Starting phenix.real_space_refine on Fri Mar 6 18:48:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hxz_0298/03_2026/6hxz_0298_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hxz_0298/03_2026/6hxz_0298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6hxz_0298/03_2026/6hxz_0298_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hxz_0298/03_2026/6hxz_0298_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hxz_0298/03_2026/6hxz_0298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hxz_0298/03_2026/6hxz_0298.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.354 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 264 5.16 5 C 21504 2.51 5 N 5880 2.21 5 O 6360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34008 Number of models: 1 Model: "" Number of chains: 1 Chain: "a" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Restraints were copied for chains: b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x Time building chain proxies: 3.09, per 1000 atoms: 0.09 Number of scatterers: 34008 At special positions: 0 Unit cell: (134.747, 134.747, 157.028, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 264 16.00 O 6360 8.00 N 5880 7.00 C 21504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.5 seconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 24 sheets defined 50.0% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'a' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU a 72 " --> pdb=" O GLU a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 80 Processing helix chain 'a' and resid 86 through 100 Processing helix chain 'a' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET a 112 " --> pdb=" O MET a 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN a 113 " --> pdb=" O PRO a 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY a 114 " --> pdb=" O THR a 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL a 117 " --> pdb=" O ASN a 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU a 121 " --> pdb=" O VAL a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL a 149 " --> pdb=" O LEU a 145 " (cutoff:3.500A) Processing helix chain 'a' and resid 155 through 161 Processing helix chain 'a' and resid 163 through 178 removed outlier: 3.766A pdb=" N GLU a 168 " --> pdb=" O SER a 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA a 169 " --> pdb=" O ASP a 165 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU a 172 " --> pdb=" O GLU a 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET a 173 " --> pdb=" O ALA a 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS a 176 " --> pdb=" O GLU a 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS a 177 " --> pdb=" O MET a 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU a 178 " --> pdb=" O ARG a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 189 Processing helix chain 'a' and resid 210 through 218 removed outlier: 3.516A pdb=" N GLU a 215 " --> pdb=" O VAL a 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA a 216 " --> pdb=" O ARG a 212 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS a 217 " --> pdb=" O ALA a 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE a 218 " --> pdb=" O ARG a 214 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU b 72 " --> pdb=" O GLU b 68 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 80 Processing helix chain 'b' and resid 86 through 100 Processing helix chain 'b' and resid 108 through 122 removed outlier: 3.570A pdb=" N MET b 112 " --> pdb=" O MET b 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN b 113 " --> pdb=" O PRO b 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY b 114 " --> pdb=" O THR b 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL b 117 " --> pdb=" O ASN b 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU b 121 " --> pdb=" O VAL b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL b 149 " --> pdb=" O LEU b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 155 through 161 Processing helix chain 'b' and resid 163 through 178 removed outlier: 3.766A pdb=" N GLU b 168 " --> pdb=" O SER b 164 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA b 169 " --> pdb=" O ASP b 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU b 172 " --> pdb=" O GLU b 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET b 173 " --> pdb=" O ALA b 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS b 176 " --> pdb=" O GLU b 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS b 177 " --> pdb=" O MET b 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU b 178 " --> pdb=" O ARG b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 189 Processing helix chain 'b' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU b 215 " --> pdb=" O VAL b 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA b 216 " --> pdb=" O ARG b 212 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS b 217 " --> pdb=" O ALA b 213 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE b 218 " --> pdb=" O ARG b 214 " (cutoff:3.500A) Processing helix chain 'c' and resid 66 through 72 removed outlier: 3.502A pdb=" N GLU c 72 " --> pdb=" O GLU c 68 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 80 Processing helix chain 'c' and resid 86 through 100 Processing helix chain 'c' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET c 112 " --> pdb=" O MET c 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY c 114 " --> pdb=" O THR c 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL c 117 " --> pdb=" O ASN c 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU c 121 " --> pdb=" O VAL c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL c 149 " --> pdb=" O LEU c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 155 through 161 Processing helix chain 'c' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU c 168 " --> pdb=" O SER c 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA c 169 " --> pdb=" O ASP c 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU c 172 " --> pdb=" O GLU c 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET c 173 " --> pdb=" O ALA c 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS c 176 " --> pdb=" O GLU c 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS c 177 " --> pdb=" O MET c 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU c 178 " --> pdb=" O ARG c 174 " (cutoff:3.500A) Processing helix chain 'c' and resid 182 through 189 Processing helix chain 'c' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU c 215 " --> pdb=" O VAL c 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA c 216 " --> pdb=" O ARG c 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS c 217 " --> pdb=" O ALA c 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE c 218 " --> pdb=" O ARG c 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU d 72 " --> pdb=" O GLU d 68 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 80 Processing helix chain 'd' and resid 86 through 100 Processing helix chain 'd' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET d 112 " --> pdb=" O MET d 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN d 113 " --> pdb=" O PRO d 109 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY d 114 " --> pdb=" O THR d 110 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL d 117 " --> pdb=" O ASN d 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU d 121 " --> pdb=" O VAL d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL d 149 " --> pdb=" O LEU d 145 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 161 Processing helix chain 'd' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU d 168 " --> pdb=" O SER d 164 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA d 169 " --> pdb=" O ASP d 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU d 172 " --> pdb=" O GLU d 168 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET d 173 " --> pdb=" O ALA d 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS d 176 " --> pdb=" O GLU d 172 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS d 177 " --> pdb=" O MET d 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU d 178 " --> pdb=" O ARG d 174 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 189 Processing helix chain 'd' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU d 215 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA d 216 " --> pdb=" O ARG d 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS d 217 " --> pdb=" O ALA d 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE d 218 " --> pdb=" O ARG d 214 " (cutoff:3.500A) Processing helix chain 'e' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU e 72 " --> pdb=" O GLU e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 76 through 80 Processing helix chain 'e' and resid 86 through 100 Processing helix chain 'e' and resid 108 through 122 removed outlier: 3.572A pdb=" N MET e 112 " --> pdb=" O MET e 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN e 113 " --> pdb=" O PRO e 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY e 114 " --> pdb=" O THR e 110 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL e 117 " --> pdb=" O ASN e 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU e 121 " --> pdb=" O VAL e 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL e 149 " --> pdb=" O LEU e 145 " (cutoff:3.500A) Processing helix chain 'e' and resid 155 through 161 Processing helix chain 'e' and resid 163 through 178 removed outlier: 3.766A pdb=" N GLU e 168 " --> pdb=" O SER e 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA e 169 " --> pdb=" O ASP e 165 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU e 172 " --> pdb=" O GLU e 168 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET e 173 " --> pdb=" O ALA e 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS e 176 " --> pdb=" O GLU e 172 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS e 177 " --> pdb=" O MET e 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU e 178 " --> pdb=" O ARG e 174 " (cutoff:3.500A) Processing helix chain 'e' and resid 182 through 189 Processing helix chain 'e' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU e 215 " --> pdb=" O VAL e 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA e 216 " --> pdb=" O ARG e 212 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS e 217 " --> pdb=" O ALA e 213 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE e 218 " --> pdb=" O ARG e 214 " (cutoff:3.500A) Processing helix chain 'f' and resid 66 through 72 removed outlier: 3.502A pdb=" N GLU f 72 " --> pdb=" O GLU f 68 " (cutoff:3.500A) Processing helix chain 'f' and resid 76 through 80 Processing helix chain 'f' and resid 86 through 100 Processing helix chain 'f' and resid 108 through 122 removed outlier: 3.572A pdb=" N MET f 112 " --> pdb=" O MET f 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN f 113 " --> pdb=" O PRO f 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY f 114 " --> pdb=" O THR f 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL f 117 " --> pdb=" O ASN f 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU f 121 " --> pdb=" O VAL f 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL f 149 " --> pdb=" O LEU f 145 " (cutoff:3.500A) Processing helix chain 'f' and resid 155 through 161 Processing helix chain 'f' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU f 168 " --> pdb=" O SER f 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA f 169 " --> pdb=" O ASP f 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU f 172 " --> pdb=" O GLU f 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET f 173 " --> pdb=" O ALA f 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS f 176 " --> pdb=" O GLU f 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS f 177 " --> pdb=" O MET f 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU f 178 " --> pdb=" O ARG f 174 " (cutoff:3.500A) Processing helix chain 'f' and resid 182 through 189 Processing helix chain 'f' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU f 215 " --> pdb=" O VAL f 211 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA f 216 " --> pdb=" O ARG f 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS f 217 " --> pdb=" O ALA f 213 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE f 218 " --> pdb=" O ARG f 214 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 72 removed outlier: 3.502A pdb=" N GLU g 72 " --> pdb=" O GLU g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 Processing helix chain 'g' and resid 86 through 100 Processing helix chain 'g' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET g 112 " --> pdb=" O MET g 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN g 113 " --> pdb=" O PRO g 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY g 114 " --> pdb=" O THR g 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL g 117 " --> pdb=" O ASN g 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU g 121 " --> pdb=" O VAL g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL g 149 " --> pdb=" O LEU g 145 " (cutoff:3.500A) Processing helix chain 'g' and resid 155 through 161 Processing helix chain 'g' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU g 168 " --> pdb=" O SER g 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA g 169 " --> pdb=" O ASP g 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU g 172 " --> pdb=" O GLU g 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET g 173 " --> pdb=" O ALA g 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS g 176 " --> pdb=" O GLU g 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS g 177 " --> pdb=" O MET g 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU g 178 " --> pdb=" O ARG g 174 " (cutoff:3.500A) Processing helix chain 'g' and resid 182 through 189 Processing helix chain 'g' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU g 215 " --> pdb=" O VAL g 211 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA g 216 " --> pdb=" O ARG g 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS g 217 " --> pdb=" O ALA g 213 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE g 218 " --> pdb=" O ARG g 214 " (cutoff:3.500A) Processing helix chain 'h' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU h 72 " --> pdb=" O GLU h 68 " (cutoff:3.500A) Processing helix chain 'h' and resid 76 through 80 Processing helix chain 'h' and resid 86 through 100 Processing helix chain 'h' and resid 108 through 122 removed outlier: 3.572A pdb=" N MET h 112 " --> pdb=" O MET h 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY h 114 " --> pdb=" O THR h 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL h 117 " --> pdb=" O ASN h 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU h 121 " --> pdb=" O VAL h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL h 149 " --> pdb=" O LEU h 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 155 through 161 Processing helix chain 'h' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU h 168 " --> pdb=" O SER h 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA h 169 " --> pdb=" O ASP h 165 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU h 172 " --> pdb=" O GLU h 168 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET h 173 " --> pdb=" O ALA h 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS h 176 " --> pdb=" O GLU h 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS h 177 " --> pdb=" O MET h 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU h 178 " --> pdb=" O ARG h 174 " (cutoff:3.500A) Processing helix chain 'h' and resid 182 through 189 Processing helix chain 'h' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU h 215 " --> pdb=" O VAL h 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA h 216 " --> pdb=" O ARG h 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS h 217 " --> pdb=" O ALA h 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE h 218 " --> pdb=" O ARG h 214 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 72 removed outlier: 3.502A pdb=" N GLU i 72 " --> pdb=" O GLU i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 80 Processing helix chain 'i' and resid 86 through 100 Processing helix chain 'i' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET i 112 " --> pdb=" O MET i 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN i 113 " --> pdb=" O PRO i 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY i 114 " --> pdb=" O THR i 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL i 117 " --> pdb=" O ASN i 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU i 121 " --> pdb=" O VAL i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL i 149 " --> pdb=" O LEU i 145 " (cutoff:3.500A) Processing helix chain 'i' and resid 155 through 161 Processing helix chain 'i' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU i 168 " --> pdb=" O SER i 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA i 169 " --> pdb=" O ASP i 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU i 172 " --> pdb=" O GLU i 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET i 173 " --> pdb=" O ALA i 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS i 176 " --> pdb=" O GLU i 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS i 177 " --> pdb=" O MET i 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU i 178 " --> pdb=" O ARG i 174 " (cutoff:3.500A) Processing helix chain 'i' and resid 182 through 189 Processing helix chain 'i' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU i 215 " --> pdb=" O VAL i 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA i 216 " --> pdb=" O ARG i 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS i 217 " --> pdb=" O ALA i 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE i 218 " --> pdb=" O ARG i 214 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 72 removed outlier: 3.502A pdb=" N GLU j 72 " --> pdb=" O GLU j 68 " (cutoff:3.500A) Processing helix chain 'j' and resid 76 through 80 Processing helix chain 'j' and resid 86 through 100 Processing helix chain 'j' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET j 112 " --> pdb=" O MET j 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN j 113 " --> pdb=" O PRO j 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY j 114 " --> pdb=" O THR j 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL j 117 " --> pdb=" O ASN j 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU j 121 " --> pdb=" O VAL j 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL j 149 " --> pdb=" O LEU j 145 " (cutoff:3.500A) Processing helix chain 'j' and resid 155 through 161 Processing helix chain 'j' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU j 168 " --> pdb=" O SER j 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA j 169 " --> pdb=" O ASP j 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU j 172 " --> pdb=" O GLU j 168 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET j 173 " --> pdb=" O ALA j 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS j 176 " --> pdb=" O GLU j 172 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS j 177 " --> pdb=" O MET j 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU j 178 " --> pdb=" O ARG j 174 " (cutoff:3.500A) Processing helix chain 'j' and resid 182 through 189 Processing helix chain 'j' and resid 210 through 218 removed outlier: 3.516A pdb=" N GLU j 215 " --> pdb=" O VAL j 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA j 216 " --> pdb=" O ARG j 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS j 217 " --> pdb=" O ALA j 213 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE j 218 " --> pdb=" O ARG j 214 " (cutoff:3.500A) Processing helix chain 'k' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU k 72 " --> pdb=" O GLU k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 80 Processing helix chain 'k' and resid 86 through 100 Processing helix chain 'k' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET k 112 " --> pdb=" O MET k 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN k 113 " --> pdb=" O PRO k 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY k 114 " --> pdb=" O THR k 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL k 117 " --> pdb=" O ASN k 