " (cutoff:3.500A) Processing helix chain 'q' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP q 34 " --> pdb=" O ASP q 30 " (cutoff:3.500A) Processing helix chain 'q' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA q 45 " --> pdb=" O VAL q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 67 through 89 Processing helix chain 'q' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER q 109 " --> pdb=" O ASP q 105 " (cutoff:3.500A) Processing helix chain 'q' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP q 117 " --> pdb=" O PRO q 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 114 through 117' Processing helix chain 'q' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL q 138 " --> pdb=" O ASP q 134 " (cutoff:3.500A) Processing helix chain 'q' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN q 155 " --> pdb=" O THR q 151 " (cutoff:3.500A) Processing helix chain 'q' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN q 161 " --> pdb=" O GLN q 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN q 162 " --> pdb=" O LEU q 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA q 173 " --> pdb=" O LEU q 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP q 176 " --> pdb=" O SER q 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET q 177 " --> pdb=" O ALA q 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE q 185 " --> pdb=" O GLN q 181 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP r 34 " --> pdb=" O ASP r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA r 45 " --> pdb=" O VAL r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 67 through 89 Processing helix chain 'r' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER r 109 " --> pdb=" O ASP r 105 " (cutoff:3.500A) Processing helix chain 'r' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP r 117 " --> pdb=" O PRO r 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 114 through 117' Processing helix chain 'r' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL r 138 " --> pdb=" O ASP r 134 " (cutoff:3.500A) Processing helix chain 'r' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN r 155 " --> pdb=" O THR r 151 " (cutoff:3.500A) Processing helix chain 'r' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN r 161 " --> pdb=" O GLN r 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN r 162 " --> pdb=" O LEU r 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA r 173 " --> pdb=" O LEU r 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP r 176 " --> pdb=" O SER r 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET r 177 " --> pdb=" O ALA r 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE r 185 " --> pdb=" O GLN r 181 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP s 34 " --> pdb=" O ASP s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA s 45 " --> pdb=" O VAL s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 67 through 89 Processing helix chain 's' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER s 109 " --> pdb=" O ASP s 105 " (cutoff:3.500A) Processing helix chain 's' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP s 117 " --> pdb=" O PRO s 114 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 114 through 117' Processing helix chain 's' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL s 138 " --> pdb=" O ASP s 134 " (cutoff:3.500A) Processing helix chain 's' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN s 155 " --> pdb=" O THR s 151 " (cutoff:3.500A) Processing helix chain 's' and resid 157 through 186 removed outlier: 3.508A pdb=" N GLN s 161 " --> pdb=" O GLN s 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN s 162 " --> pdb=" O LEU s 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA s 173 " --> pdb=" O LEU s 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP s 176 " --> pdb=" O SER s 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET s 177 " --> pdb=" O ALA s 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE s 185 " --> pdb=" O GLN s 181 " (cutoff:3.500A) Processing helix chain 't' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP t 34 " --> pdb=" O ASP t 30 " (cutoff:3.500A) Processing helix chain 't' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA t 45 " --> pdb=" O VAL t 41 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 89 Processing helix chain 't' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER t 109 " --> pdb=" O ASP t 105 " (cutoff:3.500A) Processing helix chain 't' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP t 117 " --> pdb=" O PRO t 114 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 114 through 117' Processing helix chain 't' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL t 138 " --> pdb=" O ASP t 134 " (cutoff:3.500A) Processing helix chain 't' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN t 155 " --> pdb=" O THR t 151 " (cutoff:3.500A) Processing helix chain 't' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN t 161 " --> pdb=" O GLN t 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN t 162 " --> pdb=" O LEU t 158 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA t 173 " --> pdb=" O LEU t 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP t 176 " --> pdb=" O SER t 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET t 177 " --> pdb=" O ALA t 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE t 185 " --> pdb=" O GLN t 181 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP u 34 " --> pdb=" O ASP u 30 " (cutoff:3.500A) Processing helix chain 'u' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA u 45 " --> pdb=" O VAL u 41 " (cutoff:3.500A) Processing helix chain 'u' and resid 67 through 89 Processing helix chain 'u' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER u 109 " --> pdb=" O ASP u 105 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP u 117 " --> pdb=" O PRO u 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 114 through 117' Processing helix chain 'u' and resid 134 through 143 removed outlier: 3.714A pdb=" N VAL u 138 " --> pdb=" O ASP u 134 " (cutoff:3.500A) Processing helix chain 'u' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN u 155 " --> pdb=" O THR u 151 " (cutoff:3.500A) Processing helix chain 'u' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN u 161 " --> pdb=" O GLN u 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN u 162 " --> pdb=" O LEU u 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA u 173 " --> pdb=" O LEU u 169 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP u 176 " --> pdb=" O SER u 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET u 177 " --> pdb=" O ALA u 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE u 185 " --> pdb=" O GLN u 181 " (cutoff:3.500A) Processing helix chain 'v' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP v 34 " --> pdb=" O ASP v 30 " (cutoff:3.500A) Processing helix chain 'v' and resid 41 through 65 removed outlier: 3.563A pdb=" N ALA v 45 " --> pdb=" O VAL v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 67 through 89 Processing helix chain 'v' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER v 109 " --> pdb=" O ASP v 105 " (cutoff:3.500A) Processing helix chain 'v' and resid 114 through 117 removed outlier: 3.973A pdb=" N ASP v 117 " --> pdb=" O PRO v 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 114 through 117' Processing helix chain 'v' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL v 138 " --> pdb=" O ASP v 134 " (cutoff:3.500A) Processing helix chain 'v' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN v 155 " --> pdb=" O THR v 151 " (cutoff:3.500A) Processing helix chain 'v' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN v 161 " --> pdb=" O GLN v 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN v 162 " --> pdb=" O LEU v 158 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA v 173 " --> pdb=" O LEU v 169 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP v 176 " --> pdb=" O SER v 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET v 177 " --> pdb=" O ALA v 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE v 185 " --> pdb=" O GLN v 181 " (cutoff:3.500A) Processing helix chain 'w' and resid 28 through 39 removed outlier: 3.882A pdb=" N ASP w 34 " --> pdb=" O ASP w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 65 removed outlier: 3.564A pdb=" N ALA w 45 " --> pdb=" O VAL w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 67 through 89 Processing helix chain 'w' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER w 109 " --> pdb=" O ASP w 105 " (cutoff:3.500A) Processing helix chain 'w' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP w 117 " --> pdb=" O PRO w 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 114 through 117' Processing helix chain 'w' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL w 138 " --> pdb=" O ASP w 134 " (cutoff:3.500A) Processing helix chain 'w' and resid 150 through 155 removed outlier: 3.529A pdb=" N ASN w 155 " --> pdb=" O THR w 151 " (cutoff:3.500A) Processing helix chain 'w' and resid 157 through 186 removed outlier: 3.506A pdb=" N GLN w 161 " --> pdb=" O GLN w 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN w 162 " --> pdb=" O LEU w 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA w 173 " --> pdb=" O LEU w 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP w 176 " --> pdb=" O SER w 172 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET w 177 " --> pdb=" O ALA w 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE w 185 " --> pdb=" O GLN w 181 " (cutoff:3.500A) Processing helix chain 'x' and resid 28 through 39 removed outlier: 3.881A pdb=" N ASP x 34 " --> pdb=" O ASP x 30 " (cutoff:3.500A) Processing helix chain 'x' and resid 41 through 65 removed outlier: 3.565A pdb=" N ALA x 45 " --> pdb=" O VAL x 41 " (cutoff:3.500A) Processing helix chain 'x' and resid 67 through 89 Processing helix chain 'x' and resid 104 through 113 removed outlier: 3.601A pdb=" N SER x 109 " --> pdb=" O ASP x 105 " (cutoff:3.500A) Processing helix chain 'x' and resid 114 through 117 removed outlier: 3.972A pdb=" N ASP x 117 " --> pdb=" O PRO x 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 114 through 117' Processing helix chain 'x' and resid 134 through 143 removed outlier: 3.713A pdb=" N VAL x 138 " --> pdb=" O ASP x 134 " (cutoff:3.500A) Processing helix chain 'x' and resid 150 through 155 removed outlier: 3.528A pdb=" N ASN x 155 " --> pdb=" O THR x 151 " (cutoff:3.500A) Processing helix chain 'x' and resid 157 through 186 removed outlier: 3.507A pdb=" N GLN x 161 " --> pdb=" O GLN x 157 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN x 162 " --> pdb=" O LEU x 158 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA x 173 " --> pdb=" O LEU x 169 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP x 176 " --> pdb=" O SER x 172 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET x 177 " --> pdb=" O ALA x 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE x 185 " --> pdb=" O GLN x 181 " (cutoff:3.500A) 3850 hydrogen bonds defined for protein. 11550 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: 22.43 Time building geometry restraints manager: 14.