Starting phenix.real_space_refine on Fri Mar 22 16:37:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxz_0298/03_2024/6hxz_0298_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxz_0298/03_2024/6hxz_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_0298/03_2024/6hxz_0298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxz_0298/03_2024/6hxz_0298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxz_0298/03_2024/6hxz_0298_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hxz_0298/03_2024/6hxz_0298_neut.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.354 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 264 5.16 5 C 21504 2.51 5 N 5880 2.21 5 O 6360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 17.15, per 1000 atoms: 0.50 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: 11.34 Conformation dependent library (CDL) restraints added in 6.5 seconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 24 sheets defined 50.0% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 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: 8.34 Time building geometry restraints manager: 12.53 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 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: 0.010 Normalize map: mean=0, sd=1: 2.130 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: 0.030 Extract box with map and model: 11.350 Check model and map are aligned: 0.530 Set scattering table: 0.330 Process input model: 78.530 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 34776 Z= 0.549 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 % Allowed : 3.25 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP t 118 HIS 0.007 0.002 HIS f 162 PHE 0.025 0.003 PHE p 202 TYR 0.012 0.003 TYR g 73 ARG 0.005 0.001 ARG r 214 *********************** 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 : 4.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 59 SER cc_start: 0.8432 (p) cc_final: 0.8098 (p) REVERT: a 124 THR cc_start: 0.9080 (p) cc_final: 0.8682 (t) REVERT: a 125 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8374 (t) REVERT: a 135 MET cc_start: 0.9112 (mmm) cc_final: 0.8734 (mmm) REVERT: a 139 GLU cc_start: 0.8487 (pt0) cc_final: 0.8140 (pt0) REVERT: a 149 VAL cc_start: 0.9429 (m) cc_final: 0.9145 (t) REVERT: b 59 SER cc_start: 0.8467 (p) cc_final: 0.8094 (p) REVERT: b 71 LEU cc_start: 0.8875 (mt) cc_final: 0.8610 (mt) REVERT: b 82 ASN cc_start: 0.8709 (t160) cc_final: 0.8138 (t0) REVERT: b 107 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7528 (pt0) REVERT: b 115 LEU cc_start: 0.9582 (tp) cc_final: 0.9196 (tp) REVERT: b 124 THR cc_start: 0.9031 (p) cc_final: 0.8815 (t) REVERT: b 125 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8411 (t) REVERT: b 135 MET cc_start: 0.9160 (mmm) cc_final: 0.8756 (mmm) REVERT: b 145 LEU cc_start: 0.9302 (mt) cc_final: 0.8821 (mt) REVERT: b 149 VAL cc_start: 0.9432 (m) cc_final: 0.9165 (p) REVERT: c 59 SER cc_start: 0.8430 (p) cc_final: 0.8105 (p) REVERT: c 124 THR cc_start: 0.9075 (p) cc_final: 0.8701 (t) REVERT: c 125 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8391 (t) REVERT: c 135 MET cc_start: 0.9103 (mmm) cc_final: 0.8753 (mmm) REVERT: c 139 GLU cc_start: 0.8487 (pt0) cc_final: 0.8148 (pt0) REVERT: c 149 VAL cc_start: 0.9446 (m) cc_final: 0.9149 (t) REVERT: d 59 SER cc_start: 0.8483 (p) cc_final: 0.8075 (p) REVERT: d 71 LEU cc_start: 0.8892 (mt) cc_final: 0.8587 (mt) REVERT: d 107 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7559 (pt0) REVERT: d 115 LEU cc_start: 0.9578 (tp) cc_final: 0.9043 (tp) REVERT: d 124 THR cc_start: 0.9020 (p) cc_final: 0.8739 (t) REVERT: d 125 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8406 (t) REVERT: d 135 MET cc_start: 0.9151 (mmm) cc_final: 0.8790 (mmm) REVERT: d 145 LEU cc_start: 0.9260 (mt) cc_final: 0.8820 (mt) REVERT: d 149 VAL cc_start: 0.9417 (m) cc_final: 0.9170 (t) REVERT: d 160 MET cc_start: 0.8991 (mmm) cc_final: 0.8714 (tpp) REVERT: e 59 SER cc_start: 0.8427 (p) cc_final: 0.8092 (p) REVERT: e 82 ASN cc_start: 0.8881 (t160) cc_final: 0.8675 (t0) REVERT: e 124 THR cc_start: 0.9078 (p) cc_final: 0.8707 (t) REVERT: e 125 SER cc_start: 0.8858 (OUTLIER) cc_final: 0.8364 (t) REVERT: e 135 MET cc_start: 0.9127 (mmm) cc_final: 0.8734 (mmm) REVERT: e 139 GLU cc_start: 0.8487 (pt0) cc_final: 0.8210 (pt0) REVERT: e 149 VAL cc_start: 0.9448 (m) cc_final: 0.9161 (t) REVERT: e 160 MET cc_start: 0.9060 (mmm) cc_final: 0.8844 (mmt) REVERT: f 59 SER cc_start: 0.8470 (p) cc_final: 0.8099 (p) REVERT: f 71 LEU cc_start: 0.8885 (mt) cc_final: 0.8583 (mt) REVERT: f 107 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7538 (pt0) REVERT: f 115 LEU cc_start: 0.9573 (tp) cc_final: 0.9184 (tp) REVERT: f 124 THR cc_start: 0.9009 (p) cc_final: 0.8782 (t) REVERT: f 125 SER cc_start: 0.8740 (OUTLIER) cc_final: 0.8407 (t) REVERT: f 135 MET cc_start: 0.9169 (mmm) cc_final: 0.8761 (mmm) REVERT: f 145 LEU cc_start: 0.9301 (mt) cc_final: 0.8838 (mt) REVERT: f 149 VAL cc_start: 0.9433 (m) cc_final: 0.9160 (p) REVERT: g 59 SER cc_start: 0.8437 (p) cc_final: 0.8100 (p) REVERT: g 82 ASN cc_start: 0.8873 (t160) cc_final: 0.8670 (t0) REVERT: g 124 THR cc_start: 0.9079 (p) cc_final: 0.8694 (t) REVERT: g 125 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8376 (t) REVERT: g 135 MET cc_start: 0.9131 (mmm) cc_final: 0.8742 (mmm) REVERT: g 139 GLU cc_start: 0.8489 (pt0) cc_final: 0.8151 (pt0) REVERT: g 149 VAL cc_start: 0.9450 (m) cc_final: 0.9155 (t) REVERT: g 160 MET cc_start: 0.9063 (mmm) cc_final: 0.8859 (mmt) REVERT: h 59 SER cc_start: 0.8479 (p) cc_final: 0.8089 (p) REVERT: h 71 LEU cc_start: 0.8881 (mt) cc_final: 0.8602 (mt) REVERT: h 107 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7524 (pt0) REVERT: h 115 LEU cc_start: 0.9579 (tp) cc_final: 0.9199 (tp) REVERT: h 124 THR cc_start: 0.9027 (p) cc_final: 0.8811 (t) REVERT: h 125 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8400 (t) REVERT: h 145 LEU cc_start: 0.9303 (mt) cc_final: 0.8841 (mt) REVERT: h 149 VAL cc_start: 0.9434 (m) cc_final: 0.9163 (p) REVERT: i 59 SER cc_start: 0.8367 (p) cc_final: 0.7956 (p) REVERT: i 98 GLN cc_start: 0.8325 (tt0) cc_final: 0.7641 (tt0) REVERT: i 107 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7545 (pt0) REVERT: i 115 LEU cc_start: 0.9528 (tp) cc_final: 0.8988 (tt) REVERT: i 124 THR cc_start: 0.8867 (p) cc_final: 0.8379 (t) REVERT: i 135 MET cc_start: 0.9101 (mmm) cc_final: 0.8798 (mmm) REVERT: i 149 VAL cc_start: 0.9317 (m) cc_final: 0.9073 (t) REVERT: i 160 MET cc_start: 0.9117 (mmm) cc_final: 0.8884 (tpp) REVERT: j 46 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7556 (mtt180) REVERT: j 59 SER cc_start: 0.8240 (p) cc_final: 0.7816 (p) REVERT: j 98 GLN cc_start: 0.8389 (tt0) cc_final: 0.7901 (tt0) REVERT: j 107 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7503 (pt0) REVERT: j 115 LEU cc_start: 0.9581 (tp) cc_final: 0.9033 (tp) REVERT: j 124 THR cc_start: 0.8951 (p) cc_final: 0.8587 (t) REVERT: j 125 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8548 (t) REVERT: j 135 MET cc_start: 0.9086 (mmm) cc_final: 0.8787 (mmm) REVERT: j 149 VAL cc_start: 0.9254 (m) cc_final: 0.9016 (p) REVERT: j 160 MET cc_start: 0.9122 (mmm) cc_final: 0.8665 (tpp) REVERT: k 46 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7583 (mtt180) REVERT: k 59 SER cc_start: 0.8401 (p) cc_final: 0.7970 (p) REVERT: k 98 GLN cc_start: 0.8339 (tt0) cc_final: 0.7692 (tt0) REVERT: k 107 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7550 (pt0) REVERT: k 115 LEU cc_start: 0.9518 (tp) cc_final: 0.8984 (tt) REVERT: k 124 THR cc_start: 0.8884 (p) cc_final: 0.8410 (t) REVERT: k 149 VAL cc_start: 0.9326 (m) cc_final: 0.9073 (t) REVERT: k 160 MET cc_start: 0.9102 (mmm) cc_final: 0.8873 (tpp) REVERT: l 59 SER cc_start: 0.8230 (p) cc_final: 0.7784 (p) REVERT: l 98 GLN cc_start: 0.8375 (tt0) cc_final: 0.7858 (tt0) REVERT: l 107 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7500 (pt0) REVERT: l 112 MET cc_start: 0.9477 (mmp) cc_final: 0.9266 (mmt) REVERT: l 115 LEU cc_start: 0.9597 (tp) cc_final: 0.9016 (tp) REVERT: l 124 THR cc_start: 0.9002 (p) cc_final: 0.8519 (t) REVERT: l 125 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8536 (t) REVERT: l 160 MET cc_start: 0.9082 (mmm) cc_final: 0.8645 (tpp) REVERT: l 198 TYR cc_start: 0.8977 (m-10) cc_final: 0.8056 (m-10) REVERT: m 46 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7590 (mtt180) REVERT: m 59 SER cc_start: 0.8362 (p) cc_final: 0.7922 (p) REVERT: m 98 GLN cc_start: 0.8330 (tt0) cc_final: 0.7616 (tt0) REVERT: m 107 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7553 (pt0) REVERT: m 115 LEU cc_start: 0.9530 (tp) cc_final: 0.8989 (tt) REVERT: m 124 THR cc_start: 0.8887 (p) cc_final: 0.8381 (t) REVERT: m 125 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8612 (t) REVERT: m 149 VAL cc_start: 0.9323 (m) cc_final: 0.9088 (t) REVERT: n 59 SER cc_start: 0.8251 (p) cc_final: 0.7832 (p) REVERT: n 98 GLN cc_start: 0.8370 (tt0) cc_final: 0.7866 (tt0) REVERT: n 107 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7504 (pt0) REVERT: n 115 LEU cc_start: 0.9597 (tp) cc_final: 0.9024 (tp) REVERT: n 124 THR cc_start: 0.8998 (p) cc_final: 0.8507 (t) REVERT: n 125 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8532 (t) REVERT: n 135 MET cc_start: 0.9085 (mmm) cc_final: 0.8828 (mmm) REVERT: n 160 MET cc_start: 0.9070 (mmm) cc_final: 0.8646 (tpp) REVERT: n 198 TYR cc_start: 0.8979 (m-10) cc_final: 0.8048 (m-10) REVERT: o 46 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7572 (mtt180) REVERT: o 59 SER cc_start: 0.8393 (p) cc_final: 0.7952 (p) REVERT: o 98 GLN cc_start: 0.8333 (tt0) cc_final: 0.7697 (tt0) REVERT: o 107 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7548 (pt0) REVERT: o 115 LEU cc_start: 0.9533 (tp) cc_final: 0.9021 (tt) REVERT: o 124 THR cc_start: 0.8902 (p) cc_final: 0.8423 (t) REVERT: o 125 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8589 (t) REVERT: o 149 VAL cc_start: 0.9317 (m) cc_final: 0.9064 (t) REVERT: o 160 MET cc_start: 0.9114 (mmm) cc_final: 0.8892 (tpp) REVERT: p 46 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7633 (mtt180) REVERT: p 59 SER cc_start: 0.8242 (p) cc_final: 0.7805 (p) REVERT: p 98 GLN cc_start: 0.8380 (tt0) cc_final: 0.7896 (tt0) REVERT: p 107 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7478 (pt0) REVERT: p 115 LEU cc_start: 0.9585 (tp) cc_final: 0.9027 (tp) REVERT: p 124 THR cc_start: 0.8945 (p) cc_final: 0.8584 (t) REVERT: p 125 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8545 (t) REVERT: p 149 VAL cc_start: 0.9250 (m) cc_final: 0.9014 (p) REVERT: p 160 MET cc_start: 0.9115 (mmm) cc_final: 0.8666 (tpp) REVERT: q 59 SER cc_start: 0.8344 (p) cc_final: 0.7979 (p) REVERT: q 107 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7625 (pt0) REVERT: q 124 THR cc_start: 0.8941 (p) cc_final: 0.8320 (t) REVERT: q 125 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8569 (t) REVERT: r 44 VAL cc_start: 0.9383 (m) cc_final: 0.8911 (m) REVERT: r 59 SER cc_start: 0.8601 (p) cc_final: 0.8117 (p) REVERT: r 89 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8215 (mm-40) REVERT: r 107 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7739 (pt0) REVERT: r 108 MET cc_start: 0.8642 (tpt) cc_final: 0.8370 (tpp) REVERT: r 115 LEU cc_start: 0.9597 (tp) cc_final: 0.9290 (tp) REVERT: r 124 THR cc_start: 0.9002 (p) cc_final: 0.8434 (t) REVERT: r 125 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8449 (t) REVERT: r 198 TYR cc_start: 0.8962 (m-10) cc_final: 0.8749 (m-10) REVERT: s 59 SER cc_start: 0.8329 (p) cc_final: 0.7958 (p) REVERT: s 107 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7624 (pt0) REVERT: s 124 THR cc_start: 0.8933 (p) cc_final: 0.8294 (t) REVERT: s 125 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8575 (t) REVERT: t 59 SER cc_start: 0.8596 (p) cc_final: 0.8206 (p) REVERT: t 107 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7747 (pt0) REVERT: t 108 MET cc_start: 0.8626 (tpt) cc_final: 0.8403 (tpp) REVERT: t 115 LEU cc_start: 0.9595 (tp) cc_final: 0.9266 (tp) REVERT: t 124 THR cc_start: 0.9004 (p) cc_final: 0.8422 (t) REVERT: t 125 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8430 (t) REVERT: t 198 TYR cc_start: 0.8947 (m-10) cc_final: 0.8725 (m-10) REVERT: u 59 SER cc_start: 0.8336 (p) cc_final: 0.7970 (p) REVERT: u 107 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7648 (pt0) REVERT: u 124 THR cc_start: 0.8939 (p) cc_final: 0.8352 (t) REVERT: u 125 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8573 (t) REVERT: v 44 VAL cc_start: 0.9382 (m) cc_final: 0.8925 (m) REVERT: v 59 SER cc_start: 0.8594 (p) cc_final: 0.8114 (p) REVERT: v 67 LEU cc_start: 0.8589 (mm) cc_final: 0.8064 (mm) REVERT: v 89 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8231 (mm-40) REVERT: v 107 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7732 (pt0) REVERT: v 108 MET cc_start: 0.8635 (tpt) cc_final: 0.8411 (tpp) REVERT: v 115 LEU cc_start: 0.9585 (tp) cc_final: 0.9262 (tp) REVERT: v 124 THR cc_start: 0.8998 (p) cc_final: 0.8437 (t) REVERT: v 125 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8435 (t) REVERT: v 198 TYR cc_start: 0.8951 (m-10) cc_final: 0.8737 (m-10) REVERT: w 59 SER cc_start: 0.8135 (p) cc_final: 0.7707 (p) REVERT: w 107 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7655 (pt0) REVERT: w 124 THR cc_start: 0.8947 (p) cc_final: 0.8390 (t) REVERT: w 125 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8584 (t) REVERT: x 59 SER cc_start: 0.8607 (p) cc_final: 0.8200 (p) REVERT: x 107 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7737 (pt0) REVERT: x 108 MET cc_start: 0.8636 (tpt) cc_final: 0.8413 (tpp) REVERT: x 115 LEU cc_start: 0.9594 (tp) cc_final: 0.9270 (tp) REVERT: x 124 THR cc_start: 0.8998 (p) cc_final: 0.8418 (t) REVERT: x 125 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8429 (t) REVERT: x 198 TYR cc_start: 0.8949 (m-10) cc_final: 0.8733 (m-10) outliers start: 72 outliers final: 9 residues processed: 1724 average time/residue: 0.5603 time to fit residues: 1447.6703 Evaluate side-chains 1538 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1502 time to evaluate : 3.864 ------------------------------------------------------------------------------- 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: 0.4980 chunk 208 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 319 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 238 optimal weight: 6.9990 chunk 370 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 69 HIS a 77 GLN ** a 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 162 HIS b 69 HIS b 77 GLN ** 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 77 GLN ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 162 HIS f 69 HIS f 77 GLN ** f 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 162 HIS g 69 HIS g 77 GLN ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 HIS h 69 HIS h 77 GLN ** h 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 162 HIS i 69 HIS i 77 GLN i 98 GLN i 113 ASN ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 69 HIS j 77 GLN 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 77 GLN l 98 GLN l 113 ASN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 69 HIS m 77 GLN m 98 GLN m 113 ASN ** m 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 HIS n 77 GLN n 98 GLN n 113 ASN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 69 HIS o 77 GLN o 98 GLN o 113 ASN ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 69 HIS p 77 GLN p 98 GLN p 113 ASN ** p 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 77 GLN 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 77 GLN v 113 ASN ** v 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 69 HIS w 77 GLN w 113 ASN ** w 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 162 HIS w 217 HIS x 69 HIS x 77 GLN x 113 ASN ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3196 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= 0.170 Angle : 0.614 5.891 47184 Z= 0.315 Chirality : 0.041 0.127 5160 Planarity : 0.006 0.034 6120 Dihedral : 5.349 19.692 4704 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: -4.06 (0.11), residues: 4176 helix: -2.23 (0.10), residues: 1776 sheet: -2.35 (0.32), residues: 240 loop : -3.22 (0.10), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP r 132 HIS 0.002 0.001 HIS s 162 PHE 0.014 0.002 PHE u 202 TYR 0.027 0.001 TYR h 73 ARG 0.005 0.001 ARG w 208 *********************** 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 1592 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1592 time to evaluate : 3.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 66 ASN cc_start: 0.8352 (t0) cc_final: 0.8135 (t0) REVERT: a 124 THR cc_start: 0.8987 (p) cc_final: 0.8598 (t) REVERT: a 125 SER cc_start: 0.8306 (p) cc_final: 0.8004 (t) REVERT: a 189 ASN cc_start: 0.9227 (t0) cc_final: 0.9009 (t0) REVERT: b 82 ASN cc_start: 0.8661 (t0) cc_final: 0.8389 (t0) REVERT: b 86 THR cc_start: 0.8931 (p) cc_final: 0.8688 (t) REVERT: b 107 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7325 (pt0) REVERT: b 112 MET cc_start: 0.9465 (mmp) cc_final: 0.9231 (mmt) REVERT: b 122 ASN cc_start: 0.8758 (m110) cc_final: 0.8362 (m110) REVERT: c 66 ASN cc_start: 0.8352 (t0) cc_final: 0.8125 (t0) REVERT: c 124 THR cc_start: 0.9003 (p) cc_final: 0.8611 (t) REVERT: c 125 SER cc_start: 0.8312 (p) cc_final: 0.8024 (t) REVERT: c 189 ASN cc_start: 0.9230 (t0) cc_final: 0.9012 (t0) REVERT: d 107 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7320 (pt0) REVERT: d 122 ASN cc_start: 0.8731 (m110) cc_final: 0.8394 (m110) REVERT: d 124 THR cc_start: 0.8898 (p) cc_final: 0.8608 (t) REVERT: e 66 ASN cc_start: 0.8363 (t0) cc_final: 0.8138 (t0) REVERT: e 124 THR cc_start: 0.8989 (p) cc_final: 0.8613 (t) REVERT: e 125 SER cc_start: 0.8274 (p) cc_final: 0.7991 (t) REVERT: e 189 ASN cc_start: 0.9230 (t0) cc_final: 0.9007 (t0) REVERT: f 82 ASN cc_start: 0.8653 (t0) cc_final: 0.8380 (t0) REVERT: f 86 THR cc_start: 0.8923 (p) cc_final: 0.8690 (t) REVERT: f 107 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7334 (pt0) REVERT: f 112 MET cc_start: 0.9444 (mmp) cc_final: 0.9226 (mmt) REVERT: f 122 ASN cc_start: 0.8739 (m110) cc_final: 0.8356 (m110) REVERT: g 66 ASN cc_start: 0.8378 (t0) cc_final: 0.8135 (t0) REVERT: g 124 THR cc_start: 0.8989 (p) cc_final: 0.8615 (t) REVERT: g 125 SER cc_start: 0.8291 (p) cc_final: 0.8001 (t) REVERT: g 189 ASN cc_start: 0.9227 (t0) cc_final: 0.9015 (t0) REVERT: h 82 ASN cc_start: 0.8661 (t0) cc_final: 0.8394 (t0) REVERT: h 86 THR cc_start: 0.8929 (p) cc_final: 0.8677 (t) REVERT: h 107 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7326 (pt0) REVERT: h 112 MET cc_start: 0.9466 (mmp) cc_final: 0.9237 (mmt) REVERT: h 122 ASN cc_start: 0.8726 (m110) cc_final: 0.8337 (m110) REVERT: i 44 VAL cc_start: 0.9413 (m) cc_final: 0.9116 (m) REVERT: i 66 ASN cc_start: 0.8037 (t0) cc_final: 0.7784 (t0) REVERT: i 98 GLN cc_start: 0.8640 (tt0) cc_final: 0.7697 (tt0) REVERT: i 122 ASN cc_start: 0.8672 (m110) cc_final: 0.8215 (m110) REVERT: i 124 THR cc_start: 0.8823 (p) cc_final: 0.8240 (t) REVERT: j 66 ASN cc_start: 0.8283 (t0) cc_final: 0.7929 (t0) REVERT: j 82 ASN cc_start: 0.8428 (t0) cc_final: 0.7994 (t0) REVERT: j 122 ASN cc_start: 0.8669 (m110) cc_final: 0.8383 (m110) REVERT: j 124 THR cc_start: 0.8920 (p) cc_final: 0.8329 (t) REVERT: j 188 ARG cc_start: 0.8294 (mmm160) cc_final: 0.7962 (tpt90) REVERT: j 189 ASN cc_start: 0.9156 (t0) cc_final: 0.8784 (t0) REVERT: j 198 TYR cc_start: 0.8925 (m-10) cc_final: 0.8702 (m-10) REVERT: k 44 VAL cc_start: 0.9417 (m) cc_final: 0.9104 (m) REVERT: k 66 ASN cc_start: 0.8061 (t0) cc_final: 0.7792 (t0) REVERT: k 98 GLN cc_start: 0.8632 (tt0) cc_final: 0.7668 (tt0) REVERT: k 122 ASN cc_start: 0.8681 (m110) cc_final: 0.8226 (m110) REVERT: k 124 THR cc_start: 0.8838 (p) cc_final: 0.8278 (t) REVERT: k 188 ARG cc_start: 0.8344 (mmm160) cc_final: 0.7991 (tpt90) REVERT: l 66 ASN cc_start: 0.8283 (t0) cc_final: 0.7929 (t0) REVERT: l 122 ASN cc_start: 0.8649 (m110) cc_final: 0.8360 (m110) REVERT: l 124 THR cc_start: 0.8967 (p) cc_final: 0.8363 (t) REVERT: l 188 ARG cc_start: 0.8334 (mmm160) cc_final: 0.7967 (tpt90) REVERT: l 189 ASN cc_start: 0.9154 (t0) cc_final: 0.8816 (t0) REVERT: l 198 TYR cc_start: 0.8926 (m-10) cc_final: 0.8663 (m-10) REVERT: m 44 VAL cc_start: 0.9421 (m) cc_final: 0.9115 (m) REVERT: m 66 ASN cc_start: 0.8051 (t0) cc_final: 0.7785 (t0) REVERT: m 98 GLN cc_start: 0.8655 (tt0) cc_final: 0.7806 (tt0) REVERT: m 122 ASN cc_start: 0.8691 (m110) cc_final: 0.8204 (m110) REVERT: m 124 THR cc_start: 0.8911 (p) cc_final: 0.8291 (t) REVERT: n 66 ASN cc_start: 0.8325 (t0) cc_final: 0.7967 (t0) REVERT: n 122 ASN cc_start: 0.8654 (m110) cc_final: 0.8359 (m110) REVERT: n 124 THR cc_start: 0.8955 (p) cc_final: 0.8363 (t) REVERT: n 188 ARG cc_start: 0.8325 (mmm160) cc_final: 0.7963 (tpt90) REVERT: n 189 ASN cc_start: 0.9144 (t0) cc_final: 0.8776 (t0) REVERT: n 198 TYR cc_start: 0.8912 (m-10) cc_final: 0.8664 (m-10) REVERT: o 44 VAL cc_start: 0.9411 (m) cc_final: 0.9117 (m) REVERT: o 66 ASN cc_start: 0.8045 (t0) cc_final: 0.7807 (t0) REVERT: o 98 GLN cc_start: 0.8647 (tt0) cc_final: 0.7681 (tt0) REVERT: o 122 ASN cc_start: 0.8681 (m110) cc_final: 0.8220 (m110) REVERT: o 124 THR cc_start: 0.8887 (p) cc_final: 0.8301 (t) REVERT: o 188 ARG cc_start: 0.8328 (mmm160) cc_final: 0.7980 (tpt90) REVERT: p 66 ASN cc_start: 0.8287 (t0) cc_final: 0.7930 (t0) REVERT: p 122 ASN cc_start: 0.8603 (m110) cc_final: 0.8290 (m110) REVERT: p 124 THR cc_start: 0.8928 (p) cc_final: 0.8316 (t) REVERT: p 188 ARG cc_start: 0.8297 (mmm160) cc_final: 0.7963 (tpt90) REVERT: p 189 ASN cc_start: 0.9157 (t0) cc_final: 0.8784 (t0) REVERT: p 198 TYR cc_start: 0.8914 (m-10) cc_final: 0.8691 (m-10) REVERT: q 66 ASN cc_start: 0.7846 (t0) cc_final: 0.7269 (t0) REVERT: q 103 ILE cc_start: 0.9077 (mm) cc_final: 0.8753 (mm) REVERT: q 107 GLU cc_start: 0.7833 (mt-10) cc_final: 0.6865 (tm-30) REVERT: q 108 MET cc_start: 0.8503 (tpp) cc_final: 0.8213 (tpp) REVERT: q 124 THR cc_start: 0.8858 (p) cc_final: 0.8236 (t) REVERT: r 66 ASN cc_start: 0.8158 (t0) cc_final: 0.7896 (t0) REVERT: r 67 LEU cc_start: 0.8508 (mm) cc_final: 0.8226 (mm) REVERT: r 95 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7429 (mm-30) REVERT: r 98 GLN cc_start: 0.8523 (tt0) cc_final: 0.8265 (tp40) REVERT: r 107 GLU cc_start: 0.7934 (mt-10) cc_final: 0.6976 (tm-30) REVERT: r 108 MET cc_start: 0.8682 (tpt) cc_final: 0.8425 (tpp) REVERT: r 122 ASN cc_start: 0.8685 (m110) cc_final: 0.8122 (m110) REVERT: r 124 THR cc_start: 0.8903 (p) cc_final: 0.8282 (t) REVERT: r 135 MET cc_start: 0.8866 (mmm) cc_final: 0.8406 (mmm) REVERT: r 198 TYR cc_start: 0.9017 (m-10) cc_final: 0.8779 (m-10) REVERT: s 66 ASN cc_start: 0.7821 (t0) cc_final: 0.7314 (t0) REVERT: s 103 ILE cc_start: 0.9081 (mm) cc_final: 0.8759 (mm) REVERT: s 107 GLU cc_start: 0.7848 (mt-10) cc_final: 0.6875 (tm-30) REVERT: s 108 MET cc_start: 0.8554 (tpp) cc_final: 0.8240 (tpp) REVERT: s 124 THR cc_start: 0.8850 (p) cc_final: 0.8224 (t) REVERT: t 66 ASN cc_start: 0.8132 (t0) cc_final: 0.7867 (t0) REVERT: t 67 LEU cc_start: 0.8505 (mm) cc_final: 0.8215 (mm) REVERT: t 95 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7485 (mm-30) REVERT: t 122 ASN cc_start: 0.8666 (m110) cc_final: 0.8127 (m110) REVERT: t 124 THR cc_start: 0.8857 (p) cc_final: 0.8261 (t) REVERT: t 135 MET cc_start: 0.8848 (mmm) cc_final: 0.8421 (mmm) REVERT: t 198 TYR cc_start: 0.9048 (m-10) cc_final: 0.8799 (m-10) REVERT: u 66 ASN cc_start: 0.7829 (t0) cc_final: 0.7251 (t0) REVERT: u 79 ASP cc_start: 0.8131 (m-30) cc_final: 0.7923 (m-30) REVERT: u 103 ILE cc_start: 0.9085 (mm) cc_final: 0.8760 (mm) REVERT: u 107 GLU cc_start: 0.7865 (mt-10) cc_final: 0.6879 (tm-30) REVERT: u 108 MET cc_start: 0.8523 (tpp) cc_final: 0.8211 (tpp) REVERT: u 124 THR cc_start: 0.8857 (p) cc_final: 0.8227 (t) REVERT: v 66 ASN cc_start: 0.8130 (t0) cc_final: 0.7866 (t0) REVERT: v 67 LEU cc_start: 0.8488 (mm) cc_final: 0.8232 (mm) REVERT: v 95 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7417 (mm-30) REVERT: v 98 GLN cc_start: 0.8512 (tt0) cc_final: 0.8257 (tp40) REVERT: v 107 GLU cc_start: 0.7952 (mt-10) cc_final: 0.6972 (tm-30) REVERT: v 108 MET cc_start: 0.8655 (tpt) cc_final: 0.8421 (tpp) REVERT: v 122 ASN cc_start: 0.8648 (m110) cc_final: 0.8133 (m110) REVERT: v 124 THR cc_start: 0.8900 (p) cc_final: 0.8289 (t) REVERT: v 135 MET cc_start: 0.8959 (mmm) cc_final: 0.8454 (mmm) REVERT: v 198 TYR cc_start: 0.9017 (m-10) cc_final: 0.8775 (m-10) REVERT: w 66 ASN cc_start: 0.7816 (t0) cc_final: 0.7262 (t0) REVERT: w 79 ASP cc_start: 0.8131 (m-30) cc_final: 0.7920 (m-30) REVERT: w 103 ILE cc_start: 0.9092 (mm) cc_final: 0.8779 (mm) REVERT: w 107 GLU cc_start: 0.7863 (mt-10) cc_final: 0.6852 (tm-30) REVERT: w 108 MET cc_start: 0.8576 (tpp) cc_final: 0.8230 (tpp) REVERT: w 124 THR cc_start: 0.8861 (p) cc_final: 0.8241 (t) REVERT: w 198 TYR cc_start: 0.8980 (m-10) cc_final: 0.8433 (m-10) REVERT: x 66 ASN cc_start: 0.8111 (t0) cc_final: 0.7815 (t0) REVERT: x 95 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7448 (mm-30) REVERT: x 98 GLN cc_start: 0.8513 (tt0) cc_final: 0.8223 (tp40) REVERT: x 122 ASN cc_start: 0.8691 (m110) cc_final: 0.8144 (m110) REVERT: x 124 THR cc_start: 0.8853 (p) cc_final: 0.8255 (t) REVERT: x 135 MET cc_start: 0.8811 (mmm) cc_final: 0.8479 (mmm) REVERT: x 198 TYR cc_start: 0.9040 (m-10) cc_final: 0.8806 (m-10) outliers start: 0 outliers final: 0 residues processed: 1592 average time/residue: 0.5154 time to fit residues: 1255.6482 Evaluate side-chains 1390 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1390 time to evaluate : 3.786 ------------------------------------------------------------------------------- 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: 8.9990 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 0.6980 chunk 252 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 400 optimal weight: 1.9990 chunk 330 optimal weight: 3.9990 chunk 368 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 297 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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** 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 ** i 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 162 HIS ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 175 ASN ** k 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 162 HIS ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 175 ASN ** m 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 122 ASN ** r 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 122 ASN ** t 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 175 ASN u 122 ASN ** v 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 122 ASN ** x 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 175 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 34776 Z= 0.433 Angle : 0.764 6.186 47184 Z= 0.390 Chirality : 0.048 0.150 5160 Planarity : 0.005 0.040 6120 Dihedral : 5.713 21.679 4704 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: -3.76 (0.12), residues: 4176 helix: -1.93 (0.10), residues: 2088 sheet: -2.35 (0.31), residues: 240 loop : -3.15 (0.12), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP p 132 HIS 0.002 0.001 HIS b 162 PHE 0.021 0.003 PHE u 200 TYR 0.026 0.002 TYR i 73 ARG 0.005 0.001 ARG v 208 *********************** 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 1498 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1498 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 66 ASN cc_start: 