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU k 121 " --> pdb=" O VAL k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL k 149 " --> pdb=" O LEU k 145 " (cutoff:3.500A) Processing helix chain 'k' and resid 155 through 161 Processing helix chain 'k' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU k 168 " --> pdb=" O SER k 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA k 169 " --> pdb=" O ASP k 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU k 172 " --> pdb=" O GLU k 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET k 173 " --> pdb=" O ALA k 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS k 176 " --> pdb=" O GLU k 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS k 177 " --> pdb=" O MET k 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU k 178 " --> pdb=" O ARG k 174 " (cutoff:3.500A) Processing helix chain 'k' and resid 182 through 189 Processing helix chain 'k' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU k 215 " --> pdb=" O VAL k 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA k 216 " --> pdb=" O ARG k 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS k 217 " --> pdb=" O ALA k 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE k 218 " --> pdb=" O ARG k 214 " (cutoff:3.500A) Processing helix chain 'l' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU l 72 " --> pdb=" O GLU l 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 80 Processing helix chain 'l' and resid 86 through 100 Processing helix chain 'l' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET l 112 " --> pdb=" O MET l 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN l 113 " --> pdb=" O PRO l 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY l 114 " --> pdb=" O THR l 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL l 117 " --> pdb=" O ASN l 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU l 121 " --> pdb=" O VAL l 117 " (cutoff:3.500A) Processing helix chain 'l' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL l 149 " --> pdb=" O LEU l 145 " (cutoff:3.500A) Processing helix chain 'l' and resid 155 through 161 Processing helix chain 'l' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU l 168 " --> pdb=" O SER l 164 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA l 169 " --> pdb=" O ASP l 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU l 172 " --> pdb=" O GLU l 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET l 173 " --> pdb=" O ALA l 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS l 176 " --> pdb=" O GLU l 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS l 177 " --> pdb=" O MET l 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) Processing helix chain 'l' and resid 182 through 189 Processing helix chain 'l' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU l 215 " --> pdb=" O VAL l 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA l 216 " --> pdb=" O ARG l 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS l 217 " --> pdb=" O ALA l 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE l 218 " --> pdb=" O ARG l 214 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU m 72 " --> pdb=" O GLU m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 76 through 80 Processing helix chain 'm' and resid 86 through 100 Processing helix chain 'm' and resid 108 through 122 removed outlier: 3.572A pdb=" N MET m 112 " --> pdb=" O MET m 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN m 113 " --> pdb=" O PRO m 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY m 114 " --> pdb=" O THR m 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL m 117 " --> pdb=" O ASN m 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU m 121 " --> pdb=" O VAL m 117 " (cutoff:3.500A) Processing helix chain 'm' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL m 149 " --> pdb=" O LEU m 145 " (cutoff:3.500A) Processing helix chain 'm' and resid 155 through 161 Processing helix chain 'm' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU m 168 " --> pdb=" O SER m 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA m 169 " --> pdb=" O ASP m 165 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU m 172 " --> pdb=" O GLU m 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET m 173 " --> pdb=" O ALA m 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS m 176 " --> pdb=" O GLU m 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS m 177 " --> pdb=" O MET m 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU m 178 " --> pdb=" O ARG m 174 " (cutoff:3.500A) Processing helix chain 'm' and resid 182 through 189 Processing helix chain 'm' and resid 210 through 218 removed outlier: 3.516A pdb=" N GLU m 215 " --> pdb=" O VAL m 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA m 216 " --> pdb=" O ARG m 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS m 217 " --> pdb=" O ALA m 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE m 218 " --> pdb=" O ARG m 214 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU n 72 " --> pdb=" O GLU n 68 " (cutoff:3.500A) Processing helix chain 'n' and resid 76 through 80 Processing helix chain 'n' and resid 86 through 100 Processing helix chain 'n' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET n 112 " --> pdb=" O MET n 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN n 113 " --> pdb=" O PRO n 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY n 114 " --> pdb=" O THR n 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL n 117 " --> pdb=" O ASN n 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU n 121 " --> pdb=" O VAL n 117 " (cutoff:3.500A) Processing helix chain 'n' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL n 149 " --> pdb=" O LEU n 145 " (cutoff:3.500A) Processing helix chain 'n' and resid 155 through 161 Processing helix chain 'n' and resid 163 through 178 removed outlier: 3.766A pdb=" N GLU n 168 " --> pdb=" O SER n 164 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA n 169 " --> pdb=" O ASP n 165 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU n 172 " --> pdb=" O GLU n 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET n 173 " --> pdb=" O ALA n 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS n 176 " --> pdb=" O GLU n 172 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS n 177 " --> pdb=" O MET n 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU n 178 " --> pdb=" O ARG n 174 " (cutoff:3.500A) Processing helix chain 'n' and resid 182 through 189 Processing helix chain 'n' and resid 210 through 218 removed outlier: 3.516A pdb=" N GLU n 215 " --> pdb=" O VAL n 211 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA n 216 " --> pdb=" O ARG n 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS n 217 " --> pdb=" O ALA n 213 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE n 218 " --> pdb=" O ARG n 214 " (cutoff:3.500A) Processing helix chain 'o' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU o 72 " --> pdb=" O GLU o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 76 through 80 Processing helix chain 'o' and resid 86 through 100 Processing helix chain 'o' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET o 112 " --> pdb=" O MET o 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN o 113 " --> pdb=" O PRO o 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY o 114 " --> pdb=" O THR o 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL o 117 " --> pdb=" O ASN o 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU o 121 " --> pdb=" O VAL o 117 " (cutoff:3.500A) Processing helix chain 'o' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL o 149 " --> pdb=" O LEU o 145 " (cutoff:3.500A) Processing helix chain 'o' and resid 155 through 161 Processing helix chain 'o' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU o 168 " --> pdb=" O SER o 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA o 169 " --> pdb=" O ASP o 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU o 172 " --> pdb=" O GLU o 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET o 173 " --> pdb=" O ALA o 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS o 176 " --> pdb=" O GLU o 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS o 177 " --> pdb=" O MET o 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU o 178 " --> pdb=" O ARG o 174 " (cutoff:3.500A) Processing helix chain 'o' and resid 182 through 189 Processing helix chain 'o' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU o 215 " --> pdb=" O VAL o 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA o 216 " --> pdb=" O ARG o 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS o 217 " --> pdb=" O ALA o 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE o 218 " --> pdb=" O ARG o 214 " (cutoff:3.500A) Processing helix chain 'p' and resid 66 through 72 removed outlier: 3.502A pdb=" N GLU p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 80 Processing helix chain 'p' and resid 86 through 100 Processing helix chain 'p' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET p 112 " --> pdb=" O MET p 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN p 113 " --> pdb=" O PRO p 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY p 114 " --> pdb=" O THR p 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL p 117 " --> pdb=" O ASN p 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU p 121 " --> pdb=" O VAL p 117 " (cutoff:3.500A) Processing helix chain 'p' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL p 149 " --> pdb=" O LEU p 145 " (cutoff:3.500A) Processing helix chain 'p' and resid 155 through 161 Processing helix chain 'p' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU p 168 " --> pdb=" O SER p 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA p 169 " --> pdb=" O ASP p 165 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU p 172 " --> pdb=" O GLU p 168 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET p 173 " --> pdb=" O ALA p 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS p 176 " --> pdb=" O GLU p 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS p 177 " --> pdb=" O MET p 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU p 178 " --> pdb=" O ARG p 174 " (cutoff:3.500A) Processing helix chain 'p' and resid 182 through 189 Processing helix chain 'p' and resid 210 through 218 removed outlier: 3.516A pdb=" N GLU p 215 " --> pdb=" O VAL p 211 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA p 216 " --> pdb=" O ARG p 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS p 217 " --> pdb=" O ALA p 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE p 218 " --> pdb=" O ARG p 214 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU q 72 " --> pdb=" O GLU q 68 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 80 Processing helix chain 'q' and resid 86 through 100 Processing helix chain 'q' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET q 112 " --> pdb=" O MET q 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN q 113 " --> pdb=" O PRO q 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY q 114 " --> pdb=" O THR q 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL q 117 " --> pdb=" O ASN q 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU q 121 " --> pdb=" O VAL q 117 " (cutoff:3.500A) Processing helix chain 'q' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL q 149 " --> pdb=" O LEU q 145 " (cutoff:3.500A) Processing helix chain 'q' and resid 155 through 161 Processing helix chain 'q' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU q 168 " --> pdb=" O SER q 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA q 169 " --> pdb=" O ASP q 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU q 172 " --> pdb=" O GLU q 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET q 173 " --> pdb=" O ALA q 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS q 176 " --> pdb=" O GLU q 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS q 177 " --> pdb=" O MET q 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU q 178 " --> pdb=" O ARG q 174 " (cutoff:3.500A) Processing helix chain 'q' and resid 182 through 189 Processing helix chain 'q' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU q 215 " --> pdb=" O VAL q 211 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA q 216 " --> pdb=" O ARG q 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS q 217 " --> pdb=" O ALA q 213 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE q 218 " --> pdb=" O ARG q 214 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 72 removed outlier: 3.502A pdb=" N GLU r 72 " --> pdb=" O GLU r 68 " (cutoff:3.500A) Processing helix chain 'r' and resid 76 through 80 Processing helix chain 'r' and resid 86 through 100 Processing helix chain 'r' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET r 112 " --> pdb=" O MET r 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN r 113 " --> pdb=" O PRO r 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY r 114 " --> pdb=" O THR r 110 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL r 117 " --> pdb=" O ASN r 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU r 121 " --> pdb=" O VAL r 117 " (cutoff:3.500A) Processing helix chain 'r' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL r 149 " --> pdb=" O LEU r 145 " (cutoff:3.500A) Processing helix chain 'r' and resid 155 through 161 Processing helix chain 'r' and resid 163 through 178 removed outlier: 3.766A pdb=" N GLU r 168 " --> pdb=" O SER r 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA r 169 " --> pdb=" O ASP r 165 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU r 172 " --> pdb=" O GLU r 168 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET r 173 " --> pdb=" O ALA r 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS r 176 " --> pdb=" O GLU r 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS r 177 " --> pdb=" O MET r 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU r 178 " --> pdb=" O ARG r 174 " (cutoff:3.500A) Processing helix chain 'r' and resid 182 through 189 Processing helix chain 'r' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU r 215 " --> pdb=" O VAL r 211 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA r 216 " --> pdb=" O ARG r 212 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS r 217 " --> pdb=" O ALA r 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE r 218 " --> pdb=" O ARG r 214 " (cutoff:3.500A) Processing helix chain 's' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU s 72 " --> pdb=" O GLU s 68 " (cutoff:3.500A) Processing helix chain 's' and resid 76 through 80 Processing helix chain 's' and resid 86 through 100 Processing helix chain 's' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET s 112 " --> pdb=" O MET s 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN s 113 " --> pdb=" O PRO s 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY s 114 " --> pdb=" O THR s 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL s 117 " --> pdb=" O ASN s 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU s 121 " --> pdb=" O VAL s 117 " (cutoff:3.500A) Processing helix chain 's' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL s 149 " --> pdb=" O LEU s 145 " (cutoff:3.500A) Processing helix chain 's' and resid 155 through 161 Processing helix chain 's' and resid 163 through 178 removed outlier: 3.766A pdb=" N GLU s 168 " --> pdb=" O SER s 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA s 169 " --> pdb=" O ASP s 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU s 172 " --> pdb=" O GLU s 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET s 173 " --> pdb=" O ALA s 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS s 176 " --> pdb=" O GLU s 172 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS s 177 " --> pdb=" O MET s 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU s 178 " --> pdb=" O ARG s 174 " (cutoff:3.500A) Processing helix chain 's' and resid 182 through 189 Processing helix chain 's' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU s 215 " --> pdb=" O VAL s 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA s 216 " --> pdb=" O ARG s 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS s 217 " --> pdb=" O ALA s 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE s 218 " --> pdb=" O ARG s 214 " (cutoff:3.500A) Processing helix chain 't' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU t 72 " --> pdb=" O GLU t 68 " (cutoff:3.500A) Processing helix chain 't' and resid 76 through 80 Processing helix chain 't' and resid 86 through 100 Processing helix chain 't' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET t 112 " --> pdb=" O MET t 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN t 113 " --> pdb=" O PRO t 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY t 114 " --> pdb=" O THR t 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL t 117 " --> pdb=" O ASN t 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU t 121 " --> pdb=" O VAL t 117 " (cutoff:3.500A) Processing helix chain 't' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL t 149 " --> pdb=" O LEU t 145 " (cutoff:3.500A) Processing helix chain 't' and resid 155 through 161 Processing helix chain 't' and resid 163 through 178 removed outlier: 3.768A pdb=" N GLU t 168 " --> pdb=" O SER t 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA t 169 " --> pdb=" O ASP t 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU t 172 " --> pdb=" O GLU t 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET t 173 " --> pdb=" O ALA t 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS t 176 " --> pdb=" O GLU t 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS t 177 " --> pdb=" O MET t 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU t 178 " --> pdb=" O ARG t 174 " (cutoff:3.500A) Processing helix chain 't' and resid 182 through 189 Processing helix chain 't' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU t 215 " --> pdb=" O VAL t 211 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA t 216 " --> pdb=" O ARG t 212 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS t 217 " --> pdb=" O ALA t 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE t 218 " --> pdb=" O ARG t 214 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 72 removed outlier: 3.502A pdb=" N GLU u 72 " --> pdb=" O GLU u 68 " (cutoff:3.500A) Processing helix chain 'u' and resid 76 through 80 Processing helix chain 'u' and resid 86 through 100 Processing helix chain 'u' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET u 112 " --> pdb=" O MET u 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN u 113 " --> pdb=" O PRO u 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY u 114 " --> pdb=" O THR u 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL u 117 " --> pdb=" O ASN u 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU u 121 " --> pdb=" O VAL u 117 " (cutoff:3.500A) Processing helix chain 'u' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL u 149 " --> pdb=" O LEU u 145 " (cutoff:3.500A) Processing helix chain 'u' and resid 155 through 161 Processing helix chain 'u' and resid 163 through 178 removed outlier: 3.766A pdb=" N GLU u 168 " --> pdb=" O SER u 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA u 169 " --> pdb=" O ASP u 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU u 172 " --> pdb=" O GLU u 168 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET u 173 " --> pdb=" O ALA u 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS u 176 " --> pdb=" O GLU u 172 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS u 177 " --> pdb=" O MET u 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU u 178 " --> pdb=" O ARG u 174 " (cutoff:3.500A) Processing helix chain 'u' and resid 182 through 189 Processing helix chain 'u' and resid 210 through 218 removed outlier: 3.516A pdb=" N GLU u 215 " --> pdb=" O VAL u 211 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA u 216 " --> pdb=" O ARG u 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS u 217 " --> pdb=" O ALA u 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE u 218 " --> pdb=" O ARG u 214 " (cutoff:3.500A) Processing helix