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 21898 1.34 - 1.45: 6190 1.45 - 1.57: 37162 1.57 - 1.69: 0 1.69 - 1.80: 800 Bond restraints: 66050 Sorted by residual: bond pdb=" CG1 ILE u 111 " pdb=" CD1 ILE u 111 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.43e+00 bond pdb=" CG1 ILE G 111 " pdb=" CD1 ILE G 111 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.42e+00 bond pdb=" CG1 ILE R 111 " pdb=" CD1 ILE R 111 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.41e+00 bond pdb=" CG1 ILE Q 111 " pdb=" CD1 ILE Q 111 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.41e+00 bond pdb=" CG1 ILE t 111 " pdb=" CD1 ILE t 111 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.40e+00 ... (remaining 66045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 85277 1.95 - 3.90: 3212 3.90 - 5.86: 411 5.86 - 7.81: 50 7.81 - 9.76: 200 Bond angle restraints: 89150 Sorted by residual: angle pdb=" N VAL J 91 " pdb=" CA VAL J 91 " pdb=" C VAL J 91 " ideal model delta sigma weight residual 113.42 107.69 5.73 1.17e+00 7.31e-01 2.40e+01 angle pdb=" N VAL L 91 " pdb=" CA VAL L 91 " pdb=" C VAL L 91 " ideal model delta sigma weight residual 113.42 107.70 5.72 1.17e+00 7.31e-01 2.39e+01 angle pdb=" N VAL d 91 " pdb=" CA VAL d 91 " pdb=" C VAL d 91 " ideal model delta sigma weight residual 113.42 107.71 5.71 1.17e+00 7.31e-01 2.39e+01 angle pdb=" N VAL W 91 " pdb=" CA VAL W 91 " pdb=" C VAL W 91 " ideal model delta sigma weight residual 113.42 107.71 5.71 1.17e+00 7.31e-01 2.38e+01 angle pdb=" N VAL F 91 " pdb=" CA VAL F 91 " pdb=" C VAL F 91 " ideal model delta sigma weight residual 113.42 107.71 5.71 1.17e+00 7.31e-01 2.38e+01 ... (remaining 89145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 37797 16.84 - 33.69: 2753 33.69 - 50.53: 500 50.53 - 67.38: 50 67.38 - 84.22: 150 Dihedral angle restraints: 41250 sinusoidal: 15650 harmonic: 25600 Sorted by residual: dihedral pdb=" CA LEU I 130 " pdb=" C LEU I 130 " pdb=" N GLY I 131 " pdb=" CA GLY I 131 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA LEU i 130 " pdb=" C LEU i 130 " pdb=" N GLY i 131 " pdb=" CA GLY i 131 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LEU Y 130 " pdb=" C LEU Y 130 " pdb=" N GLY Y 131 " pdb=" CA GLY Y 131 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 41247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 5602 0.037 - 0.074: 3677 0.074 - 0.111: 1028 0.111 - 0.148: 251 0.148 - 0.185: 142 Chirality restraints: 10700 Sorted by residual: chirality pdb=" CB ILE N 118 " pdb=" CA ILE N 118 " pdb=" CG1 ILE N 118 " pdb=" CG2 ILE N 118 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CB ILE b 118 " pdb=" CA ILE b 118 " pdb=" CG1 ILE b 118 " pdb=" CG2 ILE b 118 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CB ILE v 118 " pdb=" CA ILE v 118 " pdb=" CG1 ILE v 118 " pdb=" CG2 ILE v 118 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 10697 not shown) Planarity restraints: 11650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP Y 113 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO Y 114 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO Y 114 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO Y 114 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP w 113 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO w 114 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO w 114 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO w 114 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP L 113 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO L 114 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 114 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 114 " -0.018 5.00e-02 4.00e+02 ... (remaining 11647 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 218 2.30 - 2.95: 31336 2.95 - 3.60: 92475 3.60 - 4.25: 140855 4.25 - 4.90: 249779 Nonbonded interactions: 514663 Sorted by model distance: nonbonded pdb=" CD1 ILE T 185 " pdb=" ND2 ASN b 154 " model vdw 1.645 3.540 nonbonded pdb=" NE2 GLN N 78 " pdb=" CD2 LEU O 59 " model vdw 1.656 3.540 nonbonded pdb=" NE2 GLN X 78 " pdb=" CD2 LEU Y 59 " model vdw 1.656 3.540 nonbonded pdb=" NE2 GLN D 78 " pdb=" CD2 LEU E 59 " model vdw 1.656 3.540 nonbonded pdb=" NE2 GLN h 78 " pdb=" CD2 LEU i 59 " model vdw 1.656 3.540 ... (remaining 514658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.870 Check model and map are aligned: 0.390 Set scattering table: 0.470 Process input model: 91.170 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.950 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: 0.030 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 66050 Z= 0.494 Angle : 0.972 9.760 89150 Z= 0.546 Chirality : 0.052 0.185 10700 Planarity : 0.004 0.032 11650 Dihedral : 13.298 84.219 24550 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 21.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: -1.82 (0.09), residues: 8600 helix: -0.57 (0.06), residues: 6400 sheet: None (None), residues: 0 loop : -2.84 (0.12), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE g 42 TYR 0.010 0.002 TYR o 22 ARG 0.001 0.000 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1386 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1386 time to evaluate : 5.232 Fit side-chains revert: symmetry clash REVERT: A 82 ASN cc_start: 0.7649 (m-40) cc_final: 0.7242 (t0) REVERT: B 34 ASP cc_start: 0.7346 (m-30) cc_final: 0.7058 (m-30) REVERT: B 38 LYS cc_start: 0.8089 (tttp) cc_final: 0.7582 (tttm) REVERT: B 85 ASP cc_start: 0.7479 (m-30) cc_final: 0.7142 (t0) REVERT: C 34 ASP cc_start: 0.7123 (m-30) cc_final: 0.6792 (m-30) REVERT: D 79 LYS cc_start: 0.7947 (ttpp) cc_final: 0.6751 (tptm) REVERT: E 20 MET cc_start: 0.6520 (ptm) cc_final: 0.6150 (ptm) REVERT: E 38 LYS cc_start: 0.8068 (tttp) cc_final: 0.7783 (ttpp) REVERT: F 79 LYS cc_start: 0.7497 (ttpp) cc_final: 0.6900 (mttp) REVERT: G 38 LYS cc_start: 0.8161 (tttp) cc_final: 0.7715 (ttmt) REVERT: H 38 LYS cc_start: 0.7773 (tttp) cc_final: 0.7448 (ttpt) REVERT: I 30 ASP cc_start: 0.7830 (m-30) cc_final: 0.7263 (m-30) REVERT: I 34 ASP cc_start: 0.7564 (m-30) cc_final: 0.6960 (m-30) REVERT: K 148 ASN cc_start: 0.8345 (p0) cc_final: 0.8135 (p0) REVERT: L 34 ASP cc_start: 0.7596 (m-30) cc_final: 0.7114 (m-30) REVERT: L 58 ASP cc_start: 0.8148 (m-30) cc_final: 0.7863 (m-30) REVERT: L 85 ASP cc_start: 0.7485 (m-30) cc_final: 0.7138 (t0) REVERT: M 34 ASP cc_start: 0.7325 (m-30) cc_final: 0.6606 (m-30) REVERT: M 85 ASP cc_start: 0.7498 (m-30) cc_final: 0.7062 (t0) REVERT: P 38 LYS cc_start: 0.7718 (tttp) cc_final: 0.7021 (ttmt) REVERT: Q 38 LYS cc_start: 0.8016 (tttp) cc_final: 0.7736 (tttm) REVERT: U 20 MET cc_start: 0.6103 (ptm) cc_final: 0.5265 (mtm) REVERT: V 79 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7937 (ttmt) REVERT: V 85 ASP cc_start: 0.7450 (m-30) cc_final: 0.7184 (t0) REVERT: W 34 ASP cc_start: 0.7180 (m-30) cc_final: 0.6706 (m-30) REVERT: W 79 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7364 (mttt) REVERT: W 80 MET cc_start: 0.7585 (mmp) cc_final: 0.7266 (mmp) REVERT: W 183 ARG cc_start: 0.8231 (mtm110) cc_final: 0.8013 (mtm110) REVERT: X 79 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7767 (ttpp) REVERT: Y 38 LYS cc_start: 0.7891 (tttp) cc_final: 0.7682 (tttt) REVERT: Y 79 LYS cc_start: 0.8066 (ttpp) cc_final: 0.7676 (ttmm) REVERT: Z 23 ASP cc_start: 0.7654 (p0) cc_final: 0.7384 (p0) REVERT: Z 30 ASP cc_start: 0.7484 (m-30) cc_final: 0.6980 (m-30) REVERT: a 30 ASP cc_start: 0.8179 (m-30) cc_final: 0.7771 (m-30) REVERT: a 31 ASP cc_start: 0.8022 (m-30) cc_final: 0.7818 (m-30) REVERT: a 34 ASP cc_start: 0.7316 (m-30) cc_final: 0.6942 (m-30) REVERT: a 79 LYS cc_start: 0.7447 (ttpp) cc_final: 0.7150 (mttt) REVERT: b 172 SER cc_start: 0.7945 (t) cc_final: 0.7694 (m) REVERT: c 80 MET cc_start: 0.8096 (mmp) cc_final: 0.7794 (mmt) REVERT: c 164 SER cc_start: 0.9141 (m) cc_final: 0.8908 (m) REVERT: d 67 MET cc_start: 0.8479 (mtp) cc_final: 0.8269 (mtm) REVERT: e 79 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7348 (mttt) REVERT: e 113 ASP cc_start: 0.7820 (t70) cc_final: 0.7476 (t0) REVERT: f 34 ASP cc_start: 0.7448 (m-30) cc_final: 0.7204 (m-30) REVERT: f 58 ASP cc_start: 0.8585 (m-30) cc_final: 0.8331 (m-30) REVERT: f 79 LYS cc_start: 0.7764 (ttpp) cc_final: 0.7283 (mttt) REVERT: f 145 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7803 (tttm) REVERT: g 38 LYS cc_start: 0.8289 (tttp) cc_final: 0.8057 (tttt) REVERT: h 79 LYS cc_start: 0.7902 (ttpp) cc_final: 0.7279 (ttmm) REVERT: h 119 THR cc_start: 0.7856 (m) cc_final: 0.7579 (p) REVERT: i 38 LYS cc_start: 0.7803 (tttp) cc_final: 0.7544 (tttm) REVERT: j 79 LYS cc_start: 0.7523 (ttpp) cc_final: 0.6953 (mttt) REVERT: l 88 ILE cc_start: 0.7189 (mt) cc_final: 0.6942 (tt) REVERT: m 145 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8228 (tttp) REVERT: o 52 MET cc_start: 0.8202 (mtp) cc_final: 0.7968 (mtm) REVERT: o 79 LYS cc_start: 0.7864 (ttpp) cc_final: 0.7314 (mttt) REVERT: p 30 ASP cc_start: 0.7637 (m-30) cc_final: 0.7119 (m-30) REVERT: p 34 ASP cc_start: 0.7399 (m-30) cc_final: 0.7037 (m-30) REVERT: p 38 LYS cc_start: 0.8330 (tttp) cc_final: 0.8001 (ttpp) REVERT: p 79 LYS cc_start: 0.7255 (ttpp) cc_final: 0.6712 (mttt) REVERT: q 31 ASP cc_start: 0.8630 (m-30) cc_final: 0.8399 (m-30) REVERT: r 27 MET cc_start: 0.9044 (mtp) cc_final: 0.8694 (mtp) REVERT: s 20 MET cc_start: 0.6668 (ptm) cc_final: 0.6342 (ptm) REVERT: t 30 ASP cc_start: 0.8356 (m-30) cc_final: 0.8027 (m-30) REVERT: t 31 ASP cc_start: 0.8082 (m-30) cc_final: 0.7809 (m-30) REVERT: t 34 ASP cc_start: 0.7134 (m-30) cc_final: 0.6734 (m-30) REVERT: t 38 LYS cc_start: 0.7869 (tttp) cc_final: 0.7303 (ttmt) REVERT: t 63 LYS cc_start: 0.8460 (tptp) cc_final: 0.8167 (tptm) REVERT: u 38 LYS cc_start: 0.7916 (tttp) cc_final: 0.7699 (tttm) REVERT: w 145 LYS cc_start: 0.8527 (ttpp) cc_final: 0.7739 (mtpp) outliers start: 0 outliers final: 0 residues processed: 1386 average time/residue: 0.5926 time to fit residues: 1416.9276 Evaluate side-chains 896 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 896 time to evaluate : 5.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 717 optimal weight: 0.9990 chunk 644 optimal weight: 1.9990 chunk 357 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 434 optimal weight: 10.0000 chunk 344 optimal weight: 0.9980 chunk 666 optimal weight: 2.9990 chunk 257 optimal weight: 0.9980 chunk 405 optimal weight: 0.9980 chunk 495 optimal weight: 2.9990 chunk 771 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 GLN ** G 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** H 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 GLN ** J 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 GLN ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 GLN ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN O 78 GLN ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN P 68 ASN ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 GLN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN R 78 GLN ** R 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 181 GLN ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 78 GLN ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 ASN ** X 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 ASN ** Y 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 78 GLN ** Z 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN ** c 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 54 GLN ** e 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 154 ASN f 181 GLN ** g 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 GLN h 68 ASN h 78 GLN ** h 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 78 GLN ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 54 GLN ** k 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 78 GLN ** l 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 181 GLN o 154 ASN p 154 ASN p 162 GLN q 78 GLN ** q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 162 GLN ** q 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 78 GLN ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 181 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 66050 Z= 0.188 Angle : 0.586 7.283 89150 Z= 0.310 Chirality : 0.039 0.200 10700 Planarity : 0.003 0.050 11650 Dihedral : 5.926 24.886 9050 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.25 % Allowed : 7.38 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: -0.87 (0.09), residues: 8600 helix: 0.57 (0.07), residues: 6050 sheet: None (None), residues: 0 loop : -3.45 (0.09), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE J 49 TYR 0.009 0.001 TYR W 22 ARG 0.004 0.000 ARG n 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1104 time to evaluate : 5.209 Fit side-chains revert: symmetry clash REVERT: B 34 ASP cc_start: 0.7241 (m-30) cc_final: 0.6802 (m-30) REVERT: B 38 LYS cc_start: 0.8148 (tttp) cc_final: 0.7796 (tttm) REVERT: B 85 ASP cc_start: 0.7374 (m-30) cc_final: 0.7023 (t0) REVERT: B 177 MET cc_start: 0.8507 (mmm) cc_final: 0.8197 (tpt) REVERT: C 30 ASP cc_start: 0.8405 (m-30) cc_final: 0.8059 (m-30) REVERT: C 34 ASP cc_start: 0.7078 (m-30) cc_final: 0.6678 (m-30) REVERT: C 172 SER cc_start: 0.8708 (t) cc_final: 0.8452 (m) REVERT: E 20 MET cc_start: 0.6047 (ptm) cc_final: 0.5775 (ptm) REVERT: E 177 MET cc_start: 0.8297 (tpt) cc_final: 0.8039 (tpt) REVERT: F 79 LYS cc_start: 0.7496 (ttpp) cc_final: 0.6978 (mttp) REVERT: G 38 LYS cc_start: 0.8355 (tttp) cc_final: 0.7522 (ttpt) REVERT: G 172 SER cc_start: 0.8918 (t) cc_final: 0.8642 (t) REVERT: H 20 MET cc_start: 0.6690 (ptm) cc_final: 0.6407 (ptm) REVERT: H 38 LYS cc_start: 0.7878 (tttp) cc_final: 0.7438 (ttpt) REVERT: J 172 SER cc_start: 0.8671 (t) cc_final: 0.8314 (m) REVERT: K 126 ILE cc_start: 0.4865 (OUTLIER) cc_final: 0.4429 (tt) REVERT: L 85 ASP cc_start: 0.7583 (m-30) cc_final: 