0.8279 (t0) cc_final: 0.8038 (t0) REVERT: a 79 ASP cc_start: 0.8495 (m-30) cc_final: 0.8197 (m-30) REVERT: a 124 THR cc_start: 0.9137 (p) cc_final: 0.8766 (t) REVERT: b 66 ASN cc_start: 0.8221 (t0) cc_final: 0.7824 (t0) REVERT: b 107 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7425 (pt0) REVERT: b 115 LEU cc_start: 0.9678 (tp) cc_final: 0.9381 (tp) REVERT: b 122 ASN cc_start: 0.9029 (m110) cc_final: 0.8694 (m110) REVERT: b 124 THR cc_start: 0.8856 (p) cc_final: 0.8575 (t) REVERT: c 55 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7600 (tpt-90) REVERT: c 66 ASN cc_start: 0.8280 (t0) cc_final: 0.8036 (t0) REVERT: c 82 ASN cc_start: 0.8705 (t0) cc_final: 0.8394 (t0) REVERT: c 124 THR cc_start: 0.9105 (p) cc_final: 0.8841 (t) REVERT: d 66 ASN cc_start: 0.8170 (t0) cc_final: 0.7688 (t0) REVERT: d 68 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7480 (tm-30) REVERT: d 107 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7406 (pt0) REVERT: d 115 LEU cc_start: 0.9701 (tp) cc_final: 0.9481 (tp) REVERT: d 122 ASN cc_start: 0.9019 (m110) cc_final: 0.8695 (m110) REVERT: d 124 THR cc_start: 0.8955 (p) cc_final: 0.8691 (t) REVERT: d 135 MET cc_start: 0.8692 (mmm) cc_final: 0.8470 (mmm) REVERT: d 188 ARG cc_start: 0.8556 (mmm160) cc_final: 0.8302 (tpt90) REVERT: d 203 TYR cc_start: 0.9114 (t80) cc_final: 0.8840 (t80) REVERT: e 66 ASN cc_start: 0.8307 (t0) cc_final: 0.8037 (t0) REVERT: e 124 THR cc_start: 0.9136 (p) cc_final: 0.8801 (t) REVERT: f 66 ASN cc_start: 0.8242 (t0) cc_final: 0.7831 (t0) REVERT: f 107 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7419 (pt0) REVERT: f 115 LEU cc_start: 0.9680 (tp) cc_final: 0.9383 (tp) REVERT: f 122 ASN cc_start: 0.9008 (m110) cc_final: 0.8681 (m110) REVERT: f 124 THR cc_start: 0.8826 (p) cc_final: 0.8547 (t) REVERT: f 135 MET cc_start: 0.8743 (mmm) cc_final: 0.8527 (mmm) REVERT: g 55 ARG cc_start: 0.7842 (tpp80) cc_final: 0.7579 (tpt-90) REVERT: g 66 ASN cc_start: 0.8282 (t0) cc_final: 0.8047 (t0) REVERT: g 124 THR cc_start: 0.9132 (p) cc_final: 0.8777 (t) REVERT: g 197 ARG cc_start: 0.8392 (ttt180) cc_final: 0.8031 (ttt90) REVERT: h 66 ASN cc_start: 0.8225 (t0) cc_final: 0.7836 (t0) REVERT: h 107 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7420 (pt0) REVERT: h 115 LEU cc_start: 0.9681 (tp) cc_final: 0.9400 (tp) REVERT: h 122 ASN cc_start: 0.9008 (m110) cc_final: 0.8681 (m110) REVERT: h 124 THR cc_start: 0.8888 (p) cc_final: 0.8584 (t) REVERT: h 135 MET cc_start: 0.8631 (mmm) cc_final: 0.8413 (mmm) REVERT: h 188 ARG cc_start: 0.8557 (mmm160) cc_final: 0.8308 (tpt90) REVERT: i 66 ASN cc_start: 0.7997 (t0) cc_final: 0.7764 (t0) REVERT: i 67 LEU cc_start: 0.8631 (mm) cc_final: 0.8365 (mm) REVERT: i 68 GLU cc_start: 0.8465 (mp0) cc_final: 0.7903 (tm-30) REVERT: i 122 ASN cc_start: 0.8844 (m110) cc_final: 0.8459 (m110) REVERT: i 124 THR cc_start: 0.8945 (p) cc_final: 0.8359 (t) REVERT: i 143 TYR cc_start: 0.9067 (m-80) cc_final: 0.8529 (m-80) REVERT: i 172 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7937 (mm-30) REVERT: j 66 ASN cc_start: 0.8350 (t0) cc_final: 0.7902 (t0) REVERT: j 67 LEU cc_start: 0.8695 (mm) cc_final: 0.8417 (mm) REVERT: j 115 LEU cc_start: 0.9614 (tp) cc_final: 0.9174 (tp) REVERT: j 122 ASN cc_start: 0.8751 (m110) cc_final: 0.8463 (m110) REVERT: j 198 TYR cc_start: 0.9190 (m-10) cc_final: 0.8733 (m-10) REVERT: k 66 ASN cc_start: 0.7996 (t0) cc_final: 0.7761 (t0) REVERT: k 67 LEU cc_start: 0.8618 (mm) cc_final: 0.8346 (mm) REVERT: k 68 GLU cc_start: 0.8458 (mp0) cc_final: 0.7904 (tm-30) REVERT: k 122 ASN cc_start: 0.8876 (m110) cc_final: 0.8461 (m110) REVERT: k 124 THR cc_start: 0.8970 (p) cc_final: 0.8370 (t) REVERT: k 143 TYR cc_start: 0.9043 (m-80) cc_final: 0.8521 (m-80) REVERT: k 172 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7958 (mm-30) REVERT: l 66 ASN cc_start: 0.8339 (t0) cc_final: 0.7885 (t0) REVERT: l 67 LEU cc_start: 0.8696 (mm) cc_final: 0.8390 (mm) REVERT: l 105 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7963 (mp0) REVERT: l 122 ASN cc_start: 0.8757 (m110) cc_final: 0.8476 (m110) REVERT: l 197 ARG cc_start: 0.8880 (tmm-80) cc_final: 0.8080 (ttp80) REVERT: l 198 TYR cc_start: 0.9188 (m-10) cc_final: 0.8775 (m-10) REVERT: m 66 ASN cc_start: 0.8029 (t0) cc_final: 0.7742 (t0) REVERT: m 67 LEU cc_start: 0.8610 (mm) cc_final: 0.8335 (mm) REVERT: m 68 GLU cc_start: 0.8422 (mp0) cc_final: 0.7897 (tm-30) REVERT: m 122 ASN cc_start: 0.8879 (m110) cc_final: 0.8449 (m110) REVERT: m 124 THR cc_start: 0.8996 (p) cc_final: 0.8384 (t) REVERT: m 143 TYR cc_start: 0.9018 (m-80) cc_final: 0.8584 (m-80) REVERT: m 172 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7956 (mm-30) REVERT: n 66 ASN cc_start: 0.8326 (t0) cc_final: 0.7891 (t0) REVERT: n 67 LEU cc_start: 0.8696 (mm) cc_final: 0.8420 (mm) REVERT: n 105 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7948 (mp0) REVERT: n 122 ASN cc_start: 0.8750 (m110) cc_final: 0.8477 (m110) REVERT: n 197 ARG cc_start: 0.8874 (tmm-80) cc_final: 0.8075 (ttp80) REVERT: n 198 TYR cc_start: 0.9187 (m-10) cc_final: 0.8760 (m-10) REVERT: o 66 ASN cc_start: 0.8030 (t0) cc_final: 0.7759 (t0) REVERT: o 67 LEU cc_start: 0.8615 (mm) cc_final: 0.8361 (mm) REVERT: o 68 GLU cc_start: 0.8432 (mp0) cc_final: 0.7892 (tm-30) REVERT: o 122 ASN cc_start: 0.8851 (m110) cc_final: 0.8453 (m110) REVERT: o 124 THR cc_start: 0.8988 (p) cc_final: 0.8370 (t) REVERT: o 143 TYR cc_start: 0.9048 (m-80) cc_final: 0.8559 (m-80) REVERT: o 172 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7949 (mm-30) REVERT: p 66 ASN cc_start: 0.8345 (t0) cc_final: 0.7897 (t0) REVERT: p 67 LEU cc_start: 0.8685 (mm) cc_final: 0.8389 (mm) REVERT: p 115 LEU cc_start: 0.9641 (tp) cc_final: 0.9188 (tp) REVERT: p 122 ASN cc_start: 0.8778 (m110) cc_final: 0.8401 (m110) REVERT: p 135 MET cc_start: 0.8823 (mmm) cc_final: 0.8564 (mmm) REVERT: p 198 TYR cc_start: 0.9196 (m-10) cc_final: 0.8732 (m-10) REVERT: q 66 ASN cc_start: 0.7989 (t0) cc_final: 0.7508 (t0) REVERT: q 67 LEU cc_start: 0.8436 (mm) cc_final: 0.8203 (mm) REVERT: q 107 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7720 (pt0) REVERT: q 108 MET cc_start: 0.8531 (tpp) cc_final: 0.7887 (tpp) REVERT: q 124 THR cc_start: 0.8904 (p) cc_final: 0.8326 (t) REVERT: q 172 GLU cc_start: 0.8518 (mt-10) cc_final: 0.7446 (mm-30) REVERT: q 197 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7451 (mtm110) REVERT: r 82 ASN cc_start: 0.8784 (t0) cc_final: 0.8475 (t0) REVERT: r 108 MET cc_start: 0.8954 (tpt) cc_final: 0.8427 (tpp) REVERT: r 115 LEU cc_start: 0.9676 (tp) cc_final: 0.9451 (tp) REVERT: r 122 ASN cc_start: 0.9022 (m110) cc_final: 0.8629 (m110) REVERT: r 124 THR cc_start: 0.8987 (p) cc_final: 0.8450 (t) REVERT: r 135 MET cc_start: 0.8756 (mmm) cc_final: 0.8284 (mmm) REVERT: s 66 ASN cc_start: 0.7954 (t0) cc_final: 0.7473 (t0) REVERT: s 67 LEU cc_start: 0.8439 (mm) cc_final: 0.8218 (mm) REVERT: s 107 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7735 (pt0) REVERT: s 108 MET cc_start: 0.8552 (tpp) cc_final: 0.7900 (tpp) REVERT: s 124 THR cc_start: 0.8894 (p) cc_final: 0.8312 (t) REVERT: s 172 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7466 (mm-30) REVERT: s 197 ARG cc_start: 0.7981 (mtm110) cc_final: 0.7459 (mtm110) REVERT: t 82 ASN cc_start: 0.8777 (t0) cc_final: 0.8479 (t0) REVERT: t 98 GLN cc_start: 0.8542 (tp40) cc_final: 0.8132 (tp40) REVERT: t 115 LEU cc_start: 0.9658 (tp) cc_final: 0.9430 (tp) REVERT: t 122 ASN cc_start: 0.8972 (m110) cc_final: 0.8578 (m110) REVERT: t 124 THR cc_start: 0.9003 (p) cc_final: 0.8462 (t) REVERT: t 135 MET cc_start: 0.8792 (mmm) cc_final: 0.8312 (mmm) REVERT: t 198 TYR cc_start: 0.9137 (m-10) cc_final: 0.8816 (m-10) REVERT: u 66 ASN cc_start: 0.7936 (t0) cc_final: 0.7442 (t0) REVERT: u 67 LEU cc_start: 0.8445 (mm) cc_final: 0.8212 (mm) REVERT: u 107 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7741 (pt0) REVERT: u 108 MET cc_start: 0.8511 (tpp) cc_final: 0.7868 (tpp) REVERT: u 124 THR cc_start: 0.8899 (p) cc_final: 0.8323 (t) REVERT: u 172 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7444 (mm-30) REVERT: u 197 ARG cc_start: 0.7962 (mtm110) cc_final: 0.7442 (mtm110) REVERT: v 82 ASN cc_start: 0.8772 (t0) cc_final: 0.8481 (t0) REVERT: v 108 MET cc_start: 0.8955 (tpt) cc_final: 0.8420 (tpp) REVERT: v 115 LEU cc_start: 0.9677 (tp) cc_final: 0.9446 (tp) REVERT: v 122 ASN cc_start: 0.9013 (m110) cc_final: 0.8653 (m110) REVERT: v 124 THR cc_start: 0.8991 (p) cc_final: 0.8448 (t) REVERT: v 135 MET cc_start: 0.8774 (mmm) cc_final: 0.8228 (mmm) REVERT: w 66 ASN cc_start: 0.7871 (t0) cc_final: 0.7382 (t0) REVERT: w 107 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7741 (pt0) REVERT: w 108 MET cc_start: 0.8560 (tpp) cc_final: 0.7928 (tpp) REVERT: w 124 THR cc_start: 0.8907 (p) cc_final: 0.8296 (t) REVERT: x 82 ASN cc_start: 0.8754 (t0) cc_final: 0.8477 (t0) REVERT: x 98 GLN cc_start: 0.8616 (tt0) cc_final: 0.8331 (tt0) REVERT: x 115 LEU cc_start: 0.9652 (tp) cc_final: 0.9402 (tp) REVERT: x 122 ASN cc_start: 0.8981 (m110) cc_final: 0.8566 (m110) REVERT: x 124 THR cc_start: 0.8986 (p) cc_final: 0.8456 (t) REVERT: x 198 TYR cc_start: 0.9143 (m-10) cc_final: 0.8836 (m-10) outliers start: 0 outliers final: 0 residues processed: 1498 average time/residue: 0.4936 time to fit residues: 1140.0934 Evaluate side-chains 1395 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1395 time to evaluate : 3.945 ------------------------------------------------------------------------------- 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: 1.9990 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 372 optimal weight: 0.9990 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 353 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- 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** a 175 ASN b 98 GLN b 122 ASN c 77 GLN c 98 GLN ** c 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 GLN d 122 ASN d 175 ASN e 98 GLN ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 GLN f 122 ASN g 98 GLN ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 175 ASN h 98 GLN h 122 ASN i 122 ASN ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 122 ASN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 122 ASN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 122 ASN p 122 ASN q 76 GLN r 122 ASN s 76 GLN ** t 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 122 ASN t 162 HIS v 77 GLN v 122 ASN x 122 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4045 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= 0.179 Angle : 0.611 5.538 47184 Z= 0.311 Chirality : 0.042 0.134 5160 Planarity : 0.005 0.035 6120 Dihedral : 5.066 18.740 4704 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.12), residues: 4176 helix: -0.96 (0.12), residues: 1944 sheet: -1.89 (0.30), residues: 240 loop : -2.97 (0.12), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP n 132 HIS 0.001 0.000 HIS c 162 PHE 0.014 0.002 PHE m 202 TYR 0.017 0.001 TYR d 180 ARG 0.005 0.001 ARG h 212 *********************** 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 1488 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1488 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 66 ASN cc_start: 0.8300 (t0) cc_final: 0.8045 (t0) REVERT: a 79 ASP cc_start: 0.8491 (m-30) cc_final: 0.8119 (m-30) REVERT: a 122 ASN cc_start: 0.8729 (m110) cc_final: 0.8312 (m110) REVERT: a 124 THR cc_start: 0.9034 (p) cc_final: 0.8711 (t) REVERT: a 135 MET cc_start: 0.8547 (mmm) cc_final: 0.8262 (mmm) REVERT: b 79 ASP cc_start: 0.8639 (m-30) cc_final: 0.8268 (m-30) REVERT: b 122 ASN cc_start: 0.8968 (m-40) cc_final: 0.8667 (m-40) REVERT: b 135 MET cc_start: 0.8531 (mmm) cc_final: 0.8120 (mmm) REVERT: c 66 ASN cc_start: 0.8210 (t0) cc_final: 0.7957 (t0) REVERT: c 79 ASP cc_start: 0.8571 (m-30) cc_final: 0.8114 (m-30) REVERT: c 82 ASN cc_start: 0.8753 (t0) cc_final: 0.8221 (t0) REVERT: c 122 ASN cc_start: 0.8646 (m110) cc_final: 0.8236 (m110) REVERT: c 124 THR cc_start: 0.9021 (p) cc_final: 0.8793 (t) REVERT: c 135 MET cc_start: 0.8577 (mmm) cc_final: 0.8293 (mmm) REVERT: d 79 ASP cc_start: 0.8738 (m-30) cc_final: 0.8363 (m-30) REVERT: d 98 GLN cc_start: 0.8440 (tt0) cc_final: 0.7970 (tt0) REVERT: d 122 ASN cc_start: 0.8956 (m-40) cc_final: 0.8685 (m-40) REVERT: d 188 ARG cc_start: 0.8523 (mmm160) cc_final: 0.8262 (tpt90) REVERT: e 66 ASN cc_start: 0.8215 (t0) cc_final: 0.7905 (t0) REVERT: e 122 ASN cc_start: 0.8699 (m110) cc_final: 0.8321 (m110) REVERT: e 124 THR cc_start: 0.9020 (p) cc_final: 0.8734 (t) REVERT: e 135 MET cc_start: 0.8561 (mmm) cc_final: 0.8269 (mmm) REVERT: f 79 ASP cc_start: 0.8659 (m-30) cc_final: 0.8281 (m-30) REVERT: f 122 ASN cc_start: 0.8946 (m-40) cc_final: 0.8680 (m-40) REVERT: g 66 ASN cc_start: 0.8353 (t0) cc_final: 0.8083 (t0) REVERT: g 122 ASN cc_start: 0.8716 (m110) cc_final: 0.8325 (m110) REVERT: g 124 THR cc_start: 0.9023 (p) cc_final: 0.8727 (t) REVERT: h 122 ASN cc_start: 0.8930 (m-40) cc_final: 0.8692 (m-40) REVERT: h 124 THR cc_start: 0.8859 (p) cc_final: 0.8627 (t) REVERT: h 135 MET cc_start: 0.8462 (mmm) cc_final: 0.8073 (mmm) REVERT: h 188 ARG cc_start: 0.8520 (mmm160) cc_final: 0.8243 (tpt90) REVERT: i 66 ASN cc_start: 0.7865 (t0) cc_final: 0.7637 (t0) REVERT: i 68 GLU cc_start: 0.8447 (mp0) cc_final: 0.7833 (tm-30) REVERT: i 122 ASN cc_start: 0.8772 (m-40) cc_final: 0.8357 (m-40) REVERT: i 143 TYR cc_start: 0.8843 (m-80) cc_final: 0.8366 (m-80) REVERT: i 172 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7884 (mm-30) REVERT: j 66 ASN cc_start: 0.8249 (t0) cc_final: 0.7788 (t0) REVERT: j 189 ASN cc_start: 0.9035 (t0) cc_final: 0.8731 (t0) REVERT: j 197 ARG cc_start: 0.8751 (tmm-80) cc_final: 0.7767 (ttp80) REVERT: j 198 TYR cc_start: 0.8942 (m-10) cc_final: 0.8686 (m-10) REVERT: k 66 ASN cc_start: 0.7864 (t0) cc_final: 0.7630 (t0) REVERT: k 68 GLU cc_start: 0.8446 (mp0) cc_final: 0.7850 (tm-30) REVERT: k 122 ASN cc_start: 0.8770 (m-40) cc_final: 0.8379 (m-40) REVERT: k 135 MET cc_start: 0.8626 (mmm) cc_final: 0.8421 (mmm) REVERT: k 143 TYR cc_start: 0.8860 (m-80) cc_final: 0.8326 (m-80) REVERT: k 172 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7886 (mm-30) REVERT: l 66 ASN cc_start: 0.8240 (t0) cc_final: 0.7768 (t0) REVERT: l 98 GLN cc_start: 0.8502 (tt0) cc_final: 0.7650 (tt0) REVERT: l 124 THR cc_start: 0.8877 (p) cc_final: 0.8523 (t) REVERT: l 189 ASN cc_start: 0.9038 (t0) cc_final: 0.8735 (t0) REVERT: l 197 ARG cc_start: 0.8751 (tmm-80) cc_final: 0.7754 (ttp80) REVERT: l 198 TYR cc_start: 0.8931 (m-10) cc_final: 0.8688 (m-10) REVERT: m 66 ASN cc_start: 0.7910 (t0) cc_final: 0.7624 (t0) REVERT: m 68 GLU cc_start: 0.8434 (mp0) cc_final: 0.7838 (tm-30) REVERT: m 122 ASN cc_start: 0.8783 (m-40) cc_final: 0.8372 (m-40) REVERT: m 124 THR cc_start: 0.8898 (p) cc_final: 0.8329 (t) REVERT: m 143 TYR cc_start: 0.8847 (m-80) cc_final: 0.8344 (m-80) REVERT: m 172 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7859 (mm-30) REVERT: n 66 ASN cc_start: 0.8241 (t0) cc_final: 0.7787 (t0) REVERT: n 98 GLN cc_start: 0.8507 (tt0) cc_final: 0.7670 (tt0) REVERT: n 124 THR cc_start: 0.8880 (p) cc_final: 0.8532 (t) REVERT: n 189 ASN cc_start: 0.9030 (t0) cc_final: 0.8735 (t0) REVERT: n 197 ARG cc_start: 0.8746 (tmm-80) cc_final: 0.7771 (ttp80) REVERT: n 198 TYR cc_start: 0.8931 (m-10) cc_final: 0.8688 (m-10) REVERT: o 66 ASN cc_start: 0.7925 (t0) cc_final: 0.7627 (t0) REVERT: o 68 GLU cc_start: 0.8406 (mp0) cc_final: 0.7845 (tm-30) REVERT: o 122 ASN cc_start: 0.8769 (m-40) cc_final: 0.8358 (m-40) REVERT: o 135 MET cc_start: 0.8623 (mmm) cc_final: 0.8380 (mmm) REVERT: o 143 TYR cc_start: 0.8872 (m-80) cc_final: 0.8353 (m-80) REVERT: o 172 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7865 (mm-30) REVERT: p 66 ASN cc_start: 0.8252 (t0) cc_final: 0.7804 (t0) REVERT: p 189 ASN cc_start: 0.9033 (t0) cc_final: 0.8727 (t0) REVERT: p 197 ARG cc_start: 0.8755 (tmm-80) cc_final: 0.7752 (ttp80) REVERT: p 198 TYR cc_start: 0.8946 (m-10) cc_final: 0.8692 (m-10) REVERT: q 66 ASN cc_start: 0.7851 (t0) cc_final: 0.7433 (t0) REVERT: q 107 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7689 (pt0) REVERT: q 108 MET cc_start: 0.8444 (tpp) cc_final: 0.8130 (tpp) REVERT: q 124 THR cc_start: 0.8941 (p) cc_final: 0.8375 (t) REVERT: q 172 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7782 (mm-30) REVERT: q 198 TYR cc_start: 0.8940 (m-10) cc_final: 0.8720 (m-10) REVERT: q 212 ARG cc_start: 0.7416 (ptt-90) cc_final: 0.7036 (ttp-110) REVERT: r 82 ASN cc_start: 0.8663 (t0) cc_final: 0.8420 (t0) REVERT: r 122 ASN cc_start: 0.8842 (m-40) cc_final: 0.8349 (m-40) REVERT: r 124 THR cc_start: 0.8972 (p) cc_final: 0.8423 (t) REVERT: s 66 ASN cc_start: 0.7819 (t0) cc_final: 0.7376 (t0) REVERT: s 79 ASP cc_start: 0.8420 (m-30) cc_final: 0.8204 (m-30) REVERT: s 108 MET cc_start: 0.8441 (tpp) cc_final: 0.8026 (tpp) REVERT: s 124 THR cc_start: 0.8921 (p) cc_final: 0.8366 (t) REVERT: s 135 MET cc_start: 0.8722 (mmm) cc_final: 0.8470 (mmm) REVERT: s 172 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7809 (mm-30) REVERT: s 198 TYR cc_start: 0.8891 (m-10) cc_final: 0.8687 (m-10) REVERT: s 212 ARG cc_start: 0.7338 (ptt-90) cc_final: 0.6945 (ttp-110) REVERT: t 82 ASN cc_start: 0.8664 (t0) cc_final: 0.8411 (t0) REVERT: t 122 ASN cc_start: 0.8739 (m-40) cc_final: 0.8298 (m-40) REVERT: t 124 THR cc_start: 0.9008 (p) cc_final: 0.8530 (t) REVERT: t 135 MET cc_start: 0.8886 (mmm) cc_final: 0.8370 (mmm) REVERT: u 66 ASN cc_start: 0.7808 (t0) cc_final: 0.7388 (t0) REVERT: u 79 ASP cc_start: 0.8317 (m-30) cc_final: 0.8033 (m-30) REVERT: u 107 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7696 (pt0) REVERT: u 108 MET cc_start: 0.8436 (tpp) cc_final: 0.8144 (tpp) REVERT: u 124 THR cc_start: 0.8936 (p) cc_final: 0.8367 (t) REVERT: u 172 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7777 (mm-30) REVERT: u 212 ARG cc_start: 0.7413 (ptt-90) cc_final: 0.7022 (ttp-110) REVERT: v 82 ASN cc_start: 0.8647 (t0) cc_final: 0.8422 (t0) REVERT: v 108 MET cc_start: 0.8665 (tpt) cc_final: 0.8448 (tpp) REVERT: v 122 ASN cc_start: 0.8825 (m-40) cc_final: 0.8387 (m-40) REVERT: v 124 THR cc_start: 0.8997 (p) cc_final: 0.8440 (t) REVERT: w 66 ASN cc_start: 0.7825 (t0) cc_final: 0.7423 (t0) REVERT: w 108 MET cc_start: 0.8428 (tpp) cc_final: 0.8032 (tpp) REVERT: w 124 THR cc_start: 0.8941 (p) cc_final: 0.8375 (t) REVERT: w 135 MET cc_start: 0.8829 (mmm) cc_final: 0.8592 (mmm) REVERT: w 212 ARG cc_start: 0.7543 (ptt-90) cc_final: 0.7187 (ttp-110) REVERT: x 79 ASP cc_start: 0.8309 (m-30) cc_final: 0.8100 (m-30) REVERT: x 82 ASN cc_start: 0.8639 (t0) cc_final: 0.8374 (t0) REVERT: x 98 GLN cc_start: 0.8405 (tt0) cc_final: 0.8049 (tt0) REVERT: x 105 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7863 (mp0) REVERT: x 122 ASN cc_start: 0.8787 (m-40) cc_final: 0.8296 (m-40) REVERT: x 124 THR cc_start: 0.8986 (p) cc_final: 0.8495 (t) outliers start: 0 outliers final: 0 residues processed: 1488 average time/residue: 0.5194 time to fit residues: 1187.2052 Evaluate side-chains 1385 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1385 time to evaluate : 4.014 ------------------------------------------------------------------------------- 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: 3.9990 chunk 223 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 201 optimal weight: 8.9990 chunk 353 optimal weight: 0.0040 chunk 99 optimal weight: 7.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- 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** a 175 ASN b 98 GLN c 98 GLN ** c 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 175 ASN e 98 GLN ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 175 ASN f 98 GLN g 98 GLN ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 175 ASN g 217 HIS h 98 GLN h 217 HIS ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 162 HIS ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 162 HIS m 98 GLN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 162 HIS q 77 GLN q 175 ASN q 217 HIS r 162 HIS r 175 ASN s 217 HIS ** t 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 175 ASN u 217 HIS v 162 HIS v 175 ASN w 175 ASN x 162 HIS x 175 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 34776 Z= 0.380 Angle : 0.721 6.251 47184 Z= 0.363 Chirality : 0.047 0.159 5160 Planarity : 0.005 0.034 6120 Dihedral : 5.453 20.045 4704 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % 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: -2.84 (0.12), residues: 4176 helix: -0.90 (0.12), residues: 1944 sheet: -1.90 (0.30), residues: 240 loop : -2.96 (0.12), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP b 132 HIS 0.003 0.001 HIS i 162 PHE 0.018 0.003 PHE a 200 TYR 0.023 0.002 TYR v 73 ARG 0.009 0.001 ARG g 197 *********************** 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 1487 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1486 time to evaluate : 3.883 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: a 66 ASN cc_start: 0.8329 (t0) cc_final: 0.8003 (t0) REVERT: a 79 ASP cc_start: 0.8556 (m-30) cc_final: 0.8138 (m-30) REVERT: a 82 ASN cc_start: 0.8697 (t0) cc_final: 0.8211 (t0) REVERT: a 122 ASN cc_start: 0.8760 (m110) cc_final: 0.8429 (m110) REVERT: a 124 THR cc_start: 0.9071 (p) cc_final: 0.8816 (t) REVERT: a 134 MET cc_start: 0.8606 (ttt) cc_final: 0.8400 (ttt) REVERT: b 79 ASP cc_start: 0.8712 (m-30) cc_final: 0.8266 (m-30) REVERT: b 98 GLN cc_start: 0.8452 (tt0) cc_final: 0.8114 (tt0) REVERT: b 115 LEU cc_start: 0.9685 (tp) cc_final: 0.9417 (tp) REVERT: b 135 MET cc_start: 0.8723 (mmm) cc_final: 0.8289 (mmm) REVERT: b 188 ARG cc_start: 0.8309 (tpt90) cc_final: 0.7926 (tpt90) REVERT: c 66 ASN cc_start: 0.8279 (t0) cc_final: 0.8007 (t0) REVERT: c 79 ASP cc_start: 0.8574 (m-30) cc_final: 0.8218 (m-30) REVERT: c 82 ASN cc_start: 0.8706 (t0) cc_final: 0.8430 (t0) REVERT: c 122 ASN cc_start: 0.8706 (m110) cc_final: 0.8366 (m110) REVERT: c 124 THR cc_start: 0.9062 (p) cc_final: 0.8844 (t) REVERT: c 135 MET cc_start: 0.8751 (mmm) cc_final: 0.8457 (mmm) REVERT: c 160 MET cc_start: 0.8942 (mmt) cc_final: 0.8688 (mmt) REVERT: c 198 TYR cc_start: 0.9097 (m-10) cc_final: 0.8848 (m-10) REVERT: d 66 ASN cc_start: 0.8038 (t0) cc_final: 0.7589 (t0) REVERT: d 79 ASP cc_start: 0.8759 (m-30) cc_final: 0.8338 (m-30) REVERT: d 98 GLN cc_start: 0.8777 (tt0) cc_final: 0.7783 (tt0) REVERT: d 115 LEU cc_start: 0.9707 (tp) cc_final: 0.9490 (tp) REVERT: d 124 THR cc_start: 0.8864 (p) cc_final: 0.8591 (t) REVERT: d 135 MET cc_start: 0.8685 (mmm) cc_final: 0.8046 (mmm) REVERT: d 188 ARG cc_start: 0.8539 (mmm160) cc_final: 0.8338 (tpt90) REVERT: d 198 TYR cc_start: 0.9026 (m-10) cc_final: 0.8769 (m-10) REVERT: e 66 ASN cc_start: 0.8268 (t0) cc_final: 0.7976 (t0) REVERT: e 79 ASP cc_start: 0.8542 (m-30) cc_final: 0.8029 (m-30) REVERT: e 82 ASN cc_start: 0.8700 (t0) cc_final: 0.8176 (t0) REVERT: e 122 ASN cc_start: 0.8783 (m110) cc_final: 0.8450 (m110) REVERT: e 124 THR cc_start: 0.9062 (p) cc_final: 0.8837 (t) REVERT: e 134 MET cc_start: 0.8602 (ttt) cc_final: 0.8401 (ttt) REVERT: e 160 MET cc_start: 0.9297 (mmm) cc_final: 0.8961 (tpp) REVERT: f 79 ASP cc_start: 0.8717 (m-30) cc_final: 0.8264 (m-30) REVERT: f 98 GLN cc_start: 0.8480 (tt0) cc_final: 0.8130 (tt0) REVERT: f 115 LEU cc_start: 0.9678 (tp) cc_final: 0.9442 (tp) REVERT: f 188 ARG cc_start: 0.8320 (tpt90) cc_final: 0.7919 (tpt90) REVERT: g 66 ASN cc_start: 0.8324 (t0) cc_final: 0.8006 (t0) REVERT: g 82 ASN cc_start: 0.8713 (t0) cc_final: 0.8163 (t0) REVERT: g 122 ASN cc_start: 0.8806 (m110) cc_final: 0.8451 (m110) REVERT: g 124 THR cc_start: 0.9034 (p) cc_final: 0.8809 (t) REVERT: g 160 MET cc_start: 0.9288 (mmm) cc_final: 0.8940 (tpp) REVERT: g 197 ARG cc_start: 0.8420 (ttt90) cc_final: 0.7336 (ttt90) REVERT: h 79 ASP cc_start: 0.8711 (m-30) cc_final: 0.8284 (m-30) REVERT: h 98 GLN cc_start: 0.8449 (tt0) cc_final: 0.8117 (tt0) REVERT: h 115 LEU cc_start: 0.9675 (tp) cc_final: 0.9431 (tp) REVERT: h 124 THR cc_start: 0.8798 (p) cc_final: 0.8513 (t) REVERT: h 135 MET cc_start: 0.8614 (mmm) cc_final: 0.8146 (mmm) REVERT: h 188 ARG cc_start: 0.8571 (mmm160) cc_final: 0.8321 (tpt90) REVERT: h 197 ARG cc_start: 0.8496 (ttt90) cc_final: 0.8125 (ttt90) REVERT: i 66 ASN cc_start: 0.7941 (t0) cc_final: 0.7697 (t0) REVERT: i 67 LEU cc_start: 0.8565 (mm) cc_final: 0.8310 (mm) REVERT: i 68 GLU cc_start: 0.8461 (mp0) cc_final: 0.7824 (tm-30) REVERT: i 135 MET cc_start: 0.8628 (mmm) cc_final: 0.8352 (mmm) REVERT: i 143 TYR cc_start: 0.9074 (m-80) cc_final: 0.8510 (m-80) REVERT: i 172 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7728 (mm-30) REVERT: j 66 ASN cc_start: 0.8204 (t0) cc_final: 0.7706 (t0) REVERT: j 67 LEU cc_start: 0.8684 (mm) cc_final: 0.8449 (mm) REVERT: j 115 LEU cc_start: 0.9668 (tp) cc_final: 0.9342 (tp) REVERT: j 122 ASN cc_start: 0.8671 (m110) cc_final: 0.8436 (m110) REVERT: j 135 MET cc_start: 0.8666 (mmm) cc_final: 0.8361 (mmm) REVERT: k 66 ASN cc_start: 0.7919 (t0) cc_final: 0.7631 (t0) REVERT: k 67 LEU cc_start: 0.8549 (mm) cc_final: 0.8300 (mm) REVERT: k 135 MET cc_start: 0.8723 (mmm) cc_final: 0.8374 (mmm) REVERT: k 143 TYR cc_start: 0.9046 (m-80) cc_final: 0.8492 (m-80) REVERT: k 172 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7767 (mm-30) REVERT: l 66 ASN cc_start: 0.8207 (t0) cc_final: 0.7680 (t0) REVERT: l 67 LEU cc_start: 0.8669 (mm) cc_final: 0.8441 (mm) REVERT: l 105 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8016 (mp0) REVERT: l 122 ASN cc_start: 0.8699 (m110) cc_final: 0.8435 (m110) REVERT: l 135 MET cc_start: 0.8707 (mmm) cc_final: 0.8416 (mmm) REVERT: m 66 ASN cc_start: 0.7978 (t0) cc_final: 0.7622 (t0) REVERT: m 67 LEU cc_start: 0.8563 (mm) cc_final: 0.8318 (mm) REVERT: m 98 GLN cc_start: 0.8355 (tt0) cc_final: 0.7848 (tt0) REVERT: m 124 THR cc_start: 0.8989 (p) cc_final: 0.8355 (t) REVERT: m 143 TYR cc_start: 0.9057 (m-80) cc_final: 0.8499 (m-80) REVERT: m 172 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7700 (mm-30) REVERT: n 66 ASN cc_start: 0.8216 (t0) cc_final: 0.7728 (t0) REVERT: n 67 LEU cc_start: 0.8685 (mm) cc_final: 0.8452 (mm) REVERT: n 105 GLU cc_start: 0.8217 (mm-30) cc_final: 0.8012 (mp0) REVERT: n 122 ASN cc_start: 0.8692 (m110) cc_final: 0.8430 (m110) REVERT: n 135 MET cc_start: 0.8716 (mmm) cc_final: 0.8407 (mmm) REVERT: o 66 ASN cc_start: 0.7969 (t0) cc_final: 0.7681 (t0) REVERT: o 67 LEU cc_start: 0.8564 (mm) cc_final: 0.8339 (mm) REVERT: o 68 GLU cc_start: 0.8474 (mp0) cc_final: 0.7810 (tm-30) REVERT: o 135 MET cc_start: 0.8720 (mmm) cc_final: 0.8366 (mmm) REVERT: o 143 TYR cc_start: 0.9063 (m-80) cc_final: 0.8589 (m-80) REVERT: o 172 GLU cc_start: 0.8533 (mt-10) cc_final: 0.7759 (mm-30) REVERT: p 66 ASN cc_start: 0.8212 (t0) cc_final: 0.7713 (t0) REVERT: p 67 LEU cc_start: 0.8690 (mm) cc_final: 0.8449 (mm) REVERT: p 112 MET cc_start: 0.9322 (mmt) cc_final: 0.9108 (mmt) REVERT: p 115 LEU cc_start: 0.9707 (tp) cc_final: 0.9355 (tp) REVERT: q 56 MET cc_start: 0.8680 (mmm) cc_final: 0.8145 (mtt) REVERT: q 58 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7995 (mtmm) REVERT: q 66 ASN cc_start: 0.7777 (t0) cc_final: 0.7393 (t0) REVERT: q 67 LEU cc_start: 0.8577 (mm) cc_final: 0.8342 (mm) REVERT: q 82 ASN cc_start: 0.8766 (t0) cc_final: 0.8293 (t0) REVERT: q 108 MET cc_start: 0.8540 (tpp) cc_final: 0.7979 (tpp) REVERT: q 124 THR cc_start: 0.8931 (p) cc_final: 0.8335 (t) REVERT: r 54 MET cc_start: 0.8677 (tmm) cc_final: 0.8007 (ttp) REVERT: r 56 MET cc_start: 0.8485 (mtt) cc_final: 0.8004 (mtt) REVERT: r 67 LEU cc_start: 0.8445 (mm) cc_final: 0.8206 (mm) REVERT: r 82 ASN cc_start: 0.8965 (t0) cc_final: 0.8599 (t0) REVERT: r 98 