chain 'v' and resid 66 through 72 removed outlier: 3.501A pdb=" N GLU v 72 " --> pdb=" O GLU v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 80 Processing helix chain 'v' and resid 86 through 100 Processing helix chain 'v' and resid 108 through 122 removed outlier: 3.572A pdb=" N MET v 112 " --> pdb=" O MET v 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN v 113 " --> pdb=" O PRO v 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY v 114 " --> pdb=" O THR v 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL v 117 " --> pdb=" O ASN v 113 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU v 121 " --> pdb=" O VAL v 117 " (cutoff:3.500A) Processing helix chain 'v' and resid 145 through 150 removed outlier: 3.721A pdb=" N VAL v 149 " --> pdb=" O LEU v 145 " (cutoff:3.500A) Processing helix chain 'v' and resid 155 through 161 Processing helix chain 'v' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU v 168 " --> pdb=" O SER v 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA v 169 " --> pdb=" O ASP v 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU v 172 " --> pdb=" O GLU v 168 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET v 173 " --> pdb=" O ALA v 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS v 176 " --> pdb=" O GLU v 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS v 177 " --> pdb=" O MET v 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU v 178 " --> pdb=" O ARG v 174 " (cutoff:3.500A) Processing helix chain 'v' and resid 182 through 189 Processing helix chain 'v' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU v 215 " --> pdb=" O VAL v 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA v 216 " --> pdb=" O ARG v 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS v 217 " --> pdb=" O ALA v 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE v 218 " --> pdb=" O ARG v 214 " (cutoff:3.500A) Processing helix chain 'w' and resid 66 through 72 removed outlier: 3.502A pdb=" N GLU w 72 " --> pdb=" O GLU w 68 " (cutoff:3.500A) Processing helix chain 'w' and resid 76 through 80 Processing helix chain 'w' and resid 86 through 100 Processing helix chain 'w' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET w 112 " --> pdb=" O MET w 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN w 113 " --> pdb=" O PRO w 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY w 114 " --> pdb=" O THR w 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL w 117 " --> pdb=" O ASN w 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU w 121 " --> pdb=" O VAL w 117 " (cutoff:3.500A) Processing helix chain 'w' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL w 149 " --> pdb=" O LEU w 145 " (cutoff:3.500A) Processing helix chain 'w' and resid 155 through 161 Processing helix chain 'w' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU w 168 " --> pdb=" O SER w 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA w 169 " --> pdb=" O ASP w 165 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU w 172 " --> pdb=" O GLU w 168 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET w 173 " --> pdb=" O ALA w 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS w 176 " --> pdb=" O GLU w 172 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS w 177 " --> pdb=" O MET w 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU w 178 " --> pdb=" O ARG w 174 " (cutoff:3.500A) Processing helix chain 'w' and resid 182 through 189 Processing helix chain 'w' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU w 215 " --> pdb=" O VAL w 211 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA w 216 " --> pdb=" O ARG w 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS w 217 " --> pdb=" O ALA w 213 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE w 218 " --> pdb=" O ARG w 214 " (cutoff:3.500A) Processing helix chain 'x' and resid 66 through 72 removed outlier: 3.502A pdb=" N GLU x 72 " --> pdb=" O GLU x 68 " (cutoff:3.500A) Processing helix chain 'x' and resid 76 through 80 Processing helix chain 'x' and resid 86 through 100 Processing helix chain 'x' and resid 108 through 122 removed outlier: 3.571A pdb=" N MET x 112 " --> pdb=" O MET x 108 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN x 113 " --> pdb=" O PRO x 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY x 114 " --> pdb=" O THR x 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL x 117 " --> pdb=" O ASN x 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU x 121 " --> pdb=" O VAL x 117 " (cutoff:3.500A) Processing helix chain 'x' and resid 145 through 150 removed outlier: 3.722A pdb=" N VAL x 149 " --> pdb=" O LEU x 145 " (cutoff:3.500A) Processing helix chain 'x' and resid 155 through 161 Processing helix chain 'x' and resid 163 through 178 removed outlier: 3.767A pdb=" N GLU x 168 " --> pdb=" O SER x 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA x 169 " --> pdb=" O ASP x 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU x 172 " --> pdb=" O GLU x 168 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET x 173 " --> pdb=" O ALA x 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS x 176 " --> pdb=" O GLU x 172 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS x 177 " --> pdb=" O MET x 173 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU x 178 " --> pdb=" O ARG x 174 " (cutoff:3.500A) Processing helix chain 'x' and resid 182 through 189 Processing helix chain 'x' and resid 210 through 218 removed outlier: 3.515A pdb=" N GLU x 215 " --> pdb=" O VAL x 211 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA x 216 " --> pdb=" O ARG x 212 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS x 217 " --> pdb=" O ALA x 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE x 218 " --> pdb=" O ARG x 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET a 134 " --> pdb=" O VAL a 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU a 139 " --> pdb=" O ASP a 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET b 134 " --> pdb=" O VAL b 141 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU b 139 " --> pdb=" O ASP b 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET c 134 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU c 139 " --> pdb=" O ASP c 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET d 134 " --> pdb=" O VAL d 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU d 139 " --> pdb=" O ASP d 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'e' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET e 134 " --> pdb=" O VAL e 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU e 139 " --> pdb=" O ASP e 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET f 134 " --> pdb=" O VAL f 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU f 139 " --> pdb=" O ASP f 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 131 through 136 removed outlier: 3.748A pdb=" N MET g 134 " --> pdb=" O VAL g 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU g 139 " --> pdb=" O ASP g 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET h 134 " --> pdb=" O VAL h 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU h 139 " --> pdb=" O ASP h 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'i' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET i 134 " --> pdb=" O VAL i 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU i 139 " --> pdb=" O ASP i 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'j' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET j 134 " --> pdb=" O VAL j 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU j 139 " --> pdb=" O ASP j 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'k' and resid 131 through 136 removed outlier: 3.748A pdb=" N MET k 134 " --> pdb=" O VAL k 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU k 139 " --> pdb=" O ASP k 136 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'l' and resid 131 through 136 removed outlier: 3.750A pdb=" N MET l 134 " --> pdb=" O VAL l 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU l 139 " --> pdb=" O ASP l 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'm' and resid 131 through 136 removed outlier: 3.750A pdb=" N MET m 134 " --> pdb=" O VAL m 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU m 139 " --> pdb=" O ASP m 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'n' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET n 134 " --> pdb=" O VAL n 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU n 139 " --> pdb=" O ASP n 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'o' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET o 134 " --> pdb=" O VAL o 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU o 139 " --> pdb=" O ASP o 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'p' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET p 134 " --> pdb=" O VAL p 141 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU p 139 " --> pdb=" O ASP p 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'q' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET q 134 " --> pdb=" O VAL q 141 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU q 139 " --> pdb=" O ASP q 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'r' and resid 131 through 136 removed outlier: 3.750A pdb=" N MET r 134 " --> pdb=" O VAL r 141 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU r 139 " --> pdb=" O ASP r 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 's' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET s 134 " --> pdb=" O VAL s 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU s 139 " --> pdb=" O ASP s 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 't' and resid 131 through 136 removed outlier: 3.748A pdb=" N MET t 134 " --> pdb=" O VAL t 141 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU t 139 " --> pdb=" O ASP t 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'u' and resid 131 through 136 removed outlier: 3.749A pdb=" N MET u 134 " --> pdb=" O VAL u 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU u 139 " --> pdb=" O ASP u 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'v' and resid 131 through 136 removed outlier: 3.750A pdb=" N MET v 134 " --> pdb=" O VAL v 141 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU v 139 " --> pdb=" O ASP v 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'w' and resid 131 through 136 removed outlier: 3.750A pdb=" N MET w 134 " --> pdb=" O VAL w 141 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU w 139 " --> pdb=" O ASP w 136 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'x' and resid 131 through 136 removed outlier: 3.750A pdb=" N MET x 134 " --> pdb=" O VAL x 141 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU x 139 " --> pdb=" O ASP x 136 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2664 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: 6.02 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11052 1.34 - 1.45: 4871 1.45 - 1.57: 18349 1.57 - 1.68: 0 1.68 - 1.80: 504 Bond restraints: 34776 Sorted by residual: bond pdb=" N THR t 106 " pdb=" CA THR t 106 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.13e+00 bond pdb=" N THR h 106 " pdb=" CA THR h 106 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.04e+00 bond pdb=" N THR f 106 " pdb=" CA THR f 106 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.04e+00 bond pdb=" N THR v 106 " pdb=" CA THR v 106 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.04e+00 bond pdb=" N THR e 106 " pdb=" CA THR e 106 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.00e+00 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 43747 1.73 - 3.47: 2716 3.47 - 5.20: 454 5.20 - 6.93: 219 6.93 - 8.66: 48 Bond angle restraints: 47184 Sorted by residual: angle pdb=" N GLN b 76 " pdb=" CA GLN b 76 " pdb=" C GLN b 76 " ideal model delta sigma weight residual 110.55 116.23 -5.68 1.35e+00 5.49e-01 1.77e+01 angle pdb=" N GLN e 76 " pdb=" CA GLN e 76 " pdb=" C GLN e 76 " ideal model delta sigma weight residual 110.55 116.23 -5.68 1.35e+00 5.49e-01 1.77e+01 angle pdb=" N GLN v 76 " pdb=" CA GLN v 76 " pdb=" C GLN v 76 " ideal model delta sigma weight residual 110.55 116.21 -5.66 1.35e+00 5.49e-01 1.76e+01 angle pdb=" N GLN f 76 " pdb=" CA GLN f 76 " pdb=" C GLN f 76 " ideal model delta sigma weight residual 110.55 116.21 -5.66 1.35e+00 5.49e-01 1.76e+01 angle pdb=" N GLN d 76 " pdb=" CA GLN d 76 " pdb=" C GLN d 76 " ideal model delta sigma weight residual 110.55 116.21 -5.66 1.35e+00 5.49e-01 1.76e+01 ... (remaining 47179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 20160 17.40 - 34.80: 888 34.80 - 52.21: 192 52.21 - 69.61: 48 69.61 - 87.01: 24 Dihedral angle restraints: 21312 sinusoidal: 8832 harmonic: 12480 Sorted by residual: dihedral pdb=" CA ASN c 189 " pdb=" C ASN c 189 " pdb=" N LEU c 190 " pdb=" CA LEU c 190 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ASN v 189 " pdb=" C ASN v 189 " pdb=" N LEU v 190 " pdb=" CA LEU v 190 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ASN p 189 " pdb=" C ASN p 189 " pdb=" N LEU p 190 " pdb=" CA LEU p 190 " ideal model delta harmonic sigma weight residual 180.00 159.11 20.89 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 21309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3423 0.049 - 0.099: 1398 0.099 - 0.148: 219 0.148 - 0.198: 72 0.198 - 0.247: 48 Chirality restraints: 5160 Sorted by residual: chirality pdb=" CB VAL t 64 " pdb=" CA VAL t 64 " pdb=" CG1 VAL t 64 " pdb=" CG2 VAL t 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL b 64 " pdb=" CA VAL b 64 " pdb=" CG1 VAL b 64 " pdb=" CG2 VAL b 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL x 64 " pdb=" CA VAL x 64 " pdb=" CG1 VAL x 64 " pdb=" CG2 VAL x 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 5157 not shown) Planarity restraints: 6120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE u 202 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C PHE u 202 " -0.043 2.00e-02 2.50e+03 pdb=" O PHE u 202 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR u 203 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE l 202 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C PHE l 202 " -0.043 2.00e-02 2.50e+03 pdb=" O PHE l 202 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR l 203 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE c 202 " -0.013 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C PHE c 202 " 0.043 2.00e-02 2.50e+03 pdb=" O PHE c 202 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR c 203 " -0.015 2.00e-02 2.50e+03 ... (remaining 6117 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 14722 2.96 - 3.45: 32532 3.45 - 3.93: 51534 3.93 - 4.42: 59301 4.42 - 4.90: 95664 Nonbonded interactions: 253753 Sorted by model distance: nonbonded pdb=" OH TYR l 143 " pdb=" O PRO w 45 " model vdw 2.476 3.040 nonbonded pdb=" OH TYR d 143 " pdb=" O PRO p 45 " model vdw 2.487 3.040 nonbonded pdb=" OH TYR e 143 " pdb=" O PRO i 45 " model vdw 2.495 3.040 nonbonded pdb=" OH TYR c 143 " pdb=" O PRO o 45 " model vdw 2.495 3.040 nonbonded pdb=" OH TYR j 143 " pdb=" O PRO u 45 " model vdw 2.496 3.040 ... (remaining 253748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.280 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.110 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 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 0.067 34776 Z= 0.376 Angle : 1.036 8.665 47184 Z= 0.577 Chirality : 0.057 0.247 5160 Planarity : 0.008 0.048 6120 Dihedral : 11.579 87.011 13248 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 1.95 % Allowed : 3.25 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.83 (0.09), residues: 4176 helix: -3.89 (0.08), residues: 1776 sheet: -3.19 (0.30), residues: 288 loop : -4.02 (0.10), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG r 214 TYR 0.012 0.003 TYR g 73 PHE 0.025 0.003 PHE p 202 TRP 0.019 0.003 TRP t 118 HIS 0.007 0.002 HIS f 162 Details of bonding type rmsd covalent geometry : bond 0.00850 (34776) covalent geometry : angle 1.03599 (47184) hydrogen bonds : bond 0.33990 ( 936) hydrogen bonds : angle 9.85873 ( 2664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1766 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1694 time to evaluate : 1.235 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: a 59 SER cc_start: 0.8432 (p) cc_final: 0.8098 (p) REVERT: a 124 THR cc_start: 0.9080 (p) cc_final: 0.8682 (t) REVERT: a 125 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8374 (t) REVERT: a 135 MET cc_start: 0.9112 (mmm) cc_final: 0.8734 (mmm) REVERT: a 139 GLU cc_start: 0.8487 (pt0) cc_final: 0.8140 (pt0) REVERT: a 149 VAL cc_start: 0.9429 (m) cc_final: 0.9145 (t) REVERT: b 59 SER cc_start: 0.8468 (p) cc_final: 0.8094 (p) REVERT: b 71 LEU cc_start: 0.8875 (mt) cc_final: 0.8610 (mt) REVERT: b 82 ASN cc_start: 0.8709 (t160) cc_final: 0.8138 (t0) REVERT: b 107 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7528 (pt0) REVERT: b 115 LEU cc_start: 0.9582 (tp) cc_final: 0.9196 (tp) REVERT: b 124 THR cc_start: 0.9031 (p) cc_final: 0.8815 (t) REVERT: b 125 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8411 (t) REVERT: b 135 MET cc_start: 0.9160 (mmm) cc_final: 0.8756 (mmm) REVERT: b 145 LEU cc_start: 0.9302 (mt) cc_final: 0.8821 (mt) REVERT: b 149 VAL cc_start: 0.9432 (m) cc_final: 0.9165 (p) REVERT: c 59 SER cc_start: 0.8430 (p) cc_final: 0.8105 (p) REVERT: c 124 THR cc_start: 0.9075 (p) cc_final: 0.8701 (t) REVERT: c 125 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8391 (t) REVERT: c 135 MET cc_start: 0.9103 (mmm) cc_final: 0.8753 (mmm) REVERT: c 139 GLU cc_start: 0.8487 (pt0) cc_final: 0.8148 (pt0) REVERT: c 149 VAL cc_start: 0.9445 (m) cc_final: 0.9149 (t) REVERT: d 59 SER cc_start: 0.8483 (p) cc_final: 0.8075 (p) REVERT: d 71 LEU cc_start: 0.8892 (mt) cc_final: 0.8587 (mt) REVERT: d 107 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7559 (pt0) REVERT: d 115 LEU cc_start: 0.9579 (tp) cc_final: 0.9043 (tp) REVERT: d 124 THR cc_start: 0.9020 (p) cc_final: 0.8739 (t) REVERT: d 125 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8406 (t) REVERT: d 135 MET cc_start: 0.9151 (mmm) cc_final: 0.8790 (mmm) REVERT: d 145 LEU cc_start: 0.9260 (mt) cc_final: 0.8820 (mt) REVERT: d 149 VAL cc_start: 0.9417 (m) cc_final: 0.9170 (t) REVERT: d 160 MET cc_start: 0.8991 (mmm) cc_final: 0.8714 (tpp) REVERT: e 59 SER cc_start: 0.8427 (p) cc_final: 0.8092 (p) REVERT: e 82 ASN cc_start: 0.8881 (t160) cc_final: 0.8675 (t0) REVERT: e 124 THR cc_start: 0.9078 (p) cc_final: 0.8708 (t) REVERT: e 125 SER cc_start: 0.8858 (OUTLIER) cc_final: 0.8363 (t) REVERT: e 135 MET cc_start: 0.9126 (mmm) cc_final: 0.8734 (mmm) REVERT: e 139 GLU cc_start: 0.8487 (pt0) cc_final: 0.8210 (pt0) REVERT: e 149 VAL cc_start: 0.9449 (m) cc_final: 0.9161 (t) REVERT: e 160 MET cc_start: 0.9060 (mmm) cc_final: 0.8844 (mmt) REVERT: f 59 SER cc_start: 0.8470 (p) cc_final: 0.8099 (p) REVERT: f 71 LEU cc_start: 0.8885 (mt) cc_final: 0.8583 (mt) REVERT: f 107 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7538 (pt0) REVERT: f 115 LEU cc_start: 0.9573 (tp) cc_final: 0.9184 (tp) REVERT: f 124 THR cc_start: 0.9010 (p) cc_final: 0.8782 (t) REVERT: f 125 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8407 (t) REVERT: f 135 MET cc_start: 0.9169 (mmm) cc_final: 0.8761 (mmm) REVERT: f 145 LEU cc_start: 0.9301 (mt) cc_final: 0.8838 (mt) REVERT: f 149 VAL cc_start: 0.9433 (m) cc_final: 0.9160 (p) REVERT: g 59 SER cc_start: 0.8437 (p) cc_final: 0.8100 (p) REVERT: g 82 ASN cc_start: 0.8873 (t160) cc_final: 0.8670 (t0) REVERT: g 124 THR cc_start: 0.9079 (p) cc_final: 0.8694 (t) REVERT: g 125 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8376 (t) REVERT: g 135 MET cc_start: 0.9131 (mmm) cc_final: 0.8742 (mmm) REVERT: g 139 GLU cc_start: 0.8489 (pt0) cc_final: 0.8151 (pt0) REVERT: g 149 VAL cc_start: 0.9450 (m) cc_final: 0.9155 (t) REVERT: g 160 MET cc_start: 0.9063 (mmm) cc_final: 0.8859 (mmt) REVERT: h 59 SER cc_start: 0.8479 (p) cc_final: 0.8089 (p) REVERT: h 71 LEU cc_start: 0.8881 (mt) cc_final: 0.8602 (mt) REVERT: h 107 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7524 (pt0) REVERT: h 115 LEU cc_start: 0.9579 (tp) cc_final: 0.9199 (tp) REVERT: h 124 THR cc_start: 