0.7164 (t0) REVERT: L 147 ASN cc_start: 0.8525 (t0) cc_final: 0.8264 (t0) REVERT: M 34 ASP cc_start: 0.7176 (m-30) cc_final: 0.6864 (m-30) REVERT: M 85 ASP cc_start: 0.7344 (m-30) cc_final: 0.6841 (t0) REVERT: O 177 MET cc_start: 0.8177 (tpt) cc_final: 0.7816 (tpt) REVERT: P 38 LYS cc_start: 0.7773 (tttp) cc_final: 0.6964 (ttmt) REVERT: P 67 MET cc_start: 0.7729 (mtp) cc_final: 0.7472 (mtm) REVERT: Q 23 ASP cc_start: 0.7468 (p0) cc_final: 0.7074 (t0) REVERT: Q 30 ASP cc_start: 0.7391 (m-30) cc_final: 0.7179 (m-30) REVERT: R 145 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7737 (pttp) REVERT: S 58 ASP cc_start: 0.7824 (m-30) cc_final: 0.7559 (m-30) REVERT: U 20 MET cc_start: 0.6131 (ptm) cc_final: 0.5585 (mtm) REVERT: U 177 MET cc_start: 0.7909 (tpp) cc_final: 0.7506 (tpp) REVERT: V 79 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7896 (ttmt) REVERT: V 85 ASP cc_start: 0.7395 (m-30) cc_final: 0.7078 (t0) REVERT: V 90 ASP cc_start: 0.6697 (m-30) cc_final: 0.6428 (m-30) REVERT: W 34 ASP cc_start: 0.7117 (m-30) cc_final: 0.6502 (m-30) REVERT: W 67 MET cc_start: 0.7584 (mtp) cc_final: 0.7327 (mtt) REVERT: W 79 LYS cc_start: 0.7579 (ttpp) cc_final: 0.7272 (mttt) REVERT: W 80 MET cc_start: 0.7540 (mmp) cc_final: 0.7144 (mmp) REVERT: Y 20 MET cc_start: 0.6440 (ptm) cc_final: 0.5676 (ptm) REVERT: Y 38 LYS cc_start: 0.8187 (tttp) cc_final: 0.7971 (tttt) REVERT: Z 23 ASP cc_start: 0.7634 (p0) cc_final: 0.7325 (p0) REVERT: a 79 LYS cc_start: 0.7493 (ttpp) cc_final: 0.7021 (mttp) REVERT: c 108 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7219 (mp) REVERT: d 67 MET cc_start: 0.8182 (mtp) cc_final: 0.7868 (mtm) REVERT: e 79 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7282 (mttt) REVERT: g 47 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7907 (tp) REVERT: h 22 TYR cc_start: 0.7786 (m-80) cc_final: 0.7528 (m-80) REVERT: h 108 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6683 (pt) REVERT: k 172 SER cc_start: 0.8672 (t) cc_final: 0.8448 (m) REVERT: l 177 MET cc_start: 0.8585 (tpt) cc_final: 0.8296 (tpt) REVERT: m 145 LYS cc_start: 0.8355 (ttpp) cc_final: 0.7985 (tttp) REVERT: n 80 MET cc_start: 0.6663 (mmp) cc_final: 0.6452 (mmt) REVERT: n 177 MET cc_start: 0.8644 (tpp) cc_final: 0.8343 (tpt) REVERT: o 30 ASP cc_start: 0.6853 (m-30) cc_final: 0.6506 (t0) REVERT: o 79 LYS cc_start: 0.7849 (ttpp) cc_final: 0.7329 (mttt) REVERT: o 85 ASP cc_start: 0.7732 (m-30) cc_final: 0.7487 (t0) REVERT: o 113 ASP cc_start: 0.7671 (t0) cc_final: 0.7305 (t70) REVERT: p 34 ASP cc_start: 0.7432 (m-30) cc_final: 0.6863 (m-30) REVERT: p 39 LEU cc_start: 0.7966 (mt) cc_final: 0.7763 (mp) REVERT: p 79 LYS cc_start: 0.7263 (ttpp) cc_final: 0.6890 (mttt) REVERT: r 27 MET cc_start: 0.9047 (mtp) cc_final: 0.8614 (mtp) REVERT: s 30 ASP cc_start: 0.7369 (m-30) cc_final: 0.7077 (t0) REVERT: s 85 ASP cc_start: 0.6743 (m-30) cc_final: 0.6542 (m-30) REVERT: t 31 ASP cc_start: 0.7974 (m-30) cc_final: 0.7771 (m-30) REVERT: t 38 LYS cc_start: 0.7862 (tttp) cc_final: 0.7176 (ttmt) REVERT: u 172 SER cc_start: 0.8737 (t) cc_final: 0.8237 (m) REVERT: u 176 ASP cc_start: 0.8327 (m-30) cc_final: 0.8113 (m-30) REVERT: u 185 ILE cc_start: 0.8740 (mm) cc_final: 0.8449 (mm) REVERT: v 52 MET cc_start: 0.8069 (mtm) cc_final: 0.7865 (mtp) REVERT: v 176 ASP cc_start: 0.8392 (m-30) cc_final: 0.8121 (m-30) REVERT: v 177 MET cc_start: 0.8695 (tpt) cc_final: 0.8292 (tpt) REVERT: v 185 ILE cc_start: 0.8806 (mm) cc_final: 0.8597 (mm) outliers start: 164 outliers final: 35 residues processed: 1212 average time/residue: 0.5527 time to fit residues: 1191.1234 Evaluate side-chains 926 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 886 time to evaluate : 5.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain L residue 188 ILE Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 109 SER Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 142 ILE Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain V residue 127 ASN Chi-restraints excluded: chain V residue 181 GLN Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 126 ILE Chi-restraints excluded: chain c residue 108 ILE Chi-restraints excluded: chain d residue 145 LYS Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain f residue 184 THR Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain i residue 88 ILE Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain s residue 88 ILE Chi-restraints excluded: chain t residue 59 LEU Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain w residue 83 LEU Chi-restraints excluded: chain w residue 179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 428 optimal weight: 6.9990 chunk 239 optimal weight: 0.9990 chunk 642 optimal weight: 8.9990 chunk 525 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 773 optimal weight: 9.9990 chunk 835 optimal weight: 9.9990 chunk 688 optimal weight: 6.9990 chunk 766 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 620 optimal weight: 0.0370 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN E 68 ASN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN F 68 ASN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN H 68 ASN ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 GLN I 68 ASN I 78 GLN ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN K 154 ASN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** L 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN P 68 ASN ** P 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 127 ASN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 GLN R 68 ASN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 GLN S 78 GLN ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 GLN T 127 ASN ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 68 ASN ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 GLN ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 56 GLN ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 154 ASN ** X 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 ASN ** Z 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 ASN ** a 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 56 GLN b 68 ASN ** b 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 56 GLN c 68 ASN c 78 GLN ** c 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 56 GLN ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 78 GLN h 68 ASN ** h 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 ASN ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 78 GLN ** j 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 162 GLN k 56 GLN k 68 ASN k 78 GLN ** k 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 147 ASN ** k 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 56 GLN m 78 GLN m 127 ASN o 68 ASN p 68 ASN p 78 GLN ** q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 181 GLN r 68 ASN ** r 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 ASN ** s 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 162 GLN t 68 ASN t 78 GLN ** t 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 ASN ** u 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN w 78 GLN ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 66050 Z= 0.198 Angle : 0.569 8.900 89150 Z= 0.300 Chirality : 0.039 0.192 10700 Planarity : 0.003 0.048 11650 Dihedral : 5.592 23.156 9050 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.73 % Allowed : 9.63 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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 (0.09), residues: 8600 helix: 1.00 (0.07), residues: 6050 sheet: None (None), residues: 0 loop : -3.07 (0.09), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE A 64 TYR 0.013 0.001 TYR G 22 ARG 0.006 0.000 ARG n 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 908 time to evaluate : 5.284 Fit side-chains revert: symmetry clash REVERT: B 34 ASP cc_start: 0.7298 (m-30) cc_final: 0.6782 (m-30) REVERT: B 38 LYS cc_start: 0.8066 (tttp) cc_final: 0.7676 (tttm) REVERT: B 85 ASP cc_start: 0.7475 (m-30) cc_final: 0.6972 (t0) REVERT: C 172 SER cc_start: 0.8753 (t) cc_final: 0.8553 (m) REVERT: D 79 LYS cc_start: 0.7977 (ttpp) cc_final: 0.6717 (tptm) REVERT: E 177 MET cc_start: 0.8295 (tpt) cc_final: 0.7928 (tpt) REVERT: F 79 LYS cc_start: 0.7711 (ttpp) cc_final: 0.7011 (mttp) REVERT: G 31 ASP cc_start: 0.7883 (m-30) cc_final: 0.7634 (m-30) REVERT: G 38 LYS cc_start: 0.8364 (tttp) cc_final: 0.7684 (ttmt) REVERT: H 20 MET cc_start: 0.7057 (ptm) cc_final: 0.5957 (ttp) REVERT: H 38 LYS cc_start: 0.8072 (tttp) cc_final: 0.7685 (ttmt) REVERT: J 31 ASP cc_start: 0.7942 (m-30) cc_final: 0.7679 (m-30) REVERT: J 172 SER cc_start: 0.8970 (t) cc_final: 0.8538 (m) REVERT: K 126 ILE cc_start: 0.4965 (OUTLIER) cc_final: 0.4667 (tt) REVERT: L 147 ASN cc_start: 0.8722 (t0) cc_final: 0.8321 (t0) REVERT: M 34 ASP cc_start: 0.7121 (m-30) cc_final: 0.6851 (m-30) REVERT: M 85 ASP cc_start: 0.7498 (m-30) cc_final: 0.7002 (t0) REVERT: P 38 LYS cc_start: 0.7924 (tttp) cc_final: 0.7153 (ttmt) REVERT: P 67 MET cc_start: 0.7844 (mtp) cc_final: 0.7600 (mtt) REVERT: Q 23 ASP cc_start: 0.7292 (p0) cc_final: 0.6877 (t70) REVERT: Q 30 ASP cc_start: 0.7459 (m-30) cc_final: 0.7240 (m-30) REVERT: R 20 MET cc_start: 0.6613 (ptm) cc_final: 0.6261 (ttp) REVERT: R 68 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.7052 (m110) REVERT: R 145 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.7767 (pttp) REVERT: S 20 MET cc_start: 0.6932 (ttp) cc_final: 0.6684 (ttp) REVERT: S 58 ASP cc_start: 0.7750 (m-30) cc_final: 0.7440 (m-30) REVERT: U 20 MET cc_start: 0.6392 (ptm) cc_final: 0.5669 (mtm) REVERT: V 20 MET cc_start: 0.6798 (ptm) cc_final: 0.6556 (ptm) REVERT: V 38 LYS cc_start: 0.7954 (tttp) cc_final: 0.7168 (mttt) REVERT: V 79 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7893 (ttmt) REVERT: V 85 ASP cc_start: 0.7490 (m-30) cc_final: 0.7113 (t0) REVERT: V 90 ASP cc_start: 0.6779 (m-30) cc_final: 0.6543 (m-30) REVERT: V 147 ASN cc_start: 0.8689 (t0) cc_final: 0.8450 (t0) REVERT: W 34 ASP cc_start: 0.7100 (m-30) cc_final: 0.6436 (m-30) REVERT: W 67 MET cc_start: 0.7721 (mtp) cc_final: 0.7496 (mtt) REVERT: W 79 LYS cc_start: 0.7687 (ttpp) cc_final: 0.7366 (mttt) REVERT: W 80 MET cc_start: 0.7550 (mmp) cc_final: 0.7303 (mmt) REVERT: Y 38 LYS cc_start: 0.8157 (tttp) cc_final: 0.7940 (tttt) REVERT: Y 163 MET cc_start: 0.7617 (mtt) cc_final: 0.7202 (mtt) REVERT: Y 177 MET cc_start: 0.8450 (tpp) cc_final: 0.8238 (tpp) REVERT: Z 23 ASP cc_start: 0.7773 (p0) cc_final: 0.7430 (p0) REVERT: Z 126 ILE cc_start: 0.5523 (OUTLIER) cc_final: 0.5298 (tp) REVERT: a 30 ASP cc_start: 0.7745 (m-30) cc_final: 0.7434 (m-30) REVERT: a 79 LYS cc_start: 0.7606 (ttpp) cc_final: 0.7055 (mttp) REVERT: a 80 MET cc_start: 0.7739 (mmt) cc_final: 0.7377 (mmt) REVERT: d 67 MET cc_start: 0.8022 (mtp) cc_final: 0.7727 (mtm) REVERT: e 79 LYS cc_start: 0.7921 (ttpp) cc_final: 0.7301 (mttt) REVERT: f 145 LYS cc_start: 0.7882 (ttpp) cc_final: 0.7445 (ttmm) REVERT: g 47 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8097 (tp) REVERT: h 79 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7203 (ttmm) REVERT: h 108 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6493 (pt) REVERT: i 177 MET cc_start: 0.8449 (mmm) cc_final: 0.8103 (tpt) REVERT: k 68 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.7120 (m110) REVERT: k 172 SER cc_start: 0.8710 (t) cc_final: 0.8464 (m) REVERT: k 177 MET cc_start: 0.8477 (tpp) cc_final: 0.8134 (mmt) REVERT: l 172 SER cc_start: 0.8931 (t) cc_final: 0.8715 (m) REVERT: l 177 MET cc_start: 0.8582 (tpt) cc_final: 0.8184 (tpt) REVERT: m 67 MET cc_start: 0.7903 (mtp) cc_final: 0.7617 (mtt) REVERT: m 145 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8073 (tttp) REVERT: m 169 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8178 (mp) REVERT: n 177 MET cc_start: 0.8634 (tpp) cc_final: 0.8398 (tpt) REVERT: o 79 LYS cc_start: 0.7929 (ttpp) cc_final: 0.7372 (mttt) REVERT: o 85 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7477 (t0) REVERT: p 79 LYS cc_start: 0.7370 (ttpp) cc_final: 0.6922 (mttt) REVERT: s 85 ASP cc_start: 0.6796 (m-30) cc_final: 0.6569 (m-30) REVERT: t 38 LYS cc_start: 0.7971 (tttp) cc_final: 0.7368 (ttmt) REVERT: u 172 SER cc_start: 0.8778 (t) cc_final: 0.8331 (m) REVERT: v 172 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8505 (m) REVERT: v 176 ASP cc_start: 0.8437 (m-30) cc_final: 0.8197 (m-30) REVERT: v 177 MET cc_start: 0.8745 (tpt) cc_final: 0.8279 (tpt) REVERT: w 145 LYS cc_start: 0.8368 (ttpp) cc_final: 0.7969 (mmtm) outliers start: 199 outliers final: 82 residues processed: 1050 average time/residue: 0.5541 time to fit residues: 1030.9003 Evaluate side-chains 923 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 831 time to evaluate : 5.