Starting phenix.real_space_refine on Sun Mar 10 22:39:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9y_9020/03_2024/6e9y_9020.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9y_9020/03_2024/6e9y_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_9020/03_2024/6e9y_9020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9y_9020/03_2024/6e9y_9020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9y_9020/03_2024/6e9y_9020.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9y_9020/03_2024/6e9y_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-dev-5265/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: 16.56, 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: 33.19 Conformation dependent library (CDL) restraints added in 4.1 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: 2.89 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: 16.72 Time building geometry restraints manager: 34.90 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: 22950 10.71 - 21.42: 885 21.42 - 32.13: 270 32.13 - 42.84: 210 42.84 - 53.55: 30 Dihedral angle restraints: 24345 sinusoidal: 14385 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 24342 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: 0.660 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: 5.530 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 124.100 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.260 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:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.190 ------------------------------------------------------------------------------- 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 : 3.871 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 REVERT: A 57 ASP cc_start: 0.7534 (t0) cc_final: 0.7254 (p0) REVERT: A 66 GLU cc_start: 0.9006 (tt0) cc_final: 0.8569 (tm-30) REVERT: A 153 GLU cc_start: 0.8909 (tt0) cc_final: 0.8636 (tp30) REVERT: B 114 ASP cc_start: 0.8652 (t0) cc_final: 0.8334 (t0) REVERT: B 123 GLU cc_start: 0.8834 (tt0) cc_final: 0.8209 (tm-30) REVERT: B 171 ASP cc_start: 0.8099 (t0) cc_final: 0.7192 (m-30) REVERT: C 66 GLU cc_start: 0.9221 (tt0) cc_final: 0.8735 (tm-30) REVERT: D 57 ASP cc_start: 0.7252 (t0) cc_final: 0.7023 (p0) REVERT: D 66 GLU cc_start: 0.9307 (tt0) cc_final: 0.8891 (tm-30) REVERT: E 16 GLU cc_start: 0.9425 (tt0) cc_final: 0.8636 (tm-30) REVERT: E 66 GLU cc_start: 0.9267 (tt0) cc_final: 0.8955 (tm-30) REVERT: E 130 GLU cc_start: 0.9260 (tt0) cc_final: 0.9022 (tm-30) REVERT: F 66 GLU cc_start: 0.9244 (tt0) cc_final: 0.8623 (tm-30) REVERT: F 123 GLU cc_start: 0.8936 (tt0) cc_final: 0.8451 (tm-30) REVERT: F 130 GLU cc_start: 0.9416 (tt0) cc_final: 0.9098 (tm-30) REVERT: G 62 LEU cc_start: 0.9343 (tp) cc_final: 0.9121 (tt) REVERT: G 114 ASP cc_start: 0.8839 (t0) cc_final: 0.8513 (t0) REVERT: H 114 ASP cc_start: 0.8711 (t0) cc_final: 0.8313 (t0) REVERT: I 114 ASP cc_start: 0.8545 (t0) cc_final: 0.8125 (t0) REVERT: J 57 ASP cc_start: 0.7969 (t0) cc_final: 0.7718 (t0) REVERT: J 114 ASP cc_start: 0.8833 (t0) cc_final: 0.8392 (t0) REVERT: J 210 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8159 (mm-30) REVERT: K 4 LEU cc_start: 0.8995 (mt) cc_final: 0.8572 (mt) REVERT: K 114 ASP cc_start: 0.8811 (t0) cc_final: 0.8503 (t0) REVERT: K 190 GLU cc_start: 0.8902 (tt0) cc_final: 0.8623 (tp30) REVERT: L 114 ASP cc_start: 0.8398 (t0) cc_final: 0.8137 (t0) REVERT: L 206 GLU cc_start: 0.9265 (mm-30) cc_final: 0.9012 (tp30) REVERT: N 4 LEU cc_start: 0.9323 (mt) cc_final: 0.9120 (mp) REVERT: N 21 GLN cc_start: 0.9355 (mt0) cc_final: 0.8951 (tp-100) REVERT: N 36 VAL cc_start: 0.8975 (t) cc_final: 0.8595 (t) REVERT: O 112 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8444 (mp10) REVERT: O 114 ASP cc_start: 0.7958 (t0) cc_final: 