0.9027 (p) cc_final: 0.8811 (t) REVERT: h 125 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8400 (t) REVERT: h 145 LEU cc_start: 0.9303 (mt) cc_final: 0.8841 (mt) REVERT: h 149 VAL cc_start: 0.9434 (m) cc_final: 0.9163 (p) REVERT: i 59 SER cc_start: 0.8367 (p) cc_final: 0.7956 (p) REVERT: i 98 GLN cc_start: 0.8325 (tt0) cc_final: 0.7641 (tt0) REVERT: i 107 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7545 (pt0) REVERT: i 115 LEU cc_start: 0.9527 (tp) cc_final: 0.8988 (tt) REVERT: i 124 THR cc_start: 0.8867 (p) cc_final: 0.8379 (t) REVERT: i 135 MET cc_start: 0.9101 (mmm) cc_final: 0.8798 (mmm) REVERT: i 149 VAL cc_start: 0.9317 (m) cc_final: 0.9074 (t) REVERT: i 160 MET cc_start: 0.9118 (mmm) cc_final: 0.8884 (tpp) REVERT: j 46 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7557 (mtt180) REVERT: j 59 SER cc_start: 0.8240 (p) cc_final: 0.7816 (p) REVERT: j 98 GLN cc_start: 0.8389 (tt0) cc_final: 0.7901 (tt0) REVERT: j 107 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7503 (pt0) REVERT: j 115 LEU cc_start: 0.9581 (tp) cc_final: 0.9033 (tp) REVERT: j 124 THR cc_start: 0.8951 (p) cc_final: 0.8587 (t) REVERT: j 125 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8547 (t) REVERT: j 135 MET cc_start: 0.9086 (mmm) cc_final: 0.8787 (mmm) REVERT: j 149 VAL cc_start: 0.9254 (m) cc_final: 0.9016 (p) REVERT: j 160 MET cc_start: 0.9122 (mmm) cc_final: 0.8665 (tpp) REVERT: k 46 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7583 (mtt180) REVERT: k 59 SER cc_start: 0.8401 (p) cc_final: 0.7970 (p) REVERT: k 98 GLN cc_start: 0.8339 (tt0) cc_final: 0.7692 (tt0) REVERT: k 107 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7550 (pt0) REVERT: k 115 LEU cc_start: 0.9518 (tp) cc_final: 0.8984 (tt) REVERT: k 124 THR cc_start: 0.8884 (p) cc_final: 0.8411 (t) REVERT: k 149 VAL cc_start: 0.9326 (m) cc_final: 0.9073 (t) REVERT: k 160 MET cc_start: 0.9102 (mmm) cc_final: 0.8873 (tpp) REVERT: l 59 SER cc_start: 0.8230 (p) cc_final: 0.7784 (p) REVERT: l 98 GLN cc_start: 0.8375 (tt0) cc_final: 0.7859 (tt0) REVERT: l 107 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7500 (pt0) REVERT: l 112 MET cc_start: 0.9477 (mmp) cc_final: 0.9266 (mmt) REVERT: l 115 LEU cc_start: 0.9597 (tp) cc_final: 0.9016 (tp) REVERT: l 124 THR cc_start: 0.9002 (p) cc_final: 0.8519 (t) REVERT: l 125 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8536 (t) REVERT: l 160 MET cc_start: 0.9082 (mmm) cc_final: 0.8645 (tpp) REVERT: l 198 TYR cc_start: 0.8977 (m-10) cc_final: 0.8056 (m-10) REVERT: m 46 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7590 (mtt180) REVERT: m 59 SER cc_start: 0.8362 (p) cc_final: 0.7922 (p) REVERT: m 98 GLN cc_start: 0.8330 (tt0) cc_final: 0.7616 (tt0) REVERT: m 107 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7553 (pt0) REVERT: m 115 LEU cc_start: 0.9530 (tp) cc_final: 0.8990 (tt) REVERT: m 124 THR cc_start: 0.8887 (p) cc_final: 0.8381 (t) REVERT: m 125 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8612 (t) REVERT: m 149 VAL cc_start: 0.9323 (m) cc_final: 0.9088 (t) REVERT: n 59 SER cc_start: 0.8252 (p) cc_final: 0.7832 (p) REVERT: n 98 GLN cc_start: 0.8370 (tt0) cc_final: 0.7866 (tt0) REVERT: n 107 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7505 (pt0) REVERT: n 115 LEU cc_start: 0.9597 (tp) cc_final: 0.9024 (tp) REVERT: n 124 THR cc_start: 0.8998 (p) cc_final: 0.8508 (t) REVERT: n 125 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8532 (t) REVERT: n 135 MET cc_start: 0.9085 (mmm) cc_final: 0.8828 (mmm) REVERT: n 160 MET cc_start: 0.9070 (mmm) cc_final: 0.8646 (tpp) REVERT: n 198 TYR cc_start: 0.8979 (m-10) cc_final: 0.8048 (m-10) REVERT: o 46 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7572 (mtt180) REVERT: o 59 SER cc_start: 0.8393 (p) cc_final: 0.7952 (p) REVERT: o 98 GLN cc_start: 0.8333 (tt0) cc_final: 0.7697 (tt0) REVERT: o 107 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7548 (pt0) REVERT: o 115 LEU cc_start: 0.9533 (tp) cc_final: 0.9021 (tt) REVERT: o 124 THR cc_start: 0.8902 (p) cc_final: 0.8423 (t) REVERT: o 125 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8589 (t) REVERT: o 149 VAL cc_start: 0.9317 (m) cc_final: 0.9064 (t) REVERT: o 160 MET cc_start: 0.9114 (mmm) cc_final: 0.8892 (tpp) REVERT: p 46 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7633 (mtt180) REVERT: p 59 SER cc_start: 0.8242 (p) cc_final: 0.7805 (p) REVERT: p 98 GLN cc_start: 0.8380 (tt0) cc_final: 0.7895 (tt0) REVERT: p 107 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7478 (pt0) REVERT: p 115 LEU cc_start: 0.9585 (tp) cc_final: 0.9027 (tp) REVERT: p 124 THR cc_start: 0.8945 (p) cc_final: 0.8584 (t) REVERT: p 125 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8545 (t) REVERT: p 149 VAL cc_start: 0.9250 (m) cc_final: 0.9014 (p) REVERT: p 160 MET cc_start: 0.9116 (mmm) cc_final: 0.8666 (tpp) REVERT: q 59 SER cc_start: 0.8344 (p) cc_final: 0.7979 (p) REVERT: q 107 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7625 (pt0) REVERT: q 124 THR cc_start: 0.8941 (p) cc_final: 0.8320 (t) REVERT: q 125 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8569 (t) REVERT: r 44 VAL cc_start: 0.9383 (m) cc_final: 0.8911 (m) REVERT: r 59 SER cc_start: 0.8601 (p) cc_final: 0.8117 (p) REVERT: r 89 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8215 (mm-40) REVERT: r 107 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7739 (pt0) REVERT: r 108 MET cc_start: 0.8642 (tpt) cc_final: 0.8370 (tpp) REVERT: r 115 LEU cc_start: 0.9597 (tp) cc_final: 0.9290 (tp) REVERT: r 124 THR cc_start: 0.9002 (p) cc_final: 0.8434 (t) REVERT: r 125 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8449 (t) REVERT: r 198 TYR cc_start: 0.8962 (m-10) cc_final: 0.8749 (m-10) REVERT: s 59 SER cc_start: 0.8329 (p) cc_final: 0.7958 (p) REVERT: s 107 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7624 (pt0) REVERT: s 124 THR cc_start: 0.8933 (p) cc_final: 0.8294 (t) REVERT: s 125 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8575 (t) REVERT: t 59 SER cc_start: 0.8596 (p) cc_final: 0.8206 (p) REVERT: t 107 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7747 (pt0) REVERT: t 108 MET cc_start: 0.8626 (tpt) cc_final: 0.8403 (tpp) REVERT: t 115 LEU cc_start: 0.9595 (tp) cc_final: 0.9266 (tp) REVERT: t 124 THR cc_start: 0.9004 (p) cc_final: 0.8422 (t) REVERT: t 125 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8430 (t) REVERT: t 198 TYR cc_start: 0.8947 (m-10) cc_final: 0.8725 (m-10) REVERT: u 59 SER cc_start: 0.8336 (p) cc_final: 0.7970 (p) REVERT: u 107 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7649 (pt0) REVERT: u 124 THR cc_start: 0.8939 (p) cc_final: 0.8352 (t) REVERT: u 125 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8574 (t) REVERT: v 44 VAL cc_start: 0.9382 (m) cc_final: 0.8925 (m) REVERT: v 59 SER cc_start: 0.8594 (p) cc_final: 0.8114 (p) REVERT: v 67 LEU cc_start: 0.8589 (mm) cc_final: 0.8064 (mm) REVERT: v 89 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8231 (mm-40) REVERT: v 107 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7732 (pt0) REVERT: v 108 MET cc_start: 0.8635 (tpt) cc_final: 0.8411 (tpp) REVERT: v 115 LEU cc_start: 0.9585 (tp) cc_final: 0.9262 (tp) REVERT: v 124 THR cc_start: 0.8998 (p) cc_final: 0.8437 (t) REVERT: v 125 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8435 (t) REVERT: v 198 TYR cc_start: 0.8951 (m-10) cc_final: 0.8737 (m-10) REVERT: w 59 SER cc_start: 0.8135 (p) cc_final: 0.7707 (p) REVERT: w 107 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7655 (pt0) REVERT: w 124 THR cc_start: 0.8947 (p) cc_final: 0.8390 (t) REVERT: w 125 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8584 (t) REVERT: x 59 SER cc_start: 0.8607 (p) cc_final: 0.8200 (p) REVERT: x 107 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7737 (pt0) REVERT: x 108 MET cc_start: 0.8636 (tpt) cc_final: 0.8413 (tpp) REVERT: x 115 LEU cc_start: 0.9594 (tp) cc_final: 0.9270 (tp) REVERT: x 124 THR cc_start: 0.8998 (p) cc_final: 0.8418 (t) REVERT: x 125 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8428 (t) REVERT: x 198 TYR cc_start: 0.8949 (m-10) cc_final: 0.8733 (m-10) outliers start: 72 outliers final: 9 residues processed: 1724 average time/residue: 0.2399 time to fit residues: 620.4370 Evaluate side-chains 1538 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 1502 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 69 HIS a 77 GLN a 122 ASN a 162 HIS b 69 HIS b 122 ASN b 162 HIS c 69 HIS c 77 GLN ** c 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 122 ASN c 162 HIS d 69 HIS d 122 ASN d 162 HIS e 69 HIS e 122 ASN e 162 HIS f 69 HIS f 122 ASN f 162 HIS g 69 HIS g 122 ASN g 162 HIS h 69 HIS h 122 ASN h 162 HIS i 69 HIS i 98 GLN i 113 ASN i 122 ASN j 69 HIS j 98 GLN j 113 ASN j 122 ASN k 69 HIS k 98 GLN k 113 ASN k 122 ASN l 69 HIS l 98 GLN l 113 ASN l 122 ASN m 69 HIS m 98 GLN m 113 ASN m 122 ASN n 69 HIS n 98 GLN n 113 ASN n 122 ASN o 69 HIS o 98 GLN o 113 ASN o 122 ASN p 69 HIS p 98 GLN p 113 ASN p 122 ASN q 69 HIS q 113 ASN q 122 ASN q 162 HIS r 69 HIS r 77 GLN r 113 ASN r 122 ASN s 69 HIS s 113 ASN s 122 ASN s 162 HIS t 69 HIS t 113 ASN t 122 ASN u 69 HIS u 113 ASN u 122 ASN u 162 HIS v 69 HIS v 113 ASN v 122 ASN w 69 HIS w 113 ASN w 122 ASN w 162 HIS x 69 HIS x 113 ASN x 122 ASN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.129714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.110931 restraints weight = 45705.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.114513 restraints weight = 28470.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.117058 restraints weight = 19916.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.118981 restraints weight = 15003.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.120397 restraints weight = 11893.327| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34776 Z= 0.121 Angle : 0.627 6.051 47184 Z= 0.323 Chirality : 0.041 0.124 5160 Planarity : 0.006 0.036 6120 Dihedral : 5.356 19.607 4704 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.11), residues: 4176 helix: -2.21 (0.11), residues: 1776 sheet: -2.45 (0.31), residues: 240 loop : -3.19 (0.10), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG v 174 TYR 0.026 0.001 TYR b 73 PHE 0.014 0.002 PHE u 202 TRP 0.011 0.002 TRP r 132 HIS 0.003 0.001 HIS s 162 Details of bonding type rmsd covalent geometry : bond 0.00269 (34776) covalent geometry : angle 0.62705 (47184) hydrogen bonds : bond 0.03484 ( 936) hydrogen bonds : angle 4.73083 ( 2664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1651 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1651 time to evaluate : 1.155 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: a 66 ASN cc_start: 0.8349 (t0) cc_final: 0.8131 (t0) REVERT: a 124 THR cc_start: 0.9012 (p) cc_final: 0.8610 (t) REVERT: a 125 SER cc_start: 0.8282 (p) cc_final: 0.7973 (t) REVERT: a 189 ASN cc_start: 0.9186 (t0) cc_final: 0.8977 (t0) REVERT: b 86 THR cc_start: 0.8926 (p) cc_final: 0.8713 (t) REVERT: b 103 ILE cc_start: 0.9220 (mm) cc_final: 0.8587 (mm) REVERT: b 107 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7351 (pt0) REVERT: b 122 ASN cc_start: 0.8874 (m-40) cc_final: 0.8542 (m-40) REVERT: b 124 THR cc_start: 0.8934 (p) cc_final: 0.8577 (t) REVERT: c 66 ASN cc_start: 0.8348 (t0) cc_final: 0.8117 (t0) REVERT: c 124 THR cc_start: 0.9042 (p) cc_final: 0.8634 (t) REVERT: c 125 SER cc_start: 0.8300 (p) cc_final: 0.7983 (t) REVERT: c 189 ASN cc_start: 0.9190 (t0) cc_final: 0.8976 (t0) REVERT: d 107 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7315 (pt0) REVERT: d 122 ASN cc_start: 0.8810 (m-40) cc_final: 0.8484 (m-40) REVERT: d 124 THR cc_start: 0.8902 (p) cc_final: 0.8560 (t) REVERT: e 66 ASN cc_start: 0.8356 (t0) cc_final: 0.8143 (t0) REVERT: e 124 THR cc_start: 0.9014 (p) cc_final: 0.8577 (t) REVERT: e 125 SER cc_start: 0.8267 (p) cc_final: 0.7955 (t) REVERT: e 189 ASN cc_start: 0.9193 (t0) cc_final: 0.8980 (t0) REVERT: f 86 THR cc_start: 0.8928 (p) cc_final: 0.8708 (t) REVERT: f 107 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7320 (pt0) REVERT: f 122 ASN cc_start: 0.8864 (m-40) cc_final: 0.8531 (m-40) REVERT: f 124 THR cc_start: 0.8926 (p) cc_final: 0.8579 (t) REVERT: g 66 ASN cc_start: 0.8377 (t0) cc_final: 0.8146 (t0) REVERT: g 124 THR cc_start: 0.9021 (p) cc_final: 0.8616 (t) REVERT: g 125 SER cc_start: 0.8277 (p) cc_final: 0.7968 (t) REVERT: g 189 ASN cc_start: 0.9187 (t0) cc_final: 0.8980 (t0) REVERT: h 86 THR cc_start: 0.8933 (p) cc_final: 0.8700 (t) REVERT: h 107 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7342 (pt0) REVERT: h 122 ASN cc_start: 0.8842 (m-40) cc_final: 0.8483 (m-40) REVERT: h 124 THR cc_start: 0.8950 (p) cc_final: 0.8576 (t) REVERT: h 125 SER cc_start: 0.8444 (p) cc_final: 0.8243 (t) REVERT: i 44 VAL cc_start: 0.9363 (m) cc_final: 0.9111 (m) REVERT: i 66 ASN cc_start: 0.8062 (t0) cc_final: 0.7852 (t0) REVERT: i 98 GLN cc_start: 0.8593 (tt0) cc_final: 0.7649 (tt0) REVERT: i 122 ASN cc_start: 0.8759 (m-40) cc_final: 0.8398 (m-40) REVERT: i 124 THR cc_start: 0.8843 (p) cc_final: 0.8291 (t) REVERT: i 188 ARG cc_start: 0.8267 (mmm160) cc_final: 0.7903 (tpt90) REVERT: j 66 ASN cc_start: 0.8234 (t0) cc_final: 0.7953 (t0) REVERT: j 122 ASN cc_start: 0.8708 (m-40) cc_final: 0.8459 (m-40) REVERT: j 124 THR cc_start: 0.8917 (p) cc_final: 0.8280 (t) REVERT: j 188 ARG cc_start: 0.8277 (mmm160) cc_final: 0.7918 (tpt90) REVERT: j 189 ASN cc_start: 0.9108 (t0) cc_final: 0.8719 (t0) REVERT: k 44 VAL cc_start: 0.9370 (m) cc_final: 0.9105 (m) REVERT: k 66 ASN cc_start: 0.8078 (t0) cc_final: 0.7872 (t0) REVERT: k 98 GLN cc_start: 0.8586 (tt0) cc_final: 0.7559 (tt0) REVERT: k 122 ASN cc_start: 0.8772 (m-40) cc_final: 0.8422 (m-40) REVERT: k 124 THR cc_start: 0.8845 (p) cc_final: 0.8290 (t) REVERT: k 188 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7884 (tpt90) REVERT: l 66 ASN cc_start: 0.8218 (t0) cc_final: 0.8005 (t0) REVERT: l 122 ASN cc_start: 0.8772 (m-40) cc_final: 0.8524 (m-40) REVERT: l 124 THR cc_start: 0.8922 (p) cc_final: 0.8298 (t) REVERT: l 160 MET cc_start: 0.9073 (mmm) cc_final: 0.8802 (tpp) REVERT: l 188 ARG cc_start: 0.8273 (mmm160) cc_final: 0.7892 (tpt90) REVERT: l 197 ARG cc_start: 0.8654 (tmm-80) cc_final: 0.8440 (ttp80) REVERT: m 44 VAL cc_start: 0.9370 (m) cc_final: 0.9110 (m) REVERT: m 98 GLN cc_start: 0.8610 (tt0) cc_final: 0.7679 (tt0) REVERT: m 122 ASN cc_start: 0.8789 (m-40) cc_final: 0.8430 (m-40) REVERT: m 124 THR cc_start: 0.8903 (p) cc_final: 0.8333 (t) REVERT: m 188 ARG cc_start: 0.8266 (mmm160) cc_final: 0.7909 (tpt90) REVERT: n 122 ASN cc_start: 0.8771 (m-40) cc_final: 0.8515 (m-40) REVERT: n 124 THR cc_start: 0.8935 (p) cc_final: 0.8298 (t) REVERT: n 188 ARG cc_start: 0.8263 (mmm160) cc_final: 0.7885 (tpt90) REVERT: n 197 ARG cc_start: 0.8633 (tmm-80) cc_final: 0.8385 (ttp80) REVERT: o 44 VAL cc_start: 0.9364 (m) cc_final: 0.9114 (m) REVERT: o 98 GLN cc_start: 0.8605 (tt0) cc_final: 0.7571 (tt0) REVERT: o 122 ASN cc_start: 0.8756 (m-40) cc_final: 0.8416 (m-40) REVERT: o 124 THR cc_start: 0.8899 (p) cc_final: 0.8310 (t) REVERT: o 188 ARG cc_start: 0.8249 (mmm160) cc_final: 0.7881 (tpt90) REVERT: p 66 ASN cc_start: 0.8232 (t0) cc_final: 0.7958 (t0) REVERT: p 122 ASN cc_start: 0.8645 (m-40) cc_final: 0.8419 (m-40) REVERT: p 124 THR cc_start: 0.8924 (p) cc_final: 0.8283 (t) REVERT: p 188 ARG cc_start: 0.8281 (mmm160) cc_final: 0.7929 (tpt90) REVERT: p 189 ASN cc_start: 0.9100 (t0) cc_final: 0.8708 (t0) REVERT: q 66 ASN cc_start: 0.7954 (t0) cc_final: 0.7407 (t0) REVERT: q 103 ILE cc_start: 0.9041 (mm) cc_final: 0.8752 (mm) REVERT: q 107 GLU cc_start: 0.7791 (mt-10) cc_final: 0.6924 (tm-30) REVERT: q 108 MET cc_start: 0.8493 (tpp) cc_final: 0.8260 (tpp) REVERT: q 124 THR cc_start: 0.8815 (p) cc_final: 0.8149 (t) REVERT: r 66 ASN cc_start: 0.8243 (t0) cc_final: 0.8015 (t0) REVERT: r 67 LEU cc_start: 0.8556 (mm) cc_final: 0.8285 (mm) REVERT: r 95 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7315 (mm-30) REVERT: r 98 GLN cc_start: 0.8462 (tt0) cc_final: 0.8245 (tp40) REVERT: r 107 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7274 (tm-30) REVERT: r 122 ASN cc_start: 0.8832 (m-40) cc_final: 0.8434 (m-40) REVERT: r 124 THR cc_start: 0.8891 (p) cc_final: 0.8268 (t) REVERT: r 135 MET cc_start: 0.8875 (mmm) cc_final: 0.8207 (mmm) REVERT: r 188 ARG cc_start: 0.8221 (mmm160) cc_final: 0.7898 (tpt90) REVERT: r 198 TYR cc_start: 0.9008 (m-10) cc_final: 0.8794 (m-10) REVERT: s 66 ASN cc_start: 0.7952 (t0) cc_final: 0.7407 (t0) REVERT: s 79 ASP cc_start: 0.8282 (m-30) cc_final: 0.8075 (m-30) REVERT: s 103 ILE cc_start: 0.9041 (mm) cc_final: 0.8755 (mm) REVERT: s 107 GLU cc_start: 0.7805 (mt-10) cc_final: 0.6920 (tm-30) REVERT: s 108 MET cc_start: 0.8523 (tpp) cc_final: 0.8274 (tpp) REVERT: s 124 THR cc_start: 0.8805 (p) cc_final: 0.8136 (t) REVERT: t 66 ASN cc_start: 0.8219 (t0) cc_final: 0.7979 (t0) REVERT: t 67 LEU cc_start: 0.8545 (mm) cc_final: 0.8268 (mm) REVERT: t 95 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7387 (mm-30) REVERT: t 107 GLU cc_start: 0.7866 (mt-10) cc_final: 0.6976 (tm-30) REVERT: t 122 ASN cc_start: 0.8819 (m-40) cc_final: 0.8443 (m-40) REVERT: t 124 THR cc_start: 0.8875 (p) cc_final: 0.8236 (t) REVERT: t 135 MET cc_start: 0.8844 (mmm) cc_final: 0.8217 (mmm) REVERT: t 198 TYR cc_start: 0.9033 (m-10) cc_final: 0.8817 (m-10) REVERT: u 66 ASN cc_start: 0.7966 (t0) cc_final: 0.7417 (t0) REVERT: u 79 ASP cc_start: 0.8200 (m-30) cc_final: 0.7974 (m-30) REVERT: u 103 ILE cc_start: 0.9054 (mm) cc_final: 0.8768 (mm) REVERT: u 107 GLU cc_start: 0.7820 (mt-10) cc_final: 0.6917 (tm-30) REVERT: u 108 MET cc_start: 0.8510 (tpp) cc_final: 0.8197 (tpp) REVERT: u 124 THR cc_start: 0.8814 (p) cc_final: 0.8156 (t) REVERT: v 66 ASN cc_start: 0.8213 (t0) cc_final: 0.7982 (t0) REVERT: v 67 LEU cc_start: 0.8553 (mm) cc_final: 0.8279 (mm) REVERT: v 95 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7337 (mm-30) REVERT: v 98 GLN cc_start: 0.8454 (tt0) cc_final: 0.8243 (tp40) REVERT: v 107 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7273 (tm-30) REVERT: v 122 ASN cc_start: 0.8809 (m-40) cc_final: 0.8447 (m-40) REVERT: v 124 THR cc_start: 0.8890 (p) cc_final: 0.8276 (t) REVERT: v 135 MET cc_start: 0.8954 (mmm) cc_final: 0.8223 (mmm) REVERT: v 188 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7895 (tpt90) REVERT: v 198 TYR cc_start: 0.9000 (m-10) cc_final: 0.8788 (m-10) REVERT: w 66 ASN cc_start: 0.7929 (t0) cc_final: 0.7391 (t0) REVERT: w 67 LEU cc_start: 0.8416 (mm) cc_final: 0.8213 (mm) REVERT: w 79 ASP cc_start: 0.8212 (m-30) cc_final: 0.7962 (m-30) REVERT: w 103 ILE cc_start: 0.9062 (mm) cc_final: 0.8774 (mm) REVERT: w 107 GLU cc_start: 0.7817 (mt-10) cc_final: 0.6901 (tm-30) REVERT: w 108 MET cc_start: 0.8561 (tpp) cc_final: 0.8196 (tpp) REVERT: w 124 THR cc_start: 0.8828 (p) cc_final: 0.8222 (t) REVERT: x 66 ASN cc_start: 0.8215 (t0) cc_final: 0.7961 (t0) REVERT: x 67 LEU cc_start: 0.8572 (mm) cc_final: 0.8295 (mm) REVERT: x 95 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7367 (mm-30) REVERT: x 107 GLU cc_start: 0.7876 (mt-10) cc_final: 0.6971 (tm-30) REVERT: x 122 ASN cc_start: 0.8835 (m-40) cc_final: 0.8442 (m-40) REVERT: x 124 THR cc_start: 0.8880 (p) cc_final: 0.8231 (t) REVERT: x 198 TYR cc_start: 0.9030 (m-10) cc_final: 0.8818 (m-10) outliers start: 0 outliers final: 0 residues processed: 1651 average time/residue: 0.2319 time to fit residues: 582.5311 Evaluate side-chains 1427 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1427 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 203 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 376 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 98 GLN a 175 ASN c 98 GLN c 175 ASN d 98 GLN e 98 GLN e 175 ASN f 98 GLN g 98 GLN g 175 ASN h 98 GLN r 98 GLN r 175 ASN t 175 ASN v 98 GLN v 175 ASN x 175 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.121197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.105687 restraints weight = 46818.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.108567 restraints weight = 29360.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.110650 restraints weight = 20534.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.112189 restraints weight = 15434.