Starting phenix.real_space_refine on Thu Dec 7 23:39:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9y_9020/12_2023/6e9y_9020.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9y_9020/12_2023/6e9y_9020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9y_9020/12_2023/6e9y_9020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9y_9020/12_2023/6e9y_9020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9y_9020/12_2023/6e9y_9020.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9y_9020/12_2023/6e9y_9020.pdb" } resolution = 4.3 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.025 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: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 16350 2.51 5 N 4800 2.21 5 O 5085 1.98 5 H 28155 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 54450 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "B" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "C" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "E" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "G" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "H" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "I" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "J" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "K" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "L" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "M" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "N" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain: "O" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3630 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 223} Time building chain proxies: 16.14, per 1000 atoms: 0.30 Number of scatterers: 54450 At special positions: 0 Unit cell: (122.85, 122.85, 174.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 O 5085 8.00 N 4800 7.00 C 16350 6.00 H 28155 1.00 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 - 3.50 Amino acid : False - 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: 32.76 Conformation dependent library (CDL) restraints added in 4.0 seconds 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6570 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 0 sheets defined 98.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 26 removed outlier: 3.725A pdb=" N LYS A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 113 removed outlier: 3.623A pdb=" N ALA A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU A 119 " --> pdb=" O PRO A 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 170 removed outlier: 3.791A pdb=" N ALA A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 216 removed outlier: 3.570A pdb=" N ARG A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.597A pdb=" N GLU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 removed outlier: 3.725A pdb=" N LYS B 13 " --> pdb=" O GLU B 9 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 113 removed outlier: 3.623A pdb=" N ALA B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 109 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU B 119 " --> pdb=" O PRO B 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 170 removed outlier: 3.790A pdb=" N ALA B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 161 " --> pdb=" O ARG B 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 216 removed outlier: 3.569A pdb=" N ARG B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 226 removed outlier: 3.597A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 26 removed outlier: 3.725A pdb=" N LYS C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG C 20 " --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG C 43 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 55 " --> pdb=" O MET C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 113 removed outlier: 3.624A pdb=" N ALA C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG C 100 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU C 108 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU C 119 " --> pdb=" O PRO C 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 170 removed outlier: 3.790A pdb=" N ALA C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 161 " --> pdb=" O ARG C 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 197 removed outlier: 3.861A pdb=" N ALA C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 216 removed outlier: 3.570A pdb=" N ARG C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 226 removed outlier: 3.597A pdb=" N GLU C 221 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 26 removed outlier: 3.724A pdb=" N LYS D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG D 43 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 55 " --> pdb=" O MET D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 113 removed outlier: 3.623A pdb=" N ALA D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU D 108 " --> pdb=" O ARG D 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU D 119 " --> pdb=" O PRO D 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 170 removed outlier: 3.790A pdb=" N ALA D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG D 161 " --> pdb=" O ARG D 157 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 179 " --> pdb=" O ALA D 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 216 removed outlier: 3.570A pdb=" N ARG D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.596A pdb=" N GLU D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 222 " --> pdb=" O ARG D 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.725A pdb=" N LYS E 13 " --> pdb=" O GLU E 9 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG E 20 " --> pdb=" O GLU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG E 43 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 113 removed outlier: 3.624A pdb=" N ALA E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG E 100 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 108 " --> pdb=" O ARG E 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E 109 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU E 119 " --> pdb=" O PRO E 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA E 121 