0.7259 (p0) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.9293 time to fit residues: 509.7608 Evaluate side-chains 212 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.216 ------------------------------------------------------------------------------- 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: 6.9990 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 F 169 GLN G 169 GLN H 169 GLN I 169 GLN J 169 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26325 Z= 0.266 Angle : 0.677 5.827 35325 Z= 0.374 Chirality : 0.034 0.123 4350 Planarity : 0.005 0.044 4620 Dihedral : 6.003 69.925 3765 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.04 % Allowed : 0.37 % Favored : 99.59 % 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: -1.38 (0.13), residues: 3375 helix: -0.68 (0.08), residues: 3180 sheet: None (None), residues: 0 loop : -1.47 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 194 *********************** 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 277 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 3.262 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: A 32 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9278 (mm-30) REVERT: A 66 GLU cc_start: 0.9160 (tt0) cc_final: 0.8507 (tm-30) REVERT: A 153 GLU cc_start: 0.9110 (tt0) cc_final: 0.8885 (tp30) REVERT: A 180 MET cc_start: 0.9433 (mmp) cc_final: 0.9173 (mmp) REVERT: B 114 ASP cc_start: 0.8782 (t0) cc_final: 0.8428 (t0) REVERT: B 123 GLU cc_start: 0.8865 (tt0) cc_final: 0.8479 (tm-30) REVERT: B 171 ASP cc_start: 0.8210 (t0) cc_final: 0.7103 (m-30) REVERT: B 192 ILE cc_start: 0.9283 (mt) cc_final: 0.8997 (tp) REVERT: B 203 GLU cc_start: 0.8924 (tt0) cc_final: 0.8714 (tp30) REVERT: C 123 GLU cc_start: 0.8834 (tt0) cc_final: 0.8230 (tm-30) REVERT: D 57 ASP cc_start: 0.7441 (t0) cc_final: 0.6615 (p0) REVERT: F 40 MET cc_start: 0.9390 (ttp) cc_final: 0.8824 (ppp) REVERT: F 66 GLU cc_start: 0.9116 (tt0) cc_final: 0.8441 (tm-30) REVERT: F 123 GLU cc_start: 0.8828 (tt0) cc_final: 0.8386 (tm-30) REVERT: F 130 GLU cc_start: 0.9406 (tt0) cc_final: 0.9149 (tm-30) REVERT: F 190 GLU cc_start: 0.9197 (tt0) cc_final: 0.8762 (tp30) REVERT: G 114 ASP cc_start: 0.8899 (t0) cc_final: 0.8681 (t0) REVERT: H 114 ASP cc_start: 0.8825 (t0) cc_final: 0.8562 (t0) REVERT: I 114 ASP cc_start: 0.8675 (t0) cc_final: 0.8364 (t0) REVERT: I 180 MET cc_start: 0.9512 (mmp) cc_final: 0.9289 (mmp) REVERT: J 57 ASP cc_start: 0.8029 (t0) cc_final: 0.7791 (t0) REVERT: K 114 ASP cc_start: 0.8797 (t0) cc_final: 0.8480 (t0) REVERT: K 190 GLU cc_start: 0.8842 (tt0) cc_final: 0.8412 (tp30) REVERT: L 114 ASP cc_start: 0.8536 (t0) cc_final: 0.8307 (t0) REVERT: M 206 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8970 (tp30) REVERT: N 21 GLN cc_start: 0.9282 (mt0) cc_final: 0.9037 (tp-100) REVERT: N 66 GLU cc_start: 0.8982 (tt0) cc_final: 0.8690 (tm-30) REVERT: O 21 GLN cc_start: 0.9393 (mm-40) cc_final: 0.8845 (tp-100) REVERT: O 36 VAL cc_start: 0.9435 (t) cc_final: 0.8988 (p) REVERT: O 112 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8455 (mm-40) REVERT: O 114 ASP cc_start: 0.8080 (t0) cc_final: 0.7301 (p0) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.7531 time to fit residues: 325.6225 Evaluate side-chains 179 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 3.214 ------------------------------------------------------------------------------- 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: 6.9990 chunk 93 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 300 optimal weight: 10.0000 chunk 324 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 297 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 26325 Z= 0.326 Angle : 0.630 5.498 35325 Z= 0.357 Chirality : 0.032 0.138 4350 Planarity : 0.005 