GLN cc_start: 0.8620 (tt0) cc_final: 0.8263 (tt0) REVERT: r 124 THR cc_start: 0.9005 (p) cc_final: 0.8478 (t) REVERT: r 135 MET cc_start: 0.8781 (mmm) cc_final: 0.8575 (mmm) REVERT: r 197 ARG cc_start: 0.8584 (ttt90) cc_final: 0.7989 (ttt90) REVERT: s 56 MET cc_start: 0.8643 (mmm) cc_final: 0.8098 (mtt) REVERT: s 58 LYS cc_start: 0.8289 (mtmm) cc_final: 0.8013 (mtmm) REVERT: s 66 ASN cc_start: 0.7725 (t0) cc_final: 0.7320 (t0) REVERT: s 67 LEU cc_start: 0.8574 (mm) cc_final: 0.8328 (mm) REVERT: s 82 ASN cc_start: 0.8700 (t0) cc_final: 0.8200 (t0) REVERT: s 95 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7802 (mm-30) REVERT: s 108 MET cc_start: 0.8469 (tpp) cc_final: 0.7830 (tpp) REVERT: s 124 THR cc_start: 0.8916 (p) cc_final: 0.8317 (t) REVERT: s 135 MET cc_start: 0.8812 (mmm) cc_final: 0.8537 (mmm) REVERT: t 54 MET cc_start: 0.8678 (tmm) cc_final: 0.7990 (ttp) REVERT: t 56 MET cc_start: 0.8519 (mtt) cc_final: 0.8115 (mtt) REVERT: t 67 LEU cc_start: 0.8538 (mm) cc_final: 0.8318 (mm) REVERT: t 82 ASN cc_start: 0.8954 (t0) cc_final: 0.8634 (t0) REVERT: t 107 GLU cc_start: 0.7951 (pt0) cc_final: 0.6823 (tm-30) REVERT: t 115 LEU cc_start: 0.9665 (tp) cc_final: 0.9446 (tp) REVERT: t 124 THR cc_start: 0.9032 (p) cc_final: 0.8517 (t) REVERT: t 135 MET cc_start: 0.8767 (mmm) cc_final: 0.8360 (mmm) REVERT: t 197 ARG cc_start: 0.8599 (ttt90) cc_final: 0.8044 (ttt90) REVERT: u 56 MET cc_start: 0.8682 (mmm) cc_final: 0.8105 (mtt) REVERT: u 58 LYS cc_start: 0.8324 (mtmm) cc_final: 0.8051 (mtmm) REVERT: u 66 ASN cc_start: 0.7747 (t0) cc_final: 0.7407 (t0) REVERT: u 67 LEU cc_start: 0.8598 (mm) cc_final: 0.8228 (mm) REVERT: u 107 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7776 (pt0) REVERT: u 108 MET cc_start: 0.8535 (tpp) cc_final: 0.7965 (tpp) REVERT: u 124 THR cc_start: 0.8940 (p) cc_final: 0.8296 (t) REVERT: v 67 LEU cc_start: 0.8553 (mm) cc_final: 0.8303 (mm) REVERT: v 82 ASN cc_start: 0.8919 (t0) cc_final: 0.8552 (t0) REVERT: v 108 MET cc_start: 0.8793 (tpt) cc_final: 0.8444 (tpp) REVERT: v 124 THR cc_start: 0.9020 (p) cc_final: 0.8486 (t) REVERT: v 135 MET cc_start: 0.8587 (mmm) cc_final: 0.8239 (mmm) REVERT: v 197 ARG cc_start: 0.8569 (ttt90) cc_final: 0.7956 (ttt90) REVERT: w 58 LYS cc_start: 0.8302 (mtmm) cc_final: 0.8016 (mtmm) REVERT: w 66 ASN cc_start: 0.7765 (t0) cc_final: 0.7356 (t0) REVERT: w 79 ASP cc_start: 0.8437 (m-30) cc_final: 0.8212 (m-30) REVERT: w 82 ASN cc_start: 0.8744 (t0) cc_final: 0.8275 (t0) REVERT: w 95 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7777 (mm-30) REVERT: w 108 MET cc_start: 0.8488 (tpp) cc_final: 0.7844 (tpp) REVERT: w 124 THR cc_start: 0.8951 (p) cc_final: 0.8326 (t) REVERT: w 135 MET cc_start: 0.8986 (mmm) cc_final: 0.8525 (mmm) REVERT: x 79 ASP cc_start: 0.8461 (m-30) cc_final: 0.8166 (m-30) REVERT: x 82 ASN cc_start: 0.8952 (t0) cc_final: 0.8574 (t0) REVERT: x 115 LEU cc_start: 0.9639 (tp) cc_final: 0.9410 (tp) REVERT: x 122 ASN cc_start: 0.8935 (m-40) cc_final: 0.8714 (m-40) REVERT: x 124 THR cc_start: 0.9009 (p) cc_final: 0.8491 (t) REVERT: x 197 ARG cc_start: 0.8578 (ttt90) cc_final: 0.8022 (ttt90) outliers start: 1 outliers final: 0 residues processed: 1487 average time/residue: 0.4887 time to fit residues: 1139.7582 Evaluate side-chains 1400 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1400 time to evaluate : 3.621 ------------------------------------------------------------------------------- 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: 0.0170 chunk 77 optimal weight: 3.9990 chunk 231 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 394 optimal weight: 0.0030 chunk 327 optimal weight: 0.3980 chunk 182 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 overall best weight: 0.3028 ------------------------------------------------------------------------------- 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 b 175 ASN c 98 GLN c 122 ASN e 98 GLN e 122 ASN e 175 ASN f 175 ASN g 98 GLN g 122 ASN g 175 ASN h 175 ASN i 175 ASN ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 175 ASN k 175 ASN ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 175 ASN m 175 ASN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 175 ASN o 175 ASN p 175 ASN q 77 GLN ** t 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 175 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 34776 Z= 0.156 Angle : 0.602 6.983 47184 Z= 0.304 Chirality : 0.041 0.172 5160 Planarity : 0.004 0.035 6120 Dihedral : 4.829 16.949 4704 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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 (0.13), residues: 4176 helix: -0.81 (0.12), residues: 2088 sheet: -1.57 (0.31), residues: 240 loop : -2.94 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP j 132 HIS 0.001 0.000 HIS l 162 PHE 0.012 0.002 PHE m 202 TYR 0.022 0.002 TYR x 198 ARG 0.007 0.001 ARG c 197 *********************** 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 1464 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1464 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 68 GLU cc_start: 0.8447 (mp0) cc_final: 0.8080 (tm-30) REVERT: a 79 ASP cc_start: 0.8436 (m-30) cc_final: 0.8126 (m-30) REVERT: a 82 ASN cc_start: 0.8488 (t0) cc_final: 0.7780 (t0) REVERT: a 122 ASN cc_start: 0.8823 (m-40) cc_final: 0.8462 (m-40) REVERT: b 79 ASP cc_start: 0.8615 (m-30) cc_final: 0.8212 (m-30) REVERT: b 135 MET cc_start: 0.8566 (mmm) cc_final: 0.8037 (mmm) REVERT: b 136 ASP cc_start: 0.7816 (t70) cc_final: 0.7533 (t70) REVERT: b 197 ARG cc_start: 0.8367 (ttt90) cc_final: 0.6886 (ttt90) REVERT: c 66 ASN cc_start: 0.8235 (t0) cc_final: 0.7985 (t0) REVERT: c 68 GLU cc_start: 0.8404 (mp0) cc_final: 0.8128 (tm-30) REVERT: c 79 ASP cc_start: 0.8619 (m-30) cc_final: 0.8218 (m-30) REVERT: c 82 ASN cc_start: 0.8397 (t0) cc_final: 0.8023 (t0) REVERT: c 105 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8032 (mp0) REVERT: c 122 ASN cc_start: 0.8700 (m-40) cc_final: 0.8346 (m-40) REVERT: c 135 MET cc_start: 0.8682 (mmm) cc_final: 0.8391 (mmm) REVERT: d 66 ASN cc_start: 0.8019 (t0) cc_final: 0.7487 (t0) REVERT: d 79 ASP cc_start: 0.8648 (m-30) cc_final: 0.8270 (m-30) REVERT: d 98 GLN cc_start: 0.8507 (tt0) cc_final: 0.8072 (tt0) REVERT: d 112 MET cc_start: 0.9423 (mmp) cc_final: 0.9189 (mmt) REVERT: d 124 THR cc_start: 0.8831 (p) cc_final: 0.8608 (t) REVERT: d 135 MET cc_start: 0.8461 (mmm) cc_final: 0.7877 (mmm) REVERT: d 197 ARG cc_start: 0.8426 (ttt90) cc_final: 0.8150 (ttt90) REVERT: e 68 GLU cc_start: 0.8463 (mp0) cc_final: 0.8098 (tm-30) REVERT: e 79 ASP cc_start: 0.8476 (m-30) cc_final: 0.8008 (m-30) REVERT: e 82 ASN cc_start: 0.8489 (t0) cc_final: 0.7755 (t0) REVERT: e 122 ASN cc_start: 0.8784 (m-40) cc_final: 0.8462 (m-40) REVERT: f 79 ASP cc_start: 0.8612 (m-30) cc_final: 0.8241 (m-30) REVERT: f 197 ARG cc_start: 0.8336 (ttt90) cc_final: 0.6860 (ttt90) REVERT: g 68 GLU cc_start: 0.8461 (mp0) cc_final: 0.8118 (tm-30) REVERT: g 79 ASP cc_start: 0.8536 (m-30) cc_final: 0.8291 (m-30) REVERT: g 82 ASN cc_start: 0.8543 (t0) cc_final: 0.7782 (t0) REVERT: g 122 ASN cc_start: 0.8788 (m-40) cc_final: 0.8460 (m-40) REVERT: g 172 GLU cc_start: 0.7185 (tt0) cc_final: 0.6945 (tt0) REVERT: g 181 MET cc_start: 0.8146 (tpt) cc_final: 0.7714 (tmm) REVERT: g 197 ARG cc_start: 0.7927 (ttt90) cc_final: 0.6882 (ttt90) REVERT: h 79 ASP cc_start: 0.8608 (m-30) cc_final: 0.8221 (m-30) REVERT: h 135 MET cc_start: 0.8321 (mmm) cc_final: 0.7937 (mmm) REVERT: h 197 ARG cc_start: 0.8314 (ttt90) cc_final: 0.8061 (ttt90) REVERT: i 66 ASN cc_start: 0.7811 (t0) cc_final: 0.7587 (t0) REVERT: i 68 GLU cc_start: 0.8499 (mp0) cc_final: 0.7726 (tm-30) REVERT: i 82 ASN cc_start: 0.8259 (t0) cc_final: 0.7484 (t0) REVERT: i 95 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7639 (mm-30) REVERT: i 98 GLN cc_start: 0.8004 (tt0) cc_final: 0.7790 (tt0) REVERT: i 124 THR cc_start: 0.8779 (p) cc_final: 0.8378 (t) REVERT: i 135 MET cc_start: 0.8518 (mmm) cc_final: 0.8271 (mmm) REVERT: i 143 TYR cc_start: 0.8772 (m-80) cc_final: 0.8306 (m-80) REVERT: i 172 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7818 (mm-30) REVERT: j 66 ASN cc_start: 0.8115 (t0) cc_final: 0.7699 (t0) REVERT: j 135 MET cc_start: 0.8457 (mmm) cc_final: 0.8253 (mmm) REVERT: k 68 GLU cc_start: 0.8477 (mp0) cc_final: 0.7748 (tm-30) REVERT: k 95 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7580 (mm-30) REVERT: k 98 GLN cc_start: 0.8012 (tt0) cc_final: 0.7772 (tt0) REVERT: k 124 THR cc_start: 0.8787 (p) cc_final: 0.8367 (t) REVERT: k 135 MET cc_start: 0.8649 (mmm) cc_final: 0.8374 (mmm) REVERT: k 172 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7845 (mm-30) REVERT: k 188 ARG cc_start: 0.8552 (mmm160) cc_final: 0.8277 (tpt90) REVERT: l 66 ASN cc_start: 0.8138 (t0) cc_final: 0.7673 (t0) REVERT: l 98 GLN cc_start: 0.8470 (tt0) cc_final: 0.7701 (tt0) REVERT: l 197 ARG cc_start: 0.8541 (tmm-80) cc_final: 0.7472 (tmm-80) REVERT: l 198 TYR cc_start: 0.8670 (m-10) cc_final: 0.8359 (m-10) REVERT: m 66 ASN cc_start: 0.7857 (t0) cc_final: 0.7570 (t0) REVERT: m 95 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7638 (mm-30) REVERT: m 172 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7798 (mm-30) REVERT: n 66 ASN cc_start: 0.8088 (t0) cc_final: 0.7642 (t0) REVERT: n 98 GLN cc_start: 0.8482 (tt0) cc_final: 0.7707 (tt0) REVERT: n 197 ARG cc_start: 0.8538 (tmm-80) cc_final: 0.7489 (tmm-80) REVERT: n 198 TYR cc_start: 0.8695 (m-10) cc_final: 0.8338 (m-10) REVERT: o 66 ASN cc_start: 0.7820 (t0) cc_final: 0.7600 (t0) REVERT: o 68 GLU cc_start: 0.8490 (mp0) cc_final: 0.7697 (tm-30) REVERT: o 95 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7547 (mm-30) REVERT: o 98 GLN cc_start: 0.8038 (tt0) cc_final: 0.7756 (tt0) REVERT: o 124 THR cc_start: 0.8800 (p) cc_final: 0.8377 (t) REVERT: o 134 MET cc_start: 0.8725 (ttt) cc_final: 0.8460 (ttt) REVERT: o 135 MET cc_start: 0.8638 (mmm) cc_final: 0.8406 (mmm) REVERT: o 172 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7855 (mm-30) REVERT: o 188 ARG cc_start: 0.8546 (mmm160) cc_final: 0.8264 (tpt90) REVERT: p 66 ASN cc_start: 0.8123 (t0) cc_final: 0.7687 (t0) REVERT: p 112 MET cc_start: 0.9163 (mmt) cc_final: 0.8895 (mmt) REVERT: p 135 MET cc_start: 0.8138 (mmm) cc_final: 0.7887 (mmm) REVERT: p 197 ARG cc_start: 0.8566 (tmm-80) cc_final: 0.7450 (tmm-80) REVERT: p 198 TYR cc_start: 0.8698 (m-10) cc_final: 0.8388 (m-10) REVERT: q 56 MET cc_start: 0.8511 (mmm) cc_final: 0.7970 (mtt) REVERT: q 66 ASN cc_start: 0.7791 (t0) cc_final: 0.7466 (t0) REVERT: q 67 LEU cc_start: 0.8545 (mm) cc_final: 0.8068 (mm) REVERT: q 82 ASN cc_start: 0.8645 (t0) cc_final: 0.8167 (t0) REVERT: q 108 MET cc_start: 0.8351 (tpp) cc_final: 0.7989 (tpp) REVERT: q 124 THR cc_start: 0.8921 (p) cc_final: 0.8373 (t) REVERT: q 172 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7701 (mm-30) REVERT: r 82 ASN cc_start: 0.8707 (t0) cc_final: 0.8316 (t0) REVERT: r 107 GLU cc_start: 0.7702 (pt0) cc_final: 0.6395 (tm-30) REVERT: r 124 THR cc_start: 0.8966 (p) cc_final: 0.8468 (t) REVERT: r 197 ARG cc_start: 0.8410 (ttt90) cc_final: 0.7765 (ttt90) REVERT: r 215 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7440 (tm-30) REVERT: s 56 MET cc_start: 0.8521 (mmm) cc_final: 0.7928 (mtt) REVERT: s 66 ASN cc_start: 0.7778 (t0) cc_final: 0.7449 (t0) REVERT: s 67 LEU cc_start: 0.8548 (mm) cc_final: 0.8074 (mm) REVERT: s 103 ILE cc_start: 0.9294 (mm) cc_final: 0.8725 (mm) REVERT: s 107 GLU cc_start: 0.7813 (pt0) cc_final: 0.6486 (tm-30) REVERT: s 108 MET cc_start: 0.8399 (tpp) cc_final: 0.8057 (tpp) REVERT: s 124 THR cc_start: 0.8919 (p) cc_final: 0.8342 (t) REVERT: s 135 MET cc_start: 0.8731 (mmm) cc_final: 0.8530 (mmm) REVERT: s 172 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7708 (mm-30) REVERT: s 212 ARG cc_start: 0.7259 (ptt-90) cc_final: 0.6333 (tpm170) REVERT: t 82 ASN cc_start: 0.8717 (t0) cc_final: 0.8310 (t0) REVERT: t 107 GLU cc_start: 0.7793 (pt0) cc_final: 0.6492 (tm-30) REVERT: t 124 THR cc_start: 0.8962 (p) cc_final: 0.8551 (t) REVERT: t 135 MET cc_start: 0.8794 (mmm) cc_final: 0.8274 (mmm) REVERT: t 197 ARG cc_start: 0.8337 (ttt90) cc_final: 0.7925 (ttt90) REVERT: t 215 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7431 (tm-30) REVERT: u 56 MET cc_start: 0.8474 (mmm) cc_final: 0.7956 (mtt) REVERT: u 66 ASN cc_start: 0.7749 (t0) cc_final: 0.7391 (t0) REVERT: u 67 LEU cc_start: 0.8445 (mm) cc_final: 0.8106 (mm) REVERT: u 107 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7662 (pt0) REVERT: u 108 MET cc_start: 0.8347 (tpp) cc_final: 0.8118 (tpp) REVERT: u 124 THR cc_start: 0.8900 (p) cc_final: 0.8327 (t) REVERT: u 172 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7738 (mm-30) REVERT: u 212 ARG cc_start: 0.7246 (ptt-90) cc_final: 0.6387 (tpm170) REVERT: v 82 ASN cc_start: 0.8782 (t0) cc_final: 0.8459 (t0) REVERT: v 107 GLU cc_start: 0.7738 (pt0) cc_final: 0.6453 (tm-30) REVERT: v 124 THR cc_start: 0.8982 (p) cc_final: 0.8503 (t) REVERT: v 135 MET cc_start: 0.8581 (mmm) cc_final: 0.8267 (mmm) REVERT: v 197 ARG cc_start: 0.8371 (ttt90) cc_final: 0.7719 (ttt90) REVERT: v 215 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7453 (tm-30) REVERT: w 66 ASN cc_start: 0.7696 (t0) cc_final: 0.7367 (t0) REVERT: w 79 ASP cc_start: 0.8268 (m-30) cc_final: 0.7934 (m-30) REVERT: w 103 ILE cc_start: 0.9291 (mm) cc_final: 0.8712 (mm) REVERT: w 107 GLU cc_start: 0.7819 (pt0) cc_final: 0.6499 (tm-30) REVERT: w 108 MET cc_start: 0.8370 (tpp) cc_final: 0.8068 (tpp) REVERT: w 124 THR cc_start: 0.8910 (p) cc_final: 0.8336 (t) REVERT: w 135 MET cc_start: 0.8828 (mmm) cc_final: 0.8449 (mmm) REVERT: w 197 ARG cc_start: 0.8558 (tmm-80) cc_final: 0.7526 (ttp-110) REVERT: w 198 TYR cc_start: 0.8987 (m-10) cc_final: 0.8652 (m-10) REVERT: x 79 ASP cc_start: 0.8339 (m-30) cc_final: 0.7996 (m-30) REVERT: x 82 ASN cc_start: 