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL E 125 " --> pdb=" O ALA E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 170 removed outlier: 3.791A pdb=" N ALA E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS E 160 " --> pdb=" O ALA E 156 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG E 161 " --> pdb=" O ARG E 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU E 188 " --> pdb=" O ARG E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 216 removed outlier: 3.570A pdb=" N ARG E 213 " --> pdb=" O ARG E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 226 removed outlier: 3.596A pdb=" N GLU E 221 " --> pdb=" O GLU E 217 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 26 removed outlier: 3.725A pdb=" N LYS F 13 " --> pdb=" O GLU F 9 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 56 removed outlier: 3.520A pdb=" N ALA F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN F 39 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG F 43 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU F 55 " --> pdb=" O MET F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA F 61 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 113 removed outlier: 3.623A pdb=" N ALA F 99 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG F 100 " --> pdb=" O GLU F 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU F 108 " --> pdb=" O ARG F 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU F 119 " --> pdb=" O PRO F 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 170 removed outlier: 3.791A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS F 160 " --> pdb=" O ALA F 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG F 161 " --> pdb=" O ARG F 157 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 197 removed outlier: 3.861A pdb=" N ALA F 175 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS F 183 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU F 188 " --> pdb=" O ARG F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 216 removed outlier: 3.569A pdb=" N ARG F 213 " --> pdb=" O ARG F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 226 removed outlier: 3.597A pdb=" N GLU F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 26 removed outlier: 3.725A pdb=" N LYS G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG G 20 " --> pdb=" O GLU G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN G 39 " --> pdb=" O LEU G 35 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG G 43 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU G 55 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 113 removed outlier: 3.623A pdb=" N ALA G 99 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG G 100 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU G 108 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA G 109 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU G 119 " --> pdb=" O PRO G 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG G 120 " --> pdb=" O GLU G 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA G 121 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 170 removed outlier: 3.791A pdb=" N ALA G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS G 160 " --> pdb=" O ALA G 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG G 161 " --> pdb=" O ARG G 157 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS G 183 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU G 188 " --> pdb=" O ARG G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 216 removed outlier: 3.570A pdb=" N ARG G 213 " --> pdb=" O ARG G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 226 removed outlier: 3.596A pdb=" N GLU G 221 " --> pdb=" O GLU G 217 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU G 222 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU G 224 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA G 226 " --> pdb=" O LEU G 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 26 removed outlier: 3.724A pdb=" N LYS H 13 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG H 20 " --> pdb=" O GLU H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN H 39 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG H 43 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU H 55 " --> pdb=" O MET H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA H 61 " --> pdb=" O ASP H 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 113 removed outlier: 3.624A pdb=" N ALA H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG H 100 " --> pdb=" O GLU H 96 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU H 107 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU H 108 " --> pdb=" O ARG H 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA H 109 " --> pdb=" O VAL H 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU H 119 " --> pdb=" O PRO H 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL H 125 " --> pdb=" O ALA H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 170 removed outlier: 3.790A pdb=" N ALA H 159 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG H 161 " --> pdb=" O ARG H 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU H 177 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL H 179 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS H 183 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU H 187 " --> pdb=" O LYS H 183 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU H 188 " --> pdb=" O ARG H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 216 removed outlier: 3.569A pdb=" N ARG H 213 " --> pdb=" O ARG H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 226 removed outlier: 3.597A pdb=" N GLU H 221 " --> pdb=" O GLU H 217 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU H 222 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU H 224 " --> pdb=" O LYS H 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA H 226 " --> pdb=" O LEU H 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 26 removed outlier: 3.725A pdb=" N LYS I 13 " --> pdb=" O GLU I 9 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG I 20 " --> pdb=" O GLU I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN I 39 " --> pdb=" O LEU I 