0.051 4620 Dihedral : 5.629 66.322 3765 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 0.02 (0.13), residues: 3375 helix: 0.23 (0.08), residues: 3210 sheet: None (None), residues: 0 loop : -1.63 (0.56), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 150 *********************** 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 222 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 3.241 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: A 23 MET cc_start: 0.8579 (mtt) cc_final: 0.8298 (mtp) REVERT: A 66 GLU cc_start: 0.9296 (tt0) cc_final: 0.9085 (tm-30) REVERT: A 180 MET cc_start: 0.9466 (mmp) cc_final: 0.9178 (mmp) REVERT: B 114 ASP cc_start: 0.8804 (t0) cc_final: 0.8497 (t0) REVERT: B 176 ILE cc_start: 0.9490 (mt) cc_final: 0.9103 (tp) REVERT: B 192 ILE cc_start: 0.9403 (mt) cc_final: 0.9158 (tp) REVERT: B 203 GLU cc_start: 0.8983 (tt0) cc_final: 0.8691 (tp30) REVERT: F 40 MET cc_start: 0.9446 (ttp) cc_final: 0.8921 (ppp) REVERT: F 66 GLU cc_start: 0.9257 (tt0) cc_final: 0.8617 (tm-30) REVERT: F 176 ILE cc_start: 0.9255 (mt) cc_final: 0.8962 (tp) REVERT: G 40 MET cc_start: 0.9357 (tmm) cc_final: 0.9076 (ppp) REVERT: H 114 ASP cc_start: 0.8768 (t0) cc_final: 0.8497 (t0) REVERT: I 114 ASP cc_start: 0.8969 (t0) cc_final: 0.8576 (t0) REVERT: J 23 MET cc_start: 0.8947 (mmt) cc_final: 0.8730 (mmm) REVERT: J 114 ASP cc_start: 0.8836 (t0) cc_final: 0.8554 (t0) REVERT: K 57 ASP cc_start: 0.8132 (t70) cc_final: 0.7844 (t0) REVERT: L 114 ASP cc_start: 0.8532 (t0) cc_final: 0.8328 (t0) REVERT: M 66 GLU cc_start: 0.9322 (tt0) cc_final: 0.9105 (tm-30) REVERT: N 21 GLN cc_start: 0.9320 (mt0) cc_final: 0.9053 (tp-100) REVERT: N 180 MET cc_start: 0.9488 (mmm) cc_final: 0.9239 (mmm) REVERT: O 112 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8592 (tp40) REVERT: O 114 ASP cc_start: 0.8241 (t0) cc_final: 0.7298 (p0) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.6742 time to fit residues: 243.7169 Evaluate side-chains 148 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 3.214 ------------------------------------------------------------------------------- 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: 8.9990 chunk 225 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 301 optimal weight: 0.8980 chunk 318 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 overall best weight: 4.1786 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.5522 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= 0.209 Angle : 0.497 4.371 35325 Z= 0.286 Chirality : 0.030 0.116 4350 Planarity : 0.004 0.039 4620 Dihedral : 5.365 65.109 3765 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 1.08 (0.14), residues: 3375 helix: 0.90 (0.09), residues: 3150 sheet: None (None), residues: 0 loop : -0.60 (0.50), residues: 225 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 207 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.258 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: A 23 MET cc_start: 0.8554 (mtt) cc_final: 0.8276 (mtp) REVERT: A 66 GLU cc_start: 0.9327 (tt0) cc_final: 0.9024 (tm-30) REVERT: A 146 GLU cc_start: 0.9313 (tt0) cc_final: 0.8991 (tm-30) REVERT: B 114 ASP cc_start: 0.8777 (t0) cc_final: 0.8488 (t0) REVERT: B 176 ILE cc_start: 0.9471 (mt) cc_final: 0.9215 (tp) REVERT: B 192 ILE cc_start: 0.9412 (mt) cc_final: 0.9164 (tp) REVERT: B 203 GLU cc_start: 0.8986 (tt0) cc_final: 0.8689 (tp30) REVERT: F 9 GLU cc_start: 0.9284 (tt0) cc_final: 0.8903 (tp30) REVERT: F 40 MET cc_start: 0.9470 (ttp) cc_final: 0.9035 (tmm) REVERT: F 66 GLU cc_start: 0.9255 (tt0) cc_final: 0.8494 (tm-30) REVERT: F 176 ILE cc_start: 0.9202 (mt) cc_final: 0.8977 (tp) REVERT: F 190 GLU cc_start: 0.9205 (tt0) cc_final: 0.8794 (tp30) REVERT: G 40 MET cc_start: 0.9306 (tmm) cc_final: 0.9047 (ppp) REVERT: G 153 GLU cc_start: 0.9323 (tt0) cc_final: 0.9025 (tp30) REVERT: H 114 ASP cc_start: 0.8790 (t0) cc_final: 0.8514 (t0) REVERT: I 40 MET cc_start: 0.8667 (tpt) cc_final: 0.8396 (tpp) REVERT: I 114 ASP cc_start: 0.8952 (t0) cc_final: 0.8524 (t0) REVERT: J 40 MET cc_start: 0.8513 (tpp) cc_final: 0.8146 (tpp) REVERT: J 57 ASP cc_start: 0.8368 (t0) cc_final: 0.8159 (t0) REVERT: J 114 ASP cc_start: 0.8830 (t0) cc_final: 0.8557 (t0) REVERT: K 57 ASP cc_start: 0.8088 (t70) cc_final: 0.7716 (t0) REVERT: L 40 MET cc_start: 0.8723 (tpp) cc_final: 0.8387 (tpp) REVERT: M 66 GLU cc_start: 0.9277 (tt0) cc_final: 0.9054 (tm-30) REVERT: M 67 LEU cc_start: 0.9185 (mm) cc_final: 0.8984 (mm) REVERT: N 21 GLN cc_start: 0.9340 (mt0) cc_final: 0.9025 (tp-100) REVERT: N 180 MET cc_start: 0.9467 (mmm) cc_final: 0.9211 (mmm) REVERT: O 112 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8379 (tp40) REVERT: O 114 ASP cc_start: 0.8234 (t0) cc_final: 0.7191 (p0) REVERT: O 180 MET cc_start: 0.9479 (mmm) cc_final: 0.9125 (mmm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.7338 time to fit residues: 243.1454 Evaluate side-chains 157 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 3.240 ------------------------------------------------------------------------------- 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: 7.9990 chunk 181 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 237 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 220 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 162 optimal weight: 0.9990 chunk 286 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 191 ASN I 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26325 Z= 0.202 Angle : 0.472 4.647 35325 Z= 0.271 Chirality : 0.030 0.112 4350 Planarity : 0.003 0.030 4620 Dihedral : 5.195 64.828 3765 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.04 % Allowed : 1.01 % Favored : 98.96 % 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: 1.77 (0.14), residues: 3375 helix: 1.34 (0.09), residues: 3150 sheet: None (None), residues: 0 loop : -0.47 (0.49), 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 199 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 3.460 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: A 23 MET cc_start: 0.8544 (mtt) cc_final: 0.8264 (mtp) REVERT: A 66 GLU cc_start: 0.9401 (tt0) cc_final: 0.9067 (tm-30) REVERT: A 146 GLU cc_start: 0.9319 (tt0) cc_final: 0.8981 (tm-30) REVERT: B 114 ASP cc_start: 0.8749 (t0) cc_final: 0.8475 (t0) REVERT: B 176 ILE cc_start: 0.9476 (mt) cc_final: 0.9204 (tp) REVERT: B 192 ILE cc_start: 0.9429 (mt) cc_final: 0.9177 (tp) REVERT: F 9 GLU cc_start: 0.9303 (tt0) cc_final: 0.8902 (tp30) REVERT: F 40 MET cc_start: 0.9474 (ttp) cc_final: 0.9072 (tmm) REVERT: F 66 GLU cc_start: 0.9355 (tt0) cc_final: 0.8511 (tm-30) REVERT: F 176 ILE cc_start: 0.9227 (mt) cc_final: 0.8987 (tp) REVERT: F 190 GLU cc_start: 0.9236 (tt0) cc_final: 0.8842 (tp30) REVERT: G 153 GLU cc_start: 0.9356 (tt0) cc_final: 0.9030 (tp30) REVERT: H 114 ASP cc_start: 0.8776 (t0) cc_final: 0.8519 (t0) REVERT: I 40 MET cc_start: 0.8635 (tpt) cc_final: 0.8408 (tpp) REVERT: I 78 ILE cc_start: 0.9773 (mm) cc_final: 0.9568 (tp) REVERT: I 114 ASP cc_start: 0.8955 (t0) cc_final: 0.8534 (t0) REVERT: I 180 MET cc_start: 0.9478 (mmp) cc_final: 0.9259 (mmm) REVERT: J 40 MET cc_start: 0.8486 (tpp) cc_final: 0.8120 (tpp) REVERT: J 57 ASP cc_start: 0.8454 (t0) cc_final: 0.8237 (t0) REVERT: J 114 ASP cc_start: 0.8812 (t0) cc_final: 0.8549 (t0) REVERT: K 57 ASP cc_start: 0.8070 (t70) cc_final: 0.7844 (t0) REVERT: L 40 MET cc_start: 0.8774 (tpp) cc_final: 0.8407 (tpp) REVERT: N 21 GLN cc_start: 0.9332 (mt0) cc_final: 0.9011 (tp-100) REVERT: N 180 MET cc_start: 0.9435 (mmm) cc_final: 0.9180 (mmm) REVERT: O 