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 68 ASN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain L residue 27 MET Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain L residue 184 THR Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain P residue 68 ASN Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain V residue 181 GLN Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 184 THR Chi-restraints excluded: chain X residue 117 ASP Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 126 ILE Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain b residue 108 ILE Chi-restraints excluded: chain c residue 88 ILE Chi-restraints excluded: chain c residue 142 ILE Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 181 GLN Chi-restraints excluded: chain f residue 117 ASP Chi-restraints excluded: chain f residue 184 THR Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain h residue 48 MET Chi-restraints excluded: chain h residue 68 ASN Chi-restraints excluded: chain h residue 88 ILE Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain i residue 88 ILE Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain k residue 68 ASN Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 169 LEU Chi-restraints excluded: chain m residue 172 SER Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 184 THR Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain o residue 185 ILE Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain p residue 90 ASP Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 126 ILE Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain s residue 88 ILE Chi-restraints excluded: chain s residue 172 SER Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain v residue 172 SER Chi-restraints excluded: chain w residue 83 LEU Chi-restraints excluded: chain w residue 142 ILE Chi-restraints excluded: chain w residue 179 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 764 optimal weight: 7.9990 chunk 581 optimal weight: 2.9990 chunk 401 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 369 optimal weight: 6.9990 chunk 519 optimal weight: 0.0170 chunk 776 optimal weight: 0.0970 chunk 821 optimal weight: 5.9990 chunk 405 optimal weight: 0.6980 chunk 735 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 68 ASN ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN D 68 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN ** H 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 GLN I 68 ASN J 54 GLN J 56 GLN K 168 ASN L 68 ASN ** L 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN ** M 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 GLN N 161 GLN O 56 GLN ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 GLN P 68 ASN P 78 GLN ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 GLN ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 56 GLN T 155 ASN U 56 GLN ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 68 ASN ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 127 ASN ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 ASN Y 56 GLN ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 154 ASN Z 68 ASN ** Z 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 56 GLN ** a 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 154 ASN ** b 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 56 GLN f 181 GLN g 56 GLN ** g 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 ASN ** h 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 161 GLN i 56 GLN i 68 ASN ** i 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 GLN ** j 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 ASN ** k 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 56 GLN n 56 GLN o 68 ASN p 68 ASN q 154 ASN r 56 GLN r 68 ASN ** r 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 56 GLN s 68 ASN ** s 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 56 GLN ** t 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 56 GLN ** u 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 56 GLN v 82 ASN ** v 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 56 GLN ** w 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 66050 Z= 0.135 Angle : 0.498 6.747 89150 Z= 0.266 Chirality : 0.037 0.196 10700 Planarity : 0.003 0.045 11650 Dihedral : 5.111 23.148 9050 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.55 % Allowed : 10.63 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: 0.28 (0.09), residues: 8600 helix: 1.39 (0.07), residues: 5950 sheet: None (None), residues: 0 loop : -2.74 (0.09), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE A 64 TYR 0.012 0.001 TYR D 22 ARG 0.003 0.000 ARG n 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 946 time to evaluate : 5.243 Fit side-chains REVERT: A 169 LEU cc_start: 0.9233 (mt) cc_final: 0.8954 (mt) REVERT: B 34 ASP cc_start: 0.7270 (m-30) cc_final: 0.6735 (m-30) REVERT: B 38 LYS cc_start: 0.8058 (tttp) cc_final: 0.7677 (tttm) REVERT: B 85 ASP cc_start: 0.7363 (m-30) cc_final: 0.6871 (t0) REVERT: C 172 SER cc_start: 0.8696 (t) cc_final: 0.8436 (m) REVERT: C 177 MET cc_start: 0.8457 (mmm) cc_final: 0.8034 (mmt) REVERT: F 79 LYS cc_start: 0.7697 (ttpp) cc_final: 0.6983 (mttp) REVERT: F 169 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8111 (mp) REVERT: G 31 ASP cc_start: 0.7868 (m-30) cc_final: 0.7575 (m-30) REVERT: G 38 LYS cc_start: 0.8349 (tttp) cc_final: 0.7616 (ttmt) REVERT: G 79 LYS cc_start: 0.7220 (ttpp) cc_final: 0.7016 (mttt) REVERT: H 20 MET cc_start: 0.6881 (ptm) cc_final: 0.6207 (ttp) REVERT: H 38 LYS cc_start: 0.8045 (tttp) cc_final: 0.7696 (ttpt) REVERT: J 31 ASP cc_start: 0.7891 (m-30) cc_final: 0.7658 (m-30) REVERT: J 172 SER cc_start: 0.8980 (t) cc_final: 0.8701 (m) REVERT: M 34 ASP cc_start: 0.7046 (m-30) cc_final: 0.6751 (m-30) REVERT: M 85 ASP cc_start: 0.7480 (m-30) cc_final: 0.6862 (t0) REVERT: N 135 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6269 (mp) REVERT: P 38 LYS cc_start: 0.7858 (tttp) cc_final: 0.7073 (ttmt) REVERT: P 67 MET cc_start: 0.7777 (mtp) cc_final: 0.7517 (mtt) REVERT: P 169 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8402 (mp) REVERT: Q 23 ASP cc_start: 0.7242 (p0) cc_final: 0.6865 (t70) REVERT: Q 30 ASP cc_start: 0.7509 (m-30) cc_final: 0.7252 (m-30) REVERT: Q 59 LEU cc_start: 0.8355 (mt) cc_final: 0.8087 (mp) REVERT: R 20 MET cc_start: 0.6602 (ptm) cc_final: 0.6372 (ttp) REVERT: R 82 ASN cc_start: 0.8240 (t0) cc_final: 0.7875 (t0) REVERT: R 145 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7680 (pttp) REVERT: R 177 MET cc_start: 0.8798 (tpp) cc_final: 0.8357 (tpt) REVERT: S 58 ASP cc_start: 0.7754 (m-30) cc_final: 0.7449 (m-30) REVERT: U 20 MET cc_start: 0.6383 (ptm) cc_final: 0.5610 (mtm) REVERT: U 27 MET cc_start: 0.6993 (mpp) cc_final: 0.6297 (mtp) REVERT: U 145 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8345 (mtpp) REVERT: V 20 MET cc_start: 0.6631 (ptm) cc_final: 0.6304 (ptm) REVERT: V 38 LYS cc_start: 0.7979 (tttp) cc_final: 0.7209 (mttt) REVERT: V 79 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7912 (ttmt) REVERT: V 85 ASP cc_start: 0.7566 (m-30) cc_final: 0.7098 (t0) REVERT: V 90 ASP cc_start: 0.6354 (m-30) cc_final: 0.6151 (m-30) REVERT: W 34 ASP cc_start: 0.7085 (m-30) cc_final: 0.6395 (m-30) REVERT: W 67 MET cc_start: 0.7538 (mtp) cc_final: 0.7327 (mtt) REVERT: W 79 LYS cc_start: 0.7702 (ttpp) cc_final: 0.7383 (mttt) REVERT: Y 38 LYS cc_start: 0.8126 (tttp) cc_final: 0.7890 (tttt) REVERT: Y 163 MET cc_start: 0.7502 (mtt) cc_final: 0.7170 (mtt) REVERT: a 79 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7071 (mttp) REVERT: c 176 ASP cc_start: 0.8196 (m-30) cc_final: 0.7988 (m-30) REVERT: d 67 MET cc_start: 0.7875 (mtp) cc_final: 0.7569 (mtt) REVERT: e 79 LYS cc_start: 0.7909 (ttpp) cc_final: 0.7281 (mttt) REVERT: f 79 LYS cc_start: 0.7890 (ttpp) cc_final: 0.7437 (mttt) REVERT: f 85 ASP cc_start: 0.7536 (t70) cc_final: 0.7301 (t0) REVERT: g 47 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7884 (tp) REVERT: h 79 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7203 (ttmm) REVERT: h 108 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6712 (pt) REVERT: i 23 ASP cc_start: 0.7714 (p0) cc_final: 0.7419 (p0) REVERT: i 31 ASP cc_start: 0.8726 (m-30) cc_final: 0.8503 (m-30) REVERT: j 34 ASP cc_start: 0.6699 (m-30) cc_final: 0.6482 (m-30) REVERT: k 172 SER cc_start: 0.8676 (t) cc_final: 0.8461 (m) REVERT: l 30 ASP cc_start: 0.7880 (m-30) cc_final: 0.7638 (m-30) REVERT: m 67 MET cc_start: 0.7506 (mtp) cc_final: 0.7293 (mtt) REVERT: m 145 LYS cc_start: 0.8435 (ttpp) cc_final: 0.7939 (tttp) REVERT: n 19 SER cc_start: 0.6113 (m) cc_final: 0.5897 (t) REVERT: n 80 MET cc_start: 0.6784 (mmp) cc_final: 0.6532 (mmt) REVERT: o 30 ASP cc_start: 0.6800 (m-30) cc_final: 0.6593 (t0) REVERT: o 79 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7404 (mttt) REVERT: o 85 ASP cc_start: 0.7683 (m-30) cc_final: 0.7479 (t0) REVERT: p 79 LYS cc_start: 0.7459 (ttpp) cc_final: 0.6923 (mttt) REVERT: r 30 ASP cc_start: 0.7482 (m-30) cc_final: 0.7250 (m-30) REVERT: r 68 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7158 (t0) REVERT: s 30 ASP cc_start: 0.7289 (m-30) cc_final: 0.7071 (t0) REVERT: s 85 ASP cc_start: 0.6996 (m-30) cc_final: 0.6631 (m-30) REVERT: t 38 LYS cc_start: 0.7973 (tttp) cc_final: 0.7343 (ttmt) REVERT: u 172 SER cc_start: 0.8707 (t) cc_final: 0.8292 (m) REVERT: v 172 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8330 (m) REVERT: v 176 ASP cc_start: 0.8397 (m-30) cc_final: 0.8145 (m-30) REVERT: v 177 MET cc_start: 0.8719 (tpt) cc_final: 0.8114 (tpt) REVERT: w 176 ASP cc_start: 0.8162 (m-30) cc_final: 0.7923 (m-30) outliers start: 186 outliers final: 62 residues processed: 1073 average time/residue: 0.5562 time to fit residues: 1060.9282 Evaluate side-chains 917 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 847 time to evaluate : 5.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain R residue 145 LYS Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Z residue 38 LYS Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain b residue 68 ASN Chi-restraints excluded: chain c residue 88 ILE Chi-restraints excluded: chain c residue 142 ILE Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain h residue 48 MET Chi-restraints excluded: chain h residue 68 ASN Chi-restraints excluded: chain h residue 88 ILE Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain p residue 90 ASP Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain r residue 68 ASN Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 88 ILE Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain v residue 142 ILE Chi-restraints excluded: chain v residue 172 SER Chi-restraints excluded: chain w residue 179 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 684 optimal weight: 2.9990 chunk 466 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 611 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 701 optimal weight: 8.9990 chunk 567 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 419 optimal weight: 20.0000 chunk 737 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 154 ASN A 161 GLN B 154 ASN C 68 ASN C 154 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 154 ASN H 154 ASN K 68 ASN K 161 GLN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN M 68 ASN ** M 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 ASN O 154 ASN ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 ASN Q 154 ASN ** Q 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 ASN ** R 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 GLN S 68 ASN ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 154 ASN V 161 GLN ** V 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 154 ASN X 68 ASN ** X 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 ASN ** a 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 ASN a 154 ASN ** a 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 162 GLN d 127 ASN e 68 ASN e 154 ASN e 161 GLN f 68 ASN f 161 GLN g 68 ASN ** g 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 154 ASN ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 154 ASN ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 68 ASN j 154 ASN k 154 ASN ** k 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 68 ASN ** l 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 162 GLN ** o 