35 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG I 43 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU I 55 " --> pdb=" O MET I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA I 61 " --> pdb=" O ASP I 57 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 113 removed outlier: 3.624A pdb=" N ALA I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA I 109 " --> pdb=" O VAL I 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU I 119 " --> pdb=" O PRO I 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA I 121 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL I 125 " --> pdb=" O ALA I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 170 removed outlier: 3.790A pdb=" N ALA I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG I 161 " --> pdb=" O ARG I 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN I 169 " --> pdb=" O LEU I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA I 175 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL I 179 " --> pdb=" O ALA I 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS I 183 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU I 187 " --> pdb=" O LYS I 183 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU I 188 " --> pdb=" O ARG I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 216 removed outlier: 3.569A pdb=" N ARG I 213 " --> pdb=" O ARG I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 226 removed outlier: 3.596A pdb=" N GLU I 221 " --> pdb=" O GLU I 217 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU I 222 " --> pdb=" O ARG I 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU I 224 " --> pdb=" O LYS I 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA I 226 " --> pdb=" O LEU I 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 26 removed outlier: 3.725A pdb=" N LYS J 13 " --> pdb=" O GLU J 9 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG J 20 " --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA J 34 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN J 39 " --> pdb=" O LEU J 35 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG J 43 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU J 55 " --> pdb=" O MET J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA J 61 " --> pdb=" O ASP J 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU J 67 " --> pdb=" O ARG J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 113 removed outlier: 3.623A pdb=" N ALA J 99 " --> pdb=" O ALA J 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG J 100 " --> pdb=" O GLU J 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU J 107 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU J 108 " --> pdb=" O ARG J 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA J 109 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU J 110 " --> pdb=" O LEU J 106 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER J 111 " --> pdb=" O GLU J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU J 119 " --> pdb=" O PRO J 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA J 121 " --> pdb=" O VAL J 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL J 125 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 170 removed outlier: 3.791A pdb=" N ALA J 159 " --> pdb=" O ALA J 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS J 160 " --> pdb=" O ALA J 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG J 161 " --> pdb=" O ARG J 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN J 169 " --> pdb=" O LEU J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA J 175 " --> pdb=" O ASP J 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU J 177 " --> pdb=" O ALA J 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL J 179 " --> pdb=" O ALA J 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS J 183 " --> pdb=" O VAL J 179 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU J 188 " --> pdb=" O ARG J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 216 removed outlier: 3.570A pdb=" N ARG J 213 " --> pdb=" O ARG J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 226 removed outlier: 3.597A pdb=" N GLU J 221 " --> pdb=" O GLU J 217 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU J 222 " --> pdb=" O ARG J 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU J 224 " --> pdb=" O LYS J 220 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA J 226 " --> pdb=" O LEU J 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 26 removed outlier: 3.724A pdb=" N LYS K 13 " --> pdb=" O GLU K 9 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG K 20 " --> pdb=" O GLU K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA K 34 " --> pdb=" O LEU K 30 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN K 39 " --> pdb=" O LEU K 35 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG K 43 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU K 55 " --> pdb=" O MET K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA K 61 " --> pdb=" O ASP K 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 113 removed outlier: 3.623A pdb=" N ALA K 99 " --> pdb=" O ALA K 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG K 100 " --> pdb=" O GLU K 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA K 109 " --> pdb=" O VAL K 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU K 110 " --> pdb=" O LEU K 106 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU K 119 " --> pdb=" O PRO K 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG K 120 " --> pdb=" O GLU K 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA K 121 " --> pdb=" O VAL K 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL K 125 " --> pdb=" O ALA K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 170 removed outlier: 3.791A pdb=" N ALA K 159 " --> pdb=" O ALA K 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS K 160 " --> pdb=" O ALA K 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG K 161 " --> pdb=" O ARG K 157 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN K 169 " --> pdb=" O LEU K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA K 175 " --> pdb=" O ASP K 171 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU K 177 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL K 179 " --> pdb=" O ALA K 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 183 " --> pdb=" O VAL K 179 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU K 188 " --> pdb=" O ARG K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 216 removed outlier: 3.570A pdb=" N ARG K 213 " --> pdb=" O ARG K 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 216 through 226 removed outlier: 3.597A pdb=" N GLU K 221 " --> pdb=" O GLU K 217 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU K 222 " --> pdb=" O ARG K 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU K 224 " --> pdb=" O LYS K 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA K 226 " --> pdb=" O LEU K 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 26 removed outlier: 3.724A pdb=" N LYS L 13 " --> pdb=" O GLU L 9 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG L 20 " --> pdb=" O GLU L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN L 39 " --> pdb=" O LEU L 35 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG L 43 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU L 55 " --> pdb=" O MET L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA L 61 " --> pdb=" O ASP L 57 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU L 67 " --> pdb=" O ARG L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 113 removed outlier: 3.623A pdb=" N ALA L 99 " --> pdb=" O ALA L 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG L 100 " --> pdb=" O GLU L 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU L 107 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA L 109 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU L 110 " --> pdb=" O LEU L 106 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER L 111 " --> pdb=" O GLU L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU L 119 " --> pdb=" O PRO L 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG L 120 " --> pdb=" O GLU L 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA L 121 " --> pdb=" O VAL L 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 170 removed outlier: 3.791A pdb=" N ALA L 159 " --> pdb=" O ALA L 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS L 160 " --> pdb=" O ALA L 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG L 161 " --> pdb=" O ARG L 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN L 169 " --> pdb=" O LEU L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 197 removed outlier: 3.861A pdb=" N ALA L 175 " --> pdb=" O ASP L 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL L 179 " --> pdb=" O ALA L 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL L 182 " --> pdb=" O ALA L 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS L 183 " --> pdb=" O VAL L 179 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU L 188 " --> pdb=" O ARG L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 216 removed outlier: 3.569A pdb=" N ARG L 213 " --> pdb=" O ARG L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 226 removed outlier: 3.597A pdb=" N GLU L 221 " --> pdb=" O GLU L 217 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU L 222 " --> pdb=" O ARG L 218 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU L 224 " --> pdb=" O LYS L 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA L 226 " --> pdb=" O LEU L 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 26 removed outlier: 3.725A pdb=" N LYS M 13 " --> pdb=" O GLU M 9 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG M 20 " --> pdb=" O GLU M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA M 34 " --> pdb=" O LEU M 30 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN M 39 " --> pdb=" O LEU M 35 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG M 43 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU M 55 " --> pdb=" O MET M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU M 67 " --> pdb=" O ARG M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 113 removed outlier: 3.623A pdb=" N ALA M 99 " --> pdb=" O ALA M 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG M 100 " --> pdb=" O GLU M 96 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA M 109 " --> pdb=" O VAL M 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER M 111 " --> pdb=" O GLU M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU M 119 " --> pdb=" O PRO M 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG M 120 " --> pdb=" O GLU M 116 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA M 121 " --> pdb=" O VAL M 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 170 removed outlier: 3.790A pdb=" N ALA M 159 " --> pdb=" O ALA M 155 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS M 160 " --> pdb=" O ALA M 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG M 161 " --> pdb=" O ARG M 157 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN M 169 " --> pdb=" O LEU M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA M 175 " --> pdb=" O ASP M 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU M 177 " --> pdb=" O ALA M 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL M 179 " --> pdb=" O ALA M 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL M 182 " --> pdb=" O ALA M 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS M 183 " --> pdb=" O VAL M 179 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU M 187 " --> pdb=" O LYS M 183 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU M 188 " --> pdb=" O ARG M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 216 removed outlier: 3.570A pdb=" N ARG M 213 " --> pdb=" O ARG M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 226 removed outlier: 3.597A pdb=" N GLU M 221 " --> pdb=" O GLU M 217 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU M 222 " --> pdb=" O ARG M 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU M 224 " --> pdb=" O LYS M 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA M 226 " --> pdb=" O LEU M 222 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 26 removed outlier: 3.724A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG N 20 " --> pdb=" O