0.8769 (t0) cc_final: 0.8408 (t0) REVERT: x 107 GLU cc_start: 0.7770 (pt0) cc_final: 0.6393 (tm-30) REVERT: x 122 ASN cc_start: 0.8830 (m-40) cc_final: 0.8469 (m-40) REVERT: x 124 THR cc_start: 0.8946 (p) cc_final: 0.8466 (t) REVERT: x 197 ARG cc_start: 0.8378 (ttt90) cc_final: 0.7970 (ttt90) REVERT: x 215 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7451 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1464 average time/residue: 0.4800 time to fit residues: 1087.6131 Evaluate side-chains 1336 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1336 time to evaluate : 3.788 ------------------------------------------------------------------------------- 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: 5.9990 chunk 44 optimal weight: 0.4980 chunk 224 optimal weight: 0.9980 chunk 288 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 393 optimal weight: 0.6980 chunk 246 optimal weight: 9.9990 chunk 239 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 98 GLN a 217 HIS c 98 GLN ** c 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 217 HIS e 98 GLN e 175 ASN e 217 HIS g 98 GLN ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 175 ASN r 175 ASN s 175 ASN u 175 ASN v 175 ASN x 175 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34776 Z= 0.169 Angle : 0.596 6.373 47184 Z= 0.300 Chirality : 0.042 0.195 5160 Planarity : 0.004 0.032 6120 Dihedral : 4.704 17.666 4704 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -2.41 (0.13), residues: 4176 helix: -0.57 (0.12), residues: 2088 sheet: -1.41 (0.31), residues: 240 loop : -2.90 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 132 HIS 0.003 0.000 HIS o 162 PHE 0.011 0.002 PHE s 202 TYR 0.020 0.001 TYR a 198 ARG 0.005 0.000 ARG b 212 *********************** 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 1443 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1443 time to evaluate : 3.907 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: a 66 ASN cc_start: 0.8265 (t0) cc_final: 0.7997 (t0) REVERT: a 79 ASP cc_start: 0.8514 (m-30) cc_final: 0.8066 (m-30) REVERT: a 82 ASN cc_start: 0.8627 (t0) cc_final: 0.8130 (t0) REVERT: a 112 MET cc_start: 0.9269 (mmt) cc_final: 0.8926 (mmt) REVERT: a 115 LEU cc_start: 0.9462 (tp) cc_final: 0.9167 (tp) REVERT: b 79 ASP cc_start: 0.8613 (m-30) cc_final: 0.8273 (m-30) REVERT: b 95 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7462 (mm-30) REVERT: b 135 MET cc_start: 0.8612 (mmm) cc_final: 0.8065 (mmm) REVERT: c 66 ASN cc_start: 0.8231 (t0) cc_final: 0.7958 (t0) REVERT: c 68 GLU cc_start: 0.8439 (mp0) cc_final: 0.8045 (tm-30) REVERT: c 79 ASP cc_start: 0.8591 (m-30) cc_final: 0.8224 (m-30) REVERT: c 82 ASN cc_start: 0.8490 (t0) cc_final: 0.8196 (t0) REVERT: c 134 MET cc_start: 0.8835 (ttt) cc_final: 0.8582 (tmm) REVERT: d 66 ASN cc_start: 0.8003 (t0) cc_final: 0.7552 (t0) REVERT: d 79 ASP cc_start: 0.8714 (m-30) cc_final: 0.8433 (m-30) REVERT: d 105 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8121 (mp0) REVERT: d 124 THR cc_start: 0.8846 (p) cc_final: 0.8627 (t) REVERT: d 135 MET cc_start: 0.8413 (mmm) cc_final: 0.8049 (mmm) REVERT: e 68 GLU cc_start: 0.8458 (mp0) cc_final: 0.8004 (tm-30) REVERT: e 79 ASP cc_start: 0.8671 (m-30) cc_final: 0.8124 (m-30) REVERT: e 82 ASN cc_start: 0.8456 (t0) cc_final: 0.7731 (t0) REVERT: f 79 ASP cc_start: 0.8653 (m-30) cc_final: 0.8303 (m-30) REVERT: f 95 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7482 (mm-30) REVERT: f 136 ASP cc_start: 0.7659 (t70) cc_final: 0.7328 (t70) REVERT: g 66 ASN cc_start: 0.8266 (t0) cc_final: 0.7996 (t0) REVERT: g 68 GLU cc_start: 0.8449 (mp0) cc_final: 0.8065 (tm-30) REVERT: g 79 ASP cc_start: 0.8602 (m-30) cc_final: 0.8314 (m-30) REVERT: g 82 ASN cc_start: 0.8455 (t0) cc_final: 0.7772 (t0) REVERT: g 181 MET cc_start: 0.8201 (tpt) cc_final: 0.7712 (tmm) REVERT: h 79 ASP cc_start: 0.8644 (m-30) cc_final: 0.8258 (m-30) REVERT: h 95 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7535 (mm-30) REVERT: h 98 GLN cc_start: 0.8285 (tt0) cc_final: 0.8069 (tt0) REVERT: h 135 MET cc_start: 0.8310 (mmm) cc_final: 0.7715 (mmm) REVERT: h 157 ARG cc_start: 0.8461 (ttm110) cc_final: 0.8184 (ttm110) REVERT: i 66 ASN cc_start: 0.7863 (t0) cc_final: 0.7657 (t0) REVERT: i 68 GLU cc_start: 0.8514 (mp0) cc_final: 0.7741 (tm-30) REVERT: i 82 ASN cc_start: 0.8218 (t0) cc_final: 0.7448 (t0) REVERT: i 95 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7651 (mm-30) REVERT: i 98 GLN cc_start: 0.7973 (tt0) cc_final: 0.7692 (tt0) REVERT: i 124 THR cc_start: 0.8803 (p) cc_final: 0.8359 (t) REVERT: i 143 TYR cc_start: 0.8813 (m-80) cc_final: 0.8292 (m-80) REVERT: i 172 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7813 (mm-30) REVERT: j 66 ASN cc_start: 0.8087 (t0) cc_final: 0.7587 (t0) REVERT: k 95 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7613 (mm-30) REVERT: k 98 GLN cc_start: 0.7990 (tt0) cc_final: 0.7673 (tt0) REVERT: k 135 MET cc_start: 0.8599 (mmm) cc_final: 0.8273 (mmm) REVERT: k 172 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7804 (mm-30) REVERT: k 188 ARG cc_start: 0.8624 (mmm160) cc_final: 0.8246 (tpt90) REVERT: l 58 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7947 (mtmm) REVERT: l 66 ASN cc_start: 0.8081 (t0) cc_final: 0.7575 (t0) REVERT: l 95 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7858 (mm-30) REVERT: l 98 GLN cc_start: 0.8458 (tt0) cc_final: 0.7754 (tt0) REVERT: l 197 ARG cc_start: 0.8514 (tmm-80) cc_final: 0.7496 (tmm-80) REVERT: l 198 TYR cc_start: 0.8726 (m-10) cc_final: 0.8356 (m-10) REVERT: m 66 ASN cc_start: 0.7900 (t0) cc_final: 0.7651 (t0) REVERT: m 95 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7662 (mm-30) REVERT: m 124 THR cc_start: 0.8812 (p) cc_final: 0.8422 (t) REVERT: m 172 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7782 (mm-30) REVERT: n 66 ASN cc_start: 0.8056 (t0) cc_final: 0.7661 (t0) REVERT: n 98 GLN cc_start: 0.8469 (tt0) cc_final: 0.7829 (tt0) REVERT: n 135 MET cc_start: 0.8509 (mmm) cc_final: 0.8299 (mmm) REVERT: n 197 ARG cc_start: 0.8530 (tmm-80) cc_final: 0.7512 (tmm-80) REVERT: n 198 TYR cc_start: 0.8713 (m-10) cc_final: 0.8368 (m-10) REVERT: o 68 GLU cc_start: 0.8504 (mp0) cc_final: 0.7720 (tm-30) REVERT: o 95 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7588 (mm-30) REVERT: o 98 GLN cc_start: 0.7972 (tt0) cc_final: 0.7660 (tt0) REVERT: o 134 MET cc_start: 0.8690 (ttt) cc_final: 0.8424 (ttt) REVERT: o 135 MET cc_start: 0.8682 (mmm) cc_final: 0.8385 (mmm) REVERT: o 172 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7783 (mm-30) REVERT: p 66 ASN cc_start: 0.8096 (t0) cc_final: 0.7588 (t0) REVERT: p 197 ARG cc_start: 0.8534 (tmm-80) cc_final: 0.7431 (tmm-80) REVERT: p 198 TYR cc_start: 0.8723 (m-10) cc_final: 0.8359 (m-10) REVERT: q 56 MET cc_start: 0.8493 (mmm) cc_final: 0.7775 (mtt) REVERT: q 66 ASN cc_start: 0.7868 (t0) cc_final: 0.7450 (t0) REVERT: q 67 LEU cc_start: 0.8417 (mm) cc_final: 0.8193 (mm) REVERT: q 108 MET cc_start: 0.8464 (tpp) cc_final: 0.8058 (tpp) REVERT: q 124 THR cc_start: 0.8944 (p) cc_final: 0.8386 (t) REVERT: q 172 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7825 (mm-30) REVERT: r 82 ASN cc_start: 0.8797 (t0) cc_final: 0.8338 (t0) REVERT: r 95 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7771 (mm-30) REVERT: r 107 GLU cc_start: 0.7620 (pt0) cc_final: 0.6396 (tm-30) REVERT: r 108 MET cc_start: 0.8387 (tpp) cc_final: 0.7903 (tpp) REVERT: r 124 THR cc_start: 0.8979 (p) cc_final: 0.8542 (t) REVERT: r 215 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7419 (tm-30) REVERT: s 56 MET cc_start: 0.8517 (mmm) cc_final: 0.7775 (mtt) REVERT: s 66 ASN cc_start: 0.7809 (t0) cc_final: 0.7397 (t0) REVERT: s 67 LEU cc_start: 0.8451 (mm) cc_final: 0.8202 (mm) REVERT: s 103 ILE cc_start: 0.9298 (mm) cc_final: 0.8708 (mm) REVERT: s 107 GLU cc_start: 0.7825 (pt0) cc_final: 0.6597 (tm-30) REVERT: s 108 MET cc_start: 0.8481 (tpp) cc_final: 0.8115 (tpp) REVERT: s 124 THR cc_start: 0.8930 (p) cc_final: 0.8370 (t) REVERT: s 135 MET cc_start: 0.8736 (mmm) cc_final: 0.8534 (mmm) REVERT: s 172 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7865 (mm-30) REVERT: t 79 ASP cc_start: 0.8395 (m-30) cc_final: 0.8151 (m-30) REVERT: t 82 ASN cc_start: 0.8820 (t0) cc_final: 0.8453 (t0) REVERT: t 103 ILE cc_start: 0.9085 (mm) cc_final: 0.8461 (mm) REVERT: t 107 GLU cc_start: 0.7783 (pt0) cc_final: 0.6406 (tm-30) REVERT: t 124 THR cc_start: 0.8971 (p) cc_final: 0.8622 (t) REVERT: t 129 ASN cc_start: 0.8811 (p0) cc_final: 0.8560 (p0) REVERT: t 135 MET cc_start: 0.8724 (mmm) cc_final: 0.8289 (mmm) REVERT: t 215 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7376 (tm-30) REVERT: u 56 MET cc_start: 0.8490 (mmm) cc_final: 0.7712 (mtt) REVERT: u 66 ASN cc_start: 0.7737 (t0) cc_final: 0.7350 (t0) REVERT: u 107 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7661 (pt0) REVERT: u 108 MET cc_start: 0.8506 (tpp) cc_final: 0.8133 (tpp) REVERT: u 124 THR cc_start: 0.8937 (p) cc_final: 0.8392 (t) REVERT: u 172 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7755 (mm-30) REVERT: u 181 MET cc_start: 0.8194 (tpt) cc_final: 0.7958 (tpt) REVERT: v 82 ASN cc_start: 0.8805 (t0) cc_final: 0.8415 (t0) REVERT: v 107 GLU cc_start: 0.7581 (pt0) cc_final: 0.6445 (tm-30) REVERT: v 108 MET cc_start: 0.8355 (tpp) cc_final: 0.7698 (tpp) REVERT: v 124 THR cc_start: 0.8993 (p) cc_final: 0.8545 (t) REVERT: v 135 MET cc_start: 0.8532 (mmm) cc_final: 0.8186 (mmm) REVERT: v 215 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7376 (tm-30) REVERT: w 56 MET cc_start: 0.8561 (mmm) cc_final: 0.8009 (mtt) REVERT: w 66 ASN cc_start: 0.7753 (t0) cc_final: 0.7453 (t0) REVERT: w 67 LEU cc_start: 0.8476 (mm) cc_final: 0.8190 (mm) REVERT: w 79 ASP cc_start: 0.8317 (m-30) cc_final: 0.8001 (m-30) REVERT: w 103 ILE cc_start: 0.9277 (mm) cc_final: 0.8701 (mm) REVERT: w 107 GLU cc_start: 0.7831 (pt0) cc_final: 0.6685 (tm-30) REVERT: w 108 MET cc_start: 0.8476 (tpp) cc_final: 0.8110 (tpp) REVERT: w 124 THR cc_start: 0.8926 (p) cc_final: 0.8347 (t) REVERT: w 135 MET cc_start: 0.8774 (mmm) cc_final: 0.8493 (mmm) REVERT: x 79 ASP cc_start: 0.8392 (m-30) cc_final: 0.8098 (m-30) REVERT: x 82 ASN cc_start: 0.8813 (t0) cc_final: 0.8376 (t0) REVERT: x 95 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7744 (mm-30) REVERT: x 107 GLU cc_start: 0.7586 (pt0) cc_final: 0.6376 (tm-30) REVERT: x 108 MET cc_start: 0.8370 (tpp) cc_final: 0.7895 (tpp) REVERT: x 122 ASN cc_start: 0.8731 (m-40) cc_final: 0.8504 (m-40) REVERT: x 124 THR cc_start: 0.8962 (p) cc_final: 0.8579 (t) REVERT: x 215 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7383 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1443 average time/residue: 0.4729 time to fit residues: 1071.0315 Evaluate side-chains 1330 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1330 time to evaluate : 3.760 ------------------------------------------------------------------------------- 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: 1.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 309 optimal weight: 0.0170 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 GLN e 98 GLN ** j 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 217 HIS ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 217 HIS m 98 GLN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 175 ASN x 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4822 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= 0.178 Angle : 0.607 7.024 47184 Z= 0.305 Chirality : 0.042 0.162 5160 Planarity : 0.005 0.044 6120 Dihedral : 4.691 18.079 4704 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.31 (0.13), residues: 4176 helix: -0.48 (0.12), residues: 2088 sheet: -1.41 (0.30), residues: 240 loop : -2.84 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP p 132 HIS 0.004 0.000 HIS m 162 PHE 0.011 0.002 PHE i 202 TYR 0.026 0.001 TYR v 73 ARG 0.008 0.000 ARG e 212 *********************** 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 1438 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1438 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 66 ASN cc_start: 0.8252 (t0) cc_final: 0.8034 (t0) REVERT: a 79 ASP cc_start: 0.8574 (m-30) cc_final: 0.8366 (m-30) REVERT: a 82 ASN cc_start: 0.8483 (t0) cc_final: 0.8126 (t0) REVERT: b 66 ASN cc_start: 0.8217 (t0) cc_final: 0.7711 (t0) REVERT: b 95 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7462 (mm-30) REVERT: b 98 GLN cc_start: 0.8210 (tp40) cc_final: 0.7831 (tp40) REVERT: b 103 ILE cc_start: 0.8800 (mm) cc_final: 0.8501 (mm) REVERT: b 108 MET cc_start: 0.8253 (ttm) cc_final: 0.8037 (ttm) REVERT: b 135 MET cc_start: 0.8638 (mmm) cc_final: 0.8089 (mmm) REVERT: c 66 ASN cc_start: 0.8233 (t0) cc_final: 0.7950 (t0) REVERT: c 79 ASP cc_start: 0.8662 (m-30) cc_final: 0.8325 (m-30) REVERT: c 82 ASN cc_start: 0.8379 (t0) cc_final: 0.8015 (t0) REVERT: c 134 MET cc_start: 0.8793 (ttt) cc_final: 0.8566 (tmm) REVERT: d 95 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7568 (mm-30) REVERT: d 124 THR cc_start: 0.8906 (p) cc_final: 0.8701 (t) REVERT: d 135 MET cc_start: 0.8590 (mmm) cc_final: 0.7921 (mmm) REVERT: e 79 ASP cc_start: 0.8685 (m-30) cc_final: 0.8346 (m-30) REVERT: e 82 ASN cc_start: 0.8523 (t0) cc_final: 0.7718 (t0) REVERT: f 95 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7482 (mm-30) REVERT: f 98 GLN cc_start: 0.8331 (tp40) cc_final: 0.7705 (tp40) REVERT: f 103 ILE cc_start: 0.8799 (mm) cc_final: 0.8559 (mm) REVERT: f 108 MET cc_start: 0.8228 (ttm) cc_final: 0.7988 (ttm) REVERT: f 142 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7926 (mt-10) REVERT: g 66 ASN cc_start: 0.8251 (t0) cc_final: 0.8008 (t0) REVERT: g 79 ASP cc_start: 0.8611 (m-30) cc_final: 0.8295 (m-30) REVERT: g 181 MET cc_start: 0.8139 (tpt) cc_final: 0.7694 (tmm) REVERT: h 95 