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 68 ASN q 68 ASN q 136 GLN r 68 ASN ** r 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 154 ASN t 68 ASN t 154 ASN ** t 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 154 ASN ** u 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 68 ASN v 154 ASN w 127 ASN x 54 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 66050 Z= 0.404 Angle : 0.700 9.293 89150 Z= 0.359 Chirality : 0.045 0.237 10700 Planarity : 0.004 0.048 11650 Dihedral : 5.739 27.012 9050 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.44 % Allowed : 12.58 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: -0.34 (0.09), residues: 8600 helix: 0.81 (0.07), residues: 6100 sheet: None (None), residues: 0 loop : -2.89 (0.10), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE u 49 TYR 0.023 0.002 TYR s 22 ARG 0.006 0.001 ARG a 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 832 time to evaluate : 5.878 Fit side-chains REVERT: A 188 ILE cc_start: 0.3081 (OUTLIER) cc_final: 0.2773 (mt) REVERT: B 34 ASP cc_start: 0.7188 (m-30) cc_final: 0.6889 (m-30) REVERT: B 38 LYS cc_start: 0.7981 (tttp) cc_final: 0.7573 (tttm) REVERT: B 85 ASP cc_start: 0.7594 (m-30) cc_final: 0.6975 (t0) REVERT: E 177 MET cc_start: 0.8235 (tpt) cc_final: 0.7901 (tpt) REVERT: F 79 LYS cc_start: 0.7795 (ttpp) cc_final: 0.6994 (mttp) REVERT: F 169 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8132 (mp) REVERT: F 177 MET cc_start: 0.8618 (tpt) cc_final: 0.8309 (tpt) REVERT: G 23 ASP cc_start: 0.7239 (p0) cc_final: 0.6861 (t0) REVERT: G 38 LYS cc_start: 0.8363 (tttp) cc_final: 0.7796 (ttmt) REVERT: G 79 LYS cc_start: 0.7321 (ttpp) cc_final: 0.6972 (mttt) REVERT: G 145 LYS cc_start: 0.8462 (tttp) cc_final: 0.8141 (ttmm) REVERT: H 20 MET cc_start: 0.7197 (ptm) cc_final: 0.6238 (ttp) REVERT: H 38 LYS cc_start: 0.8013 (tttp) cc_final: 0.7580 (ttpt) REVERT: J 31 ASP cc_start: 0.7979 (m-30) cc_final: 0.7732 (m-30) REVERT: M 34 ASP cc_start: 0.7110 (m-30) cc_final: 0.6874 (m-30) REVERT: M 85 ASP cc_start: 0.7931 (m-30) cc_final: 0.7292 (t0) REVERT: N 135 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6350 (mp) REVERT: P 38 LYS cc_start: 0.8017 (tttp) cc_final: 0.7237 (ttmt) REVERT: P 169 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8076 (mp) REVERT: Q 23 ASP cc_start: 0.7438 (p0) cc_final: 0.6920 (t0) REVERT: Q 169 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8391 (mp) REVERT: R 31 ASP cc_start: 0.7871 (t0) cc_final: 0.7602 (t0) REVERT: S 23 ASP cc_start: 0.7200 (p0) cc_final: 0.6910 (p0) REVERT: T 161 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: U 20 MET cc_start: 0.6807 (ptm) cc_final: 0.5350 (mtp) REVERT: V 38 LYS cc_start: 0.7856 (tttp) cc_final: 0.7072 (mttt) REVERT: V 79 LYS cc_start: 0.8232 (ttpp) cc_final: 0.7898 (ttmt) REVERT: V 85 ASP cc_start: 0.7712 (m-30) cc_final: 0.7209 (t0) REVERT: W 79 LYS cc_start: 0.7729 (ttpp) cc_final: 0.7312 (mttt) REVERT: W 134 ASP cc_start: 0.6720 (p0) cc_final: 0.6467 (p0) REVERT: Y 163 MET cc_start: 0.7810 (mtt) cc_final: 0.7432 (mtt) REVERT: a 79 LYS cc_start: 0.7749 (ttpp) cc_final: 0.7177 (mttt) REVERT: b 177 MET cc_start: 0.8622 (tpp) cc_final: 0.8407 (tpt) REVERT: c 169 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8293 (mp) REVERT: d 20 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6405 (ptt) REVERT: d 161 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: e 79 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7300 (mttt) REVERT: f 145 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7490 (ttmm) REVERT: g 47 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8181 (tp) REVERT: h 79 LYS cc_start: 0.7896 (ttpp) cc_final: 0.7300 (ttmm) REVERT: h 108 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6551 (pt) REVERT: h 145 LYS cc_start: 0.7941 (tttm) cc_final: 0.7433 (ttmm) REVERT: j 177 MET cc_start: 0.8593 (tpt) cc_final: 0.8369 (tpt) REVERT: k 31 ASP cc_start: 0.8122 (m-30) cc_final: 0.7737 (m-30) REVERT: k 68 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7468 (m110) REVERT: k 177 MET cc_start: 0.8342 (tpp) cc_final: 0.8049 (mmt) REVERT: l 30 ASP cc_start: 0.8199 (m-30) cc_final: 0.7992 (m-30) REVERT: m 145 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8148 (tttp) REVERT: m 169 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8427 (mp) REVERT: n 19 SER cc_start: 0.6272 (m) cc_final: 0.5816 (t) REVERT: n 177 MET cc_start: 0.8504 (tpp) cc_final: 0.8261 (tpt) REVERT: o 68 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7748 (m110) REVERT: o 79 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7368 (mttt) REVERT: o 85 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7542 (t0) REVERT: p 79 LYS cc_start: 0.7563 (ttpp) cc_final: 0.6857 (mttt) REVERT: q 59 LEU cc_start: 0.8691 (mt) cc_final: 0.8474 (mp) REVERT: r 30 ASP cc_start: 0.7913 (m-30) cc_final: 0.7633 (m-30) REVERT: r 68 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7601 (t0) REVERT: s 85 ASP cc_start: 0.7007 (m-30) cc_final: 0.6651 (m-30) REVERT: s 135 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6361 (mp) REVERT: v 23 ASP cc_start: 0.6751 (t0) cc_final: 0.6421 (p0) REVERT: v 145 LYS cc_start: 0.8445 (tttp) cc_final: 0.7984 (ttmm) REVERT: v 172 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8341 (p) REVERT: v 177 MET cc_start: 0.8698 (tpt) cc_final: 0.8222 (tpt) REVERT: w 34 ASP cc_start: 0.7063 (m-30) cc_final: 0.6647 (m-30) REVERT: w 145 LYS cc_start: 0.8464 (ttpp) cc_final: 0.8158 (mmtm) REVERT: w 161 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: x 177 MET cc_start: 0.8364 (tpt) cc_final: 0.8154 (tpt) outliers start: 251 outliers final: 115 residues processed: 1029 average time/residue: 0.5959 time to fit residues: 1084.9563 Evaluate side-chains 911 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 777 time to evaluate : 5.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 68 ASN Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 177 MET Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 161 GLN Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain U residue 172 SER Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain V residue 181 GLN Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 184 THR Chi-restraints excluded: chain X residue 68 ASN Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 188 ILE Chi-restraints excluded: chain Z residue 68 ASN Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain a residue 52 MET Chi-restraints excluded: chain a residue 68 ASN Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain c residue 88 ILE Chi-restraints excluded: chain c residue 142 ILE Chi-restraints excluded: chain c residue 169 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain c residue 188 ILE Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain d residue 161 GLN Chi-restraints excluded: chain d residue 169 LEU Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 181 GLN Chi-restraints excluded: chain e residue 184 THR Chi-restraints excluded: chain f residue 117 ASP Chi-restraints excluded: chain g residue 20 MET Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain g residue 126 ILE Chi-restraints excluded: chain h residue 48 MET Chi-restraints excluded: chain h residue 88 ILE Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain i residue 88 ILE Chi-restraints excluded: chain i residue 111 ILE Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain k residue 68 ASN Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 169 LEU Chi-restraints excluded: chain m residue 172 SER Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain n residue 184 THR Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 172 SER Chi-restraints excluded: chain o residue 175 SER Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain o residue 185 ILE Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain p residue 108 ILE Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 188 ILE Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain r residue 20 MET Chi-restraints excluded: chain r residue 68 ASN Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain s residue 135 LEU Chi-restraints excluded: chain s residue 172 SER Chi-restraints excluded: chain t residue 172 SER Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain v residue 20 MET Chi-restraints excluded: chain v residue 172 SER Chi-restraints excluded: chain w residue 83 LEU Chi-restraints excluded: chain w residue 152 THR Chi-restraints excluded: chain w residue 161 GLN Chi-restraints excluded: chain w residue 179 SER Chi-restraints excluded: chain w residue 188 ILE Chi-restraints excluded: chain x residue 19 SER Chi-restraints excluded: chain x residue 172 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 276 optimal weight: 3.9990 chunk 739 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 482 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 822 optimal weight: 5.9990 chunk 682 optimal weight: 5.9990 chunk 380 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 431 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN C 68 ASN C 136 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN K 68 ASN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN M 68 ASN N 68 ASN N 78 GLN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 ASN Q 78 GLN R 54 GLN ** R 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 54 GLN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 ASN U 161 GLN ** V 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 ASN ** X 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 54 GLN f 68 ASN ** g 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 154 ASN h 68 ASN ** h 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 78 GLN k 147 ASN ** l 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 68 ASN p 68 ASN ** r 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 162 GLN t 68 ASN ** u 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 66050 Z= 0.332 Angle : 0.633 9.030 89150 Z= 0.328 Chirality : 0.042 0.295 10700 Planarity : 0.004 0.052 11650 Dihedral : 5.604 25.948 9050 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.78 % Allowed : 13.90 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: -0.27 (0.09), residues: 8600 helix: 0.88 (0.07), residues: 6000 sheet: None (None), residues: 0 loop : -2.78 (0.10), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE Q 49 TYR 0.016 0.001 TYR Z 22 ARG 0.003 0.000 ARG n 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 782 time to evaluate : 5.272 Fit side-chains REVERT: A 177 MET cc_start: 0.8228 (tpt) cc_final: 0.7964 (tpt) REVERT: A 188 ILE cc_start: 0.3145 (OUTLIER) cc_final: 0.2812 (mt) REVERT: B 34 ASP cc_start: 0.7214 (m-30) cc_final: 0.6658 (m-30) REVERT: B 38 LYS cc_start: 0.7913 (tttp) cc_final: 0.7648 (tttm) REVERT: B 85 ASP cc_start: 0.7452 (m-30) cc_final: 0.6813 (t0) REVERT: C 90 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6852 (t0) REVERT: D 79 LYS cc_start: 0.7909 (ttpp) cc_final: 0.6729 (tptm) REVERT: E 135 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6288 (mp) REVERT: F 63 LYS cc_start: 0.8326 (tptp) cc_final: 0.8120 (tptt) REVERT: F 79 LYS cc_start: 0.7763 (ttpp) cc_final: 0.7073 (mttp) REVERT: F 169 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8153 (mp) REVERT: G 23 ASP cc_start: 0.7262 (p0) cc_final: 0.6838 (t0) REVERT: G 38 LYS cc_start: 0.8338 (tttp) cc_final: 0.7770 (ttmt) REVERT: G 79 LYS cc_start: 0.7383 (ttpp) cc_final: 0.7086 (mttt) REVERT: G 145 LYS cc_start: 0.8405 (tttp) cc_final: 0.8097 (ttmm) REVERT: H 20 MET cc_start: 0.7242 (ptm) cc_final: 0.6463 (ttp) REVERT: H 38 LYS cc_start: 0.7983 (tttp) cc_final: 0.7547 (ttpt) REVERT: H 67 MET cc_start: 0.8343 (mtp) cc_final: 0.8137 (mtp) REVERT: J 172 SER cc_start: 0.8971 (t) cc_final: 0.8709 (m) REVERT: M 34 ASP cc_start: 0.7164 (m-30) cc_final: 0.6934 (m-30) REVERT: M 85 ASP cc_start: 0.7718 (m-30) cc_final: 0.6990 (t0) REVERT: P 38 LYS cc_start: 0.8033 (tttp) cc_final: 0.7250 (ttmt) REVERT: P 169 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8164 (mp) REVERT: Q 23 ASP cc_start: 0.7447 (p0) cc_final: 0.6907 (t0) REVERT: Q 169 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8515 (mp) REVERT: S 23 ASP cc_start: 0.7075 (p0) cc_final: 0.6761 (p0) REVERT: S 31 ASP cc_start: 0.8069 (m-30) cc_final: 0.7642 (m-30) REVERT: T 147 ASN cc_start: 0.8836 (t0) cc_final: 0.8577 (t0) REVERT: U 20 MET cc_start: 0.6813 (ptm) cc_final: 0.5353 (mtp) REVERT: U 27 MET cc_start: 0.7344 (mpp) cc_final: 0.7132 (mpp) REVERT: V 38 LYS cc_start: 0.7751 (tttp) cc_final: 0.6958 (mttt) REVERT: V 79 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7894 (ttmt) REVERT: V 85 ASP cc_start: 0.7713 (m-30) cc_final: 0.7182 (t0) REVERT: V 135 LEU cc_start: 0.7683 (tp) cc_final: 0.7407 (mp) REVERT: W 79 LYS cc_start: 0.7754 (ttpp) cc_final: 0.7319 (mttt) REVERT: Y 163 MET cc_start: 0.7726 (mtt) cc_final: 0.7352 (mtt) REVERT: a 79 LYS cc_start: 0.7768 (ttpp) cc_final: 0.7082 (mttp) REVERT: b 139 LYS cc_start: 0.7637 (tmmt) cc_final: 0.7420 (tttp) REVERT: d 20 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6358 (ptt) REVERT: e 79 LYS cc_start: 0.8016 (ttpp) cc_final: 0.7298 (mttt) REVERT: f 38 LYS cc_start: 0.8672 (tttt) cc_final: 0.8457 (tttt) REVERT: f 79 LYS cc_start: 0.7748 (ttpp) cc_final: 0.7175 (mttt) REVERT: g 47 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8102 (tp) REVERT: h 79 LYS cc_start: 0.7899 (ttpp) cc_final: 0.7303 (ttmm) REVERT: h 108 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6677 (pt) REVERT: h 145 LYS cc_start: 0.7932 (tttm) cc_final: 0.7475 (ttmm) REVERT: j 177 MET cc_start: 0.8593 (tpt) cc_final: 0.8267 (tpt) REVERT: k 31 ASP cc_start: 0.8141 (m-30) cc_final: 0.7679 (m-30) REVERT: k 145 LYS cc_start: 0.8803 (tttm) cc_final: 0.8554 (tttm) REVERT: k 177 MET cc_start: 0.8421 (tpp) cc_final: 0.8052 (mmt) REVERT: l 30 ASP cc_start: 0.8173 (m-30) cc_final: 0.7913 (m-30) REVERT: m 145 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8115 (tttp) REVERT: n 19 SER cc_start: 0.6194 (m) cc_final: 0.5826 (t) REVERT: n 177 MET cc_start: 0.8492 (tpp) cc_final: 0.8269 (tpt) REVERT: o 79 LYS cc_start: 0.8061 (ttpp) cc_final: 0.7420 (mttt) REVERT: o 85 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7484 (t0) REVERT: p 79 LYS cc_start: 0.7489 (ttpp) cc_final: 0.6807 (mttt) REVERT: q 59 LEU cc_start: 0.8707 (mt) cc_final: 0.8463 (mp) REVERT: r 30 ASP cc_start: 0.7948 (m-30) cc_final: 0.7674 (m-30) REVERT: r 67 MET cc_start: 0.8320 (mtp) cc_final: 0.8073 (mtp) REVERT: s 85 ASP cc_start: 0.6659 (m-30) cc_final: 0.6444 (m-30) REVERT: s 135 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6351 (mp) REVERT: u 27 MET cc_start: 0.8683 (mtp) cc_final: 0.8471 (mtt) REVERT: v 145 LYS cc_start: 0.8432 (tttp) cc_final: 0.7740 (mtpp) REVERT: v 172 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8355 (p) REVERT: v 177 MET cc_start: 0.8793 (tpt) cc_final: 0.8326 (tpt) REVERT: w 145 LYS cc_start: 0.8269 (ttpp) cc_final: 0.8011 (mmtt) REVERT: x 161 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7951 (tt0) outliers start: 203 outliers final: 122 residues processed: 932 average time/residue: 0.5914 time to fit residues: 968.3092 Evaluate side-chains 892 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 757 time to evaluate : 5.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 169 LEU Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 111 ILE Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain U residue 172 SER Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 181 GLN Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 152 THR Chi-restraints excluded: chain W residue 184 THR Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 188 ILE Chi-restraints excluded: chain Z residue 27 MET Chi-restraints excluded: chain Z residue 38 LYS Chi-restraints excluded: chain Z residue 68 ASN Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain a residue 52 MET Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain c residue 88 ILE Chi-restraints excluded: chain c residue 142 ILE Chi-restraints excluded: chain c residue 149 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain d residue 169 LEU Chi-restraints excluded: chain e residue 68 ASN Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 181 GLN Chi-restraints excluded: chain f residue 68 ASN Chi-restraints excluded: chain f residue 184 THR Chi-restraints excluded: chain g residue 20 MET Chi-restraints excluded: chain g residue 47 LEU Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain h residue 48 MET Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain i residue 88 ILE Chi-restraints excluded: chain i residue 111 ILE Chi-restraints excluded: chain j residue 172 SER Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 142 ILE Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 88 ILE Chi-restraints excluded: chain m residue 172 SER Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain n residue 184 THR Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 175 SER Chi-restraints excluded: chain o residue 181 GLN Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain p residue 152 THR Chi-restraints excluded: chain p residue 184 THR Chi-restraints excluded: chain p residue 188 ILE Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 117 ASP Chi-restraints excluded: chain q residue 175 SER Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain s residue 135 LEU Chi-restraints excluded: chain s residue 172 SER Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain v residue 172 SER Chi-restraints excluded: chain w residue 83 LEU Chi-restraints excluded: chain w residue 135 LEU Chi-restraints excluded: chain w residue 179 SER Chi-restraints excluded: chain w residue 188 ILE Chi-restraints excluded: chain x residue 161 GLN Chi-restraints excluded: chain x residue 172 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 792 optimal weight: 6.9990 chunk 92 optimal weight: 0.0070 chunk 468 optimal weight: 0.0670 chunk 600 optimal weight: 2.9990 chunk 465 optimal weight: 0.9980 chunk 692 optimal weight: 10.0000 chunk 459 optimal weight: 9.9990 chunk 819 optimal weight: 1.9990 chunk 512 optimal weight: 6.9990 chunk 499 optimal weight: 9.9990 chunk 378 optimal weight: 2.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN C 68 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN H 161 GLN K 68 ASN L 68 ASN ** L 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN M 68 ASN P 54 GLN P 68 ASN Q 54 GLN R 127 ASN S 54 GLN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 68 ASN X 68 ASN ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 56 GLN ** Z 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 54 GLN b 78 GLN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 162 GLN f 68 ASN ** g 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 56 GLN h 68 ASN ** h 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 ASN j 68 ASN j 162 GLN ** k 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 68 ASN q 56 GLN q 136 GLN r 68 ASN ** r 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 127 ASN t 68 ASN u 54 GLN u 78 GLN ** w 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 66050 Z= 0.136 Angle : 0.502 8.198 89150 Z= 0.267 Chirality : 0.037 0.249 10700 Planarity : 0.003 0.052 11650 Dihedral : 4.930 23.550 9050 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.90 % Allowed : 14.93 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: 0.36 (0.09), residues: 8600 helix: 1.41 (0.07), residues: 5950 sheet: None (None), residues: 0 loop : -2.60 (0.10), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE L 49 TYR 0.013 0.001 TYR D 22 ARG 0.002 0.000 ARG d 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 835 time to evaluate : 5.339 Fit side-chains REVERT: A 35 LEU cc_start: 0.8357 (tp) cc_final: 0.8144 (tp) REVERT: A 175 SER cc_start: 0.8869 (t) cc_final: 0.8443 (p) REVERT: A 177 MET cc_start: 0.8224 (tpt) cc_final: 0.7923 (tpt) REVERT: A 188 ILE cc_start: 0.3155 (OUTLIER) cc_final: 0.2831 (mp) REVERT: B 34 ASP cc_start: 0.7185 (m-30) cc_final: 0.6725 (m-30) REVERT: B 85 ASP cc_start: 0.7343 (m-30) cc_final: 0.6811 (t0) REVERT: C 169 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8465 (mt) REVERT: C 177 MET cc_start: 0.8474 (mmm) cc_final: 0.8102 (mmp) REVERT: C 185 ILE cc_start: 0.9048 (mm) cc_final: 0.8690 (mm) REVERT: D 79 LYS cc_start: 0.7890 (ttpp) cc_final: 0.6701 (tptm) REVERT: D 177 MET cc_start: 0.8824 (tpp) cc_final: 0.7891 (mmt) REVERT: E 87 LYS cc_start: 0.6310 (tptt) cc_final: 0.6107 (tptt) REVERT: E 135 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6366 (mp) REVERT: F 79 LYS cc_start: 0.7812 (ttpp) cc_final: 0.7038 (mttp) REVERT: G 30 ASP cc_start: 0.6910 (m-30) cc_final: 0.6617 (m-30) REVERT: G 38 LYS cc_start: 0.8412 (tttp) cc_final: 0.7726 (ttmt) REVERT: G 79 LYS cc_start: 0.7271 (ttpp) cc_final: 0.7026 (mttt) REVERT: H 38 LYS cc_start: 0.8033 (tttp) cc_final: 0.7649 (ttpt) REVERT: J 172 SER cc_start: 0.9019 (t) cc_final: 0.8696 (m) REVERT: M 34 ASP cc_start: 0.6994 (m-30) cc_final: 0.6740 (m-30) REVERT: M 85 ASP cc_start: 0.7641 (m-30) cc_final: 0.6868 (t0) REVERT: O 163 MET cc_start: 0.7552 (mtt) cc_final: 0.7265 (mtt) REVERT: P 38 LYS cc_start: 0.7705 (tttp) cc_final: 0.7082 (ttmt) REVERT: P 67 MET cc_start: 0.7892 (mtp) cc_final: 0.7655 (mtt) REVERT: P 169 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8189 (mp) REVERT: Q 23 ASP cc_start: 0.7446 (p0) cc_final: 0.6944 (t0) REVERT: T 38 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7583 (tptt) REVERT: U 20 MET cc_start: 0.6801 (ptm) cc_final: 0.5774 (mtp) REVERT: U 145 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8390 (mtpp) REVERT: V 38 LYS cc_start: 0.7827 (tttp) cc_final: 0.6988 (mttt) REVERT: V 79 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7923 (ttmt) REVERT: V 85 ASP cc_start: 0.7711 (m-30) cc_final: 0.7131 (t0) REVERT: V 177 MET cc_start: 0.8929 (mmm) cc_final: 0.8709 (mmt) REVERT: W 67 MET cc_start: 0.7569 (mtp) cc_final: 0.7356 (mtt) REVERT: W 79 LYS cc_start: 0.7735 (ttpp) cc_final: 0.7397 (mttt) REVERT: Y 163 MET cc_start: 0.7545 (mtt) cc_final: 0.7304 (mtt) REVERT: Z 20 MET cc_start: 0.7196 (ptm) cc_final: 0.6002 (ttm) REVERT: Z 38 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7630 (tmtt) REVERT: a 79 LYS cc_start: 0.7738 (ttpp) cc_final: 0.7077 (mttp) REVERT: d 20 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6224 (ptt) REVERT: e 79 LYS cc_start: 0.7950 (ttpp) cc_final: 0.7228 (mttt) REVERT: e 126 ILE cc_start: 0.5240 (OUTLIER) cc_final: 0.4822 (mt) REVERT: f 79 LYS cc_start: 0.7746 (ttpp) cc_final: 0.7277 (mttt) REVERT: f 85 ASP cc_start: 0.7528 (t70) cc_final: 0.7318 (t0) REVERT: h 79 LYS cc_start: 0.7880 (ttpp) cc_final: 0.7305 (ttmm) REVERT: i 20 MET cc_start: 0.6808 (ptp) cc_final: 0.6351 (mtp) REVERT: i 177 MET cc_start: 0.8598 (tpt) cc_final: 0.7996 (tpt) REVERT: k 31 ASP cc_start: 0.8145 (m-30) cc_final: 0.7650 (m-30) REVERT: k 79 LYS cc_start: 0.7603 (ttpp) cc_final: 0.7013 (mttt) REVERT: k 177 MET cc_start: 0.8474 (tpp) cc_final: 0.8182 (mmt) REVERT: l 30 ASP cc_start: 0.7878 (m-30) cc_final: 0.7619 (m-30) REVERT: n 19 SER cc_start: 0.6222 (m) cc_final: 0.5847 (t) REVERT: n 80 MET cc_start: 0.6983 (mmp) cc_final: 0.6725 (mmt) REVERT: n 177 MET cc_start: 0.8500 (tpp) cc_final: 0.8168 (tpt) REVERT: o 35 LEU cc_start: 0.8208 (tp) cc_final: 0.7970 (tp) REVERT: o 79 LYS cc_start: 0.7970 (ttpp) cc_final: 0.7396 (mttt) REVERT: o 85 ASP cc_start: 0.7633 (m-30) cc_final: 0.7398 (t0) REVERT: p 67 MET cc_start: 0.7235 (ptp) cc_final: 0.6961 (ptm) REVERT: p 79 LYS cc_start: 0.7501 (ttpp) cc_final: 0.6860 (mttt) REVERT: q 177 MET cc_start: 0.8795 (tpt) cc_final: 0.8576 (tpp) REVERT: r 30 ASP cc_start: 0.7466 (m-30) cc_final: 0.7249 (m-30) REVERT: r 169 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8542 (mt) REVERT: s 30 ASP cc_start: 0.7271 (m-30) cc_final: 0.6975 (t0) REVERT: t 48 MET cc_start: 0.8101 (tmm) cc_final: 0.7776 (ttp) REVERT: u 115 ARG cc_start: 0.6713 (ptt180) cc_final: 0.6406 (ptt90) REVERT: u 172 SER cc_start: 0.8746 (t) cc_final: 0.8355 (m) REVERT: v 177 MET cc_start: 0.8711 (tpt) cc_final: 0.8155 (tpt) REVERT: x 177 MET cc_start: 0.8512 (tpt) cc_final: 0.8205 (tpt) outliers start: 139 outliers final: 73 residues processed: 936 average time/residue: 0.5808 time to fit residues: 959.8003 Evaluate side-chains 884 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 803 time to evaluate : 5.