GLU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA N 34 " --> pdb=" O LEU N 30 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN N 39 " --> pdb=" O LEU N 35 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG N 43 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU N 55 " --> pdb=" O MET N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA N 61 " --> pdb=" O ASP N 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU N 67 " --> pdb=" O ARG N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 113 removed outlier: 3.623A pdb=" N ALA N 99 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG N 100 " --> pdb=" O GLU N 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU N 107 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU N 108 " --> pdb=" O ARG N 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA N 109 " --> pdb=" O VAL N 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU N 110 " --> pdb=" O LEU N 106 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU N 119 " --> pdb=" O PRO N 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG N 120 " --> pdb=" O GLU N 116 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA N 121 " --> pdb=" O VAL N 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL N 125 " --> pdb=" O ALA N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 170 removed outlier: 3.790A pdb=" N ALA N 159 " --> pdb=" O ALA N 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS N 160 " --> pdb=" O ALA N 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG N 161 " --> pdb=" O ARG N 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN N 169 " --> pdb=" O LEU N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA N 175 " --> pdb=" O ASP N 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL N 179 " --> pdb=" O ALA N 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL N 182 " --> pdb=" O ALA N 178 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS N 183 " --> pdb=" O VAL N 179 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU N 187 " --> pdb=" O LYS N 183 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU N 188 " --> pdb=" O ARG N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 216 removed outlier: 3.569A pdb=" N ARG N 213 " --> pdb=" O ARG N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 216 through 226 removed outlier: 3.597A pdb=" N GLU N 221 " --> pdb=" O GLU N 217 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU N 222 " --> pdb=" O ARG N 218 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU N 224 " --> pdb=" O LYS N 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA N 226 " --> pdb=" O LEU N 222 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 26 removed outlier: 3.725A pdb=" N LYS O 13 " --> pdb=" O GLU O 9 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG O 20 " --> pdb=" O GLU O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 56 removed outlier: 3.521A pdb=" N ALA O 34 " --> pdb=" O LEU O 30 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN O 39 " --> pdb=" O LEU O 35 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG O 43 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU O 55 " --> pdb=" O MET O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 83 removed outlier: 4.062A pdb=" N ALA O 61 " --> pdb=" O ASP O 57 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU O 67 " --> pdb=" O ARG O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 113 removed outlier: 3.624A pdb=" N ALA O 99 " --> pdb=" O ALA O 95 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG O 100 " --> pdb=" O GLU O 96 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU O 107 " --> pdb=" O LYS O 103 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU O 108 " --> pdb=" O ARG O 104 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA O 109 " --> pdb=" O VAL O 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER O 111 " --> pdb=" O GLU O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 140 removed outlier: 3.696A pdb=" N LEU O 119 " --> pdb=" O PRO O 115 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG O 120 " --> pdb=" O GLU O 116 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA O 121 " --> pdb=" O VAL O 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 170 removed outlier: 3.791A pdb=" N ALA O 159 " --> pdb=" O ALA O 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS O 160 " --> pdb=" O ALA O 156 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG O 161 " --> pdb=" O ARG O 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN O 169 " --> pdb=" O LEU O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 197 removed outlier: 3.860A pdb=" N ALA O 175 " --> pdb=" O ASP O 171 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL O 179 " --> pdb=" O ALA O 175 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL O 182 " --> pdb=" O ALA O 178 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS O 183 " --> pdb=" O VAL O 179 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU O 188 " --> pdb=" O ARG O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 216 removed outlier: 3.570A pdb=" N ARG O 213 " --> pdb=" O ARG O 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 216 through 226 removed outlier: 3.597A pdb=" N GLU O 221 " --> pdb=" O GLU O 217 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU O 222 " --> pdb=" O ARG O 218 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU O 224 " --> pdb=" O LYS O 220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA O 226 " --> pdb=" O LEU O 222 " (cutoff:3.500A) 2296 hydrogen bonds defined for protein. 6888 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: 15.84 Time building geometry restraints manager: 34.