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.113257 restraints weight = 12313.725| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 34776 Z= 0.253 Angle : 0.728 5.866 47184 Z= 0.373 Chirality : 0.047 0.130 5160 Planarity : 0.005 0.059 6120 Dihedral : 5.498 20.263 4704 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.12), residues: 4176 helix: -1.78 (0.11), residues: 2064 sheet: -2.31 (0.31), residues: 240 loop : -3.03 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG w 197 TYR 0.027 0.002 TYR i 73 PHE 0.019 0.003 PHE u 200 TRP 0.014 0.002 TRP g 132 HIS 0.003 0.001 HIS c 162 Details of bonding type rmsd covalent geometry : bond 0.00591 (34776) covalent geometry : angle 0.72845 (47184) hydrogen bonds : bond 0.03789 ( 936) hydrogen bonds : angle 4.61688 ( 2664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1523 time to evaluate : 1.029 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: a 66 ASN cc_start: 0.8345 (t0) cc_final: 0.8133 (t0) REVERT: a 79 ASP cc_start: 0.8458 (m-30) cc_final: 0.8018 (m-30) REVERT: a 82 ASN cc_start: 0.8836 (t0) cc_final: 0.8636 (t0) REVERT: a 124 THR cc_start: 0.9138 (p) cc_final: 0.8776 (t) REVERT: a 197 ARG cc_start: 0.8327 (ttt180) cc_final: 0.7882 (mtm110) REVERT: b 66 ASN cc_start: 0.8198 (t0) cc_final: 0.7897 (t0) REVERT: b 98 GLN cc_start: 0.8744 (tp40) cc_final: 0.8404 (tp40) REVERT: b 107 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7476 (pt0) REVERT: b 115 LEU cc_start: 0.9694 (tp) cc_final: 0.9464 (tp) REVERT: b 122 ASN cc_start: 0.9016 (m-40) cc_final: 0.8767 (m-40) REVERT: b 124 THR cc_start: 0.8998 (p) cc_final: 0.8724 (t) REVERT: b 135 MET cc_start: 0.8646 (mmm) cc_final: 0.8421 (mmm) REVERT: b 136 ASP cc_start: 0.8049 (t70) cc_final: 0.7739 (t70) REVERT: c 66 ASN cc_start: 0.8325 (t0) cc_final: 0.8104 (t0) REVERT: c 82 ASN cc_start: 0.8662 (t0) cc_final: 0.8031 (t0) REVERT: c 124 THR cc_start: 0.9140 (p) cc_final: 0.8792 (t) REVERT: c 197 ARG cc_start: 0.8374 (ttt180) cc_final: 0.7936 (mtm110) REVERT: d 66 ASN cc_start: 0.8102 (t0) cc_final: 0.7718 (t0) REVERT: d 68 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7469 (tm-30) REVERT: d 107 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7402 (pt0) REVERT: d 122 ASN cc_start: 0.8999 (m-40) cc_final: 0.8788 (m-40) REVERT: d 124 THR cc_start: 0.8956 (p) cc_final: 0.8711 (t) REVERT: d 135 MET cc_start: 0.8660 (mmm) cc_final: 0.8459 (mmm) REVERT: d 188 ARG cc_start: 0.8408 (mmm160) cc_final: 0.8175 (tpt90) REVERT: e 66 ASN cc_start: 0.8343 (t0) cc_final: 0.8134 (t0) REVERT: e 124 THR cc_start: 0.9125 (p) cc_final: 0.8743 (t) REVERT: e 157 ARG cc_start: 0.8605 (ttm110) cc_final: 0.8318 (ttm110) REVERT: e 197 ARG cc_start: 0.8342 (ttt180) cc_final: 0.7903 (mtm110) REVERT: f 66 ASN cc_start: 0.8219 (t0) cc_final: 0.7698 (t0) REVERT: f 115 LEU cc_start: 0.9681 (tp) cc_final: 0.9451 (tp) REVERT: f 122 ASN cc_start: 0.8984 (m-40) cc_final: 0.8772 (m-40) REVERT: f 124 THR cc_start: 0.8970 (p) cc_final: 0.8732 (t) REVERT: f 135 MET cc_start: 0.8654 (mmm) cc_final: 0.8425 (mmm) REVERT: f 188 ARG cc_start: 0.8077 (tpt90) cc_final: 0.7843 (tpt90) REVERT: g 66 ASN cc_start: 0.8334 (t0) cc_final: 0.8126 (t0) REVERT: g 124 THR cc_start: 0.9124 (p) cc_final: 0.8737 (t) REVERT: g 157 ARG cc_start: 0.8627 (ttm110) cc_final: 0.8337 (ttm110) REVERT: g 197 ARG cc_start: 0.8338 (ttt180) cc_final: 0.7901 (mtm110) REVERT: h 66 ASN cc_start: 0.8218 (t0) cc_final: 0.7716 (t0) REVERT: h 115 LEU cc_start: 0.9681 (tp) cc_final: 0.9445 (tp) REVERT: h 122 ASN cc_start: 0.9006 (m-40) cc_final: 0.8797 (m-40) REVERT: h 124 THR cc_start: 0.9032 (p) cc_final: 0.8773 (t) REVERT: h 135 MET cc_start: 0.8684 (mmm) cc_final: 0.8030 (mmm) REVERT: i 66 ASN cc_start: 0.8155 (t0) cc_final: 0.7914 (t0) REVERT: i 67 LEU cc_start: 0.8662 (mm) cc_final: 0.8406 (mm) REVERT: i 122 ASN cc_start: 0.8929 (m-40) cc_final: 0.8704 (m-40) REVERT: i 124 THR cc_start: 0.8918 (p) cc_final: 0.8358 (t) REVERT: i 135 MET cc_start: 0.8759 (mmm) cc_final: 0.8092 (mmm) REVERT: i 172 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7870 (mm-30) REVERT: j 66 ASN cc_start: 0.8265 (t0) cc_final: 0.7942 (t0) REVERT: j 67 LEU cc_start: 0.8712 (mm) cc_final: 0.8489 (mm) REVERT: j 79 ASP cc_start: 0.8313 (m-30) cc_final: 0.8076 (m-30) REVERT: j 198 TYR cc_start: 0.9127 (m-10) cc_final: 0.8819 (m-10) REVERT: k 66 ASN cc_start: 0.8115 (t0) cc_final: 0.7869 (t0) REVERT: k 67 LEU cc_start: 0.8663 (mm) cc_final: 0.8405 (mm) REVERT: k 122 ASN cc_start: 0.8935 (m-40) cc_final: 0.8699 (m-40) REVERT: k 124 THR cc_start: 0.8927 (p) cc_final: 0.8346 (t) REVERT: k 172 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7886 (mm-30) REVERT: l 66 ASN cc_start: 0.8266 (t0) cc_final: 0.7926 (t0) REVERT: l 67 LEU cc_start: 0.8731 (mm) cc_final: 0.8482 (mm) REVERT: l 142 GLU cc_start: 0.8435 (mp0) cc_final: 0.8196 (mp0) REVERT: l 160 MET cc_start: 0.9155 (mmm) cc_final: 0.8947 (tpp) REVERT: l 198 TYR cc_start: 0.9105 (m-10) cc_final: 0.8783 (m-10) REVERT: m 67 LEU cc_start: 0.8624 (mm) cc_final: 0.8410 (mm) REVERT: m 122 ASN cc_start: 0.8956 (m-40) cc_final: 0.8694 (m-40) REVERT: m 124 THR cc_start: 0.8983 (p) cc_final: 0.8392 (t) REVERT: m 172 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7834 (mm-30) REVERT: n 66 ASN cc_start: 0.8147 (t0) cc_final: 0.7827 (t0) REVERT: n 198 TYR cc_start: 0.9107 (m-10) cc_final: 0.8791 (m-10) REVERT: o 67 LEU cc_start: 0.8624 (mm) cc_final: 0.8405 (mm) REVERT: o 122 ASN cc_start: 0.8925 (m-40) cc_final: 0.8697 (m-40) REVERT: o 124 THR cc_start: 0.8944 (p) cc_final: 0.8353 (t) REVERT: o 172 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7870 (mm-30) REVERT: p 66 ASN cc_start: 0.8270 (t0) cc_final: 0.7944 (t0) REVERT: p 67 LEU cc_start: 0.8719 (mm) cc_final: 0.8491 (mm) REVERT: p 198 TYR cc_start: 0.9123 (m-10) cc_final: 0.8819 (m-10) REVERT: q 66 ASN cc_start: 0.8008 (t0) cc_final: 0.7489 (t0) REVERT: q 108 MET cc_start: 0.8534 (tpp) cc_final: 0.8090 (tpp) REVERT: q 124 THR cc_start: 0.8877 (p) cc_final: 0.8295 (t) REVERT: q 172 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7587 (mm-30) REVERT: q 197 ARG cc_start: 0.7902 (mtm110) cc_final: 0.7439 (mtm110) REVERT: r 108 MET cc_start: 0.8490 (tpp) cc_final: 0.7982 (tpp) REVERT: r 115 LEU cc_start: 0.9655 (tp) cc_final: 0.9452 (tp) REVERT: r 122 ASN cc_start: 0.8940 (m-40) cc_final: 0.8678 (m-40) REVERT: r 124 THR cc_start: 0.8960 (p) cc_final: 0.8447 (t) REVERT: r 218 ILE cc_start: 0.7940 (mm) cc_final: 0.7729 (mp) REVERT: s 66 ASN cc_start: 0.7991 (t0) cc_final: 0.7489 (t0) REVERT: s 108 MET cc_start: 0.8561 (tpp) cc_final: 0.8114 (tpp) REVERT: s 124 THR cc_start: 0.8864 (p) cc_final: 0.8313 (t) REVERT: s 172 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7649 (mm-30) REVERT: s 197 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7465 (mtm110) REVERT: t 98 GLN cc_start: 0.8605 (tp40) cc_final: 0.8228 (tp40) REVERT: t 107 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7783 (mt-10) REVERT: t 108 MET cc_start: 0.8623 (tpp) cc_final: 0.7999 (tpp) REVERT: t 115 LEU cc_start: 0.9654 (tp) cc_final: 0.9418 (tp) REVERT: t 122 ASN cc_start: 0.8952 (m-40) cc_final: 0.8722 (m-40) REVERT: t 124 THR cc_start: 0.8970 (p) cc_final: 0.8464 (t) REVERT: t 198 TYR cc_start: 0.9112 (m-10) cc_final: 0.8832 (m-10) REVERT: u 66 ASN cc_start: 0.8000 (t0) cc_final: 0.7451 (t0) REVERT: u 108 MET cc_start: 0.8539 (tpp) cc_final: 0.8083 (tpp) REVERT: u 124 THR cc_start: 0.8878 (p) cc_final: 0.8325 (t) REVERT: u 135 MET cc_start: 0.8834 (mmm) cc_final: 0.8521 (mmm) REVERT: u 172 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7591 (mm-30) REVERT: u 197 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7474 (mtm110) REVERT: v 108 MET cc_start: 0.8465 (tpp) cc_final: 0.7958 (tpp) REVERT: v 115 LEU cc_start: 0.9657 (tp) cc_final: 0.9443 (tp) REVERT: v 124 THR cc_start: 0.8970 (p) cc_final: 0.8457 (t) REVERT: v 135 MET cc_start: 0.8754 (mmm) cc_final: 0.8115 (mmm) REVERT: v 218 ILE cc_start: 0.7937 (mm) cc_final: 0.7728 (mp) REVERT: w 66 ASN cc_start: 0.7954 (t0) cc_final: 0.7482 (t0) REVERT: w 67 LEU cc_start: 0.8482 (mm) cc_final: 0.8229 (mm) REVERT: w 79 ASP cc_start: 0.8509 (m-30) cc_final: 0.8281 (m-30) REVERT: w 108 MET cc_start: 0.8566 (tpp) cc_final: 0.8097 (tpp) REVERT: w 124 THR cc_start: 0.8887 (p) cc_final: 0.8324 (t) REVERT: w 198 TYR cc_start: 0.9045 (m-10) cc_final: 0.8657 (m-10) REVERT: x 98 GLN cc_start: 0.8589 (tp40) cc_final: 0.8246 (tp40) REVERT: x 107 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7785 (mt-10) REVERT: x 108 MET cc_start: 0.8637 (tpp) cc_final: 0.8023 (tpp) REVERT: x 115 LEU cc_start: 0.9645 (tp) cc_final: 0.9421 (tp) REVERT: x 122 ASN cc_start: 0.8950 (m-40) cc_final: 0.8708 (m-40) REVERT: x 124 THR cc_start: 0.8957 (p) cc_final: 0.8453 (t) REVERT: x 198 TYR cc_start: 0.9102 (m-10) cc_final: 0.8843 (m-10) outliers start: 0 outliers final: 0 residues processed: 1523 average time/residue: 0.2135 time to fit residues: 508.9184 Evaluate side-chains 1404 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1404 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 45 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 384 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 54 optimal weight: 0.0470 chunk 372 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 190 optimal weight: 0.0980 chunk 144 optimal weight: 5.9990 chunk 173 optimal weight: 0.0980 overall best weight: 0.2278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 98 GLN b 217 HIS c 77 GLN c 98 GLN e 98 GLN f 98 GLN f 217 HIS g 98 GLN h 217 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.130749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.112738 restraints weight = 45412.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.116225 restraints weight = 28352.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.118504 restraints weight = 19658.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.120365 restraints weight = 15152.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.121859 restraints weight = 11963.398| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 34776 Z= 0.105 Angle : 0.596 5.737 47184 Z= 0.304 Chirality : 0.041 0.133 5160 Planarity : 0.005 0.048 6120 Dihedral : 4.834 18.483 4704 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.12), residues: 4176 helix: -0.87 (0.12), residues: 1944 sheet: -1.76 (0.31), residues: 240 loop : -2.93 (0.11), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG t 208 TYR 0.015 0.001 TYR c 180 PHE 0.014 0.002 PHE d 202 TRP 0.015 0.001 TRP r 132 HIS 0.001 0.000 HIS i 162 Details of bonding type rmsd covalent geometry : bond 0.00235 (34776) covalent geometry : angle 0.59556 (47184) hydrogen bonds : bond 0.02640 ( 936) hydrogen bonds : angle 3.92761 ( 2664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1479 time to evaluate : 1.041 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: a 66 ASN cc_start: 0.8236 (t0) cc_final: 0.7988 (t0) REVERT: a 79 ASP cc_start: 0.8393 (m-30) cc_final: 0.8114 (m-30) REVERT: a 124 THR cc_start: 0.9077 (p) cc_final: 0.8714 (t) REVERT: a 135 MET cc_start: 0.8532 (mmm) cc_final: 0.8329 (mmm) REVERT: b 79 ASP cc_start: 0.8547 (m-30) cc_final: 0.8215 (m-30) REVERT: b 112 MET cc_start: 0.9425 (mmp) cc_final: 0.9151 (mmt) REVERT: b 122 ASN cc_start: 0.8941 (m-40) cc_final: 0.8693 (m-40) REVERT: c 66 ASN cc_start: 0.8240 (t0) cc_final: 0.7967 (t0) REVERT: c 82 ASN cc_start: 0.8622 (t0) cc_final: 0.7969 (t0) REVERT: c 124 THR cc_start: 0.9107 (p) cc_final: 0.8758 (t) REVERT: c 135 MET cc_start: 0.8523 (mmm) cc_final: 0.8297 (mmm) REVERT: d 79 ASP cc_start: 0.8523 (m-30) cc_final: 0.8208 (m-30) REVERT: d 112 MET cc_start: 0.9418 (mmp) cc_final: 0.9197 (mmt) REVERT: d 122 ASN cc_start: 0.8860 (m-40) cc_final: 0.8559 (m-40) REVERT: d 135 MET cc_start: 0.8385 (mmm) cc_final: 0.7887 (mmm) REVERT: e 66 ASN cc_start: 0.8219 (t0) cc_final: 0.7920 (t0) REVERT: e 79 ASP cc_start: 0.8380 (m-30) cc_final: 0.7958 (m-30) REVERT: e 124 THR cc_start: 0.9052 (p) cc_final: 0.8688 (t) REVERT: e 135 MET cc_start: 0.8526 (mmm) cc_final: 0.8314 (mmm) REVERT: e 157 ARG cc_start: 0.8499 (ttm110) cc_final: 0.8240 (ttm110) REVERT: f 79 ASP cc_start: 0.8550 (m-30) cc_final: 0.8234 (m-30) REVERT: f 112 MET cc_start: 0.9401 (mmp) cc_final: 0.9181 (mmt) REVERT: f 122 ASN cc_start: 0.8819 (m-40) cc_final: 0.8548 (m-40) REVERT: g 66 ASN cc_start: 0.8297 (t0) cc_final: 0.8039 (t0) REVERT: g 124 THR cc_start: 0.9057 (p) cc_final: 0.8689 (t) REVERT: g 135 MET cc_start: 0.8563 (mmm) cc_final: 0.8350 (mmm) REVERT: g 157 ARG cc_start: 0.8533 (ttm110) cc_final: 0.8260 (ttm110) REVERT: h 79 ASP cc_start: 0.8546 (m-30) cc_final: 0.8194 (m-30) REVERT: h 122 ASN cc_start: 0.8903 (m-40) cc_final: 0.8630 (m-40) REVERT: h 135 MET cc_start: 0.8452 (mmm) cc_final: 0.7992 (mmm) REVERT: i 79 ASP cc_start: 0.8244 (m-30) cc_final: 0.8029 (m-30) REVERT: i 95 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7249 (mm-30) REVERT: i 98 GLN cc_start: 0.8025 (tt0) cc_final: 0.7786 (tt0) REVERT: i 122 ASN cc_start: 0.8688 (m-40) cc_final: 0.8481 (m-40) REVERT: i 124 THR cc_start: 0.8881 (p) cc_final: 0.8390 (t) REVERT: i 135 MET cc_start: 0.8653 (mmm) cc_final: 0.8087 (mmm) REVERT: i 172 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7743 (mm-30) REVERT: j 66 ASN cc_start: 0.8182 (t0) cc_final: 0.7927 (t0) REVERT: j 108 MET cc_start: 0.8396 (tpp) cc_final: 0.7930 (tpp) REVERT: j 135 MET cc_start: 0.8200 (mmm) cc_final: 0.7899 (mmm) REVERT: k 95 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7329 (mm-30) REVERT: k 98 GLN cc_start: 0.8501 (tt0) cc_final: 0.8211 (tt0) REVERT: k 122 ASN cc_start: 0.8678 (m-40) cc_final: 0.8457 (m-40) REVERT: k 124 THR cc_start: 0.8878 (p) cc_final: 0.8389 (t) REVERT: k 172 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7752 (mm-30) REVERT: l 66 ASN cc_start: 0.8197 (t0) cc_final: 0.7931 (t0) REVERT: l 189 ASN cc_start: 0.8979 (t0) cc_final: 0.8679 (t0) REVERT: l 197 ARG cc_start: 0.8568 (tmm-80) cc_final: 0.7654 (ttp80) REVERT: l 198 TYR cc_start: 0.8962 (m-10) cc_final: 0.8713 (m-10) REVERT: m 95 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7208 (mm-30) REVERT: m 98 GLN cc_start: 0.8044 (tt0) cc_final: 0.7728 (tt0) REVERT: m 122 ASN cc_start: 0.8776 (m-40) cc_final: 0.8495 (m-40) REVERT: m 124 THR cc_start: 0.8909 (p) cc_final: 0.8426 (t) REVERT: m 172 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7807 (mm-30) REVERT: n 66 ASN cc_start: 0.8012 (t0) cc_final: 0.7729 (t0) REVERT: n 135 MET cc_start: 0.8146 (mmm) cc_final: 0.7848 (mmm) REVERT: n 189 ASN cc_start: 0.8963 (t0) cc_final: 0.8668 (t0) REVERT: n 197 ARG cc_start: 0.8544 (tmm-80) cc_final: 0.7642 (ttp80) REVERT: n 198 TYR cc_start: 0.8955 (m-10) cc_final: 0.8712 (m-10) REVERT: o 79 ASP cc_start: 0.8112 (m-30) cc_final: 0.7848 (m-30) REVERT: o 95 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7294 (mm-30) REVERT: o 98 GLN cc_start: 0.8495 (tt0) cc_final: 0.8210 (tt0) REVERT: o 122 ASN cc_start: 0.8677 (m-40) cc_final: 0.8453 (m-40) REVERT: o 124 THR cc_start: 0.8896 (p) cc_final: 0.8409 (t) REVERT: o 172 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7742 (mm-30) REVERT: p 66 ASN cc_start: 0.8175 (t0) cc_final: 0.7940 (t0) REVERT: p 108 MET cc_start: 0.8428 (tpp) cc_final: 0.7962 (tpp) REVERT: p 135 MET cc_start: 0.8348 (mmm) cc_final: 0.7687 (mmm) REVERT: q 58 LYS cc_start: 0.8310 (mtmm) cc_final: 0.8098 (mtmm) REVERT: q 66 ASN cc_start: 0.7731 (t0) cc_final: 0.7241 (t0) REVERT: q 107 GLU cc_start: 0.7748 (pt0) cc_final: 0.6554 (tm-30) REVERT: q 112 MET cc_start: 0.9273 (mmp) cc_final: 0.9047 (mmt) REVERT: q 124 THR cc_start: 0.8894 (p) cc_final: 0.8347 (t) REVERT: q 135 MET cc_start: 0.8704 (mmm) cc_final: 0.8442 (mmm) REVERT: q 172 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7880 (mm-30) REVERT: q 188 ARG cc_start: 0.8251 (tpt90) cc_final: 0.7897 (tpt90) REVERT: r 79 ASP cc_start: 0.8402 (m-30) cc_final: 0.8172 (m-30) REVERT: r 82 ASN cc_start: 0.8430 (t0) cc_final: 0.8048 (t0) REVERT: r 107 GLU cc_start: 0.7597 (pt0) cc_final: 0.6513 (tm-30) REVERT: r 122 ASN cc_start: 0.8808 (m-40) cc_final: 0.8441 (m-40) REVERT: r 124 THR cc_start: 0.8936 (p) cc_final: 0.8382 (t) REVERT: r 197 ARG cc_start: 0.8487 (ttt90) cc_final: 0.6828 (ttt90) REVERT: s 58 LYS cc_start: 0.8383 (mtmm) cc_final: 0.8088 (mtmm) REVERT: s 66 ASN cc_start: 0.7743 (t0) cc_final: 0.7285 (t0) REVERT: s 107 GLU cc_start: 0.7733 (pt0) cc_final: 0.6566 (tm-30) REVERT: s 112 MET cc_start: 0.9284 (mmp) cc_final: 0.9062 (mmt) REVERT: s 124 THR cc_start: 0.8876 (p) cc_final: 0.8353 (t) REVERT: s 172 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7949 (mm-30) REVERT: t 82 ASN cc_start: 0.8435 (t0) cc_final: 0.8057 (t0) REVERT: t 108 MET cc_start: 0.8528 (tpp) cc_final: 0.7937 (tpp) REVERT: t 122 ASN cc_start: 0.8788 (m-40) cc_final: 0.8409 (m-40) REVERT: t 124 THR cc_start: 0.8987 (p) cc_final: 0.8423 (t) REVERT: t 215 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7135 (tm-30) REVERT: u 66 ASN cc_start: 0.7703 (t0) cc_final: 0.7274 (t0) REVERT: u 107 GLU cc_start: 0.7752 (pt0) cc_final: 0.6582 (tm-30) REVERT: u 112 MET cc_start: 0.9266 (mmp) cc_final: 0.9056 (mmt) REVERT: u 124 THR cc_start: 0.8892 (p) cc_final: 0.8357 (t) REVERT: u 135 MET cc_start: 0.8720 (mmm) cc_final: 0.8350 (mmm) REVERT: u 172 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7772 (mm-30) REVERT: u 188 ARG cc_start: 0.8245 (tpt90) cc_final: 0.7883 (tpt90) REVERT: v 82 ASN cc_start: 0.8516 (t0) cc_final: 0.8152 (t0) REVERT: v 107 GLU cc_start: 0.7580 (pt0) cc_final: 0.6517 (tm-30) REVERT: v 124 THR cc_start: 0.8960 (p) cc_final: 0.8390 (t) REVERT: v 197 ARG cc_start: 0.8455 (ttt90) cc_final: 0.6801 (ttt90) REVERT: w 66 ASN cc_start: 0.7718 (t0) cc_final: 0.7290 (t0) REVERT: w 107 GLU cc_start: 0.7702 (pt0) cc_final: 0.6565 (tm-30) REVERT: w 112 MET cc_start: 0.9295 (mmp) cc_final: 0.9057 (mmt) REVERT: w 124 THR cc_start: 0.8907 (p) cc_final: 0.8376 (t) REVERT: w 135 MET cc_start: 0.8707 (mmm) cc_final: 0.8490 (mmm) REVERT: w 212 ARG cc_start: 0.7003 (ptt-90) cc_final: 0.6784 (ttp-110) REVERT: x 56 MET cc_start: 0.8149 (mtt) cc_final: 0.7921 (mtt) REVERT: x 82 ASN cc_start: 0.8464 (t0) cc_final: 0.8085 (t0) REVERT: x 108 MET cc_start: 0.8562 (tpp) cc_final: 0.7988 (tpp) REVERT: x 122 ASN cc_start: 0.8776 (m-40) cc_final: 0.8375 (m-40) REVERT: x 124 THR cc_start: 0.8966 (p) cc_final: 0.8410 (t) outliers start: 0 outliers final: 0 residues processed: 1479 average time/residue: 0.2088 time to fit residues: 485.1690 Evaluate side-chains 1339 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1339 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 65 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 270 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 327 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 98 GLN c 98 GLN ** c 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 GLN e 98 GLN f 98 GLN g 98 GLN h 98 GLN j 162 HIS l 162 HIS n 162 HIS p 162 HIS q 175 ASN r 162 HIS r 175 ASN s 175 ASN ** t 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 162 HIS t 175 ASN u 175 ASN v 162 HIS v 175 ASN ** x 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 162 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.121957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.104084 restraints weight = 47531.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.107190 restraints weight = 30499.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.109483 restraints weight = 21816.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.110858 restraints weight = 16776.