112 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8322 (tp40) REVERT: O 114 ASP cc_start: 0.8187 (t0) cc_final: 0.7202 (p0) REVERT: O 180 MET cc_start: 0.9492 (mmm) cc_final: 0.9155 (mmm) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.6766 time to fit residues: 222.2911 Evaluate side-chains 156 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 3.237 ------------------------------------------------------------------------------- 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: 10.0000 chunk 63 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 319 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 J 191 ASN J 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 26325 Z= 0.327 Angle : 0.583 4.991 35325 Z= 0.339 Chirality : 0.031 0.118 4350 Planarity : 0.004 0.062 4620 Dihedral : 5.044 63.323 3765 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 1.11 (0.14), residues: 3375 helix: 0.91 (0.09), residues: 3210 sheet: None (None), residues: 0 loop : -1.06 (0.56), 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 173 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 3.291 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: A 23 MET cc_start: 0.8531 (mtt) cc_final: 0.8267 (mtp) REVERT: A 66 GLU cc_start: 0.9437 (tt0) cc_final: 0.9178 (tm-30) REVERT: B 114 ASP cc_start: 0.8801 (t0) cc_final: 0.8541 (t0) REVERT: B 176 ILE cc_start: 0.9506 (mt) cc_final: 0.9232 (tp) REVERT: B 192 ILE cc_start: 0.9429 (mt) cc_final: 0.9184 (tp) REVERT: F 40 MET cc_start: 0.9457 (ttp) cc_final: 0.9037 (tmm) REVERT: F 66 GLU cc_start: 0.9457 (tt0) cc_final: 0.8706 (tm-30) REVERT: F 176 ILE cc_start: 0.9240 (mt) cc_final: 0.9017 (tp) REVERT: F 190 GLU cc_start: 0.9237 (tt0) cc_final: 0.8821 (tp30) REVERT: G 180 MET cc_start: 0.9496 (mmp) cc_final: 0.9292 (mmp) REVERT: I 23 MET cc_start: 0.9141 (mmp) cc_final: 0.8719 (mmm) REVERT: I 40 MET cc_start: 0.8706 (tpt) cc_final: 0.8440 (tpp) REVERT: I 114 ASP cc_start: 0.9059 (t0) cc_final: 0.8655 (t0) REVERT: J 40 MET cc_start: 0.8581 (tpp) cc_final: 0.8231 (tpp) REVERT: J 57 ASP cc_start: 0.8397 (t0) cc_final: 0.8181 (t0) REVERT: J 114 ASP cc_start: 0.8792 (t0) cc_final: 0.8553 (t0) REVERT: K 57 ASP cc_start: 0.8047 (t70) cc_final: 0.7738 (t0) REVERT: N 21 GLN cc_start: 0.9388 (mt0) cc_final: 0.9030 (tp-100) REVERT: N 180 MET cc_start: 0.9455 (mmm) cc_final: 0.9202 (mmm) REVERT: O 112 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8373 (tp40) REVERT: O 114 ASP cc_start: 0.8329 (t0) cc_final: 0.7296 (p0) REVERT: O 180 MET cc_start: 0.9480 (mmm) cc_final: 0.9262 (mmp) REVERT: O 203 GLU cc_start: 0.8827 (tt0) cc_final: 0.8570 (tm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.6451 time to fit residues: 186.4128 Evaluate side-chains 143 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.258 ------------------------------------------------------------------------------- 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: 20.0000 chunk 35 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 233 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 178 optimal weight: 7.9990 chunk 318 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 193 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 216 GLN O 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 26325 Z= 0.346 Angle : 0.609 5.955 35325 Z= 0.353 Chirality : 0.031 0.112 4350 Planarity : 0.005 0.073 4620 Dihedral : 5.016 66.017 3765 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3375 helix: 0.53 (0.09), residues: 3225 sheet: None (None), residues: 0 loop : -0.66 (0.58), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 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 171 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 3.267 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: A 66 GLU cc_start: 0.9522 (tt0) cc_final: 0.9233 (tm-30) REVERT: B 114 ASP cc_start: 0.8766 (t0) cc_final: 0.8520 (t0) REVERT: B 176 ILE cc_start: 0.9514 (mt) cc_final: 0.9233 (tp) REVERT: B 192 ILE cc_start: 0.9442 (mt) cc_final: 0.9216 (tp) REVERT: F 66 GLU cc_start: 0.9472 (tt0) cc_final: 0.8751 (tm-30) REVERT: F 176 ILE cc_start: 0.9282 (mt) cc_final: 0.9077 (tp) REVERT: F 180 MET cc_start: 0.9356 (mmp) cc_final: 0.9132 (mmm) REVERT: F 190 GLU cc_start: 0.9285 (tt0) cc_final: 0.8858 (tp30) REVERT: G 40 MET cc_start: 0.9318 (tmm) cc_final: 0.9110 (tmm) REVERT: I 40 MET cc_start: 0.8648 (tpt) cc_final: 0.8355 (tpp) REVERT: I 114 ASP cc_start: 0.9104 (t0) cc_final: 0.8732 (t0) REVERT: J 40 MET cc_start: 0.8631 (tpp) cc_final: 0.8261 (tpp) REVERT: J 57 ASP cc_start: 0.8448 (t0) cc_final: 0.8239 (t0) REVERT: J 114 ASP cc_start: 0.8880 (t0) cc_final: 0.8639 (t0) REVERT: J 180 MET cc_start: 0.9454 (mmm) cc_final: 0.9227 (mmm) REVERT: L 114 ASP cc_start: 0.8635 (t0) cc_final: 0.8430 (t0) REVERT: M 66 GLU cc_start: 0.9474 (tt0) cc_final: 0.9197 (tm-30) REVERT: N 21 GLN cc_start: 0.9385 (mt0) cc_final: 0.9103 (tp-100) REVERT: N 40 MET cc_start: 0.8801 (ppp) cc_final: 0.8583 (ppp) REVERT: N 180 MET cc_start: 0.9457 (mmm) cc_final: 0.9204 (mmm) REVERT: O 112 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8409 (tp40) REVERT: O 114 ASP cc_start: 0.8413 (t0) cc_final: 0.7379 (p0) REVERT: O 203 GLU cc_start: 0.8978 (tt0) cc_final: 0.8695 (tm-30) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.6402 time to fit residues: 185.7189 Evaluate side-chains 142 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 3.232 ------------------------------------------------------------------------------- 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: 4.9990 chunk 189 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 202 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 26325 Z= 0.189 Angle : 0.474 4.344 35325 Z= 0.271 Chirality : 0.030 0.120 4350 Planarity : 0.004 0.062 4620 Dihedral : 4.903 65.378 3765 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 1.53 (0.14), residues: 3375 helix: 1.18 (0.09), residues: 3210 sheet: None (None), residues: 0 loop : -0.93 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 181 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 3.368 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: A 16 GLU cc_start: 0.9572 (tt0) cc_final: 0.9240 (tm-30) REVERT: A 66 GLU cc_start: 0.9512 (tt0) cc_final: 0.9094 (tm-30) REVERT: A 146 GLU cc_start: 0.9241 (tt0) cc_final: 0.8978 (tm-30) REVERT: B 114 ASP cc_start: 0.8747 (t0) cc_final: 0.8514 (t0) REVERT: B 176 ILE cc_start: 0.9511 (mt) cc_final: 0.9228 (tp) REVERT: B 192 ILE cc_start: 0.9427 (mt) cc_final: 0.9198 (tp) REVERT: F 16 GLU cc_start: 0.9294 (tt0) cc_final: 0.8963 (tm-30) REVERT: F 66 GLU cc_start: 0.9432 (tt0) cc_final: 0.8676 (tm-30) REVERT: F 180 MET cc_start: 0.9344 (mmp) cc_final: 0.9127 (mmp) REVERT: F 190 GLU cc_start: 0.9264 (tt0) cc_final: 0.8873 (tp30) REVERT: G 16 GLU cc_start: 0.9616 (tt0) cc_final: 0.9262 (tm-30) REVERT: H 16 GLU cc_start: 0.9530 (tt0) cc_final: 0.9015 (tm-30) REVERT: I 16 GLU cc_start: 0.9303 (tt0) cc_final: 0.8744 (tm-30) REVERT: I 114 ASP cc_start: 0.9036 (t0) cc_final: 0.8706 (t0) REVERT: J 40 MET cc_start: 0.8575 (tpp) cc_final: 0.8186 (tpp) REVERT: J 57 ASP cc_start: 0.8398 (t0) cc_final: 0.8185 (t0) REVERT: J 114 ASP cc_start: 0.8786 (t0) cc_final: 0.8544 (t0) REVERT: K 40 MET cc_start: 0.8637 (tpp) cc_final: 0.8250 (tpp) REVERT: N 21 GLN cc_start: 0.9394 (mt0) cc_final: 0.9089 (tp-100) REVERT: N 40 MET cc_start: 0.8791 (ppp) cc_final: 0.8580 (ppp) REVERT: N 180 MET cc_start: 0.9435 (mmm) cc_final: 0.9164 (mmm) REVERT: O 112 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8382 (tp40) REVERT: O 114 ASP cc_start: 0.8337 (t0) cc_final: 0.7289 (p0) REVERT: O 203 GLU cc_start: 0.8888 (tt0) cc_final: 0.8630 (tm-30) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.6818 time to fit residues: 207.4367 Evaluate side-chains 149 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.242 ------------------------------------------------------------------------------- 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: 6.9990 chunk 304 optimal weight: 5.9990 chunk 278 optimal weight: 9.9990 chunk 296 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 267 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8339 moved from start: 0.6995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26325 Z= 0.212 Angle : 0.484 5.026 35325 Z= 0.278 Chirality : 0.030 0.113 4350 Planarity : 0.004 0.050 4620 Dihedral : 4.722 64.808 3765 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 1.80 (0.14), residues: 3375 helix: 1.35 (0.09), residues: 3210 sheet: None (None), residues: 0 loop : -0.91 (0.48), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 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 183 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 3.318 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: A 16 GLU cc_start: 0.9568 (tt0) cc_final: 0.9265 (tm-30) REVERT: A 66 GLU cc_start: 0.9512 (tt0) cc_final: 0.9111 (tm-30) REVERT: A 146 GLU cc_start: 0.9284 (tt0) cc_final: 0.9019 (tm-30) REVERT: B 114 ASP cc_start: 0.8742 (t0) cc_final: 0.8483 (t0) REVERT: B 176 ILE cc_start: 0.9546 (mt) cc_final: 0.9272 (tp) REVERT: B 192 ILE cc_start: 0.9467 (mt) cc_final: 0.9191 (tp) REVERT: F 16 GLU cc_start: 0.9288 (tt0) cc_final: 0.8968 (tm-30) REVERT: F 66 GLU cc_start: 0.9414 (tt0) cc_final: 0.8637 (tm-30) REVERT: F 180 MET cc_start: 0.9359 (mmp) cc_final: 0.9103 (mmp) REVERT: F 190 GLU cc_start: 0.9262 (tt0) cc_final: 0.8882 (tp30) REVERT: G 16 GLU cc_start: 0.9577 (tt0) cc_final: 0.9216 (tm-30) REVERT: H 16 GLU cc_start: 0.9552 (tt0) cc_final: 0.9028 (tm-30) REVERT: I 16 GLU cc_start: 0.9357 (tt0) cc_final: 0.8746 (tm-30) REVERT: I 23 MET cc_start: 0.8850 (mmp) cc_final: 0.8485 (mmm) REVERT: I 114 ASP cc_start: 0.9039 (t0) cc_final: 0.8711 (t0) REVERT: I 123 GLU cc_start: 0.9055 (tt0) cc_final: 0.8513 (tm-30) REVERT: J 40 MET cc_start: 0.8625 (tpp) cc_final: 0.8248 (tpp) REVERT: J 57 ASP cc_start: 0.8400 (t0) cc_final: 0.8180 (t0) REVERT: J 114 ASP cc_start: 0.8779 (t0) cc_final: 0.8538 (t0) REVERT: J 180 MET cc_start: 0.9445 (mmm) cc_final: 0.9204 (mmm) REVERT: K 40 MET cc_start: 0.8642 (tpp) cc_final: 0.8263 (tpp) REVERT: N 21 GLN cc_start: 0.9375 (mt0) cc_final: 0.9079 (tp-100) REVERT: N 40 MET cc_start: 0.8774 (ppp) cc_final: 0.8566 (ppp) REVERT: N 180 MET cc_start: 0.9422 (mmm) cc_final: 0.9172 (mmm) REVERT: O 112 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8507 (tp40) REVERT: O 114 ASP cc_start: 0.8341 (t0) cc_final: 0.7269 (p0) REVERT: O 203 GLU cc_start: 0.8925 (tt0) cc_final: 0.8651 (tm-30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.6886 time to fit residues: 211.1036 Evaluate side-chains 153 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.210 ------------------------------------------------------------------------------- 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: 6.9990 chunk 313 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 328 optimal weight: 5.9990 chunk 302 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 202 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.7136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26325 Z= 0.147 Angle : 0.435 5.190 35325 Z= 0.245 Chirality : 0.029 0.118 4350 Planarity : 0.003 0.043 4620 Dihedral : 4.622 65.409 3765 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 