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 28155 1.03 - 1.23: 0 1.23 - 1.42: 9630 1.42 - 1.62: 16575 1.62 - 1.81: 120 Bond restraints: 54480 Sorted by residual: bond pdb=" CB VAL H 105 " pdb=" CG2 VAL H 105 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CB VAL O 105 " pdb=" CG2 VAL O 105 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.28e+00 bond pdb=" CB VAL G 105 " pdb=" CG2 VAL G 105 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.27e+00 bond pdb=" CB VAL K 105 " pdb=" CG2 VAL K 105 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.27e+00 bond pdb=" CB VAL D 105 " pdb=" CG2 VAL D 105 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.27e+00 ... (remaining 54475 not shown) Histogram of bond angle deviations from ideal: 99.99 - 105.89: 285 105.89 - 111.79: 67684 111.79 - 117.69: 11233 117.69 - 123.59: 16869 123.59 - 129.49: 3619 Bond angle restraints: 99690 Sorted by residual: angle pdb=" CB PRO D 115 " pdb=" CA PRO D 115 " pdb=" HA PRO D 115 " ideal model delta sigma weight residual 109.00 115.51 -6.51 3.00e+00 1.11e-01 4.70e+00 angle pdb=" CB PRO H 115 " pdb=" CA PRO H 115 " pdb=" HA PRO H 115 " ideal model delta sigma weight residual 109.00 115.46 -6.46 3.00e+00 1.11e-01 4.64e+00 angle pdb=" CB PRO M 115 " pdb=" CA PRO M 115 " pdb=" HA PRO M 115 " ideal model delta sigma weight residual 109.00 115.46 -6.46 3.00e+00 1.11e-01 4.63e+00 angle pdb=" CB PRO E 115 " pdb=" CA PRO E 115 " pdb=" HA PRO E 115 " ideal model delta sigma weight residual 109.00 115.45 -6.45 3.00e+00 1.11e-01 4.63e+00 angle pdb=" CB PRO A 115 " pdb=" CA PRO A 115 " pdb=" HA PRO A 115 " ideal model delta sigma weight residual 109.00 115.45 -6.45 3.00e+00 1.11e-01 4.62e+00 ... (remaining 99685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.71: 22230 10.71 - 21.42: 840 21.42 - 32.13: 210 32.13 - 42.84: 135 42.84 - 53.55: 15 Dihedral angle restraints: 23430 sinusoidal: 13470 harmonic: 9960 Sorted by residual: dihedral pdb=" CA ALA D 118 " pdb=" C ALA D 118 " pdb=" N LEU D 119 " pdb=" CA LEU D 119 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ALA E 118 " pdb=" C ALA E 118 " pdb=" N LEU E 119 " pdb=" CA LEU E 119 " ideal model delta harmonic sigma weight residual -180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ALA L 118 " pdb=" C ALA L 118 " pdb=" N LEU L 119 " pdb=" CA LEU L 119 " ideal model delta harmonic sigma weight residual -180.00 -160.59 -19.41 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 23427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 2328 0.024 - 0.049: 1013 0.049 - 0.073: 717 0.073 - 0.097: 178 0.097 - 0.122: 114 Chirality restraints: 4350 Sorted by residual: chirality pdb=" CB VAL J 162 " pdb=" CA VAL J 162 " pdb=" CG1 VAL J 162 " pdb=" CG2 VAL J 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.70e-01 chirality pdb=" CB VAL E 162 " pdb=" CA VAL E 162 " pdb=" CG1 VAL E 162 " pdb=" CG2 VAL E 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CB VAL M 162 " pdb=" CA VAL M 162 " pdb=" CG1 VAL M 162 " pdb=" CG2 VAL M 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 4347 not shown) Planarity restraints: 7965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 171 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.27e+00 pdb=" N PRO B 172 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 172 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 172 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 171 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO H 172 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO H 172 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 172 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 171 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO F 172 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO F 172 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 172 " -0.021 5.00e-02 4.00e+02 ... (remaining 7962 not shown) Histogram of nonbonded interaction distances: 0.41 - 1.25: 100 1.25 - 2.08: 1495 2.08 - 2.92: 157179 2.92 - 3.76: 212266 3.76 - 4.60: 380825 Warning: very small nonbonded interaction distances. Nonbonded interactions: 751865 Sorted by model distance: nonbonded pdb=" HD2 PRO K 172 " pdb=" HE1 MET L 40 " model vdw 0.407 2.440 nonbonded pdb=" HD2 PRO H 172 " pdb=" HE1 MET I 40 " model vdw 0.408 2.440 nonbonded pdb=" HD2 PRO I 172 " pdb=" HE1 MET J 40 " model vdw 0.408 2.440 nonbonded pdb=" HD2 PRO D 172 " pdb=" HE1 MET E 40 " model vdw 0.408 2.440 nonbonded pdb=" HD2 PRO J 172 " pdb=" HE1 MET K 40 " model vdw 0.408 2.440 ... (remaining 751860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.610 Extract box with map and model: 5.480 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 124.490 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 0.050 26325 Z= 0.507 Angle : 0.731 4.490 35325 Z= 0.436 Chirality : 0.039 0.122 4350 Planarity : 0.003 0.038 4620 Dihedral : 7.511 40.496 10590 Min Nonbonded Distance : 1.433 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.13), residues: 3375 helix: -2.65 (0.07), residues: 2820 sheet: None (None), residues: 0 loop : 0.94 (0.32), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG I 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.9354 time to fit residues: 514.7087 Evaluate side-chains 192 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 3.177 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 299 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN B 169 GLN C 169 GLN D 21 GLN D 169 GLN E 169 GLN F 169 GLN G 169 GLN H 169 GLN I 169 GLN J 169 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26325 Z= 0.270 Angle : 0.667 5.864 35325 Z= 0.372 Chirality : 0.033 0.123 4350 Planarity : 0.005 0.044 4620 Dihedral : 5.797 64.081 3765 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 3375 helix: -0.75 (0.08), residues: 3180 sheet: None (None), residues: 0 loop : -1.67 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.7699 time to fit residues: 311.8387 Evaluate side-chains 159 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 3.734 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 300 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 297 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 240 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 GLN N 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26325 Z= 0.325 Angle : 0.640 5.984 35325 Z= 0.363 Chirality : 0.032 0.123 4350 Planarity : 0.005 0.083 4620 Dihedral : 5.525 64.388 3765 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 3375 helix: 0.17 (0.08), residues: 3210 sheet: None (None), residues: 0 loop : -2.05 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.7079 time to fit residues: 245.6472 Evaluate side-chains 128 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 3.