Starting phenix.real_space_refine (version: dev) on Mon Dec 19 02:10:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxz_0298/12_2022/6hxz_0298_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxz_0298/12_2022/6hxz_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxz_0298/12_2022/6hxz_0298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxz_0298/12_2022/6hxz_0298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxz_0298/12_2022/6hxz_0298_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxz_0298/12_2022/6hxz_0298_neut.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "a ARG 55": "NH1" <-> "NH2" Residue "a ARG 174": "NH1" <-> "NH2" Residue "b ARG 55": "NH1" <-> "NH2" Residue "b ARG 174": "NH1" <-> "NH2" Residue "c ARG 55": "NH1" <-> "NH2" Residue "c ARG 174": "NH1" <-> "NH2" Residue "d ARG 55": "NH1" <-> "NH2" Residue "d ARG 174": "NH1" <-> "NH2" Residue "e ARG 55": "NH1" <-> "NH2" Residue "e ARG 174": "NH1" <-> "NH2" Residue "f ARG 55": "NH1" <-> "NH2" Residue "f ARG 174": "NH1" <-> "NH2" Residue "g ARG 55": "NH1" <-> "NH2" Residue "g ARG 174": "NH1" <-> "NH2" Residue "h ARG 55": "NH1" <-> "NH2" Residue "h ARG 174": "NH1" <-> "NH2" Residue "i ARG 55": "NH1" <-> "NH2" Residue "i ARG 174": "NH1" <-> "NH2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 174": "NH1" <-> "NH2" Residue "k ARG 55": "NH1" <-> "NH2" Residue "k ARG 174": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l ARG 174": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 174": "NH1" <-> "NH2" Residue "n ARG 55": "NH1" <-> "NH2" Residue "n ARG 174": "NH1" <-> "NH2" Residue "o ARG 55": "NH1" <-> "NH2" Residue "o ARG 174": "NH1" <-> "NH2" Residue "p ARG 55": "NH1" <-> "NH2" Residue "p ARG 174": "NH1" <-> "NH2" Residue "q ARG 55": "NH1" <-> "NH2" Residue "q ARG 174": "NH1" <-> "NH2" Residue "r ARG 55": "NH1" <-> "NH2" Residue "r ARG 174": "NH1" <-> "NH2" Residue "s ARG 55": "NH1" <-> "NH2" Residue "s ARG 174": "NH1" <-> "NH2" Residue "t ARG 55": "NH1" <-> "NH2" Residue "t ARG 174": "NH1" <-> "NH2" Residue "u ARG 55": "NH1" <-> "NH2" Residue "u ARG 174": "NH1" <-> "NH2" Residue "v ARG 55": "NH1" <-> "NH2" Residue "v ARG 174": "NH1" <-> "NH2" Residue "w ARG 55": "NH1" <-> "NH2" Residue "w ARG 174": "NH1" <-> "NH2" Residue "x ARG 55": "NH1" <-> "NH2" Residue "x ARG 174": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 34008 Number of models: 1 Model: "" Number of chains: 24 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} Chain: "b" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "c" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "d" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "e" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "f" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "g" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "h" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "i" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "j" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "k" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "l" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "m" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "n" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "o" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "p" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "q" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "r" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "s" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "t" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "u" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "v" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "w" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "x" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1417 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Time building chain proxies: 18.57, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.18 Conformation dependent library (CDL) restraints added in 5.2 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: 1.43 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: 9.14 Time building geometry restraints manager: 14.18 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: 98.28 - 105.45: 1152 105.45 - 112.62: 17363 112.62 - 119.79: 12848 119.79 - 126.96: 15351 126.96 - 134.13: 470 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 2.440 nonbonded pdb=" OH TYR d 143 " pdb=" O PRO p 45 " model vdw 2.487 2.440 nonbonded pdb=" OH TYR e 143 " pdb=" O PRO i 45 " model vdw 2.495 2.440 nonbonded pdb=" OH TYR c 143 " pdb=" O PRO o 45 " model vdw 2.495 2.440 nonbonded pdb=" OH TYR j 143 " pdb=" O PRO u 45 " model vdw 2.496 2.440 ... (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 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 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. 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.590 Check model and map are aligned: 0.520 Convert atoms to be neutral: 0.310 Process input model: 79.520 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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= 0.549 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 72 poor density : 1694 time to evaluate : 3.963 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 outliers start: 72 outliers final: 9 residues processed: 1724 average time/residue: 0.5221 time to fit residues: 1353.0356 Evaluate side-chains 1498 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1489 time to evaluate : 4.002 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.9147 time to fit residues: 16.1073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.8980 chunk 309 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 319 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 370 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 69 HIS ** a 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 162 HIS b 69 HIS ** b 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 162 HIS c 69 HIS c 77 GLN ** c 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 162 HIS d 69 HIS ** d 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 162 HIS e 69 HIS ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 162 HIS f 69 HIS ** f 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 162 HIS g 69 HIS ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 HIS h 69 HIS ** h 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 162 