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.112235 restraints weight = 13953.021| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 34776 Z= 0.276 Angle : 0.740 6.314 47184 Z= 0.374 Chirality : 0.048 0.156 5160 Planarity : 0.005 0.040 6120 Dihedral : 5.329 20.216 4704 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.12), residues: 4176 helix: -1.10 (0.12), residues: 2064 sheet: -1.67 (0.31), residues: 240 loop : -2.67 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG w 197 TYR 0.026 0.002 TYR v 73 PHE 0.020 0.003 PHE w 200 TRP 0.012 0.002 TRP d 132 HIS 0.002 0.001 HIS a 69 Details of bonding type rmsd covalent geometry : bond 0.00645 (34776) covalent geometry : angle 0.73956 (47184) hydrogen bonds : bond 0.03592 ( 936) hydrogen bonds : angle 4.61890 ( 2664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1482 time to evaluate : 1.206 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: a 66 ASN cc_start: 0.8324 (t0) cc_final: 0.8043 (t0) REVERT: a 79 ASP cc_start: 0.8591 (m-30) cc_final: 0.8150 (m-30) REVERT: a 82 ASN cc_start: 0.8744 (t0) cc_final: 0.8415 (t0) REVERT: a 98 GLN cc_start: 0.8373 (tt0) cc_final: 0.8157 (tt0) REVERT: a 124 THR cc_start: 0.9110 (p) cc_final: 0.8805 (t) REVERT: a 135 MET cc_start: 0.8644 (mmm) cc_final: 0.8327 (mmm) REVERT: a 160 MET cc_start: 0.9220 (mmm) cc_final: 0.8749 (mmt) REVERT: b 79 ASP cc_start: 0.8686 (m-30) cc_final: 0.8293 (m-30) REVERT: b 115 LEU cc_start: 0.9695 (tp) cc_final: 0.9475 (tp) REVERT: b 122 ASN cc_start: 0.8994 (m-40) cc_final: 0.8763 (m-40) REVERT: b 124 THR cc_start: 0.8941 (p) cc_final: 0.8655 (t) REVERT: b 135 MET cc_start: 0.8757 (mmm) cc_final: 0.8287 (mmm) REVERT: b 156 LEU cc_start: 0.9043 (tp) cc_final: 0.8838 (tp) REVERT: c 66 ASN cc_start: 0.8389 (t0) cc_final: 0.8079 (t0) REVERT: c 79 ASP cc_start: 0.8601 (m-30) cc_final: 0.8099 (m-30) REVERT: c 82 ASN cc_start: 0.8651 (t0) cc_final: 0.8030 (t0) REVERT: c 98 GLN cc_start: 0.8376 (tt0) cc_final: 0.8139 (tt0) REVERT: c 124 THR cc_start: 0.9125 (p) cc_final: 0.8824 (t) REVERT: c 135 MET cc_start: 0.8632 (mmm) cc_final: 0.8315 (mmm) REVERT: c 160 MET cc_start: 0.9226 (mmm) cc_final: 0.8846 (mmt) REVERT: d 66 ASN cc_start: 0.8074 (t0) cc_final: 0.7703 (t0) REVERT: d 79 ASP cc_start: 0.8730 (m-30) cc_final: 0.8326 (m-30) REVERT: d 122 ASN cc_start: 0.8970 (m-40) cc_final: 0.8692 (m-40) REVERT: d 124 THR cc_start: 0.8883 (p) cc_final: 0.8598 (t) REVERT: d 156 LEU cc_start: 0.9062 (tp) cc_final: 0.8807 (tp) REVERT: e 66 ASN cc_start: 0.8397 (t0) cc_final: 0.8097 (t0) REVERT: e 82 ASN cc_start: 0.8706 (t0) cc_final: 0.8056 (t0) REVERT: e 98 GLN cc_start: 0.8376 (tt0) cc_final: 0.8081 (tt0) REVERT: e 124 THR cc_start: 0.9091 (p) cc_final: 0.8814 (t) REVERT: e 135 MET cc_start: 0.8628 (mmm) cc_final: 0.8313 (mmm) REVERT: e 157 ARG cc_start: 0.8579 (ttm110) cc_final: 0.8205 (ttm110) REVERT: e 160 MET cc_start: 0.9209 (mmm) cc_final: 0.8988 (tpp) REVERT: f 79 ASP cc_start: 0.8679 (m-30) cc_final: 0.8277 (m-30) REVERT: f 115 LEU cc_start: 0.9693 (tp) cc_final: 0.9467 (tp) REVERT: f 122 ASN cc_start: 0.8948 (m-40) cc_final: 0.8689 (m-40) REVERT: f 124 THR cc_start: 0.8836 (p) cc_final: 0.8556 (t) REVERT: f 135 MET cc_start: 0.8737 (mmm) cc_final: 0.8222 (mmm) REVERT: g 66 ASN cc_start: 0.8438 (t0) cc_final: 0.8107 (t0) REVERT: g 79 ASP cc_start: 0.8605 (m-30) cc_final: 0.8072 (m-30) REVERT: g 82 ASN cc_start: 0.8629 (t0) cc_final: 0.8057 (t0) REVERT: g 98 GLN cc_start: 0.8372 (tt0) cc_final: 0.8058 (tt0) REVERT: g 124 THR cc_start: 0.9096 (p) cc_final: 0.8794 (t) REVERT: g 135 MET cc_start: 0.8724 (mmm) cc_final: 0.8377 (mmm) REVERT: h 79 ASP cc_start: 0.8593 (m-30) cc_final: 0.8359 (m-30) REVERT: h 115 LEU cc_start: 0.9679 (tp) cc_final: 0.9421 (tp) REVERT: h 122 ASN cc_start: 0.9000 (m-40) cc_final: 0.8740 (m-40) REVERT: h 124 THR cc_start: 0.8931 (p) cc_final: 0.8638 (t) REVERT: h 135 MET cc_start: 0.8801 (mmm) cc_final: 0.8179 (mmm) REVERT: i 68 GLU cc_start: 0.8332 (mp0) cc_final: 0.8098 (tm-30) REVERT: i 82 ASN cc_start: 0.8452 (t0) cc_final: 0.7971 (t0) REVERT: i 122 ASN cc_start: 0.8899 (m-40) cc_final: 0.8646 (m-40) REVERT: i 124 THR cc_start: 0.9039 (p) cc_final: 0.8502 (t) REVERT: i 172 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7833 (mm-30) REVERT: j 66 ASN cc_start: 0.8222 (t0) cc_final: 0.7831 (t0) REVERT: j 67 LEU cc_start: 0.8678 (mm) cc_final: 0.8448 (mm) REVERT: j 122 ASN cc_start: 0.8621 (m-40) cc_final: 0.8360 (m-40) REVERT: k 68 GLU cc_start: 0.8315 (mp0) cc_final: 0.8099 (tm-30) REVERT: k 82 ASN cc_start: 0.8467 (t0) cc_final: 0.7975 (t0) REVERT: k 122 ASN cc_start: 0.8837 (m-40) cc_final: 0.8623 (m-40) REVERT: k 124 THR cc_start: 0.9042 (p) cc_final: 0.8503 (t) REVERT: k 172 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7803 (mm-30) REVERT: l 66 ASN cc_start: 0.8225 (t0) cc_final: 0.7828 (t0) REVERT: l 67 LEU cc_start: 0.8699 (mm) cc_final: 0.8470 (mm) REVERT: l 189 ASN cc_start: 0.8986 (t0) cc_final: 0.8679 (t0) REVERT: l 198 TYR cc_start: 0.9168 (m-10) cc_final: 0.8775 (m-10) REVERT: m 56 MET cc_start: 0.8722 (mmm) cc_final: 0.8462 (mtt) REVERT: m 68 GLU cc_start: 0.8296 (mp0) cc_final: 0.8069 (tm-30) REVERT: m 122 ASN cc_start: 0.8937 (m-40) cc_final: 0.8677 (m-40) REVERT: m 124 THR cc_start: 0.9059 (p) cc_final: 0.8484 (t) REVERT: m 172 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7771 (mm-30) REVERT: n 66 ASN cc_start: 0.8025 (t0) cc_final: 0.7707 (t0) REVERT: n 122 ASN cc_start: 0.8628 (m-40) cc_final: 0.8411 (m-40) REVERT: n 189 ASN cc_start: 0.8987 (t0) cc_final: 0.8688 (t0) REVERT: n 198 TYR cc_start: 0.9160 (m-10) cc_final: 0.8778 (m-10) REVERT: o 56 MET cc_start: 0.8675 (mmm) cc_final: 0.8429 (mtt) REVERT: o 68 GLU cc_start: 0.8322 (mp0) cc_final: 0.8090 (tm-30) REVERT: o 82 ASN cc_start: 0.8477 (t0) cc_final: 0.7987 (t0) REVERT: o 122 ASN cc_start: 0.8873 (m-40) cc_final: 0.8629 (m-40) REVERT: o 124 THR cc_start: 0.9055 (p) cc_final: 0.8505 (t) REVERT: o 172 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7787 (mm-30) REVERT: p 66 ASN cc_start: 0.8229 (t0) cc_final: 0.7838 (t0) REVERT: p 67 LEU cc_start: 0.8689 (mm) cc_final: 0.8471 (mm) REVERT: q 66 ASN cc_start: 0.7906 (t0) cc_final: 0.7403 (t0) REVERT: q 67 LEU cc_start: 0.8573 (mm) cc_final: 0.8368 (mm) REVERT: q 108 MET cc_start: 0.8565 (tpp) cc_final: 0.7894 (tpp) REVERT: q 124 THR cc_start: 0.8956 (p) cc_final: 0.8328 (t) REVERT: q 135 MET cc_start: 0.8795 (mmm) cc_final: 0.8440 (mmm) REVERT: q 172 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7614 (mm-30) REVERT: q 197 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7544 (mtm110) REVERT: r 82 ASN cc_start: 0.8639 (t0) cc_final: 0.8232 (t0) REVERT: r 108 MET cc_start: 0.8569 (tpp) cc_final: 0.7908 (tpp) REVERT: r 122 ASN cc_start: 0.8920 (m-40) cc_final: 0.8602 (m-40) REVERT: r 124 THR cc_start: 0.9017 (p) cc_final: 0.8470 (t) REVERT: r 135 MET cc_start: 0.8683 (mmm) cc_final: 0.8474 (mmm) REVERT: r 197 ARG cc_start: 0.8394 (ttt90) cc_final: 0.8097 (ttt90) REVERT: s 66 ASN cc_start: 0.7954 (t0) cc_final: 0.7397 (t0) REVERT: s 67 LEU cc_start: 0.8573 (mm) cc_final: 0.8353 (mm) REVERT: s 108 MET cc_start: 0.8603 (tpp) cc_final: 0.7940 (tpp) REVERT: s 124 THR cc_start: 0.8960 (p) cc_final: 0.8323 (t) REVERT: s 208 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7704 (mmm-85) REVERT: t 82 ASN cc_start: 0.8606 (t0) cc_final: 0.8193 (t0) REVERT: t 108 MET cc_start: 0.8673 (tpp) cc_final: 0.8016 (tpp) REVERT: t 122 ASN cc_start: 0.8975 (m-40) cc_final: 0.8661 (m-40) REVERT: t 124 THR cc_start: 0.9036 (p) cc_final: 0.8497 (t) REVERT: t 135 MET cc_start: 0.8702 (mmm) cc_final: 0.8396 (mmm) REVERT: t 215 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7365 (tm-30) REVERT: u 66 ASN cc_start: 0.7827 (t0) cc_final: 0.7246 (t0) REVERT: u 67 LEU cc_start: 0.8500 (mm) cc_final: 0.8275 (mm) REVERT: u 79 ASP cc_start: 0.8428 (m-30) cc_final: 0.8186 (m-30) REVERT: u 108 MET cc_start: 0.8582 (tpp) cc_final: 0.7919 (tpp) REVERT: u 124 THR cc_start: 0.8965 (p) cc_final: 0.8318 (t) REVERT: v 67 LEU cc_start: 0.8629 (mm) cc_final: 0.8402 (mm) REVERT: v 82 ASN cc_start: 0.8627 (t0) cc_final: 0.8351 (t0) REVERT: v 108 MET cc_start: 0.8511 (tpp) cc_final: 0.7874 (tpp) REVERT: v 115 LEU cc_start: 0.9644 (tp) cc_final: 0.9443 (tp) REVERT: v 124 THR cc_start: 0.9013 (p) cc_final: 0.8461 (t) REVERT: v 135 MET cc_start: 0.8715 (mmm) cc_final: 0.8374 (mmm) REVERT: v 197 ARG cc_start: 0.8396 (ttt90) cc_final: 0.8077 (ttt90) REVERT: w 58 LYS cc_start: 0.8411 (mtmm) cc_final: 0.8137 (mtmm) REVERT: w 66 ASN cc_start: 0.7711 (t0) cc_final: 0.7195 (t0) REVERT: w 79 ASP cc_start: 0.8489 (m-30) cc_final: 0.8165 (m-30) REVERT: w 82 ASN cc_start: 0.8718 (t0) cc_final: 0.8247 (t0) REVERT: w 108 MET cc_start: 0.8619 (tpp) cc_final: 0.7940 (tpp) REVERT: w 124 THR cc_start: 0.8974 (p) cc_final: 0.8344 (t) REVERT: w 135 MET cc_start: 0.8776 (mmm) cc_final: 0.8467 (mmm) REVERT: w 198 TYR cc_start: 0.9184 (m-10) cc_final: 0.8913 (m-10) REVERT: x 67 LEU cc_start: 0.8643 (mm) cc_final: 0.8390 (mm) REVERT: x 82 ASN cc_start: 0.8625 (t0) cc_final: 0.8220 (t0) REVERT: x 108 MET cc_start: 0.8719 (tpp) cc_final: 0.8047 (tpp) REVERT: x 122 ASN cc_start: 0.8993 (m-40) cc_final: 0.8682 (m-40) REVERT: x 124 THR cc_start: 0.9028 (p) cc_final: 0.8492 (t) outliers start: 0 outliers final: 0 residues processed: 1482 average time/residue: 0.2058 time to fit residues: 484.9727 Evaluate side-chains 1374 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1374 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 200 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 224 optimal weight: 0.0040 chunk 129 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 325 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 308 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 217 HIS c 217 HIS d 98 GLN f 98 GLN g 217 HIS h 98 GLN r 127 ASN t 127 ASN v 127 ASN x 127 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.129203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.111044 restraints weight = 45612.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.114375 restraints weight = 28750.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.116436 restraints weight = 20150.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.118375 restraints weight = 15791.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.119564 restraints weight = 12479.601| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34776 Z= 0.117 Angle : 0.609 6.392 47184 Z= 0.309 Chirality : 0.042 0.134 5160 Planarity : 0.005 0.044 6120 Dihedral : 4.970 18.425 4704 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.13), residues: 4176 helix: -0.77 (0.12), residues: 2064 sheet: -1.59 (0.30), residues: 240 loop : -2.71 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 197 TYR 0.025 0.001 TYR v 73 PHE 0.012 0.002 PHE k 202 TRP 0.019 0.001 TRP p 132 HIS 0.001 0.000 HIS j 162 Details of bonding type rmsd covalent geometry : bond 0.00273 (34776) covalent geometry : angle 0.60934 (47184) hydrogen bonds : bond 0.02729 ( 936) hydrogen bonds : angle 4.08905 ( 2664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1436 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1436 time to evaluate : 1.191 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: a 66 ASN cc_start: 0.8361 (t0) cc_final: 0.8110 (t0) REVERT: a 79 ASP cc_start: 0.8561 (m-30) cc_final: 0.8113 (m-30) REVERT: a 82 ASN cc_start: 0.8612 (t0) cc_final: 0.8266 (t0) REVERT: a 124 THR cc_start: 0.9050 (p) cc_final: 0.8817 (t) REVERT: a 135 MET cc_start: 0.8561 (mmm) cc_final: 0.8342 (mmm) REVERT: a 197 ARG cc_start: 0.8411 (ttt90) cc_final: 0.7318 (ttt90) REVERT: b 79 ASP cc_start: 0.8588 (m-30) cc_final: 0.8238 (m-30) REVERT: b 112 MET cc_start: 0.9435 (mmp) cc_final: 0.9182 (mmt) REVERT: b 122 ASN cc_start: 0.8901 (m-40) cc_final: 0.8642 (m-40) REVERT: b 135 MET cc_start: 0.8690 (mmm) cc_final: 0.8225 (mmm) REVERT: c 66 ASN cc_start: 0.8374 (t0) cc_final: 0.8125 (t0) REVERT: c 79 ASP cc_start: 0.8553 (m-30) cc_final: 0.8069 (m-30) REVERT: c 82 ASN cc_start: 0.8629 (t0) cc_final: 0.7957 (t0) REVERT: c 124 THR cc_start: 0.9055 (p) cc_final: 0.8836 (t) REVERT: c 135 MET cc_start: 0.8529 (mmm) cc_final: 0.8294 (mmm) REVERT: c 160 MET cc_start: 0.9073 (mmm) cc_final: 0.8812 (mmt) REVERT: c 174 ARG cc_start: 0.9134 (tpp80) cc_final: 0.8859 (tpp80) REVERT: d 79 ASP cc_start: 0.8548 (m-30) cc_final: 0.8194 (m-30) REVERT: d 112 MET cc_start: 0.9403 (mmp) cc_final: 0.9153 (mmt) REVERT: d 122 ASN cc_start: 0.8822 (m-40) cc_final: 0.8557 (m-40) REVERT: d 124 THR cc_start: 0.8812 (p) cc_final: 0.8581 (t) REVERT: d 135 MET cc_start: 0.8514 (mmm) cc_final: 0.8160 (mmm) REVERT: d 197 ARG cc_start: 0.8476 (ttt90) cc_final: 0.8166 (ttt90) REVERT: e 66 ASN cc_start: 0.8418 (t0) cc_final: 0.8131 (t0) REVERT: e 79 ASP cc_start: 0.8541 (m-30) cc_final: 0.8045 (m-30) REVERT: e 82 ASN cc_start: 0.8475 (t0) cc_final: 0.7782 (t0) REVERT: e 124 THR cc_start: 0.9027 (p) cc_final: 0.8809 (t) REVERT: e 157 ARG cc_start: 0.8478 (ttm110) cc_final: 0.8133 (ttm110) REVERT: f 79 ASP cc_start: 0.8603 (m-30) cc_final: 0.8218 (m-30) REVERT: f 98 GLN cc_start: 0.8204 (tt0) cc_final: 0.7775 (tt0) REVERT: f 122 ASN cc_start: 0.8754 (m-40) cc_final: 0.8534 (m-40) REVERT: f 135 MET cc_start: 0.8562 (mmm) cc_final: 0.8050 (mmm) REVERT: g 66 ASN cc_start: 0.8417 (t0) cc_final: 0.8159 (t0) REVERT: g 68 GLU cc_start: 0.8389 (mp0) cc_final: 0.8087 (tm-30) REVERT: g 79 ASP cc_start: 0.8570 (m-30) cc_final: 0.8102 (m-30) REVERT: g 82 ASN cc_start: 0.8699 (t0) cc_final: 0.8469 (t0) REVERT: g 124 THR cc_start: 0.9024 (p) cc_final: 0.8816 (t) REVERT: g 135 MET cc_start: 0.8565 (mmm) cc_final: 0.8354 (mmm) REVERT: g 197 ARG cc_start: 0.8421 (ttt90) cc_final: 0.7270 (ttt90) REVERT: h 79 ASP cc_start: 0.8486 (m-30) cc_final: 0.8083 (m-30) REVERT: h 98 GLN cc_start: 0.8181 (tt0) cc_final: 0.7825 (tt0) REVERT: h 122 ASN cc_start: 0.8882 (m-40) cc_final: 0.8618 (m-40) REVERT: h 135 MET cc_start: 0.8701 (mmm) cc_final: 0.8105 (mmm) REVERT: i 68 GLU cc_start: 0.8260 (mp0) cc_final: 0.7978 (tm-30) REVERT: i 82 ASN cc_start: 0.8320 (t0) cc_final: 0.7628 (t0) REVERT: i 95 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7560 (mm-30) REVERT: i 122 ASN cc_start: 0.8699 (m-40) cc_final: 0.8486 (m-40) REVERT: i 124 THR cc_start: 0.8928 (p) cc_final: 0.8456 (t) REVERT: i 135 MET cc_start: 0.8453 (mmm) cc_final: 0.8162 (mmm) REVERT: i 172 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7859 (mm-30) REVERT: j 66 ASN cc_start: 0.8182 (t0) cc_final: 0.7850 (t0) REVERT: j 124 THR cc_start: 0.8936 (p) cc_final: 0.8585 (t) REVERT: k 68 GLU cc_start: 0.8266 (mp0) cc_final: 0.7999 (tm-30) REVERT: k 82 ASN cc_start: 0.8325 (t0) cc_final: 0.7683 (t0) REVERT: k 95 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7554 (mm-30) REVERT: k 124 THR cc_start: 0.8921 (p) cc_final: 0.8437 (t) REVERT: k 172 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7866 (mm-30) REVERT: l 66 ASN cc_start: 0.8172 (t0) cc_final: 0.7834 (t0) REVERT: l 107 GLU cc_start: 0.7346 (pt0) cc_final: 0.7140 (pt0) REVERT: l 124 THR cc_start: 0.8909 (p) cc_final: 0.8651 (t) REVERT: l 189 ASN cc_start: 0.8915 (t0) cc_final: 0.8685 (t0) REVERT: l 198 TYR cc_start: 0.9056 (m-10) cc_final: 0.8720 (m-10) REVERT: m 56 MET cc_start: 0.8673 (mmm) cc_final: 0.8321 (mtt) REVERT: m 68 GLU cc_start: 0.8315 (mp0) cc_final: 0.7910 (tm-30) REVERT: m 95 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7549 (mm-30) REVERT: m 98 GLN cc_start: 0.8028 (tt0) cc_final: 0.7820 (tt0) REVERT: m 122 ASN cc_start: 0.8704 (m-40) cc_final: 0.8502 (m-40) REVERT: m 124 THR cc_start: 0.8925 (p) cc_final: 0.8467 (t) REVERT: m 134 MET cc_start: 0.8662 (ttt) cc_final: 0.8365 (ttt) REVERT: m 172 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7845 (mm-30) REVERT: n 66 ASN cc_start: 0.8003 (t0) cc_final: 0.7679 (t0) REVERT: n 107 GLU cc_start: 0.7334 (pt0) cc_final: 0.7126 (pt0) REVERT: n 124 THR cc_start: 0.8947 (p) cc_final: 0.8622 (t) REVERT: n 189 ASN cc_start: 0.8902 (t0) cc_final: 0.8667 (t0) REVERT: n 198 TYR cc_start: 0.9048 (m-10) cc_final: 0.8711 (m-10) REVERT: o 56 MET cc_start: 0.8628 (mmm) cc_final: 0.8191 (mtt) REVERT: o 68 GLU cc_start: 0.8322 (mp0) cc_final: 0.7911 (tm-30) REVERT: o 82 ASN cc_start: 0.8349 (t0) cc_final: 0.7727 (t0) REVERT: o 95 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7552 (mm-30) REVERT: o 122 ASN cc_start: 0.8681 (m-40) cc_final: 0.8471 (m-40) REVERT: o 124 THR cc_start: 0.8939 (p) cc_final: 0.8467 (t) REVERT: o 135 MET cc_start: 0.8483 (mmm) cc_final: 0.8265 (mmm) REVERT: o 172 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7802 (mm-30) REVERT: p 66 ASN cc_start: 0.8177 (t0) cc_final: 0.7868 (t0) REVERT: q 56 MET cc_start: 0.8542 (mmm) cc_final: 0.8105 (mtt) REVERT: q 58 LYS cc_start: 0.8348 (mtmm) cc_final: 0.8139 (mtmm) REVERT: q 66 ASN cc_start: 0.7766 (t0) cc_final: 0.7145 (t0) REVERT: q 67 LEU cc_start: 0.8507 (mm) cc_final: 0.8272 (mm) REVERT: q 107 GLU cc_start: 0.7722 (pt0) cc_final: 0.6579 (tm-30) REVERT: q 108 MET cc_start: 0.8478 (tpp) cc_final: 0.8108 (tpp) REVERT: q 124 THR cc_start: 0.8933 (p) cc_final: 0.8368 (t) REVERT: q 172 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7788 (mm-30) REVERT: q 188 ARG cc_start: 0.8311 (tpt90) cc_final: 0.7993 (tpt90) REVERT: q 212 ARG cc_start: 0.7267 (ptt-90) cc_final: 0.6894 (ttp-110) REVERT: r 54 MET cc_start: 0.8467 (tmm) cc_final: 0.8123 (ttp) REVERT: r 82 ASN cc_start: 0.8535 (t0) cc_final: 0.8209 (t0) REVERT: r 107 GLU cc_start: 0.7766 (pt0) cc_final: 0.6418 (tm-30) REVERT: r 122 ASN cc_start: 0.8888 (m-40) cc_final: 0.8505 (m-40) REVERT: r 124 THR cc_start: 0.8970 (p) cc_final: 0.8491 (t) REVERT: r 135 MET cc_start: 0.8572 (mmm) cc_final: 0.8322 (mmm) REVERT: s 56 MET cc_start: 0.8535 (mmm) cc_final: 0.7952 (mtt) REVERT: s 58 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8122 (mtmm) REVERT: s 66 ASN cc_start: 0.7775 (t0) cc_final: 0.7286 (t0) REVERT: s 67 LEU cc_start: 0.8487 (mm) cc_final: 0.8237 (mm) REVERT: s 79 ASP cc_start: 0.8405 (m-30) cc_final: 0.8147 (m-30) REVERT: s 107 GLU cc_start: 0.7768 (pt0) cc_final: 0.6569 (tm-30) REVERT: s 108 MET cc_start: 0.8513 (tpp) cc_final: 0.8110 (tpp) REVERT: s 124 THR cc_start: 0.8894 (p) cc_final: 0.8376 (t) REVERT: s 172 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7767 (mm-30) REVERT: t 54 MET cc_start: 0.8443 (tmm) cc_final: 0.8112 (ttp) REVERT: t 82 ASN cc_start: 0.8479 (t0) cc_final: 0.8158 (t0) REVERT: t 108 MET cc_start: 0.8564 (tpp) cc_final: 0.7995 (tpp) REVERT: t 122 ASN cc_start: 0.8907 (m-40) cc_final: 0.8506 (m-40) REVERT: t 124 THR cc_start: 0.8964 (p) cc_final: 0.8553 (t) REVERT: t 135 MET cc_start: 0.8678 (mmm) cc_final: 0.8417 (mmm) REVERT: t 215 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7371 (tm-30) REVERT: u 66 ASN cc_start: 0.7699 (t0) cc_final: 0.7230 (t0) REVERT: u 67 LEU cc_start: 0.8426 (mm) cc_final: 0.8218 (mm) REVERT: u 79 ASP cc_start: 0.8246 (m-30) cc_final: 0.7953 (m-30) REVERT: u 107 GLU cc_start: 0.7701 (pt0) cc_final: 0.6567 (tm-30) REVERT: u 108 MET cc_start: 0.8477 (tpp) cc_final: 0.8110 (tpp) REVERT: u 124 THR cc_start: 0.8877 (p) cc_final: 0.8380 (t) REVERT: u 172 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7780 (mm-30) REVERT: u 181 MET cc_start: 0.8328 (tpt) cc_final: 0.8069 (mmm) REVERT: v 82 ASN cc_start: 0.8516 (t0) cc_final: 0.8229 (t0) REVERT: v 107 GLU cc_start: 0.7711 (pt0) cc_final: 0.6424 (tm-30) REVERT: v 124 THR cc_start: 0.8963 (p) cc_final: 0.8555 (t) REVERT: v 135 MET cc_start: 0.8709 (mmm) cc_final: 0.8282 (mmm) REVERT: w 58 LYS cc_start: 0.8243 (mtmm) cc_final: 0.8039 (mtmm) REVERT: w 66 ASN cc_start: 0.7690 (t0) cc_final: 0.7380 (t0) REVERT: w 79 ASP cc_start: 0.8447 (m-30) cc_final: 0.7878 (m-30) REVERT: w 107 GLU cc_start: 0.7757 (pt0) cc_final: 0.6556 (tm-30) REVERT: w 108 MET cc_start: 0.8512 (tpp) cc_final: 0.8106 (tpp) REVERT: w 124 THR cc_start: 0.8891 (p) cc_final: 0.8375 (t) REVERT: x 82 ASN cc_start: 0.8490 (t0) cc_final: 0.8197 (t0) REVERT: x 108 MET cc_start: 0.8598 (tpp) cc_final: 0.7995 (tpp) REVERT: x 122 ASN cc_start: 0.8904 (m-40) cc_final: 0.8479 (m-40) REVERT: x 124 THR cc_start: 0.8961 (p) cc_final: 0.8539 (t) outliers start: 0 outliers final: 0 residues processed: 1436 average time/residue: 0.2090 time to fit residues: 475.7146 Evaluate side-chains 1326 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1326 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 130 optimal weight: 0.9980 chunk 318 optimal weight: 4.9990 chunk 375 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 359 optimal weight: 0.0070 chunk 42 optimal weight: 0.1980 chunk 271 optimal weight: 0.9990 chunk 249 optimal weight: 5.9990 chunk 339 optimal weight: 0.2980 chunk 165 optimal weight: 4.