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7600 (mm-30) REVERT: h 105 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8122 (mp0) REVERT: h 135 MET cc_start: 0.8426 (mmm) cc_final: 0.7785 (mmm) REVERT: i 66 ASN cc_start: 0.7857 (t0) cc_final: 0.7617 (t0) REVERT: i 82 ASN cc_start: 0.8268 (t0) cc_final: 0.7492 (t0) REVERT: i 95 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7654 (mm-30) REVERT: i 124 THR cc_start: 0.8817 (p) cc_final: 0.8396 (t) REVERT: i 172 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7754 (mm-30) REVERT: i 188 ARG cc_start: 0.8634 (mmm160) cc_final: 0.8269 (tpt90) REVERT: j 58 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7941 (mtmm) REVERT: j 66 ASN cc_start: 0.8063 (t0) cc_final: 0.7610 (t0) REVERT: j 107 GLU cc_start: 0.7251 (pt0) cc_final: 0.7012 (pt0) REVERT: k 95 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7620 (mm-30) REVERT: k 124 THR cc_start: 0.8806 (p) cc_final: 0.8394 (t) REVERT: k 135 MET cc_start: 0.8628 (mmm) cc_final: 0.7928 (mmm) REVERT: k 172 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7781 (mm-30) REVERT: k 188 ARG cc_start: 0.8630 (mmm160) cc_final: 0.8272 (tpt90) REVERT: l 58 LYS cc_start: 0.8242 (mtmm) cc_final: 0.8012 (mtmm) REVERT: l 66 ASN cc_start: 0.8055 (t0) cc_final: 0.7574 (t0) REVERT: l 95 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7852 (mm-30) REVERT: l 98 GLN cc_start: 0.8306 (tt0) cc_final: 0.7618 (tt0) REVERT: l 197 ARG cc_start: 0.8535 (tmm-80) cc_final: 0.7467 (tmm-80) REVERT: l 198 TYR cc_start: 0.8696 (m-10) cc_final: 0.8348 (m-10) REVERT: m 66 ASN cc_start: 0.7919 (t0) cc_final: 0.7669 (t0) REVERT: m 95 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7708 (mm-30) REVERT: m 124 THR cc_start: 0.8828 (p) cc_final: 0.8423 (t) REVERT: m 172 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7774 (mm-30) REVERT: n 66 ASN cc_start: 0.8061 (t0) cc_final: 0.7634 (t0) REVERT: n 98 GLN cc_start: 0.8317 (tt0) cc_final: 0.7637 (tt0) REVERT: n 135 MET cc_start: 0.8554 (mmm) cc_final: 0.8300 (mmm) REVERT: n 197 ARG cc_start: 0.8548 (tmm-80) cc_final: 0.7496 (tmm-80) REVERT: n 198 TYR cc_start: 0.8701 (m-10) cc_final: 0.8364 (m-10) REVERT: o 95 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7610 (mm-30) REVERT: o 124 THR cc_start: 0.8827 (p) cc_final: 0.8414 (t) REVERT: o 134 MET cc_start: 0.8680 (ttt) cc_final: 0.8391 (ttt) REVERT: o 135 MET cc_start: 0.8676 (mmm) cc_final: 0.7947 (mmm) REVERT: o 172 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7813 (mm-30) REVERT: p 58 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7992 (mtmm) REVERT: p 66 ASN cc_start: 0.8080 (t0) cc_final: 0.7574 (t0) REVERT: p 197 ARG cc_start: 0.8579 (tmm-80) cc_final: 0.7437 (tmm-80) REVERT: p 198 TYR cc_start: 0.8701 (m-10) cc_final: 0.8372 (m-10) REVERT: q 56 MET cc_start: 0.8557 (mmm) cc_final: 0.7857 (mtt) REVERT: q 66 ASN cc_start: 0.7844 (t0) cc_final: 0.7443 (t0) REVERT: q 67 LEU cc_start: 0.8416 (mm) cc_final: 0.8196 (mm) REVERT: q 103 ILE cc_start: 0.9319 (mm) cc_final: 0.8699 (mm) REVERT: q 107 GLU cc_start: 0.7770 (pt0) cc_final: 0.6513 (tm-30) REVERT: q 108 MET cc_start: 0.8541 (tpp) cc_final: 0.8171 (tpp) REVERT: q 122 ASN cc_start: 0.8678 (m-40) cc_final: 0.8433 (m-40) REVERT: q 124 THR cc_start: 0.8932 (p) cc_final: 0.8397 (t) REVERT: q 172 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7698 (mm-30) REVERT: r 82 ASN cc_start: 0.8830 (t0) cc_final: 0.8334 (t0) REVERT: r 107 GLU cc_start: 0.7560 (pt0) cc_final: 0.6299 (tm-30) REVERT: r 124 THR cc_start: 0.8966 (p) cc_final: 0.8545 (t) REVERT: r 215 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7388 (tm-30) REVERT: s 66 ASN cc_start: 0.7867 (t0) cc_final: 0.7385 (t0) REVERT: s 103 ILE cc_start: 0.9314 (mm) cc_final: 0.9096 (mm) REVERT: s 107 GLU cc_start: 0.7786 (pt0) cc_final: 0.6631 (tm-30) REVERT: s 108 MET cc_start: 0.8540 (tpp) cc_final: 0.8136 (tpp) REVERT: s 122 ASN cc_start: 0.8706 (m-40) cc_final: 0.8502 (m-40) REVERT: s 124 THR cc_start: 0.8920 (p) cc_final: 0.8359 (t) REVERT: s 135 MET cc_start: 0.8772 (mmm) cc_final: 0.8571 (mmm) REVERT: s 172 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7681 (mm-30) REVERT: s 212 ARG cc_start: 0.7237 (ptt-90) cc_final: 0.6332 (tpm170) REVERT: t 79 ASP cc_start: 0.8503 (m-30) cc_final: 0.8120 (m-30) REVERT: t 82 ASN cc_start: 0.8826 (t0) cc_final: 0.8520 (t0) REVERT: t 103 ILE cc_start: 0.9071 (mm) cc_final: 0.8546 (mm) REVERT: t 107 GLU cc_start: 0.7724 (pt0) cc_final: 0.6298 (tm-30) REVERT: t 124 THR cc_start: 0.8928 (p) cc_final: 0.8692 (t) REVERT: t 215 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7356 (tm-30) REVERT: u 66 ASN cc_start: 0.7781 (t0) cc_final: 0.7324 (t0) REVERT: u 107 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7606 (pt0) REVERT: u 108 MET cc_start: 0.8461 (tpp) cc_final: 0.8083 (tpp) REVERT: u 124 THR cc_start: 0.8899 (p) cc_final: 0.8402 (t) REVERT: u 172 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7747 (mm-30) REVERT: u 198 TYR cc_start: 0.8840 (m-10) cc_final: 0.8613 (m-10) REVERT: v 82 ASN cc_start: 0.8794 (t0) cc_final: 0.8424 (t0) REVERT: v 107 GLU cc_start: 0.7553 (pt0) cc_final: 0.6348 (tm-30) REVERT: v 124 THR cc_start: 0.8984 (p) cc_final: 0.8563 (t) REVERT: v 135 MET cc_start: 0.8625 (mmm) cc_final: 0.8191 (mmm) REVERT: v 215 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7348 (tm-30) REVERT: w 56 MET cc_start: 0.8578 (mmm) cc_final: 0.7962 (mtt) REVERT: w 66 ASN cc_start: 0.7784 (t0) cc_final: 0.7413 (t0) REVERT: w 79 ASP cc_start: 0.8273 (m-30) cc_final: 0.8021 (m-30) REVERT: w 103 ILE cc_start: 0.9297 (mm) cc_final: 0.9066 (mm) REVERT: w 107 GLU cc_start: 0.7808 (pt0) cc_final: 0.6624 (tm-30) REVERT: w 108 MET cc_start: 0.8573 (tpp) cc_final: 0.8146 (tpp) REVERT: w 122 ASN cc_start: 0.8686 (m-40) cc_final: 0.8465 (m-40) REVERT: w 124 THR cc_start: 0.8912 (p) cc_final: 0.8367 (t) REVERT: w 135 MET cc_start: 0.8796 (mmm) cc_final: 0.8496 (mmm) REVERT: w 181 MET cc_start: 0.7977 (tpt) cc_final: 0.7754 (mmm) REVERT: x 79 ASP cc_start: 0.8489 (m-30) cc_final: 0.8125 (m-30) REVERT: x 82 ASN cc_start: 0.8839 (t0) cc_final: 0.8460 (t0) REVERT: x 107 GLU cc_start: 0.7531 (pt0) cc_final: 0.6329 (tm-30) REVERT: x 122 ASN cc_start: 0.8654 (m-40) cc_final: 0.8447 (m-40) REVERT: x 124 THR cc_start: 0.8934 (p) cc_final: 0.8621 (t) REVERT: x 197 ARG cc_start: 0.8345 (ttt90) cc_final: 0.7959 (ttt90) REVERT: x 215 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7417 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1438 average time/residue: 0.4822 time to fit residues: 1077.2015 Evaluate side-chains 1334 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1334 time to evaluate : 3.694 ------------------------------------------------------------------------------- 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: 8.9990 chunk 376 optimal weight: 0.0050 chunk 343 optimal weight: 0.0000 chunk 366 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 159 optimal weight: 0.0370 chunk 287 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 331 optimal weight: 7.9990 chunk 346 optimal weight: 0.4980 chunk 365 optimal weight: 10.0000 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 98 GLN ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 217 HIS e 158 GLN f 98 GLN i 98 GLN j 122 ASN k 98 GLN l 122 ASN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 217 HIS o 98 GLN p 217 HIS q 175 ASN r 98 GLN r 175 ASN s 175 ASN u 175 ASN v 175 ASN x 175 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 34776 Z= 0.153 Angle : 0.586 7.669 47184 Z= 0.295 Chirality : 0.041 0.180 5160 Planarity : 0.005 0.069 6120 Dihedral : 4.446 17.247 4704 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.03 % Allowed : 0.41 % Favored : 99.57 % 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: -2.14 (0.13), residues: 4176 helix: -0.33 (0.12), residues: 2088 sheet: -1.21 (0.29), residues: 240 loop : -2.79 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP n 132 HIS 0.003 0.000 HIS m 162 PHE 0.011 0.001 PHE h 202 TYR 0.024 0.001 TYR b 198 ARG 0.009 0.000 ARG e 212 *********************** 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 1412 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1411 time to evaluate : 4.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 82 ASN cc_start: 0.8311 (t0) cc_final: 0.7882 (t0) REVERT: a 188 ARG cc_start: 0.8158 (tpt90) cc_final: 0.7931 (tpt90) REVERT: b 79 ASP cc_start: 0.8573 (m-30) cc_final: 0.8329 (m-30) REVERT: b 95 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7456 (mm-30) REVERT: b 98 GLN cc_start: 0.8157 (tp40) cc_final: 0.7756 (tp40) REVERT: b 103 ILE cc_start: 0.8863 (mm) cc_final: 0.8549 (mm) REVERT: b 108 MET cc_start: 0.8206 (ttm) cc_final: 0.8000 (ttm) REVERT: b 135 MET cc_start: 0.8570 (mmm) cc_final: 0.8035 (mmm) REVERT: b 139 GLU cc_start: 0.8260 (pt0) cc_final: 0.8060 (mt-10) REVERT: c 66 ASN cc_start: 0.8133 (t0) cc_final: 0.7888 (t0) REVERT: c 79 ASP cc_start: 0.8683 (m-30) cc_final: 0.8211 (m-30) REVERT: c 95 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7361 (mm-30) REVERT: d 95 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7472 (mm-30) REVERT: d 98 GLN cc_start: 0.8120 (tp40) cc_final: 0.7779 (tp40) REVERT: d 108 MET cc_start: 0.8173 (ttm) cc_final: 0.7969 (ttm) REVERT: d 135 MET cc_start: 0.8697 (mmm) cc_final: 0.8092 (mmm) REVERT: e 55 ARG cc_start: 0.7861 (tpp80) cc_final: 0.7656 (tpt-90) REVERT: e 82 ASN cc_start: 0.8437 (t0) cc_final: 0.7649 (t0) REVERT: f 95 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7432 (mm-30) REVERT: f 98 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7667 (tp40) REVERT: f 103 ILE cc_start: 0.8870 (mm) cc_final: 0.8552 (mm) REVERT: f 142 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7879 (mt-10) REVERT: g 66 ASN cc_start: 0.8259 (t0) cc_final: 0.8030 (t0) REVERT: g 79 ASP cc_start: 0.8490 (m-30) cc_final: 0.8180 (m-30) REVERT: g 181 MET cc_start: 0.7866 (tpt) cc_final: 0.7531 (tmm) REVERT: h 95 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7555 (mm-30) REVERT: h 135 MET cc_start: 0.8398 (mmm) cc_final: 0.7809 (mmm) REVERT: i 66 ASN cc_start: 0.7791 (t0) cc_final: 0.7562 (t0) REVERT: i 82 ASN cc_start: 0.8145 (t0) cc_final: 0.7350 (t0) REVERT: i 95 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7709 (mm-30) REVERT: i 124 THR cc_start: 0.8807 (p) cc_final: 0.8442 (t) REVERT: i 134 MET cc_start: 0.8399 (ttt) cc_final: 0.8176 (ttt) REVERT: i 143 TYR cc_start: 0.8770 (m-80) cc_final: 0.8245 (m-80) REVERT: i 172 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7706 (mm-30) REVERT: j 58 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7911 (mtmm) REVERT: j 66 ASN cc_start: 0.8021 (t0) cc_final: 0.7501 (t0) REVERT: j 95 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7566 (mm-30) REVERT: j 177 LYS cc_start: 0.8307 (mmmm) cc_final: 0.8079 (tptp) REVERT: k 124 THR cc_start: 0.8739 (p) cc_final: 0.8379 (t) REVERT: k 135 MET cc_start: 0.8593 (mmm) cc_final: 0.7901 (mmm) REVERT: k 172 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7751 (mm-30) REVERT: l 58 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7933 (mtmm) REVERT: l 66 ASN cc_start: 0.8014 (t0) cc_final: 0.7534 (t0) REVERT: l 79 ASP cc_start: 0.8317 (m-30) cc_final: 0.8075 (m-30) REVERT: l 95 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7615 (mm-30) REVERT: l 105 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8148 (mm-30) REVERT: l 197 ARG cc_start: 0.8509 (tmm-80) cc_final: 0.7454 (tmm-80) REVERT: m 91 ASP cc_start: 0.8503 (m-30) cc_final: 0.8289 (m-30) REVERT: m 95 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7367 (mm-30) REVERT: m 124 THR cc_start: 0.8750 (p) cc_final: 0.8393 (t) REVERT: m 172 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7764 (mm-30) REVERT: n 58 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7847 (mtmm) REVERT: n 66 ASN cc_start: 0.7945 (t0) cc_final: 0.7569 (t0) REVERT: n 135 MET cc_start: 0.8554 (mmm) cc_final: 0.8322 (mmm) REVERT: n 177 LYS cc_start: 0.8284 (mmmm) cc_final: 0.8046 (tptp) REVERT: n 197 ARG cc_start: 0.8472 (tmm-80) cc_final: 0.7450 (tmm-80) REVERT: o 56 MET cc_start: 0.8614 (mmm) cc_final: 0.8147 (mtt) REVERT: o 124 THR cc_start: 0.8760 (p) cc_final: 0.8385 (t) REVERT: o 135 MET cc_start: 0.8651 (mmm) cc_final: 0.7917 (mmm) REVERT: o 172 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7785 (mm-30) REVERT: p 66 ASN cc_start: 0.8049 (t0) cc_final: 0.7541 (t0) REVERT: p 79 ASP cc_start: 0.8316 (m-30) cc_final: 0.8073 (m-30) REVERT: p 95 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7624 (mm-30) REVERT: p 112 MET cc_start: 0.9312 (mmt) cc_final: 0.8927 (mmt) REVERT: p 197 ARG cc_start: 0.8492 (tmm-80) cc_final: 0.7365 (tmm-80) REVERT: q 66 ASN cc_start: 0.7893 (t0) cc_final: 0.7391 (t0) REVERT: q 103 ILE cc_start: 0.9284 (mm) cc_final: 0.8607 (mm) REVERT: q 107 GLU cc_start: 0.7708 (pt0) cc_final: 0.6513 (tm-30) REVERT: q 124 THR cc_start: 0.8915 (p) cc_final: 0.8400 (t) REVERT: q 172 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7681 (mm-30) REVERT: q 181 MET cc_start: 0.8205 (tpt) cc_final: 0.7801 (mmm) REVERT: r 82 ASN cc_start: 0.8812 (t0) cc_final: 0.8571 (t0) REVERT: r 108 MET cc_start: 0.8318 (tpp) cc_final: 0.7606 (tpp) REVERT: r 124 THR cc_start: 0.8938 (p) cc_final: 0.8527 (t) REVERT: r 197 ARG cc_start: 0.8241 (ttt90) cc_final: 0.7922 (ttt90) REVERT: r 204 GLU cc_start: 0.8219 (pt0) cc_final: 0.7957 (pt0) REVERT: r 215 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7283 (tm-30) REVERT: s 56 MET cc_start: 0.8468 (mmm) cc_final: 0.7722 (mtt) REVERT: s 66 ASN cc_start: 0.7799 (t0) cc_final: 0.7358 (t0) REVERT: s 103 ILE cc_start: 0.9282 (mm) cc_final: 0.8629 (mm) REVERT: s 107 GLU cc_start: 0.7715 (pt0) cc_final: 0.6517 (tm-30) REVERT: s 124 THR