2.54 (0.14), residues: 3375 helix: 1.84 (0.09), residues: 3210 sheet: None (None), residues: 0 loop : -1.05 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 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 195 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.424 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: A 16 GLU cc_start: 0.9568 (tt0) cc_final: 0.9244 (tm-30) REVERT: A 66 GLU cc_start: 0.9488 (tt0) cc_final: 0.9081 (tm-30) REVERT: A 146 GLU cc_start: 0.9268 (tt0) cc_final: 0.9007 (tm-30) REVERT: A 192 ILE cc_start: 0.9364 (mt) cc_final: 0.9052 (tp) REVERT: B 114 ASP cc_start: 0.8706 (t0) cc_final: 0.8447 (t0) REVERT: B 176 ILE cc_start: 0.9554 (mt) cc_final: 0.9277 (tp) REVERT: B 192 ILE cc_start: 0.9468 (mt) cc_final: 0.9174 (tp) REVERT: F 16 GLU cc_start: 0.9271 (tt0) cc_final: 0.8925 (tm-30) REVERT: F 66 GLU cc_start: 0.9395 (tt0) cc_final: 0.8652 (tm-30) REVERT: F 180 MET cc_start: 0.9364 (mmp) cc_final: 0.9105 (mmp) REVERT: F 190 GLU cc_start: 0.9262 (tt0) cc_final: 0.8922 (tp30) REVERT: G 16 GLU cc_start: 0.9587 (tt0) cc_final: 0.9254 (tm-30) REVERT: G 40 MET cc_start: 0.9288 (tmm) cc_final: 0.9059 (tmm) REVERT: G 114 ASP cc_start: 0.8734 (t0) cc_final: 0.8514 (t0) REVERT: G 153 GLU cc_start: 0.9401 (tt0) cc_final: 0.9077 (tp30) REVERT: H 16 GLU cc_start: 0.9523 (tt0) cc_final: 0.8995 (tm-30) REVERT: H 132 LEU cc_start: 0.9732 (mt) cc_final: 0.9444 (tp) REVERT: I 16 GLU cc_start: 0.9317 (tt0) cc_final: 0.8697 (tm-30) REVERT: I 114 ASP cc_start: 0.8964 (t0) cc_final: 0.8639 (t0) REVERT: I 123 GLU cc_start: 0.9034 (tt0) cc_final: 0.8489 (tm-30) REVERT: J 40 MET cc_start: 0.8510 (tpp) cc_final: 0.8101 (tpp) REVERT: J 57 ASP cc_start: 0.8340 (t0) cc_final: 0.8111 (t0) REVERT: J 114 ASP cc_start: 0.8741 (t0) cc_final: 0.8498 (t0) REVERT: J 180 MET cc_start: 0.9435 (mmm) cc_final: 0.9183 (mmm) REVERT: K 40 MET cc_start: 0.8554 (tpp) cc_final: 0.8157 (tpp) REVERT: N 21 GLN cc_start: 0.9360 (mt0) cc_final: 0.9089 (tp-100) REVERT: N 40 MET cc_start: 0.8769 (ppp) cc_final: 0.8569 (ppp) REVERT: N 180 MET cc_start: 0.9400 (mmm) cc_final: 0.9152 (mmm) REVERT: O 112 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8664 (tp40) REVERT: O 114 ASP cc_start: 0.8284 (t0) cc_final: 0.7211 (p0) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.6456 time to fit residues: 209.2491 Evaluate side-chains 154 residues out of total 2685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 3.263 ------------------------------------------------------------------------------- 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: 8.9990 chunk 278 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 241 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 262 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.046609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.036819 restraints weight = 468523.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.038730 restraints weight = 235966.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.040061 restraints weight = 145797.767| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.7261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26325 Z= 0.255 Angle : 0.515 4.661 35325 Z= 0.298 Chirality : 0.030 0.112 4350 Planarity : 0.004 0.041 4620 Dihedral : 4.559 64.789 3765 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % 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: 2.09 (0.14), residues: 3375 helix: 1.53 (0.09), residues: 3225 sheet: None (None), residues: 0 loop : -0.80 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 70 =============================================================================== Job complete usr+sys time: 6397.98 seconds wall clock time: 112 minutes 20.11 seconds (6740.11 seconds total)