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 181 GLN Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain U residue 48 MET Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 38 LYS Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain b residue 184 THR Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 126 ILE Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain h residue 48 MET Chi-restraints excluded: chain h residue 68 ASN Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain j residue 68 ASN Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 126 ILE Chi-restraints excluded: chain q residue 175 SER Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 169 LEU Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain w residue 135 LEU Chi-restraints excluded: chain x residue 172 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 506 optimal weight: 10.0000 chunk 327 optimal weight: 2.9990 chunk 489 optimal weight: 0.0070 chunk 246 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 520 optimal weight: 20.0000 chunk 558 optimal weight: 4.9990 chunk 405 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 643 optimal weight: 3.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN C 68 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 GLN J 43 GLN J 54 GLN K 68 ASN L 68 ASN M 68 ASN ** M 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 GLN P 162 GLN Q 54 GLN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 GLN V 68 ASN X 68 ASN X 162 GLN ** Z 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 ASN b 68 ASN f 68 ASN f 181 GLN ** g 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 ASN ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 68 ASN p 78 GLN ** r 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 68 ASN u 54 GLN ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 66050 Z= 0.229 Angle : 0.560 8.481 89150 Z= 0.292 Chirality : 0.040 0.264 10700 Planarity : 0.003 0.052 11650 Dihedral : 5.087 24.480 9050 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.99 % Allowed : 15.21 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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 (0.09), residues: 8600 helix: 1.38 (0.07), residues: 6000 sheet: None (None), residues: 0 loop : -2.65 (0.10), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE Q 49 TYR 0.015 0.001 TYR w 110 ARG 0.002 0.000 ARG K 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 787 time to evaluate : 5.231 Fit side-chains REVERT: A 175 SER cc_start: 0.8976 (t) cc_final: 0.8506 (p) REVERT: A 177 MET cc_start: 0.8233 (tpt) cc_final: 0.7945 (tpt) REVERT: A 188 ILE cc_start: 0.3171 (OUTLIER) cc_final: 0.2858 (mp) REVERT: B 34 ASP cc_start: 0.7193 (m-30) cc_final: 0.6694 (m-30) REVERT: B 85 ASP cc_start: 0.7448 (m-30) cc_final: 0.6834 (t0) REVERT: C 177 MET cc_start: 0.8481 (mmm) cc_final: 0.8043 (mmt) REVERT: D 79 LYS cc_start: 0.7874 (ttpp) cc_final: 0.6684 (tptm) REVERT: E 135 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6198 (mp) REVERT: F 79 LYS cc_start: 0.7813 (ttpp) cc_final: 0.7001 (mttp) REVERT: G 20 MET cc_start: 0.6271 (ptm) cc_final: 0.5715 (ttp) REVERT: G 30 ASP cc_start: 0.7030 (m-30) cc_final: 0.6669 (m-30) REVERT: G 38 LYS cc_start: 0.8387 (tttp) cc_final: 0.7768 (ttmt) REVERT: G 79 LYS cc_start: 0.7287 (ttpp) cc_final: 0.6977 (mttt) REVERT: H 38 LYS cc_start: 0.8106 (tttp) cc_final: 0.7731 (ttpt) REVERT: J 172 SER cc_start: 0.9006 (t) cc_final: 0.8687 (m) REVERT: M 34 ASP cc_start: 0.7088 (m-30) cc_final: 0.6831 (m-30) REVERT: M 85 ASP cc_start: 0.7796 (m-30) cc_final: 0.7061 (t0) REVERT: O 48 MET cc_start: 0.8090 (tmm) cc_final: 0.7873 (tmm) REVERT: O 163 MET cc_start: 0.7650 (mtt) cc_final: 0.7373 (mtt) REVERT: P 38 LYS cc_start: 0.7996 (tttp) cc_final: 0.7235 (ttmt) REVERT: P 103 LEU cc_start: 0.8013 (mt) cc_final: 0.7744 (mt) REVERT: P 169 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8193 (mp) REVERT: Q 23 ASP cc_start: 0.7515 (p0) cc_final: 0.6966 (t0) REVERT: U 20 MET cc_start: 0.6883 (ptm) cc_final: 0.5807 (mtp) REVERT: V 20 MET cc_start: 0.6867 (ptm) cc_final: 0.6483 (ptm) REVERT: V 38 LYS cc_start: 0.7838 (tttp) cc_final: 0.7013 (mttt) REVERT: V 79 LYS cc_start: 0.8264 (ttpp) cc_final: 0.7934 (ttmt) REVERT: V 85 ASP cc_start: 0.7773 (m-30) cc_final: 0.7189 (t0) REVERT: V 177 MET cc_start: 0.8914 (mmm) cc_final: 0.8657 (mmt) REVERT: W 34 ASP cc_start: 0.7750 (t0) cc_final: 0.6990 (m-30) REVERT: W 79 LYS cc_start: 0.7803 (ttpp) cc_final: 0.7369 (mttt) REVERT: Y 163 MET cc_start: 0.7677 (mtt) cc_final: 0.7336 (mtt) REVERT: Z 20 MET cc_start: 0.7350 (ptm) cc_final: 0.6133 (ttm) REVERT: a 79 LYS cc_start: 0.7743 (ttpp) cc_final: 0.7138 (mttp) REVERT: a 80 MET cc_start: 0.7654 (mmt) cc_final: 0.7200 (mmt) REVERT: b 135 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6123 (mp) REVERT: d 20 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6280 (ptt) REVERT: e 79 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7287 (mttt) REVERT: e 126 ILE cc_start: 0.5368 (OUTLIER) cc_final: 0.4836 (mt) REVERT: f 79 LYS cc_start: 0.7747 (ttpp) cc_final: 0.7186 (mttt) REVERT: f 188 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8023 (mp) REVERT: g 67 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7876 (mtp) REVERT: h 145 LYS cc_start: 0.7845 (tttm) cc_final: 0.7311 (ttmm) REVERT: h 177 MET cc_start: 0.8834 (tpp) cc_final: 0.8368 (mmt) REVERT: j 177 MET cc_start: 0.8584 (tpt) cc_final: 0.8262 (tpt) REVERT: k 31 ASP cc_start: 0.8132 (m-30) cc_final: 0.7788 (m-30) REVERT: k 145 LYS cc_start: 0.8747 (tttm) cc_final: 0.8530 (tttm) REVERT: k 177 MET cc_start: 0.8445 (tpp) cc_final: 0.8086 (mmt) REVERT: l 30 ASP cc_start: 0.7916 (m-30) cc_final: 0.7677 (m-30) REVERT: m 67 MET cc_start: 0.8073 (mtt) cc_final: 0.7808 (mtt) REVERT: n 19 SER cc_start: 0.6436 (m) cc_final: 0.5994 (t) REVERT: n 80 MET cc_start: 0.7143 (mmp) cc_final: 0.6799 (mmt) REVERT: n 177 MET cc_start: 0.8497 (tpp) cc_final: 0.8154 (tpt) REVERT: o 35 LEU cc_start: 0.8213 (tp) cc_final: 0.7988 (tp) REVERT: o 79 LYS cc_start: 0.7993 (ttpp) cc_final: 0.7408 (mttt) REVERT: o 85 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7430 (t0) REVERT: p 79 LYS cc_start: 0.7527 (ttpp) cc_final: 0.6865 (mttt) REVERT: r 30 ASP cc_start: 0.7587 (m-30) cc_final: 0.7333 (m-30) REVERT: s 20 MET cc_start: 0.6163 (ptm) cc_final: 0.5753 (ttp) REVERT: s 22 TYR cc_start: 0.8214 (m-80) cc_final: 0.7951 (m-80) REVERT: u 115 ARG cc_start: 0.6700 (ptt180) cc_final: 0.6364 (ptt90) REVERT: u 145 LYS cc_start: 0.8508 (tttm) cc_final: 0.8134 (mtpp) REVERT: u 172 SER cc_start: 0.8899 (t) cc_final: 0.8483 (m) REVERT: v 177 MET cc_start: 0.8764 (tpt) cc_final: 0.8210 (tpt) REVERT: w 108 ILE cc_start: 0.6652 (tp) cc_final: 0.6061 (pt) REVERT: w 145 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7943 (mmtt) outliers start: 145 outliers final: 101 residues processed: 904 average time/residue: 0.5717 time to fit residues: 907.1413 Evaluate side-chains 883 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 773 time to evaluate : 5.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 181 GLN Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain X residue 143 SER Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 68 ASN Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain a residue 184 THR Chi-restraints excluded: chain b residue 68 ASN Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain d residue 169 LEU Chi-restraints excluded: chain e residue 30 ASP Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 126 ILE Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain e residue 181 GLN Chi-restraints excluded: chain f residue 68 ASN Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain h residue 48 MET Chi-restraints excluded: chain h residue 68 ASN Chi-restraints excluded: chain h residue 88 ILE Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 80 MET Chi-restraints excluded: chain o residue 85 ASP Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 175 SER Chi-restraints excluded: chain o residue 184 THR Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain p residue 188 ILE Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 126 ILE Chi-restraints excluded: chain q residue 175 SER Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain t residue 184 THR Chi-restraints excluded: chain u residue 169 LEU Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain w residue 83 LEU Chi-restraints excluded: chain w residue 135 LEU Chi-restraints excluded: chain x residue 172 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 745 optimal weight: 0.5980 chunk 784 optimal weight: 0.7980 chunk 716 optimal weight: 4.9990 chunk 763 optimal weight: 0.8980 chunk 459 optimal weight: 10.0000 chunk 332 optimal weight: 2.9990 chunk 599 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 689 optimal weight: 0.9990 chunk 722 optimal weight: 9.9990 chunk 760 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 68 ASN B 127 ASN C 68 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN K 56 GLN K 68 ASN L 56 GLN L 68 ASN ** L 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN ** M 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 127 ASN T 54 GLN ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 78 GLN ** b 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 ASN f 181 GLN ** g 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 ASN i 68 ASN j 68 ASN ** k 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 127 ASN o 54 GLN o 68 ASN p 56 GLN r 78 GLN t 68 ASN u 54 GLN ** v 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 66050 Z= 0.122 Angle : 0.491 10.420 89150 Z= 0.261 Chirality : 0.037 0.263 10700 Planarity : 0.003 0.050 11650 Dihedral : 4.656 25.281 9050 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.29 % Allowed : 15.90 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: 0.63 (0.09), residues: 8600 helix: 1.61 (0.07), residues: 6050 sheet: None (None), residues: 0 loop : -2.65 (0.10), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE A 64 TYR 0.012 0.001 TYR G 22 ARG 0.002 0.000 ARG v 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 811 time to evaluate : 5.223 Fit side-chains revert: symmetry clash REVERT: A 175 SER cc_start: 0.8846 (t) cc_final: 0.8409 (p) REVERT: A 177 MET cc_start: 0.8192 (tpt) cc_final: 0.7887 (tpt) REVERT: A 188 ILE cc_start: 0.3303 (OUTLIER) cc_final: 0.3004 (mp) REVERT: B 34 ASP cc_start: 0.7160 (m-30) cc_final: 0.6705 (m-30) REVERT: B 85 ASP cc_start: 0.7408 (m-30) cc_final: 0.6770 (t0) REVERT: C 48 MET cc_start: 0.7832 (tmm) cc_final: 0.7559 (ttp) REVERT: C 177 MET cc_start: 0.8467 (mmm) cc_final: 0.8136 (mmp) REVERT: C 185 ILE cc_start: 0.9045 (mm) cc_final: 0.8670 (mm) REVERT: D 79 LYS cc_start: 0.7871 (ttpp) cc_final: 0.6671 (tptm) REVERT: D 177 MET cc_start: 0.8837 (tpp) cc_final: 0.7930 (mmt) REVERT: E 135 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6399 (mp) REVERT: F 79 LYS cc_start: 0.7780 (ttpp) cc_final: 0.6994 (mttp) REVERT: G 20 MET cc_start: 0.6205 (ptm) cc_final: 0.5785 (ttp) REVERT: G 30 ASP cc_start: 0.6750 (m-30) cc_final: 0.6431 (m-30) REVERT: G 38 LYS cc_start: 0.8416 (tttp) cc_final: 0.7741 (ttmt) REVERT: G 79 LYS cc_start: 0.7250 (ttpp) cc_final: 0.6999 (mttt) REVERT: H 38 LYS cc_start: 0.7948 (tttp) cc_final: 0.7572 (ttpt) REVERT: I 20 MET cc_start: 0.6905 (ttm) cc_final: 0.6665 (ttp) REVERT: J 48 MET cc_start: 0.8070 (tmm) cc_final: 0.7747 (ttt) REVERT: M 34 ASP cc_start: 0.6974 (m-30) cc_final: 0.6724 (m-30) REVERT: M 85 ASP cc_start: 0.7743 (m-30) cc_final: 0.6879 (t0) REVERT: O 163 MET cc_start: 0.7552 (mtt) cc_final: 0.7325 (mtt) REVERT: P 38 LYS cc_start: 0.7698 (tttp) cc_final: 0.7086 (ttmt) REVERT: P 67 MET cc_start: 0.7939 (mtp) cc_final: 0.7607 (mtt) REVERT: P 103 LEU cc_start: 0.7970 (mt) cc_final: 0.7722 (mt) REVERT: P 169 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8119 (mt) REVERT: Q 23 ASP cc_start: 0.7511 (p0) cc_final: 0.7043 (t0) REVERT: T 38 LYS cc_start: 0.7928 (tttt) cc_final: 0.7580 (tptt) REVERT: T 181 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: U 145 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8353 (mtpp) REVERT: V 20 MET cc_start: 0.6647 (ptm) cc_final: 0.6096 (ptm) REVERT: V 38 LYS cc_start: 0.7868 (tttp) cc_final: 0.7040 (mttt) REVERT: V 79 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7893 (ttmt) REVERT: V 85 ASP cc_start: 0.7741 (m-30) cc_final: 0.7161 (t0) REVERT: W 34 ASP cc_start: 0.7658 (t0) cc_final: 0.7309 (m-30) REVERT: W 79 LYS cc_start: 0.7753 (ttpp) cc_final: 0.7387 (mttt) REVERT: W 115 ARG cc_start: 0.6911 (ptt180) cc_final: 0.6683 (ptt180) REVERT: Y 143 SER cc_start: 0.7814 (OUTLIER) cc_final: 0.7554 (m) REVERT: Y 163 MET cc_start: 0.7517 (mtt) cc_final: 0.7244 (mtt) REVERT: Z 20 MET cc_start: 0.7147 (ptm) cc_final: 0.6103 (ttm) REVERT: Z 38 LYS cc_start: 0.7930 (tttp) cc_final: 0.7600 (tmtt) REVERT: a 79 LYS cc_start: 0.7703 (ttpp) cc_final: 0.7147 (mttt) REVERT: b 135 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6060 (mp) REVERT: d 20 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6354 (ptt) REVERT: e 79 LYS cc_start: 0.7989 (ttpp) cc_final: 0.7286 (mttt) REVERT: f 79 LYS cc_start: 0.7699 (ttpp) cc_final: 0.7175 (mttt) REVERT: f 85 ASP cc_start: 0.7488 (t70) cc_final: 0.7271 (t0) REVERT: f 188 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7826 (mp) REVERT: g 67 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7766 (mtp) REVERT: h 79 LYS cc_start: 0.7859 (ttpp) cc_final: 0.7272 (ttmm) REVERT: k 177 MET cc_start: 0.8513 (tpp) cc_final: 0.8216 (mmt) REVERT: m 148 ASN cc_start: 0.9226 (p0) cc_final: 0.8954 (p0) REVERT: n 19 SER cc_start: 0.6392 (m) cc_final: 0.6019 (t) REVERT: n 80 MET cc_start: 0.7089 (mmp) cc_final: 0.6752 (mmt) REVERT: n 177 MET cc_start: 0.8483 (tpp) cc_final: 0.8189 (tpt) REVERT: o 79 LYS cc_start: 0.7949 (ttpp) cc_final: 0.7397 (mttt) REVERT: o 85 ASP cc_start: 0.7608 (m-30) cc_final: 0.7207 (t0) REVERT: p 67 MET cc_start: 0.7188 (ptp) cc_final: 0.6979 (ptm) REVERT: p 79 LYS cc_start: 0.7480 (ttpp) cc_final: 0.6808 (mttt) REVERT: r 135 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6173 (mp) REVERT: s 20 MET cc_start: 0.6315 (ptm) cc_final: 0.5851 (ttp) REVERT: s 30 ASP cc_start: 0.7251 (m-30) cc_final: 0.7025 (t0) REVERT: u 115 ARG cc_start: 0.6650 (ptt180) cc_final: 0.6322 (ptt90) REVERT: v 66 ASP cc_start: 0.7874 (m-30) cc_final: 0.7665 (m-30) REVERT: x 177 MET cc_start: 0.8423 (tpt) cc_final: 0.8181 (tpt) outliers start: 94 outliers final: 63 residues processed: 880 average time/residue: 0.5598 time to fit residues: 867.8456 Evaluate side-chains 849 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 776 time to evaluate : 7.