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 98 GLN c 98 GLN ** c 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 GLN d 217 HIS e 98 GLN f 98 GLN g 98 GLN h 98 GLN i 98 GLN q 175 ASN r 175 ASN s 175 ASN t 175 ASN u 175 ASN v 175 ASN w 175 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.131851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.114203 restraints weight = 44897.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.117662 restraints weight = 27828.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.120187 restraints weight = 19240.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.122017 restraints weight = 14343.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.123346 restraints weight = 11301.391| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 34776 Z= 0.107 Angle : 0.603 6.329 47184 Z= 0.304 Chirality : 0.042 0.232 5160 Planarity : 0.005 0.040 6120 Dihedral : 4.627 16.975 4704 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.13), residues: 4176 helix: -0.57 (0.12), residues: 2064 sheet: -1.27 (0.31), residues: 240 loop : -2.67 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG e 212 TYR 0.018 0.001 TYR h 180 PHE 0.010 0.002 PHE q 202 TRP 0.017 0.001 TRP n 132 HIS 0.001 0.000 HIS m 162 Details of bonding type rmsd covalent geometry : bond 0.00248 (34776) covalent geometry : angle 0.60262 (47184) hydrogen bonds : bond 0.02560 ( 936) hydrogen bonds : angle 3.91443 ( 2664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1425 time to evaluate : 1.269 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: a 66 ASN cc_start: 0.8191 (t0) cc_final: 0.7949 (t0) REVERT: a 68 GLU cc_start: 0.8356 (mp0) cc_final: 0.8003 (tm-30) REVERT: a 79 ASP cc_start: 0.8564 (m-30) cc_final: 0.8176 (m-30) REVERT: a 82 ASN cc_start: 0.8524 (t0) cc_final: 0.8143 (t0) REVERT: a 124 THR cc_start: 0.9019 (p) cc_final: 0.8807 (t) REVERT: a 135 MET cc_start: 0.8550 (mmm) cc_final: 0.8212 (mmm) REVERT: b 79 ASP cc_start: 0.8453 (m-30) cc_final: 0.8113 (m-30) REVERT: b 95 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7267 (mm-30) REVERT: b 108 MET cc_start: 0.8041 (tpp) cc_final: 0.7293 (tpp) REVERT: b 135 MET cc_start: 0.8419 (mmm) cc_final: 0.7971 (mmm) REVERT: b 142 GLU cc_start: 0.8218 (tt0) cc_final: 0.7983 (tt0) REVERT: c 68 GLU cc_start: 0.8412 (mp0) cc_final: 0.8019 (tm-30) REVERT: c 79 ASP cc_start: 0.8577 (m-30) cc_final: 0.8271 (m-30) REVERT: c 124 THR cc_start: 0.9038 (p) cc_final: 0.8830 (t) REVERT: c 135 MET cc_start: 0.8532 (mmm) cc_final: 0.8176 (mmm) REVERT: d 79 ASP cc_start: 0.8454 (m-30) cc_final: 0.8076 (m-30) REVERT: d 95 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7440 (mm-30) REVERT: d 112 MET cc_start: 0.9373 (mmp) cc_final: 0.9121 (mmt) REVERT: d 122 ASN cc_start: 0.8765 (m-40) cc_final: 0.8495 (m-40) REVERT: d 124 THR cc_start: 0.8820 (p) cc_final: 0.8570 (t) REVERT: d 135 MET cc_start: 0.8399 (mmm) cc_final: 0.8101 (mmm) REVERT: d 197 ARG cc_start: 0.8243 (ttt90) cc_final: 0.7968 (ttt90) REVERT: e 68 GLU cc_start: 0.8379 (mp0) cc_final: 0.7985 (tm-30) REVERT: e 79 ASP cc_start: 0.8385 (m-30) cc_final: 0.8029 (m-30) REVERT: e 82 ASN cc_start: 0.8582 (t0) cc_final: 0.7878 (t0) REVERT: f 54 MET cc_start: 0.7393 (ttp) cc_final: 0.7080 (ttp) REVERT: f 79 ASP cc_start: 0.8492 (m-30) cc_final: 0.8265 (m-30) REVERT: f 95 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7466 (mm-30) REVERT: f 98 GLN cc_start: 0.8254 (tt0) cc_final: 0.7588 (tt0) REVERT: f 135 MET cc_start: 0.8549 (mmm) cc_final: 0.7999 (mmm) REVERT: g 66 ASN cc_start: 0.8334 (t0) cc_final: 0.8101 (t0) REVERT: g 68 GLU cc_start: 0.8373 (mp0) cc_final: 0.8092 (tm-30) REVERT: g 79 ASP cc_start: 0.8510 (m-30) cc_final: 0.8144 (m-30) REVERT: g 82 ASN cc_start: 0.8637 (t0) cc_final: 0.8336 (t0) REVERT: g 95 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7486 (mm-30) REVERT: g 135 MET cc_start: 0.8575 (mmm) cc_final: 0.8191 (mmm) REVERT: h 54 MET cc_start: 0.7445 (ttp) cc_final: 0.7083 (ttp) REVERT: h 79 ASP cc_start: 0.8395 (m-30) cc_final: 0.8079 (m-30) REVERT: h 95 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7448 (mm-30) REVERT: h 98 GLN cc_start: 0.8257 (tt0) cc_final: 0.7979 (tt0) REVERT: h 122 ASN cc_start: 0.8670 (m-40) cc_final: 0.8468 (m-40) REVERT: h 135 MET cc_start: 0.8706 (mmm) cc_final: 0.8065 (mmm) REVERT: i 56 MET cc_start: 0.8662 (mmm) cc_final: 0.8263 (mmm) REVERT: i 82 ASN cc_start: 0.8159 (t0) cc_final: 0.7293 (t0) REVERT: i 95 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7513 (mm-30) REVERT: i 122 ASN cc_start: 0.8665 (m-40) cc_final: 0.8404 (m-40) REVERT: i 124 THR cc_start: 0.8853 (p) cc_final: 0.8424 (t) REVERT: i 135 MET cc_start: 0.8512 (mmm) cc_final: 0.8256 (mmm) REVERT: j 66 ASN cc_start: 0.8093 (t0) cc_final: 0.7662 (t0) REVERT: k 82 ASN cc_start: 0.8184 (t0) cc_final: 0.7278 (t0) REVERT: k 95 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7545 (mm-30) REVERT: k 98 GLN cc_start: 0.7900 (tt0) cc_final: 0.7534 (tt0) REVERT: k 124 THR cc_start: 0.8872 (p) cc_final: 0.8410 (t) REVERT: k 134 MET cc_start: 0.8685 (ttt) cc_final: 0.8477 (ttt) REVERT: l 66 ASN cc_start: 0.8070 (t0) cc_final: 0.7725 (t0) REVERT: l 198 TYR cc_start: 0.8949 (m-10) cc_final: 0.8604 (m-10) REVERT: m 68 GLU cc_start: 0.8353 (mp0) cc_final: 0.7883 (tm-30) REVERT: m 95 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7529 (mm-30) REVERT: m 124 THR cc_start: 0.8894 (p) cc_final: 0.8434 (t) REVERT: m 172 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7780 (mm-30) REVERT: n 66 ASN cc_start: 0.7976 (t0) cc_final: 0.7765 (t0) REVERT: n 95 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7714 (mm-30) REVERT: n 124 THR cc_start: 0.8957 (p) cc_final: 0.8538 (t) REVERT: n 135 MET cc_start: 0.8458 (mmm) cc_final: 0.8116 (mmm) REVERT: n 198 TYR cc_start: 0.8930 (m-10) cc_final: 0.8589 (m-10) REVERT: o 68 GLU cc_start: 0.8330 (mp0) cc_final: 0.7902 (tm-30) REVERT: o 82 ASN cc_start: 0.8206 (t0) cc_final: 0.7348 (t0) REVERT: o 95 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7554 (mm-30) REVERT: o 98 GLN cc_start: 0.7888 (tt0) cc_final: 0.7542 (tt0) REVERT: o 122 ASN cc_start: 0.8601 (m-40) cc_final: 0.8401 (m-40) REVERT: o 124 THR cc_start: 0.8894 (p) cc_final: 0.8437 (t) REVERT: o 135 MET cc_start: 0.8498 (mmm) cc_final: 0.8246 (mmm) REVERT: o 172 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7782 (mm-30) REVERT: p 66 ASN cc_start: 0.8120 (t0) cc_final: 0.7824 (t0) REVERT: p 135 MET cc_start: 0.8578 (mmm) cc_final: 0.7905 (mmm) REVERT: p 136 ASP cc_start: 0.7693 (t70) cc_final: 0.7480 (t70) REVERT: p 197 ARG cc_start: 0.8374 (tmm-80) cc_final: 0.7630 (ttp80) REVERT: p 198 TYR cc_start: 0.8980 (m-10) cc_final: 0.8724 (m-10) REVERT: q 67 LEU cc_start: 0.8539 (mm) cc_final: 0.8283 (mm) REVERT: q 103 ILE cc_start: 0.9242 (mm) cc_final: 0.8582 (mm) REVERT: q 107 GLU cc_start: 0.7713 (pt0) cc_final: 0.6625 (tm-30) REVERT: q 108 MET cc_start: 0.8428 (tpp) cc_final: 0.8179 (tpp) REVERT: q 124 THR cc_start: 0.8908 (p) cc_final: 0.8326 (t) REVERT: q 172 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7664 (mm-30) REVERT: q 188 ARG cc_start: 0.8357 (tpt90) cc_final: 0.8013 (tpt90) REVERT: r 82 ASN cc_start: 0.8587 (t0) cc_final: 0.8169 (t0) REVERT: r 107 GLU cc_start: 0.7446 (pt0) cc_final: 0.6346 (tm-30) REVERT: r 108 MET cc_start: 0.8266 (tpp) cc_final: 0.7774 (tpp) REVERT: r 122 ASN cc_start: 0.8825 (m-40) cc_final: 0.8426 (m-40) REVERT: r 124 THR cc_start: 0.8923 (p) cc_final: 0.8486 (t) REVERT: r 135 MET cc_start: 0.8598 (mmm) cc_final: 0.8293 (mmm) REVERT: s 66 ASN cc_start: 0.7773 (t0) cc_final: 0.7277 (t0) REVERT: s 103 ILE cc_start: 0.9241 (mm) cc_final: 0.8589 (mm) REVERT: s 107 GLU cc_start: 0.7728 (pt0) cc_final: 0.6611 (tm-30) REVERT: s 108 MET cc_start: 0.8471 (tpp) cc_final: 0.8230 (tpp) REVERT: s 124 THR cc_start: 0.8840 (p) cc_final: 0.8331 (t) REVERT: s 172 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7725 (mm-30) REVERT: t 82 ASN cc_start: 0.8521 (t0) cc_final: 0.8084 (t0) REVERT: t 108 MET cc_start: 0.8579 (tpp) cc_final: 0.8046 (tpp) REVERT: t 122 ASN cc_start: 0.8877 (m-40) cc_final: 0.8521 (m-40) REVERT: t 124 THR cc_start: 0.8882 (p) cc_final: 0.8611 (t) REVERT: t 135 MET cc_start: 0.8658 (mmm) cc_final: 0.8288 (mmm) REVERT: t 215 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7290 (tm-30) REVERT: u 56 MET cc_start: 0.8618 (mmm) cc_final: 0.8057 (mtt) REVERT: u 66 ASN cc_start: 0.7776 (t0) cc_final: 0.7215 (t0) REVERT: u 79 ASP cc_start: 0.8175 (m-30) cc_final: 0.7878 (m-30) REVERT: u 103 ILE cc_start: 0.9257 (mm) cc_final: 0.8293 (mm) REVERT: u 107 GLU cc_start: 0.7712 (pt0) cc_final: 0.6626 (tm-30) REVERT: u 108 MET cc_start: 0.8426 (tpp) cc_final: 0.8188 (tpp) REVERT: u 124 THR cc_start: 0.8836 (p) cc_final: 0.8323 (t) REVERT: u 172 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7733 (mm-30) REVERT: v 82 ASN cc_start: 0.8506 (t0) cc_final: 0.8133 (t0) REVERT: v 107 GLU cc_start: 0.7426 (pt0) cc_final: 0.6362 (tm-30) REVERT: v 108 MET cc_start: 0.8236 (tpp) cc_final: 0.7712 (tpp) REVERT: v 124 THR cc_start: 0.8932 (p) cc_final: 0.8521 (t) REVERT: v 135 MET cc_start: 0.8616 (mmm) cc_final: 0.8121 (mmm) REVERT: v 197 ARG cc_start: 0.8226 (ttt90) cc_final: 0.6767 (ttt90) REVERT: w 56 MET cc_start: 0.8554 (mmm) cc_final: 0.8047 (mtt) REVERT: w 66 ASN cc_start: 0.7899 (t0) cc_final: 0.7403 (t0) REVERT: w 79 ASP cc_start: 0.8301 (m-30) cc_final: 0.7822 (m-30) REVERT: w 103 ILE cc_start: 0.9224 (mm) cc_final: 0.8299 (mm) REVERT: w 107 GLU cc_start: 0.7697 (pt0) cc_final: 0.6572 (tm-30) REVERT: w 108 MET cc_start: 0.8477 (tpp) cc_final: 0.8211 (tpp) REVERT: w 124 THR cc_start: 0.8826 (p) cc_final: 0.8342 (t) REVERT: x 54 MET cc_start: 0.8063 (tmm) cc_final: 0.7847 (ttp) REVERT: x 56 MET cc_start: 0.8223 (mtt) cc_final: 0.7852 (mtt) REVERT: x 82 ASN cc_start: 0.8551 (t0) cc_final: 0.8112 (t0) REVERT: x 108 MET cc_start: 0.8584 (tpp) cc_final: 0.8068 (tpp) REVERT: x 122 ASN cc_start: 0.8885 (m-40) cc_final: 0.8461 (m-40) REVERT: x 124 THR cc_start: 0.8917 (p) cc_final: 0.8506 (t) REVERT: x 197 ARG cc_start: 0.8224 (ttt90) cc_final: 0.6632 (ttt90) REVERT: x 215 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7257 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1425 average time/residue: 0.2069 time to fit residues: 468.0061 Evaluate side-chains 1309 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1309 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 106 optimal weight: 5.9990 chunk 321 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 394 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 98 GLN m 98 GLN q 217 HIS s 217 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.127575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.112685 restraints weight = 44958.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.115560 restraints weight = 28517.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.117713 restraints weight = 19851.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.119174 restraints weight = 14940.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.120319 restraints weight = 11878.071| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34776 Z= 0.138 Angle : 0.629 7.125 47184 Z= 0.318 Chirality : 0.043 0.214 5160 Planarity : 0.005 0.048 6120 Dihedral : 4.770 17.037 4704 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.13), residues: 4176 helix: -0.49 (0.12), residues: 2064 sheet: -1.25 (0.30), residues: 240 loop : -2.57 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG e 212 TYR 0.025 0.001 TYR a 73 PHE 0.013 0.002 PHE q 200 TRP 0.010 0.001 TRP f 132 HIS 0.002 0.000 HIS m 162 Details of bonding type rmsd covalent geometry : bond 0.00328 (34776) covalent geometry : angle 0.62895 (47184) hydrogen bonds : bond 0.02865 ( 936) hydrogen bonds : angle 4.11846 ( 2664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1408 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1408 time to evaluate : 1.172 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: a 79 ASP cc_start: 0.8646 (m-30) cc_final: 0.8152 (m-30) REVERT: a 82 ASN cc_start: 0.8562 (t0) cc_final: 0.8283 (t0) REVERT: a 124 THR cc_start: 0.9139 (p) cc_final: 0.8875 (t) REVERT: a 135 MET cc_start: 0.8511 (mmm) cc_final: 0.8170 (mmm) REVERT: b 66 ASN cc_start: 0.8153 (t0) cc_final: 0.7749 (t0) REVERT: b 95 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7280 (mm-30) REVERT: b 98 GLN cc_start: 0.8374 (tp40) cc_final: 0.8127 (tp40) REVERT: b 108 MET cc_start: 0.7993 (tpp) cc_final: 0.7159 (tpp) REVERT: b 135 MET cc_start: 0.8640 (mmm) cc_final: 0.8016 (mmm) REVERT: b 142 GLU cc_start: 0.8076 (tt0) cc_final: 0.7865 (tt0) REVERT: c 79 ASP cc_start: 0.8502 (m-30) cc_final: 0.8194 (m-30) REVERT: c 124 THR cc_start: 0.9171 (p) cc_final: 0.8921 (t) REVERT: c 135 MET cc_start: 0.8459 (mmm) cc_final: 0.8112 (mmm) REVERT: d 68 GLU cc_start: 0.8318 (mp0) cc_final: 0.7974 (mp0) REVERT: d 79 ASP cc_start: 0.8470 (m-30) cc_final: 0.8135 (m-30) REVERT: d 95 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7412 (mm-30) REVERT: d 122 ASN cc_start: 0.8876 (m-40) cc_final: 0.8568 (m-40) REVERT: d 124 THR cc_start: 0.8901 (p) cc_final: 0.8643 (t) REVERT: d 135 MET cc_start: 0.8552 (mmm) cc_final: 0.8141 (mmm) REVERT: d 197 ARG cc_start: 0.8216 (ttt90) cc_final: 0.7935 (ttt90) REVERT: e 79 ASP cc_start: 0.8549 (m-30) cc_final: 0.8131 (m-30) REVERT: e 82 ASN cc_start: 0.8518 (t0) cc_final: 0.7898 (t0) REVERT: e 174 ARG cc_start: 0.9042 (tpp80) cc_final: 0.8749 (tpp80) REVERT: f 95 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7442 (mm-30) REVERT: f 98 GLN cc_start: 0.8095 (tt0) cc_final: 0.7513 (tt0) REVERT: f 135 MET cc_start: 0.8370 (mmm) cc_final: 0.8023 (mmm) REVERT: f 157 ARG cc_start: 0.8453 (ttm110) cc_final: 0.8244 (ttm110) REVERT: g 79 ASP cc_start: 0.8554 (m-30) cc_final: 0.8161 (m-30) REVERT: g 82 ASN cc_start: 0.8586 (t0) cc_final: 0.8295 (t0) REVERT: g 135 MET cc_start: 0.8586 (mmm) cc_final: 0.8260 (mmm) REVERT: h 79 ASP cc_start: 0.8393 (m-30) cc_final: 0.8092 (m-30) REVERT: h 95 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7419 (mm-30) REVERT: h 135 MET cc_start: 0.8778 (mmm) cc_final: 0.8069 (mmm) REVERT: h 157 ARG cc_start: 0.8511 (ttm110) cc_final: 0.8282 (ttm110) REVERT: i 56 MET cc_start: 0.8639 (mmm) cc_final: 0.8181 (mmm) REVERT: i 82 ASN cc_start: 0.8113 (t0) cc_final: 0.7315 (t0) REVERT: i 95 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7453 (mm-30) REVERT: i 122 ASN cc_start: 0.8686 (m-40) cc_final: 0.8468 (m-40) REVERT: i 124 THR cc_start: 0.8934 (p) cc_final: 0.8483 (t) REVERT: i 135 MET cc_start: 0.8481 (mmm) cc_final: 0.8252 (mmm) REVERT: i 172 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7803 (mm-30) REVERT: j 66 ASN cc_start: 0.8007 (t0) cc_final: 0.7708 (t0) REVERT: j 134 MET cc_start: 0.8512 (ttt) cc_final: 0.8310 (ttt) REVERT: k 82 ASN cc_start: 0.8149 (t0) cc_final: 0.7322 (t0) REVERT: k 95 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7490 (mm-30) REVERT: k 124 THR cc_start: 0.8961 (p) cc_final: 0.8461 (t) REVERT: k 172 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7863 (mm-30) REVERT: l 66 ASN cc_start: 0.7978 (t0) cc_final: 0.7750 (t0) REVERT: l 124 THR cc_start: 0.9032 (p) cc_final: 0.8757 (t) REVERT: l 198 TYR cc_start: 0.8995 (m-10) cc_final: 0.8637 (m-10) REVERT: m 95 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7487 (mm-30) REVERT: m 124 THR cc_start: 0.8969 (p) cc_final: 0.8487 (t) REVERT: n 124 THR cc_start: 0.8984 (p) cc_final: 0.8563 (t) REVERT: n 135 MET cc_start: 0.8465 (mmm) cc_final: 0.8009 (mmm) REVERT: n 198 TYR cc_start: 0.8988 (m-10) cc_final: 0.8636 (m-10) REVERT: o 82 ASN cc_start: 0.8198 (t0) cc_final: 0.7380 (t0) REVERT: o 95 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7545 (mm-30) REVERT: o 124 THR cc_start: 0.8969 (p) cc_final: 0.8489 (t) REVERT: o 135 MET cc_start: 0.8427 (mmm) cc_final: 0.8218 (mmm) REVERT: p 66 ASN cc_start: 0.8028 (t0) cc_final: 0.7811 (t0) REVERT: p 95 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7657 (mm-30) REVERT: p 135 MET cc_start: 0.8730 (mmm) cc_final: 0.8095 (mmm) REVERT: q 66 ASN cc_start: 0.7798 (t0) cc_final: 0.7356 (t0) REVERT: q 98 GLN cc_start: 0.8147 (tp40) cc_final: 0.7798 (tp40) REVERT: q 103 ILE cc_start: 0.9122 (mm) cc_final: 0.8302 (mm) REVERT: q 107 GLU cc_start: 0.7779 (pt0) cc_final: 0.6616 (tm-30) REVERT: q 108 MET cc_start: 0.8517 (tpp) cc_final: 0.7922 (tpp) REVERT: q 122 ASN cc_start: 0.8641 (m-40) cc_final: 0.8427 (m-40) REVERT: q 124 THR cc_start: 0.8939 (p) cc_final: 0.8470 (t) REVERT: q 172 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7890 (mm-30) REVERT: r 82 ASN cc_start: 0.8609 (t0) cc_final: 0.8126 (t0) REVERT: r 107 GLU cc_start: 0.7394 (pt0) cc_final: 0.6427 (tm-30) REVERT: r 108 MET cc_start: 0.8372 (tpp) cc_final: 0.7848 (tpp) REVERT: r 122 ASN cc_start: 0.8960 (m-40) cc_final: 0.8552 (m-40) REVERT: r 124 THR cc_start: 0.8980 (p) cc_final: 0.8520 (t) REVERT: r 135 MET cc_start: 0.8540 (mmm) cc_final: 0.8192 (mmm) REVERT: s 66 ASN cc_start: 0.7645 (t0) cc_final: 0.7310 (t0) REVERT: s 98 GLN cc_start: 0.8129 (tp40) cc_final: 0.7773 (tp40) REVERT: s 103 ILE cc_start: 0.9109 (mm) cc_final: 0.8291 (mm) REVERT: s 107 GLU cc_start: 0.7800 (pt0) cc_final: 0.6554 (tm-30) REVERT: s 108 MET cc_start: 0.8569 (tpp) cc_final: 0.7921 (tpp) REVERT: s 113 ASN cc_start: 0.9139 (m-40) cc_final: 0.8457 (m-40) REVERT: s 124 THR cc_start: 0.8859 (p) cc_final: 0.8463 (t) REVERT: s 172 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7713 (mm-30) REVERT: t 66 ASN cc_start: 0.7807 (t0) cc_final: 0.7564 (t0) REVERT: t 82 ASN cc_start: 0.8541 (t0) cc_final: 0.8160 (t0) REVERT: t 108 MET cc_start: 0.8554 (tpp) cc_final: 0.8004 (tpp) REVERT: t 115 LEU cc_start: 0.9594 (tp) cc_final: 0.9382 (tp) REVERT: t 122 ASN cc_start: 0.8932 (m-40) cc_final: 0.8598 (m-40) REVERT: t 124 THR cc_start: 0.8922 (p) cc_final: 0.8649 (t) REVERT: t 135 MET cc_start: 0.8725 (mmm) cc_final: 0.8307 (mmm) REVERT: u 66 ASN cc_start: 0.7733 (t0) cc_final: 0.7213 (t0) REVERT: u 67 LEU cc_start: 0.8471 (mm) cc_final: 0.8218 (mm) REVERT: u 79 ASP cc_start: 0.8141 (m-30) cc_final: 0.7886 (m-30) REVERT: u 107 GLU cc_start: 0.7735 (pt0) cc_final: 0.6541 (tm-30) REVERT: u 108 MET cc_start: 0.8447 (tpp) cc_final: 0.7785 (tpp) REVERT: u 124 THR cc_start: 0.8862 (p) cc_final: 0.8447 (t) REVERT: u 172 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7760 (mm-30) REVERT: v 82 ASN cc_start: 0.8502 (t0) cc_final: 0.8227 (t0) REVERT: v 107 GLU cc_start: 0.7355 (pt0) cc_final: 0.6301 (tm-30) REVERT: v 124 THR cc_start: 0.8940 (p) cc_final: 0.8594 (t) REVERT: v 135 MET cc_start: 0.8693 (mmm) cc_final: 0.8455 (mmm) REVERT: w 66 ASN cc_start: 0.7799 (t0) cc_final: 0.7380 (t0) REVERT: w 67 LEU cc_start: 0.8441 (mm) cc_final: 0.8230 (mm) REVERT: w 107 GLU cc_start: 0.7692 (pt0) cc_final: 0.6472 (tm-30) REVERT: w 108 MET cc_start: 0.8500 (tpp) cc_final: 0.7867 (tpp) REVERT: w 124 THR cc_start: 0.8872 (p) cc_final: 0.8443 (t) REVERT: x 54 MET cc_start: 0.8075 (tmm) cc_final: 0.7814 (ttp) REVERT: x 82 ASN cc_start: 0.8561 (t0) cc_final: 0.8207 (t0) REVERT: x 108 MET cc_start: 0.8554 (tpp) cc_final: 0.8013 (tpp) REVERT: x 122 ASN cc_start: 0.8932 (m-40) cc_final: 0.8547 (m-40) REVERT: x 124 THR cc_start: 0.8959 (p) cc_final: 0.8575 (t) REVERT: x 197 ARG cc_start: 0.8134 (ttt90) cc_final: 0.6544 (ttt90) outliers start: 0 outliers final: 0 residues processed: 1408 average time/residue: 0.2064 time to fit residues: 460.7250 Evaluate side-chains 1300 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1300 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 233 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 386 optimal weight: 4.9990 chunk 369 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 GLN h 98 GLN i 98 GLN k 98 GLN m 98 GLN o 98 GLN r 175 ASN s 175 ASN t 175 ASN u 175 ASN v 175 ASN w 175 ASN w 217 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.127293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.108793 restraints weight = 45741.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.111998 restraints weight = 29484.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.114521 restraints weight = 21273.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.116288 restraints weight = 16150.