HIS i 69 HIS i 98 GLN i 113 ASN ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 69 HIS j 98 GLN j 113 ASN ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 69 HIS k 77 GLN k 98 GLN k 113 ASN ** k 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 69 HIS l 98 GLN l 113 ASN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 69 HIS m 98 GLN m 113 ASN ** m 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 HIS n 98 GLN n 113 ASN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 69 HIS o 98 GLN o 113 ASN ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 69 HIS p 98 GLN p 113 ASN p 122 ASN q 69 HIS q 113 ASN ** q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 162 HIS r 69 HIS r 77 GLN r 113 ASN ** r 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS s 77 GLN s 113 ASN ** s 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 162 HIS t 69 HIS t 113 ASN ** t 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 69 HIS u 113 ASN ** u 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 162 HIS v 69 HIS v 113 ASN ** v 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 69 HIS w 113 ASN ** w 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 162 HIS x 69 HIS x 113 ASN ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3280 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= 0.179 Angle : 0.626 6.011 47184 Z= 0.323 Chirality : 0.042 0.132 5160 Planarity : 0.006 0.032 6120 Dihedral : 5.441 19.834 4704 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.11), residues: 4176 helix: -2.32 (0.10), residues: 1776 sheet: -2.26 (0.33), residues: 240 loop : -3.27 (0.10), residues: 2160 *********************** 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 1540 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1540 time to evaluate : 3.943 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 outliers start: 0 outliers final: 0 residues processed: 1540 average time/residue: 0.4786 time to fit residues: 1147.0637 Evaluate side-chains 1350 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1350 time to evaluate : 3.905 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 0.0270 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 371 optimal weight: 7.9990 chunk 400 optimal weight: 2.9990 chunk 330 optimal weight: 3.9990 chunk 368 optimal weight: 7.9990 chunk 126 optimal weight: 0.4980 chunk 297 optimal weight: 7.9990 overall best weight: 2.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 98 GLN ** a 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 98 GLN ** b 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 175 ASN b 217 HIS c 98 GLN ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 175 ASN d 98 GLN ** d 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 217 HIS e 98 GLN ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 GLN ** f 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 175 ASN f 217 HIS g 98 GLN ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 GLN ** h 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 175 ASN h 217 HIS i 98 GLN ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 175 ASN ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 175 ASN k 98 GLN ** k 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 175 ASN ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 175 ASN m 98 GLN ** m 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 175 ASN ** n 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 175 ASN o 98 GLN ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 175 ASN p 175 ASN ** q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 175 ASN ** r 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 175 ASN ** s 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 175 ASN ** t 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 175 ASN ** u 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 175 ASN ** v 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 175 ASN ** w 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 175 ASN ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 175 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 34776 Z= 0.309 Angle : 0.676 5.835 47184 Z= 0.346 Chirality : 0.046 0.132 5160 Planarity : 0.005 0.057 6120 Dihedral : 5.387 19.568 4704 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.11), residues: 4176 helix: -1.96 (0.10), residues: 2088 sheet: -2.25 (0.31), residues: 240 loop : -3.16 (0.12), residues: 1848 *********************** 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 1539 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1539 time to evaluate : 4.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1539 average time/residue: 0.5050 time to fit residues: 1221.5076 Evaluate side-chains 1426 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1426 time to evaluate : 3.993 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 192 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 249 optimal weight: 0.9990 chunk 372 optimal weight: 0.5980 chunk 394 optimal weight: 4.9990 chunk 194 optimal weight: 0.5980 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 98 GLN a 122 ASN a 175 ASN b 122 ASN c 77 GLN c 98 GLN c 113 ASN c 122 ASN c 175 ASN d 98 GLN ** d 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 175 ASN e 98 GLN ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 175 ASN f 122 ASN g 98 GLN ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 175 ASN h 122 ASN ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4130 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= 0.162 Angle : 0.602 5.654 47184 Z= 0.306 Chirality : 0.043 0.140 5160 Planarity : 0.005 0.042 6120 Dihedral : 4.871 17.655 4704 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.12), residues: 4176 helix: -1.07 (0.12), residues: 1944 sheet: -1.69 (0.32), residues: 240 loop : -2.95 (0.12), residues: 1992 *********************** 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 1483 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1483 time to evaluate : 3.951 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 outliers start: 0 outliers final: 0 residues processed: 1483 average time/residue: 0.4831 time to fit residues: 1109.3132 Evaluate side-chains 1357 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1357 time to evaluate : 3.