cc_start: 0.8912 (p) cc_final: 0.8419 (t) REVERT: s 135 MET cc_start: 0.8739 (mmm) cc_final: 0.8530 (mmm) REVERT: s 172 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7759 (mm-30) REVERT: t 79 ASP cc_start: 0.8430 (m-30) cc_final: 0.8135 (m-30) REVERT: t 82 ASN cc_start: 0.8793 (t0) cc_final: 0.8590 (t0) REVERT: t 135 MET cc_start: 0.8708 (mmm) cc_final: 0.7793 (mmm) REVERT: t 197 ARG cc_start: 0.8214 (ttt90) cc_final: 0.7881 (ttt90) REVERT: t 215 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7339 (tm-30) REVERT: u 56 MET cc_start: 0.8483 (mmm) cc_final: 0.7743 (mtt) REVERT: u 66 ASN cc_start: 0.7701 (t0) cc_final: 0.7252 (t0) REVERT: u 103 ILE cc_start: 0.9180 (mm) cc_final: 0.8912 (mm) REVERT: u 107 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6665 (tm-30) REVERT: u 108 MET cc_start: 0.8416 (tpp) cc_final: 0.8065 (tpp) REVERT: u 124 THR cc_start: 0.8839 (p) cc_final: 0.8325 (t) REVERT: u 172 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7748 (mm-30) REVERT: u 181 MET cc_start: 0.7830 (tpt) cc_final: 0.7584 (mmm) REVERT: v 107 GLU cc_start: 0.7466 (pt0) cc_final: 0.6366 (tm-30) REVERT: v 108 MET cc_start: 0.8349 (tpp) cc_final: 0.7870 (tpp) REVERT: v 124 THR cc_start: 0.8954 (p) cc_final: 0.8549 (t) REVERT: v 135 MET cc_start: 0.8482 (mmm) cc_final: 0.8139 (mmm) REVERT: v 197 ARG cc_start: 0.8247 (ttt90) cc_final: 0.7936 (ttt90) REVERT: v 215 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7325 (tm-30) REVERT: w 56 MET cc_start: 0.8592 (mmm) cc_final: 0.7987 (mtt) REVERT: w 66 ASN cc_start: 0.7739 (t0) cc_final: 0.7403 (t0) REVERT: w 79 ASP cc_start: 0.8180 (m-30) cc_final: 0.7785 (m-30) REVERT: w 103 ILE cc_start: 0.9260 (mm) cc_final: 0.8604 (mm) REVERT: w 107 GLU cc_start: 0.7779 (pt0) cc_final: 0.6478 (tm-30) REVERT: w 124 THR cc_start: 0.8929 (p) cc_final: 0.8411 (t) REVERT: w 135 MET cc_start: 0.8764 (mmm) cc_final: 0.8487 (mmm) REVERT: w 181 MET cc_start: 0.7864 (tpt) cc_final: 0.7605 (mmm) REVERT: w 197 ARG cc_start: 0.8531 (tmm-80) cc_final: 0.8120 (tmm-80) REVERT: x 79 ASP cc_start: 0.8377 (m-30) cc_final: 0.8028 (m-30) REVERT: x 82 ASN cc_start: 0.8817 (t0) cc_final: 0.8553 (t0) REVERT: x 108 MET cc_start: 0.8282 (tpp) cc_final: 0.7673 (tpp) REVERT: x 122 ASN cc_start: 0.8620 (m-40) cc_final: 0.8391 (m-40) REVERT: x 124 THR cc_start: 0.8902 (p) cc_final: 0.8649 (t) REVERT: x 135 MET cc_start: 0.8574 (mmm) cc_final: 0.8335 (mmm) REVERT: x 142 GLU cc_start: 0.8364 (mp0) cc_final: 0.8118 (mt-10) REVERT: x 197 ARG cc_start: 0.8145 (ttt90) cc_final: 0.7844 (ttt90) REVERT: x 215 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7321 (tm-30) outliers start: 1 outliers final: 0 residues processed: 1412 average time/residue: 0.4826 time to fit residues: 1067.5779 Evaluate side-chains 1301 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1300 time to evaluate : 3.966 ------------------------------------------------------------------------------- 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: 7.9990 chunk 387 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 3.9990 chunk 374 optimal weight: 2.9990 chunk 323 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 250 optimal weight: 0.2980 chunk 198 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 82 ASN ** c 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 98 GLN k 98 GLN m 98 GLN ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 98 GLN t 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 34776 Z= 0.350 Angle : 0.719 8.127 47184 Z= 0.362 Chirality : 0.047 0.224 5160 Planarity : 0.005 0.051 6120 Dihedral : 5.050 19.219 4704 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 0.03 % Allowed : 0.19 % Favored : 99.78 % 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: -2.41 (0.13), residues: 4176 helix: -0.63 (0.11), residues: 2232 sheet: -1.47 (0.30), residues: 240 loop : -2.95 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP b 118 HIS 0.006 0.001 HIS n 162 PHE 0.018 0.003 PHE r 200 TYR 0.025 0.002 TYR r 73 ARG 0.009 0.001 ARG x 55 ********************** 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 1476 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1475 time to evaluate : 4.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 103 ILE cc_start: 0.9083 (mm) cc_final: 0.8568 (mm) REVERT: a 107 GLU cc_start: 0.7236 (pt0) cc_final: 0.6857 (pp20) REVERT: b 95 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7496 (mm-30) REVERT: b 98 GLN cc_start: 0.8375 (tp40) cc_final: 0.7915 (tp40) REVERT: b 108 MET cc_start: 0.8410 (ttm) cc_final: 0.8103 (ttm) REVERT: b 135 MET cc_start: 0.8777 (mmm) cc_final: 0.8205 (mmm) REVERT: b 156 LEU cc_start: 0.8973 (tp) cc_final: 0.8755 (tp) REVERT: c 66 ASN cc_start: 0.8267 (t0) cc_final: 0.7987 (t0) REVERT: c 68 GLU cc_start: 0.8394 (mp0) cc_final: 0.7981 (tm-30) REVERT: c 79 ASP cc_start: 0.8632 (m-30) cc_final: 0.8368 (m-30) REVERT: c 112 MET cc_start: 0.9383 (mmt) cc_final: 0.9012 (mmt) REVERT: c 197 ARG cc_start: 0.8821 (ptm-80) cc_final: 0.8613 (ptm-80) REVERT: d 66 ASN cc_start: 0.7991 (t0) cc_final: 0.7561 (t0) REVERT: d 135 MET cc_start: 0.8646 (mmm) cc_final: 0.8325 (mmm) REVERT: e 66 ASN cc_start: 0.8231 (t0) cc_final: 0.7917 (t0) REVERT: e 68 GLU cc_start: 0.8582 (mp0) cc_final: 0.8069 (tm-30) REVERT: e 82 ASN cc_start: 0.8618 (t0) cc_final: 0.7955 (t0) REVERT: f 66 ASN cc_start: 0.8212 (t0) cc_final: 0.7873 (t0) REVERT: f 115 LEU cc_start: 0.9672 (tp) cc_final: 0.9471 (tp) REVERT: g 66 ASN cc_start: 0.8353 (t0) cc_final: 0.8114 (t0) REVERT: g 68 GLU cc_start: 0.8652 (mp0) cc_final: 0.8174 (tm-30) REVERT: g 82 ASN cc_start: 0.8255 (t0) cc_final: 0.7991 (t0) REVERT: g 134 MET cc_start: 0.8494 (ttm) cc_final: 0.8264 (ttt) REVERT: g 188 ARG cc_start: 0.8442 (mmm160) cc_final: 0.8069 (tpt90) REVERT: h 79 ASP cc_start: 0.8798 (m-30) cc_final: 0.8302 (m-30) REVERT: h 95 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7577 (mm-30) REVERT: h 135 MET cc_start: 0.8384 (mmm) cc_final: 0.7873 (mmm) REVERT: i 66 ASN cc_start: 0.7870 (t0) cc_final: 0.7596 (t0) REVERT: i 82 ASN cc_start: 0.8327 (t0) cc_final: 0.7739 (t0) REVERT: i 95 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7528 (mm-30) REVERT: i 98 GLN cc_start: 0.8191 (tt0) cc_final: 0.7847 (tt0) REVERT: j 66 ASN cc_start: 0.8079 (t0) cc_final: 0.7601 (t0) REVERT: j 124 THR cc_start: 0.9033 (p) cc_final: 0.8686 (t) REVERT: j 177 LYS cc_start: 0.8319 (mmmm) cc_final: 0.8026 (tptp) REVERT: k 143 TYR cc_start: 0.9037 (m-80) cc_final: 0.8465 (m-80) REVERT: k 172 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7701 (mt-10) REVERT: k 188 ARG cc_start: 0.8668 (mmm160) cc_final: 0.8310 (tpt90) REVERT: l 66 ASN cc_start: 0.8085 (t0) cc_final: 0.7600 (t0) REVERT: l 124 THR cc_start: 0.9054 (p) cc_final: 0.8700 (t) REVERT: l 177 LYS cc_start: 0.8312 (mmmm) cc_final: 0.8030 (tptp) REVERT: m 95 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7521 (mm-30) REVERT: m 143 TYR cc_start: 0.9011 (m-80) cc_final: 0.8493 (m-80) REVERT: m 172 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7810 (mt-10) REVERT: m 188 ARG cc_start: 0.8670 (mmm160) cc_final: 0.8305 (tpt90) REVERT: n 66 ASN cc_start: 0.8095 (t0) cc_final: 0.7612 (t0) REVERT: n 122 ASN cc_start: 0.8718 (m110) cc_final: 0.8481 (m110) REVERT: n 124 THR cc_start: 0.9062 (p) cc_final: 0.8858 (t) REVERT: n 177 LYS cc_start: 0.8341 (mmmm) cc_final: 0.8089 (tptp) REVERT: o 108 MET cc_start: 0.8388 (ttm) cc_final: 0.8186 (ttp) REVERT: o 143 TYR cc_start: 0.8973 (m-80) cc_final: 0.8423 (m-80) REVERT: o 172 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8226 (mt-10) REVERT: p 66 ASN cc_start: 0.8069 (t0) cc_final: 0.7588 (t0) REVERT: p 177 LYS cc_start: 0.8345 (mmmm) cc_final: 0.8069 (tptp) REVERT: q 56 MET cc_start: 0.8634 (mmm) cc_final: 0.8155 (mtt) REVERT: q 66 ASN cc_start: 0.7877 (t0) cc_final: 0.7413 (t0) REVERT: q 82 ASN cc_start: 0.8449 (t0) cc_final: 0.7988 (t0) REVERT: q 98 GLN cc_start: 0.8489 (tp40) cc_final: 0.8225 (tp40) REVERT: q 103 ILE cc_start: 0.9140 (mm) cc_final: 0.8142 (mm) REVERT: q 107 GLU cc_start: 0.7790 (pt0) cc_final: 0.6322 (tm-30) REVERT: q 108 MET cc_start: 0.8620 (tpp) cc_final: 0.7675 (tpp) REVERT: q 124 THR cc_start: 0.8956 (p) cc_final: 0.8477 (t) REVERT: q 172 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7758 (mm-30) REVERT: r 82 ASN cc_start: 0.8832 (t0) cc_final: 0.8520 (t0) REVERT: r 107 GLU cc_start: 0.7605 (pt0) cc_final: 0.6361 (tm-30) REVERT: r 108 MET cc_start: 0.8516 (tpp) cc_final: 0.7666 (tpp) REVERT: r 124 THR cc_start: 0.9019 (p) cc_final: 0.8609 (t) REVERT: r 129 ASN cc_start: 0.8873 (p0) cc_final: 0.8669 (p0) REVERT: r 139 GLU cc_start: 0.8429 (pt0) cc_final: 0.8193 (mt-10) REVERT: r 197 ARG cc_start: 0.8421 (ttt90) cc_final: 0.7949 (ttt90) REVERT: r 215 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7350 (tm-30) REVERT: s 56 MET cc_start: 0.8704 (mmm) cc_final: 0.8152 (mtt) REVERT: s 66 ASN cc_start: 0.7861 (t0) cc_final: 0.7411 (t0) REVERT: s 67 LEU cc_start: 0.8561 (mm) cc_final: 0.8179 (mm) REVERT: s 82 ASN cc_start: 0.8575 (t0) cc_final: 0.8168 (t0) REVERT: s 98 GLN cc_start: 0.8506 (tp40) cc_final: 0.8211 (tp40) REVERT: s 103 ILE cc_start: 0.9128 (mm) cc_final: 0.8111 (mm) REVERT: s 107 GLU cc_start: 0.7750 (pt0) cc_final: 0.6331 (tm-30) REVERT: s 108 MET cc_start: 0.8623 (tpp) cc_final: 0.7677 (tpp) REVERT: s 122 ASN cc_start: 0.8836 (m-40) cc_final: 0.8635 (m-40) REVERT: s 124 THR cc_start: 0.8949 (p) cc_final: 0.8445 (t) REVERT: s 135 MET cc_start: 0.8841 (mmm) cc_final: 0.8598 (mmm) REVERT: s 172 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7764 (mm-30) REVERT: t 79 ASP cc_start: 0.8516 (m-30) cc_final: 0.8243 (m-30) REVERT: t 82 ASN cc_start: 0.8844 (t0) cc_final: 0.8551 (t0) REVERT: t 108 MET cc_start: 0.8684 (tpp) cc_final: 0.7912 (tpp) REVERT: t 115 LEU cc_start: 0.9643 (tp) cc_final: 0.9439 (tp) REVERT: t 197 ARG cc_start: 0.8376 (ttt90) cc_final: 0.7929 (ttt90) REVERT: t 215 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7394 (tm-30) REVERT: u 56 MET cc_start: 0.8704 (mmm) cc_final: 0.8162 (mtt) REVERT: u 66 ASN cc_start: 0.7747 (t0) cc_final: 0.7259 (t0) REVERT: u 67 LEU cc_start: 0.8457 (mm) cc_final: 0.8250 (mm) REVERT: u 82 ASN cc_start: 0.8702 (t0) cc_final: 0.8141 (t0) REVERT: u 108 MET cc_start: 0.8465 (tpp) cc_final: 0.8028 (tpp) REVERT: u 124 THR cc_start: 0.8890 (p) cc_final: 0.8341 (t) REVERT: u 172 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7851 (mm-30) REVERT: v 82 ASN cc_start: 0.8895 (t0) cc_final: 0.8632 (t0) REVERT: v 107 GLU cc_start: 0.7580 (pt0) cc_final: 0.6408 (tm-30) REVERT: v 108 MET cc_start: 0.8552 (tpp) cc_final: 0.7930 (tpp) REVERT: v 115 LEU cc_start: 0.9643 (tp) cc_final: 0.9432 (tp) REVERT: v 124 THR cc_start: 0.9070 (p) cc_final: 0.8668 (t) REVERT: v 135 MET cc_start: 0.8756 (mmm) cc_final: 0.8222 (mmm) REVERT: v 197 ARG cc_start: 0.8426 (ttt90) cc_final: 0.7941 (ttt90) REVERT: v 215 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7399 (tm-30) REVERT: w 66 ASN cc_start: 0.7917 (t0) cc_final: 0.7526 (t0) REVERT: w 79 ASP cc_start: 0.8434 (m-30) cc_final: 0.8034 (m-30) REVERT: w 82 ASN cc_start: 0.8592 (t0) cc_final: 0.8093 (t0) REVERT: w 98 GLN cc_start: 0.8503 (tp40) cc_final: 0.8255 (tp40) REVERT: w 103 ILE cc_start: 0.9120 (mm) cc_final: 0.8110 (mm) REVERT: w 107 GLU cc_start: 0.7783 (pt0) cc_final: 0.6332 (tm-30) REVERT: w 108 MET cc_start: 0.8600 (tpp) cc_final: 0.7663 (tpp) REVERT: w 122 ASN cc_start: 0.8787 (m-40) cc_final: 0.8586 (m-40) REVERT: w 124 THR cc_start: 0.8954 (p) cc_final: 0.8475 (t) REVERT: w 135 MET cc_start: 0.8830 (mmm) cc_final: 0.8459 (mmm) REVERT: x 56 MET cc_start: 0.8636 (mmm) cc_final: 0.8152 (mtt) REVERT: x 68 GLU cc_start: 0.8456 (mp0) cc_final: 0.7795 (tm-30) REVERT: x 79 ASP cc_start: 0.8453 (m-30) cc_final: 0.8163 (m-30) REVERT: x 82 ASN cc_start: 0.8842 (t0) cc_final: 0.8490 (t0) REVERT: x 107 GLU cc_start: 0.7573 (pt0) cc_final: 0.6429 (tm-30) REVERT: x 108 MET cc_start: 0.8552 (tpp) cc_final: 0.7755 (tpp) REVERT: x 124 THR cc_start: 0.8995 (p) cc_final: 0.8718 (t) REVERT: x 197 ARG cc_start: 0.8400 (ttt90) cc_final: 0.7886 (ttt90) REVERT: x 215 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7407 (tm-30) outliers start: 1 outliers final: 0 residues processed: 1475 average time/residue: 0.5022 time to fit residues: 1163.3824 Evaluate side-chains 1376 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1376 time to evaluate : 3.814 ------------------------------------------------------------------------------- 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: 3.9990 chunk 344 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 298 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 332 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 98 GLN q 175 ASN r 98 GLN r 175 ASN s 175 ASN u 175 ASN v 98 GLN v 175 ASN x 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.125746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.107498 restraints weight = 46003.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.110631 restraints weight = 29844.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.112852 restraints weight = 21487.457| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34776 Z= 0.275 Angle : 0.678 8.227 47184 Z= 0.342 Chirality : 0.045 0.197 5160 Planarity : 0.005 0.065 6120 Dihedral : 5.013 19.644 4704 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -2.38 (0.13), residues: 4176 helix: -0.60 (0.12), residues: 2232 sheet: -1.49 (0.30), residues: 240 loop : -2.94 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP l 132 HIS 0.004 0.001 HIS o 162 PHE 0.014 0.002 PHE r 200 TYR 0.026 0.002 TYR r 203 ARG 0.008 0.001 ARG e 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14684.81 seconds wall clock time: 258 minutes 22.44 seconds (15502.44 seconds total)