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.117566 restraints weight = 12898.669| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34776 Z= 0.175 Angle : 0.668 7.606 47184 Z= 0.339 Chirality : 0.045 0.202 5160 Planarity : 0.005 0.042 6120 Dihedral : 4.936 17.323 4704 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.13), residues: 4176 helix: -0.50 (0.12), residues: 2040 sheet: -1.44 (0.30), residues: 240 loop : -2.43 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG e 212 TYR 0.024 0.001 TYR t 73 PHE 0.015 0.002 PHE q 200 TRP 0.013 0.001 TRP n 132 HIS 0.002 0.000 HIS o 162 Details of bonding type rmsd covalent geometry : bond 0.00412 (34776) covalent geometry : angle 0.66830 (47184) hydrogen bonds : bond 0.03029 ( 936) hydrogen bonds : angle 4.30169 ( 2664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1431 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1431 time to evaluate : 0.981 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: a 82 ASN cc_start: 0.8568 (t0) cc_final: 0.8196 (t0) REVERT: a 124 THR cc_start: 0.9128 (p) cc_final: 0.8867 (t) REVERT: b 66 ASN cc_start: 0.7712 (t0) cc_final: 0.7128 (t0) REVERT: b 95 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7343 (mm-30) REVERT: b 108 MET cc_start: 0.8036 (tpp) cc_final: 0.7156 (tpp) REVERT: b 115 LEU cc_start: 0.9671 (tp) cc_final: 0.9448 (tp) REVERT: b 135 MET cc_start: 0.8580 (mmm) cc_final: 0.8100 (mmm) REVERT: b 145 LEU cc_start: 0.9130 (mt) cc_final: 0.8624 (mt) REVERT: c 79 ASP cc_start: 0.8623 (m-30) cc_final: 0.8357 (m-30) REVERT: c 82 ASN cc_start: 0.8479 (t0) cc_final: 0.7686 (t0) REVERT: c 124 THR cc_start: 0.9132 (p) cc_final: 0.8864 (t) REVERT: d 68 GLU cc_start: 0.8440 (mp0) cc_final: 0.8226 (mp0) REVERT: d 79 ASP cc_start: 0.8489 (m-30) cc_final: 0.8261 (m-30) REVERT: d 95 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7490 (mm-30) REVERT: d 122 ASN cc_start: 0.8851 (m-40) cc_final: 0.8577 (m-40) REVERT: d 124 THR cc_start: 0.8921 (p) cc_final: 0.8517 (t) REVERT: d 135 MET cc_start: 0.8668 (mmm) cc_final: 0.8241 (mmm) REVERT: d 142 GLU cc_start: 0.8202 (tt0) cc_final: 0.7957 (tt0) REVERT: d 156 LEU cc_start: 0.8975 (tp) cc_final: 0.8767 (tp) REVERT: d 197 ARG cc_start: 0.8402 (ttt90) cc_final: 0.8004 (ttt90) REVERT: e 55 ARG cc_start: 0.7903 (tpp80) cc_final: 0.7701 (tpt-90) REVERT: e 79 ASP cc_start: 0.8630 (m-30) cc_final: 0.8183 (m-30) REVERT: f 95 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7525 (mm-30) REVERT: f 98 GLN cc_start: 0.8382 (tt0) cc_final: 0.7571 (tt0) REVERT: f 135 MET cc_start: 0.8540 (mmm) cc_final: 0.8175 (mmm) REVERT: f 142 GLU cc_start: 0.8155 (tt0) cc_final: 0.7950 (tt0) REVERT: g 79 ASP cc_start: 0.8618 (m-30) cc_final: 0.8232 (m-30) REVERT: g 82 ASN cc_start: 0.8685 (t0) cc_final: 0.8407 (t0) REVERT: g 125 SER cc_start: 0.8427 (p) cc_final: 0.8214 (t) REVERT: h 79 ASP cc_start: 0.8467 (m-30) cc_final: 0.8171 (m-30) REVERT: h 95 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7463 (mm-30) REVERT: h 135 MET cc_start: 0.8791 (mmm) cc_final: 0.8070 (mmm) REVERT: h 142 GLU cc_start: 0.8225 (tt0) cc_final: 0.7969 (tt0) REVERT: h 157 ARG cc_start: 0.8535 (ttm110) cc_final: 0.8296 (ttm110) REVERT: i 56 MET cc_start: 0.8631 (mmm) cc_final: 0.8216 (mmm) REVERT: i 68 GLU cc_start: 0.8362 (mp0) cc_final: 0.7977 (tm-30) REVERT: i 82 ASN cc_start: 0.8136 (t0) cc_final: 0.7419 (t0) REVERT: i 95 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7565 (mm-30) REVERT: i 122 ASN cc_start: 0.8647 (m-40) cc_final: 0.8402 (m-40) REVERT: i 124 THR cc_start: 0.8954 (p) cc_final: 0.8514 (t) REVERT: i 172 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7872 (mm-30) REVERT: j 66 ASN cc_start: 0.8129 (t0) cc_final: 0.7690 (t0) REVERT: j 112 MET cc_start: 0.9399 (mmt) cc_final: 0.9097 (mmt) REVERT: j 115 LEU cc_start: 0.9636 (tp) cc_final: 0.9326 (tp) REVERT: j 134 MET cc_start: 0.8588 (ttt) cc_final: 0.8344 (ttt) REVERT: k 82 ASN cc_start: 0.8215 (t0) cc_final: 0.7498 (t0) REVERT: k 95 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7602 (mm-30) REVERT: k 108 MET cc_start: 0.8425 (tpp) cc_final: 0.7756 (tpp) REVERT: k 124 THR cc_start: 0.9000 (p) cc_final: 0.8541 (t) REVERT: k 172 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7884 (mm-30) REVERT: l 66 ASN cc_start: 0.8060 (t0) cc_final: 0.7698 (t0) REVERT: l 112 MET cc_start: 0.9427 (mmt) cc_final: 0.9111 (mmt) REVERT: l 115 LEU cc_start: 0.9624 (tp) cc_final: 0.9301 (tp) REVERT: l 124 THR cc_start: 0.9077 (p) cc_final: 0.8709 (t) REVERT: l 181 MET cc_start: 0.8227 (tpt) cc_final: 0.7780 (mmm) REVERT: l 198 TYR cc_start: 0.9020 (m-10) cc_final: 0.8666 (m-10) REVERT: m 95 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7580 (mm-30) REVERT: m 124 THR cc_start: 0.8986 (p) cc_final: 0.8571 (t) REVERT: m 172 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7684 (mm-30) REVERT: n 135 MET cc_start: 0.8605 (mmm) cc_final: 0.8013 (mmm) REVERT: n 181 MET cc_start: 0.8218 (tpt) cc_final: 0.7779 (mmm) REVERT: n 198 TYR cc_start: 0.9020 (m-10) cc_final: 0.8662 (m-10) REVERT: o 82 ASN cc_start: 0.8285 (t0) cc_final: 0.7523 (t0) REVERT: o 95 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7626 (mm-30) REVERT: o 108 MET cc_start: 0.8437 (tpp) cc_final: 0.7755 (tpp) REVERT: o 124 THR cc_start: 0.9016 (p) cc_final: 0.8544 (t) REVERT: o 135 MET cc_start: 0.8570 (mmm) cc_final: 0.8359 (mmm) REVERT: p 66 ASN cc_start: 0.8088 (t0) cc_final: 0.7761 (t0) REVERT: p 135 MET cc_start: 0.8750 (mmm) cc_final: 0.8159 (mmm) REVERT: q 66 ASN cc_start: 0.7703 (t0) cc_final: 0.7297 (t0) REVERT: q 98 GLN cc_start: 0.8246 (tp40) cc_final: 0.7774 (tp40) REVERT: q 103 ILE cc_start: 0.9150 (mm) cc_final: 0.8760 (mm) REVERT: q 107 GLU cc_start: 0.7770 (pt0) cc_final: 0.6532 (tm-30) REVERT: q 108 MET cc_start: 0.8648 (tpp) cc_final: 0.8013 (tpp) REVERT: q 124 THR cc_start: 0.8974 (p) cc_final: 0.8476 (t) REVERT: q 172 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7849 (mm-30) REVERT: q 208 ARG cc_start: 0.7975 (mmm-85) cc_final: 0.7617 (mmm-85) REVERT: r 82 ASN cc_start: 0.8662 (t0) cc_final: 0.8225 (t0) REVERT: r 107 GLU cc_start: 0.7568 (pt0) cc_final: 0.6455 (tm-30) REVERT: r 122 ASN cc_start: 0.8956 (m-40) cc_final: 0.8566 (m-40) REVERT: r 124 THR cc_start: 0.9013 (p) cc_final: 0.8640 (t) REVERT: r 135 MET cc_start: 0.8689 (mmm) cc_final: 0.8130 (mmm) REVERT: r 197 ARG cc_start: 0.8324 (ttt90) cc_final: 0.6855 (ttt90) REVERT: s 66 ASN cc_start: 0.7739 (t0) cc_final: 0.7300 (t0) REVERT: s 79 ASP cc_start: 0.8356 (m-30) cc_final: 0.8105 (m-30) REVERT: s 98 GLN cc_start: 0.8249 (tp40) cc_final: 0.7788 (tp40) REVERT: s 103 ILE cc_start: 0.9140 (mm) cc_final: 0.8779 (mm) REVERT: s 107 GLU cc_start: 0.7778 (pt0) cc_final: 0.6489 (tm-30) REVERT: s 108 MET cc_start: 0.8673 (tpp) cc_final: 0.8068 (tpp) REVERT: s 124 THR cc_start: 0.8860 (p) cc_final: 0.8409 (t) REVERT: s 142 GLU cc_start: 0.8428 (mp0) cc_final: 0.8047 (mt-10) REVERT: s 172 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7788 (mm-30) REVERT: t 82 ASN cc_start: 0.8646 (t0) cc_final: 0.8394 (t0) REVERT: t 108 MET cc_start: 0.8627 (tpp) cc_final: 0.8107 (tpp) REVERT: t 122 ASN cc_start: 0.8928 (m-40) cc_final: 0.8586 (m-40) REVERT: t 124 THR cc_start: 0.8965 (p) cc_final: 0.8710 (t) REVERT: t 135 MET cc_start: 0.8745 (mmm) cc_final: 0.8013 (mmm) REVERT: u 66 ASN cc_start: 0.7734 (t0) cc_final: 0.7263 (t0) REVERT: u 79 ASP cc_start: 0.8258 (m-30) cc_final: 0.7728 (m-30) REVERT: u 82 ASN cc_start: 0.8728 (t0) cc_final: 0.8084 (t0) REVERT: u 103 ILE cc_start: 0.9203 (mm) cc_final: 0.8796 (mm) REVERT: u 107 GLU cc_start: 0.7903 (pt0) cc_final: 0.6564 (tm-30) REVERT: u 108 MET cc_start: 0.8606 (tpp) cc_final: 0.7972 (tpp) REVERT: u 124 THR cc_start: 0.8858 (p) cc_final: 0.8434 (t) REVERT: u 172 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7802 (mm-30) REVERT: v 68 GLU cc_start: 0.8161 (mp0) cc_final: 0.7946 (tm-30) REVERT: v 82 ASN cc_start: 0.8607 (t0) cc_final: 0.8269 (t0) REVERT: v 108 MET cc_start: 0.8453 (tpp) cc_final: 0.7821 (tpp) REVERT: v 124 THR cc_start: 0.8992 (p) cc_final: 0.8638 (t) REVERT: v 135 MET cc_start: 0.8705 (mmm) cc_final: 0.7879 (mmm) REVERT: v 197 ARG cc_start: 0.8314 (ttt90) cc_final: 0.6842 (ttt90) REVERT: w 56 MET cc_start: 0.8719 (mmm) cc_final: 0.8179 (mtt) REVERT: w 66 ASN cc_start: 0.7689 (t0) cc_final: 0.7302 (t0) REVERT: w 68 GLU cc_start: 0.8653 (mp0) cc_final: 0.8438 (mp0) REVERT: w 79 ASP cc_start: 0.8261 (m-30) cc_final: 0.7651 (m-30) REVERT: w 82 ASN cc_start: 0.8631 (t0) cc_final: 0.8051 (t0) REVERT: w 103 ILE cc_start: 0.9173 (mm) cc_final: 0.8812 (mm) REVERT: w 107 GLU cc_start: 0.7782 (pt0) cc_final: 0.6495 (tm-30) REVERT: w 108 MET cc_start: 0.8565 (tpp) cc_final: 0.7935 (tpp) REVERT: w 124 THR cc_start: 0.8874 (p) cc_final: 0.8443 (t) REVERT: x 82 ASN cc_start: 0.8627 (t0) cc_final: 0.8342 (t0) REVERT: x 108 MET cc_start: 0.8686 (tpp) cc_final: 0.8136 (tpp) REVERT: x 122 ASN cc_start: 0.8956 (m-40) cc_final: 0.8579 (m-40) REVERT: x 124 THR cc_start: 0.9005 (p) cc_final: 0.8629 (t) outliers start: 0 outliers final: 0 residues processed: 1431 average time/residue: 0.2101 time to fit residues: 481.2273 Evaluate side-chains 1314 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1314 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 322 optimal weight: 8.9990 chunk 203 optimal weight: 0.0870 chunk 344 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 350 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 98 GLN i 98 GLN j 175 ASN k 98 GLN l 98 GLN l 175 ASN m 98 GLN o 98 GLN p 175 ASN q 175 ASN t 98 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.132591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.114070 restraints weight = 45078.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.117471 restraints weight = 28572.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.120036 restraints weight = 20150.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.121917 restraints weight = 15203.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.123245 restraints weight = 12093.209| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34776 Z= 0.116 Angle : 0.627 8.154 47184 Z= 0.320 Chirality : 0.043 0.192 5160 Planarity : 0.005 0.043 6120 Dihedral : 4.715 16.811 4704 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.13), residues: 4176 helix: -0.36 (0.12), residues: 2040 sheet: -1.33 (0.29), residues: 240 loop : -2.42 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 197 TYR 0.023 0.001 TYR t 73 PHE 0.011 0.002 PHE i 202 TRP 0.018 0.001 TRP p 132 HIS 0.002 0.000 HIS o 162 Details of bonding type rmsd covalent geometry : bond 0.00270 (34776) covalent geometry : angle 0.62700 (47184) hydrogen bonds : bond 0.02594 ( 936) hydrogen bonds : angle 4.07494 ( 2664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1428 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1428 time to evaluate : 1.203 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: a 124 THR cc_start: 0.9102 (p) cc_final: 0.8901 (t) REVERT: a 135 MET cc_start: 0.8505 (mmm) cc_final: 0.7780 (mmm) REVERT: b 66 ASN cc_start: 0.7522 (t0) cc_final: 0.7099 (t0) REVERT: b 95 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7348 (mm-30) REVERT: b 108 MET cc_start: 0.7871 (tpp) cc_final: 0.7176 (tpp) REVERT: b 135 MET cc_start: 0.8360 (mmm) cc_final: 0.8083 (mmm) REVERT: c 124 THR cc_start: 0.9102 (p) cc_final: 0.8864 (t) REVERT: c 135 MET cc_start: 0.8523 (mmm) cc_final: 0.7816 (mmm) REVERT: c 174 ARG cc_start: 0.9106 (tpp80) cc_final: 0.8906 (tpp80) REVERT: d 68 GLU cc_start: 0.8426 (mp0) cc_final: 0.8219 (mp0) REVERT: d 79 ASP cc_start: 0.8412 (m-30) cc_final: 0.8143 (m-30) REVERT: d 95 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7445 (mm-30) REVERT: d 122 ASN cc_start: 0.8720 (m-40) cc_final: 0.8470 (m-40) REVERT: d 135 MET cc_start: 0.8533 (mmm) cc_final: 0.8111 (mmm) REVERT: d 142 GLU cc_start: 0.8121 (tt0) cc_final: 0.7849 (tt0) REVERT: d 197 ARG cc_start: 0.8211 (ttt90) cc_final: 0.7829 (ttt90) REVERT: e 79 ASP cc_start: 0.8477 (m-30) cc_final: 0.8068 (m-30) REVERT: f 95 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7458 (mm-30) REVERT: f 98 GLN cc_start: 0.8150 (tt0) cc_final: 0.7797 (tt0) REVERT: f 135 MET cc_start: 0.8518 (mmm) cc_final: 0.7982 (mmm) REVERT: f 142 GLU cc_start: 0.8099 (tt0) cc_final: 0.7815 (tt0) REVERT: g 79 ASP cc_start: 0.8553 (m-30) cc_final: 0.8127 (m-30) REVERT: g 82 ASN cc_start: 0.8585 (t0) cc_final: 0.8247 (t0) REVERT: g 95 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7250 (mm-30) REVERT: h 95 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7441 (mm-30) REVERT: h 135 MET cc_start: 0.8770 (mmm) cc_final: 0.8029 (mmm) REVERT: i 68 GLU cc_start: 0.8377 (mp0) cc_final: 0.8016 (tm-30) REVERT: i 82 ASN cc_start: 0.8072 (t0) cc_final: 0.7344 (t0) REVERT: i 95 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7475 (mm-30) REVERT: i 122 ASN cc_start: 0.8633 (m-40) cc_final: 0.8386 (m-40) REVERT: i 124 THR cc_start: 0.8880 (p) cc_final: 0.8475 (t) REVERT: j 66 ASN cc_start: 0.8043 (t0) cc_final: 0.7611 (t0) REVERT: j 197 ARG cc_start: 0.8222 (tmm-80) cc_final: 0.7677 (ttp80) REVERT: k 82 ASN cc_start: 0.8087 (t0) cc_final: 0.7350 (t0) REVERT: k 95 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7529 (mm-30) REVERT: k 124 THR cc_start: 0.8925 (p) cc_final: 0.8486 (t) REVERT: l 66 ASN cc_start: 0.8025 (t0) cc_final: 0.7750 (t0) REVERT: l 124 THR cc_start: 0.9029 (p) cc_final: 0.8757 (t) REVERT: l 197 ARG cc_start: 0.8382 (tmm-80) cc_final: 0.7982 (tmm-80) REVERT: m 108 MET cc_start: 0.8305 (tpp) cc_final: 0.7677 (tpp) REVERT: m 124 THR cc_start: 0.8921 (p) cc_final: 0.8485 (t) REVERT: m 134 MET cc_start: 0.8460 (ttt) cc_final: 0.8245 (ttt) REVERT: m 197 ARG cc_start: 0.8261 (ttp-110) cc_final: 0.8060 (mtm110) REVERT: m 198 TYR cc_start: 0.9050 (m-10) cc_final: 0.8768 (m-10) REVERT: n 66 ASN cc_start: 0.8081 (t0) cc_final: 0.7859 (t0) REVERT: n 135 MET cc_start: 0.8402 (mmm) cc_final: 0.7875 (mmm) REVERT: n 197 ARG cc_start: 0.8378 (tmm-80) cc_final: 0.7983 (tmm-80) REVERT: o 82 ASN cc_start: 0.8123 (t0) cc_final: 0.7343 (t0) REVERT: o 95 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7513 (mm-30) REVERT: o 124 THR cc_start: 0.8930 (p) cc_final: 0.8448 (t) REVERT: o 134 MET cc_start: 0.8693 (ttt) cc_final: 0.8480 (ttt) REVERT: o 135 MET cc_start: 0.8537 (mmm) cc_final: 0.8243 (mmm) REVERT: o 197 ARG cc_start: 0.7271 (mtm110) cc_final: 0.6785 (mtm-85) REVERT: p 66 ASN cc_start: 0.8043 (t0) cc_final: 0.7687 (t0) REVERT: p 135 MET cc_start: 0.8695 (mmm) cc_final: 0.8091 (mmm) REVERT: p 197 ARG cc_start: 0.8248 (tmm-80) cc_final: 0.7719 (ttp80) REVERT: q 66 ASN cc_start: 0.7856 (t0) cc_final: 0.7381 (t0) REVERT: q 98 GLN cc_start: 0.8152 (tp40) cc_final: 0.7825 (tp40) REVERT: q 103 ILE cc_start: 0.9075 (mm) cc_final: 0.8191 (mm) REVERT: q 107 GLU cc_start: 0.7614 (pt0) cc_final: 0.6332 (tm-30) REVERT: q 108 MET cc_start: 0.8519 (tpp) cc_final: 0.7850 (tpp) REVERT: q 113 ASN cc_start: 0.9120 (m-40) cc_final: 0.8393 (m-40) REVERT: q 124 THR cc_start: 0.8902 (p) cc_final: 0.8344 (t) REVERT: r 108 MET cc_start: 0.8303 (tpp) cc_final: 0.7765 (tpp) REVERT: r 122 ASN cc_start: 0.8863 (m-40) cc_final: 0.8453 (m-40) REVERT: r 124 THR cc_start: 0.8917 (p) cc_final: 0.8597 (t) REVERT: r 135 MET cc_start: 0.8522 (mmm) cc_final: 0.8288 (mmm) REVERT: r 215 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7156 (tm-30) REVERT: s 66 ASN cc_start: 0.7760 (t0) cc_final: 0.7179 (t0) REVERT: s 98 GLN cc_start: 0.8149 (tp40) cc_final: 0.7769 (tp40) REVERT: s 103 ILE cc_start: 0.9066 (mm) cc_final: 0.8189 (mm) REVERT: s 107 GLU cc_start: 0.7494 (pt0) cc_final: 0.6250 (tm-30) REVERT: s 108 MET cc_start: 0.8575 (tpp) cc_final: 0.7900 (tpp) REVERT: s 113 ASN cc_start: 0.9106 (m-40) cc_final: 0.8435 (m-40) REVERT: s 124 THR cc_start: 0.8799 (p) cc_final: 0.8472 (t) REVERT: s 142 GLU cc_start: 0.8397 (mp0) cc_final: 0.7988 (mt-10) REVERT: s 172 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7681 (mm-30) REVERT: t 108 MET cc_start: 0.8491 (tpp) cc_final: 0.8020 (tpp) REVERT: t 122 ASN cc_start: 0.8844 (m-40) cc_final: 0.8502 (m-40) REVERT: t 124 THR cc_start: 0.8898 (p) cc_final: 0.8679 (t) REVERT: t 135 MET cc_start: 0.8687 (mmm) cc_final: 0.8275 (mmm) REVERT: t 215 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7220 (tm-30) REVERT: u 66 ASN cc_start: 0.7773 (t0) cc_final: 0.7281 (t0) REVERT: u 67 LEU cc_start: 0.8454 (mm) cc_final: 0.8229 (mm) REVERT: u 82 ASN cc_start: 0.8654 (t0) cc_final: 0.7949 (t0) REVERT: u 107 GLU cc_start: 0.7613 (pt0) cc_final: 0.6274 (tm-30) REVERT: u 108 MET cc_start: 0.8439 (tpp) cc_final: 0.7751 (tpp) REVERT: u 113 ASN cc_start: 0.9079 (m-40) cc_final: 0.8469 (m-40) REVERT: u 124 THR cc_start: 0.8800 (p) cc_final: 0.8528 (t) REVERT: u 142 GLU cc_start: 0.8379 (mp0) cc_final: 0.7971 (mt-10) REVERT: u 172 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7716 (mm-30) REVERT: v 68 GLU cc_start: 0.8350 (mp0) cc_final: 0.7959 (tm-30) REVERT: v 86 THR cc_start: 0.8632 (t) cc_final: 0.8386 (t) REVERT: v 108 MET cc_start: 0.8349 (tpp) cc_final: 0.7904 (tpp) REVERT: v 124 THR cc_start: 0.8915 (p) cc_final: 0.8592 (t) REVERT: v 135 MET cc_start: 0.8691 (mmm) cc_final: 0.8413 (mmm) REVERT: v 197 ARG cc_start: 0.8193 (ttt90) cc_final: 0.6798 (ttt90) REVERT: w 56 MET cc_start: 0.8575 (mmm) cc_final: 0.8018 (mtt) REVERT: w 66 ASN cc_start: 0.7768 (t0) cc_final: 0.7351 (t0) REVERT: w 82 ASN cc_start: 0.8664 (t0) cc_final: 0.7960 (t0) REVERT: w 107 GLU cc_start: 0.7514 (pt0) cc_final: 0.6231 (tm-30) REVERT: w 108 MET cc_start: 0.8444 (tpp) cc_final: 0.7787 (tpp) REVERT: w 113 ASN cc_start: 0.9059 (m-40) cc_final: 0.8380 (m-40) REVERT: w 124 THR cc_start: 0.8800 (p) cc_final: 0.8532 (t) REVERT: w 142 GLU cc_start: 0.8344 (mp0) cc_final: 0.7956 (mt-10) REVERT: w 198 TYR cc_start: 0.8926 (m-10) cc_final: 0.8671 (m-10) REVERT: x 64 VAL cc_start: 0.9094 (p) cc_final: 0.8885 (t) REVERT: x 108 MET cc_start: 0.8544 (tpp) cc_final: 0.8042 (tpp) REVERT: x 122 ASN cc_start: 0.8915 (m-40) cc_final: 0.8501 (m-40) REVERT: x 124 THR cc_start: 0.8921 (p) cc_final: 0.8621 (t) REVERT: x 215 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7235 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1428 average time/residue: 0.2020 time to fit residues: 459.7896 Evaluate side-chains 1319 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1319 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 232 optimal weight: 0.0470 chunk 157 optimal weight: 7.9990 chunk 146 optimal weight: 0.0980 chunk 34 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 66 optimal weight: 0.0970 chunk 278 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 251 optimal weight: 0.7980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 175 ASN o 175 ASN q 175 ASN r 175 ASN t 175 ASN u 175 ASN u 217 HIS v 175 ASN w 175 ASN x 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.136219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.117652 restraints weight = 44391.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.121129 restraints weight = 28161.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.123771 restraints weight = 19827.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.125664 restraints weight = 14958.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.127009 restraints weight = 11862.054| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34776 Z= 0.113 Angle : 0.615 8.113 47184 Z= 0.314 Chirality : 0.042 0.220 5160 Planarity : 0.005 0.042 6120 Dihedral : 4.503 16.490 4704 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.13), residues: 4176 helix: -0.19 (0.12), residues: 2040 sheet: -1.21 (0.28), residues: 240 loop : -2.38 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 197 TYR 0.030 0.001 TYR u 73 PHE 0.012 0.002 PHE a 202 TRP 0.016 0.001 TRP j 132 HIS 0.001 0.000 HIS c 69 Details of bonding type rmsd covalent geometry : bond 0.00260 (34776) covalent geometry : angle 0.61535 (47184) hydrogen bonds : bond 0.02488 ( 936) hydrogen bonds : angle 3.96305 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7790.14 seconds wall clock time: 133 minutes 52.61 seconds (8032.61 seconds total)