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 336 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 353 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 98 GLN ** a 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN b 98 GLN c 98 GLN c 175 ASN d 98 GLN ** d 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 98 GLN ** e 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 175 ASN f 98 GLN g 98 GLN ** g 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 175 ASN h 98 GLN i 98 GLN ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 162 HIS j 77 GLN ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 162 HIS k 98 GLN ** k 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 162 HIS ** l 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 162 HIS m 77 GLN m 98 GLN ** m 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 162 HIS n 77 GLN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 77 GLN o 98 GLN ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 162 HIS p 77 GLN p 162 HIS ** q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 175 ASN ** r 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 162 HIS ** s 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 175 ASN ** t 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 162 HIS ** u 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 175 ASN v 77 GLN ** v 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 162 HIS ** w 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 77 GLN ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 162 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.047 34776 Z= 0.480 Angle : 0.794 7.305 47184 Z= 0.400 Chirality : 0.050 0.160 5160 Planarity : 0.006 0.043 6120 Dihedral : 5.619 20.527 4704 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.12), residues: 4176 helix: -1.21 (0.12), residues: 1944 sheet: -1.84 (0.30), residues: 240 loop : -2.95 (0.12), residues: 1992 *********************** 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 1562 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1557 time to evaluate : 4.219 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 outliers start: 5 outliers final: 0 residues processed: 1562 average time/residue: 0.4778 time to fit residues: 1170.7658 Evaluate side-chains 1442 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1442 time to evaluate : 3.894 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 2.9990 chunk 355 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 394 optimal weight: 0.7980 chunk 327 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 98 GLN c 175 ASN d 98 GLN ** d 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 113 ASN ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 175 ASN j 98 GLN ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 175 ASN ** k 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 175 ASN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 175 ASN m 77 GLN ** m 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 175 ASN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 175 ASN o 77 GLN ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 175 ASN p 98 GLN p 175 ASN ** q 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 175 ASN ** s 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 175 ASN ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 175 ASN ** w 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 175 ASN ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 175 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 34776 Z= 0.174 Angle : 0.631 8.484 47184 Z= 0.320 Chirality : 0.043 0.161 5160 Planarity : 0.005 0.060 6120 Dihedral : 5.020 17.550 4704 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.12), residues: 4176 helix: -0.82 (0.12), residues: 1944 sheet: -1.54 (0.31), residues: 240 loop : -2.79 (0.12), residues: 1992 *********************** 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 1455 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1455 time to evaluate : 3.882 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 outliers start: 0 outliers final: 0 residues processed: 1455 average time/residue: 0.5056 time to fit residues: 1151.9418 Evaluate side-chains 1330 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1330 time to evaluate : 4.059 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 288 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 0.0040 chunk 393 optimal weight: 0.7980 chunk 246 optimal weight: 10.0000 chunk 239 optimal weight: 0.3980 chunk 181 optimal weight: 2.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 98 GLN a 113 ASN a 175 ASN c 98 GLN c 175 ASN d 98 GLN ** d 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 98 GLN ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN g 113 ASN ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 98 GLN ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 98 GLN ** k 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 98 GLN ** m 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 98 GLN ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 175 ASN ** r 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 175 ASN s 217 HIS ** t 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 175 ASN u 217 HIS ** v 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4727 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= 0.177 Angle : 0.614 6.616 47184 Z= 0.309 Chirality : 0.043 0.198 5160 Planarity : 0.005 0.054 6120 Dihedral : 4.812 19.197 4704 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.13), residues: 4176 helix: -0.96 (0.12), residues: 2088 sheet: -1.34 (0.32), residues: 240 loop : -2.79 (0.13), residues: 1848 *********************** 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 1426 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1426 time to evaluate : 4.027 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 outliers start: 0 outliers final: 0 residues processed: 1426 average time/residue: 0.4806 time to fit residues: 1068.5358 Evaluate side-chains 1313 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1313 time to evaluate : 4.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.0470 chunk 157 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 250 optimal weight: 0.6980 chunk 267 optimal weight: 5.9990 chunk 194 optimal weight: 0.0010 chunk 36 optimal weight: 3.9990 chunk 309 optimal weight: 0.0970 overall best weight: 0.