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 33 optimal weight: 0.0000 chunk 143 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 301 optimal weight: 0.6980 chunk 318 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 285 optimal weight: 0.0770 chunk 85 optimal weight: 3.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 26325 Z= 0.123 Angle : 0.441 4.542 35325 Z= 0.246 Chirality : 0.030 0.117 4350 Planarity : 0.003 0.040 4620 Dihedral : 5.247 62.935 3765 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.14), residues: 3375 helix: 1.27 (0.09), residues: 3210 sheet: None (None), residues: 0 loop : -1.29 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.7675 time to fit residues: 251.3802 Evaluate side-chains 139 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 3.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 272 optimal weight: 0.8980 chunk 220 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 286 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26325 Z= 0.233 Angle : 0.501 4.462 35325 Z= 0.287 Chirality : 0.030 0.112 4350 Planarity : 0.003 0.029 4620 Dihedral : 4.934 57.313 3765 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.14), residues: 3375 helix: 1.46 (0.09), residues: 3150 sheet: None (None), residues: 0 loop : -0.35 (0.48), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.7181 time to fit residues: 202.2955 Evaluate side-chains 131 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.197 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 319 optimal weight: 20.0000 chunk 265 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 ASN D 191 ASN F 169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26325 Z= 0.286 Angle : 0.548 4.394 35325 Z= 0.316 Chirality : 0.031 0.115 4350 Planarity : 0.004 0.038 4620 Dihedral : 4.737 57.882 3765 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.14), residues: 3375 helix: 1.19 (0.09), residues: 3210 sheet: None (None), residues: 0 loop : -0.87 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.6831 time to fit residues: 182.4853 Evaluate side-chains 121 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 3.234 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 181 optimal weight: 0.0870 chunk 233 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 318 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 overall best weight: 4.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.6634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26325 Z= 0.202 Angle : 0.474 5.352 35325 Z= 0.272 Chirality : 0.030 0.115 4350 Planarity : 0.004 0.067 4620 Dihedral : 4.635 57.426 3765 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.14), residues: 3375 helix: 1.49 (0.09), residues: 3210 sheet: None (None), residues: 0 loop : -0.75 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.6742 time to fit residues: 189.1246 Evaluate side-chains 128 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 3.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 chunk 157 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26325 Z= 0.227 Angle : 0.488 4.463 35325 Z= 0.281 Chirality : 0.030 0.126 4350 Planarity : 0.004 0.063 4620 Dihedral : 4.515 57.013 3765 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.14), residues: 3375 helix: 1.50 (0.09), residues: 3210 sheet: None (None), residues: 0 loop : -0.73 (0.50), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.6528 time to fit residues: 176.9412 Evaluate side-chains 127 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 3.218 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.9990 chunk 304 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 295 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.6994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 26325 Z= 0.138 Angle : 0.427 5.184 35325 Z= 0.239 Chirality : 0.029 0.114 4350 Planarity : 0.003 0.052 4620 Dihedral : 4.410 57.624 3765 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.14), residues: 3375 helix: 2.01 (0.09), residues: 3210 sheet: None (None), residues: 0 loop : -0.84 (0.48), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.6806 time to fit residues: 195.4255 Evaluate side-chains 131 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 5.9990 chunk 313 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 328 optimal weight: 10.0000 chunk 302 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26325 Z= 0.206 Angle : 0.464 5.454 35325 Z= 0.267 Chirality : 0.030 0.112 4350 Planarity : 0.003 0.051 4620 Dihedral : 4.309 55.963 3765 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.14), residues: 3375 helix: 1.93 (0.09), residues: 3210 sheet: None (None), residues: 0 loop : -0.84 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6750 Ramachandran restraints generated. 3375 Oldfield, 0 Emsley, 3375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.6736 time to fit residues: 185.5330 Evaluate side-chains 129 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 3.211 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 241 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.048373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.037885 restraints weight = 462484.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.039870 restraints weight = 243693.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.041261 restraints weight = 154859.576| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.7243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26325 Z= 0.193 Angle : 0.455 4.604 35325 Z= 0.261 Chirality : 0.029 0.113 4350 Planarity : 0.003 0.050 4620 Dihedral : 4.253 55.703 3765 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.14), residues: 3375 helix: 1.97 (0.09), residues: 3210 sheet: None (None), residues: 0 loop : -0.84 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 127 =============================================================================== Job complete usr+sys time: 6246.49 seconds wall clock time: 109 minutes 49.86 seconds (6589.86 seconds total)