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain M residue 68 ASN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 181 GLN Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain S residue 30 ASP Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 181 GLN Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain c residue 184 THR Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain e residue 30 ASP Chi-restraints excluded: chain e residue 48 MET Chi-restraints excluded: chain f residue 68 ASN Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain h residue 48 MET Chi-restraints excluded: chain h residue 68 ASN Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 126 ILE Chi-restraints excluded: chain q residue 175 SER Chi-restraints excluded: chain r residue 135 LEU Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain w residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 501 optimal weight: 10.0000 chunk 807 optimal weight: 2.9990 chunk 492 optimal weight: 6.9990 chunk 382 optimal weight: 7.9990 chunk 561 optimal weight: 9.9990 chunk 846 optimal weight: 10.0000 chunk 779 optimal weight: 0.9990 chunk 674 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 chunk 520 optimal weight: 0.8980 chunk 413 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN C 68 ASN C 78 GLN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** M 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 GLN P 155 ASN R 78 GLN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 ASN b 68 ASN e 127 ASN f 68 ASN ** g 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 ASN i 54 GLN i 68 ASN k 54 GLN ** k 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 68 ASN t 68 ASN u 54 GLN ** v 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 66050 Z= 0.217 Angle : 0.553 10.003 89150 Z= 0.288 Chirality : 0.040 0.282 10700 Planarity : 0.003 0.051 11650 Dihedral : 4.858 23.619 9050 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.40 % Allowed : 15.88 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: 0.63 (0.09), residues: 8600 helix: 1.61 (0.07), residues: 6000 sheet: None (None), residues: 0 loop : -2.56 (0.10), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE p 64 TYR 0.013 0.001 TYR G 22 ARG 0.003 0.000 ARG d 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17200 Ramachandran restraints generated. 8600 Oldfield, 0 Emsley, 8600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 755 time to evaluate : 5.208 Fit side-chains revert: symmetry clash REVERT: A 175 SER cc_start: 0.8971 (t) cc_final: 0.8482 (p) REVERT: A 177 MET cc_start: 0.8239 (tpt) cc_final: 0.7947 (tpt) REVERT: A 188 ILE cc_start: 0.3323 (OUTLIER) cc_final: 0.3016 (mp) REVERT: B 34 ASP cc_start: 0.7131 (m-30) cc_final: 0.6584 (m-30) REVERT: B 85 ASP cc_start: 0.7514 (m-30) cc_final: 0.6824 (t0) REVERT: C 48 MET cc_start: 0.7970 (tmm) cc_final: 0.7559 (ttp) REVERT: D 79 LYS cc_start: 0.7864 (ttpp) cc_final: 0.6680 (tptm) REVERT: E 135 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6215 (mp) REVERT: F 79 LYS cc_start: 0.7779 (ttpp) cc_final: 0.6967 (mttp) REVERT: G 20 MET cc_start: 0.6251 (ptm) cc_final: 0.5806 (ttp) REVERT: G 79 LYS cc_start: 0.7333 (ttpp) cc_final: 0.7090 (mttt) REVERT: H 38 LYS cc_start: 0.8078 (tttp) cc_final: 0.7725 (ttpt) REVERT: J 80 MET cc_start: 0.7072 (mmt) cc_final: 0.6754 (mmp) REVERT: M 34 ASP cc_start: 0.7075 (m-30) cc_final: 0.6820 (m-30) REVERT: M 85 ASP cc_start: 0.7848 (m-30) cc_final: 0.7091 (t0) REVERT: P 38 LYS cc_start: 0.7988 (tttp) cc_final: 0.7248 (ttmt) REVERT: P 103 LEU cc_start: 0.8009 (mt) cc_final: 0.7730 (mt) REVERT: P 169 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8063 (mp) REVERT: Q 23 ASP cc_start: 0.7462 (p0) cc_final: 0.6968 (t0) REVERT: T 38 LYS cc_start: 0.7973 (tttt) cc_final: 0.7638 (tptt) REVERT: T 181 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: U 20 MET cc_start: 0.6906 (ptm) cc_final: 0.5842 (mtp) REVERT: V 20 MET cc_start: 0.6758 (ptm) cc_final: 0.6290 (ptm) REVERT: V 38 LYS cc_start: 0.7824 (tttp) cc_final: 0.7002 (mttt) REVERT: V 79 LYS cc_start: 0.8250 (ttpp) cc_final: 0.7928 (ttmt) REVERT: V 85 ASP cc_start: 0.7796 (m-30) cc_final: 0.7217 (t0) REVERT: W 34 ASP cc_start: 0.7719 (t0) cc_final: 0.7304 (m-30) REVERT: W 79 LYS cc_start: 0.7797 (ttpp) cc_final: 0.7359 (mttt) REVERT: W 115 ARG cc_start: 0.7095 (ptt180) cc_final: 0.6867 (ptt180) REVERT: Y 163 MET cc_start: 0.7677 (mtt) cc_final: 0.7318 (mtt) REVERT: Z 20 MET cc_start: 0.7269 (ptm) cc_final: 0.6202 (ttm) REVERT: Z 38 LYS cc_start: 0.7965 (tttp) cc_final: 0.7684 (tmtt) REVERT: a 79 LYS cc_start: 0.7719 (ttpp) cc_final: 0.7074 (mttp) REVERT: a 80 MET cc_start: 0.7802 (mmt) cc_final: 0.7403 (mmt) REVERT: b 135 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6124 (mp) REVERT: b 177 MET cc_start: 0.8812 (tpp) cc_final: 0.8451 (tpt) REVERT: c 48 MET cc_start: 0.8046 (tmm) cc_final: 0.7475 (ttp) REVERT: d 20 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6243 (ptt) REVERT: e 79 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7343 (mttt) REVERT: f 79 LYS cc_start: 0.7738 (ttpp) cc_final: 0.7184 (mttt) REVERT: f 85 ASP cc_start: 0.7609 (t70) cc_final: 0.7349 (t0) REVERT: f 188 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7972 (mp) REVERT: g 67 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7814 (mtp) REVERT: j 177 MET cc_start: 0.8574 (tpt) cc_final: 0.8288 (tpt) REVERT: k 31 ASP cc_start: 0.8117 (m-30) cc_final: 0.7780 (m-30) REVERT: k 145 LYS cc_start: 0.8691 (tttm) cc_final: 0.8462 (tttm) REVERT: k 177 MET cc_start: 0.8484 (tpp) cc_final: 0.8068 (mmt) REVERT: n 19 SER cc_start: 0.6583 (m) cc_final: 0.6112 (t) REVERT: n 80 MET cc_start: 0.7041 (mmp) cc_final: 0.6654 (mmt) REVERT: n 177 MET cc_start: 0.8484 (tpp) cc_final: 0.8171 (tpt) REVERT: o 79 LYS cc_start: 0.7977 (ttpp) cc_final: 0.7402 (mttt) REVERT: o 85 ASP cc_start: 0.7761 (m-30) cc_final: 0.7387 (t0) REVERT: p 67 MET cc_start: 0.7519 (ptp) cc_final: 0.7215 (ptm) REVERT: p 79 LYS cc_start: 0.7464 (ttpp) cc_final: 0.6775 (mttt) REVERT: q 177 MET cc_start: 0.8767 (tpp) cc_final: 0.8516 (mmt) REVERT: r 30 ASP cc_start: 0.7506 (m-30) cc_final: 0.7190 (t0) REVERT: s 20 MET cc_start: 0.6429 (ptm) cc_final: 0.5949 (ttp) REVERT: s 30 ASP cc_start: 0.7295 (m-30) cc_final: 0.7006 (t0) REVERT: t 172 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8273 (m) REVERT: u 115 ARG cc_start: 0.6690 (ptt180) cc_final: 0.6340 (ptt90) REVERT: u 145 LYS cc_start: 0.8426 (tttm) cc_final: 0.8073 (mtpp) REVERT: w 34 ASP cc_start: 0.6968 (m-30) cc_final: 0.6527 (m-30) REVERT: w 108 ILE cc_start: 0.6659 (tp) cc_final: 0.6094 (pt) REVERT: x 177 MET cc_start: 0.8429 (tpt) cc_final: 0.8218 (tpt) outliers start: 102 outliers final: 82 residues processed: 836 average time/residue: 0.5744 time to fit residues: 842.5244 Evaluate side-chains 843 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 752 time to evaluate : 5.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain L residue 68 ASN Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain O residue 111 ILE Chi-restraints excluded: chain O residue 143 SER Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 109 SER Chi-restraints excluded: chain Q residue 172 SER Chi-restraints excluded: chain Q residue 181 GLN Chi-restraints excluded: chain Q residue 184 THR Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain T residue 175 SER Chi-restraints excluded: chain T residue 181 GLN Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain V residue 28 SER Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain b residue 68 ASN Chi-restraints excluded: chain b residue 135 LEU Chi-restraints excluded: chain d residue 20 MET Chi-restraints excluded: chain d residue 169 LEU Chi-restraints excluded: chain e residue 30 ASP Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain f residue 30 ASP Chi-restraints excluded: chain f residue 68 ASN Chi-restraints excluded: chain f residue 188 ILE Chi-restraints excluded: chain g residue 67 MET Chi-restraints excluded: chain g residue 88 ILE Chi-restraints excluded: chain g residue 117 ASP Chi-restraints excluded: chain h residue 48 MET Chi-restraints excluded: chain h residue 68 ASN Chi-restraints excluded: chain i residue 59 LEU Chi-restraints excluded: chain i residue 68 ASN Chi-restraints excluded: chain j residue 184 THR Chi-restraints excluded: chain k residue 179 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 184 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 179 SER Chi-restraints excluded: chain n residue 27 MET Chi-restraints excluded: chain n residue 172 SER Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 117 ASP Chi-restraints excluded: chain o residue 175 SER Chi-restraints excluded: chain p residue 88 ILE Chi-restraints excluded: chain q residue 52 MET Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 126 ILE Chi-restraints excluded: chain q residue 175 SER Chi-restraints excluded: chain r residue 169 LEU Chi-restraints excluded: chain s residue 80 MET Chi-restraints excluded: chain t residue 172 SER Chi-restraints excluded: chain t residue 179 SER Chi-restraints excluded: chain u residue 142 ILE Chi-restraints excluded: chain w residue 135 LEU Chi-restraints excluded: chain w residue 179 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 535 optimal weight: 5.9990 chunk 718 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 621 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 675 optimal weight: 6.9990 chunk 282 optimal weight: 20.0000 chunk 693 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN B 68 ASN C 68 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN I 155 ASN K 68 ASN ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** M 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 68 ASN f 68 ASN ** g 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 68 ASN ** i 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 82 ASN ** o 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.188801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148931 restraints weight = 62287.140| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.36 r_work: 0.3029 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 66050 Z= 0.254 Angle : 0.574 10.070 89150 Z= 0.298 Chirality : 0.040 0.273 10700 Planarity : 0.003 0.052 11650 Dihedral : 4.956 23.473 9050 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.70 % Allowed : 15.71 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.58 % 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: 0.48 (0.09), residues: 8600 helix: 1.47 (0.07), residues: 6000 sheet: None (None), residues: 0 loop : -2.56 (0.10), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE p 64 TYR 0.013 0.001 TYR G 22 ARG 0.003 0.000 ARG n 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16047.54 seconds wall clock time: 279 minutes 22.66 seconds (16762.66 seconds total)