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 175 ASN c 98 GLN c 175 ASN d 98 GLN ** d 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 98 GLN ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 98 GLN ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 98 GLN ** k 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 98 GLN m 122 ASN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 98 GLN ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 217 HIS r 175 ASN ** s 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 175 ASN ** u 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 175 ASN ** w 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 175 ASN ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 175 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 34776 Z= 0.159 Angle : 0.613 6.891 47184 Z= 0.308 Chirality : 0.042 0.173 5160 Planarity : 0.005 0.061 6120 Dihedral : 4.615 18.142 4704 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.13), residues: 4176 helix: -0.85 (0.12), residues: 2088 sheet: -1.29 (0.31), residues: 240 loop : -2.75 (0.13), residues: 1848 *********************** 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 1402 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1402 time to evaluate : 4.032 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 outliers start: 0 outliers final: 0 residues processed: 1402 average time/residue: 0.4888 time to fit residues: 1079.8299 Evaluate side-chains 1296 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1296 time to evaluate : 3.997 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 5.9990 chunk 376 optimal weight: 0.9980 chunk 343 optimal weight: 0.9980 chunk 366 optimal weight: 3.9990 chunk 220 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 331 optimal weight: 8.9990 chunk 346 optimal weight: 0.9990 chunk 365 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 175 ASN c 98 GLN c 175 ASN d 98 GLN ** d 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 98 GLN ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 122 ASN i 98 GLN ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 175 ASN ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 98 GLN ** k 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 98 GLN m 175 ASN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 98 GLN ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 98 GLN ** v 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 34776 Z= 0.175 Angle : 0.624 7.507 47184 Z= 0.311 Chirality : 0.043 0.183 5160 Planarity : 0.005 0.077 6120 Dihedral : 4.591 17.949 4704 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.13), residues: 4176 helix: -0.77 (0.12), residues: 2088 sheet: -1.24 (0.30), residues: 240 loop : -2.73 (0.13), residues: 1848 *********************** 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 1382 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1382 time to evaluate : 4.238 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 outliers start: 0 outliers final: 0 residues processed: 1382 average time/residue: 0.4707 time to fit residues: 1022.3408 Evaluate side-chains 1285 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1285 time to evaluate : 3.954 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 2.9990 chunk 387 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 269 optimal weight: 6.9990 chunk 406 optimal weight: 0.0070 chunk 374 optimal weight: 3.9990 chunk 323 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 198 optimal weight: 0.6980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 175 ASN c 175 ASN ** d 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 122 ASN ** i 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 98 GLN ** k 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 217 HIS ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 77 GLN m 98 GLN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 175 ASN ** s 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 175 ASN ** u 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 175 ASN ** w 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 217 HIS ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 175 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 34776 Z= 0.193 Angle : 0.631 7.778 47184 Z= 0.314 Chirality : 0.044 0.181 5160 Planarity : 0.005 0.051 6120 Dihedral : 4.584 17.323 4704 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.13), residues: 4176 helix: -0.67 (0.12), residues: 2088 sheet: -1.25 (0.29), residues: 240 loop : -2.70 (0.13), residues: 1848 ********************** 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 1382 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1382 time to evaluate : 3.624 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 outliers start: 0 outliers final: 0 residues processed: 1382 average time/residue: 0.4780 time to fit residues: 1040.4833 Evaluate side-chains 1288 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1288 time to evaluate : 4.131 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 0.9990 chunk 344 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 332 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 175 ASN c 175 ASN ** d 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 175 ASN ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 98 GLN ** k 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 175 ASN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 175 ASN ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.132362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.113892 restraints weight = 45100.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.117216 restraints weight = 28994.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.119704 restraints weight = 20583.266| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5267 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= 0.198 Angle : 0.637 8.847 47184 Z= 0.318 Chirality : 0.044 0.184 5160 Planarity : 0.005 0.070 6120 Dihedral : 4.572 17.362 4704 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.13), residues: 4176 helix: -0.61 (0.12), residues: 2088 sheet: -1.30 (0.29), residues: 240 loop : -2.70 (0.13), residues: 1848 =============================================================================== Job complete usr+sys time: 14204.15 seconds wall clock time: 249 minutes 28.98 seconds (14968.98 seconds total)