Starting phenix.real_space_refine on Mon Apr 15 14:21:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opd_17049/04_2024/8opd_17049.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opd_17049/04_2024/8opd_17049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opd_17049/04_2024/8opd_17049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opd_17049/04_2024/8opd_17049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opd_17049/04_2024/8opd_17049.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opd_17049/04_2024/8opd_17049.pdb" } resolution = 3.5 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= -0.001 sd= 0.049 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 288 5.16 5 C 22128 2.51 5 N 6096 2.21 5 O 6528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Aa GLU 68": "OE1" <-> "OE2" Residue "Aa ARG 191": "NH1" <-> "NH2" Residue "Ab GLU 68": "OE1" <-> "OE2" Residue "Ab ARG 191": "NH1" <-> "NH2" Residue "Ac GLU 68": "OE1" <-> "OE2" Residue "Ac ARG 191": "NH1" <-> "NH2" Residue "Ad GLU 68": "OE1" <-> "OE2" Residue "Ad ARG 191": "NH1" <-> "NH2" Residue "Ae GLU 68": "OE1" <-> "OE2" Residue "Ae ARG 191": "NH1" <-> "NH2" Residue "Af GLU 68": "OE1" <-> "OE2" Residue "Af ARG 191": "NH1" <-> "NH2" Residue "Ag GLU 68": "OE1" <-> "OE2" Residue "Ag ARG 191": "NH1" <-> "NH2" Residue "Ah GLU 68": "OE1" <-> "OE2" Residue "Ah ARG 191": "NH1" <-> "NH2" Residue "Ai GLU 68": "OE1" <-> "OE2" Residue "Ai ARG 191": "NH1" <-> "NH2" Residue "Aj GLU 68": "OE1" <-> "OE2" Residue "Aj ARG 191": "NH1" <-> "NH2" Residue "Ak GLU 68": "OE1" <-> "OE2" Residue "Ak ARG 191": "NH1" <-> "NH2" Residue "Al GLU 68": "OE1" <-> "OE2" Residue "Al ARG 191": "NH1" <-> "NH2" Residue "Am GLU 68": "OE1" <-> "OE2" Residue "Am ARG 191": "NH1" <-> "NH2" Residue "An GLU 68": "OE1" <-> "OE2" Residue "An ARG 191": "NH1" <-> "NH2" Residue "Ao GLU 68": "OE1" <-> "OE2" Residue "Ao ARG 191": "NH1" <-> "NH2" Residue "Ap GLU 68": "OE1" <-> "OE2" Residue "Ap ARG 191": "NH1" <-> "NH2" Residue "Aq GLU 68": "OE1" <-> "OE2" Residue "Aq ARG 191": "NH1" <-> "NH2" Residue "Ar GLU 68": "OE1" <-> "OE2" Residue "Ar ARG 191": "NH1" <-> "NH2" Residue "As GLU 68": "OE1" <-> "OE2" Residue "As ARG 191": "NH1" <-> "NH2" Residue "At GLU 68": "OE1" <-> "OE2" Residue "At ARG 191": "NH1" <-> "NH2" Residue "Au GLU 68": "OE1" <-> "OE2" Residue "Au ARG 191": "NH1" <-> "NH2" Residue "Av GLU 68": "OE1" <-> "OE2" Residue "Av ARG 191": "NH1" <-> "NH2" Residue "Aw GLU 68": "OE1" <-> "OE2" Residue "Aw ARG 191": "NH1" <-> "NH2" Residue "Ax GLU 68": "OE1" <-> "OE2" Residue "Ax ARG 191": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35040 Number of models: 1 Model: "" Number of chains: 24 Chain: "Aa" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ab" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ac" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ad" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ae" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Af" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ag" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ah" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ai" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Aj" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ak" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Al" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Am" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "An" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ao" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ap" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Aq" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ar" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "As" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "At" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Au" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Av" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Aw" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ax" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1460 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Time building chain proxies: 16.68, per 1000 atoms: 0.48 Number of scatterers: 35040 At special positions: 0 Unit cell: (137.127, 137.127, 164.765, 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 288 16.00 O 6528 8.00 N 6096 7.00 C 22128 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: 12.87 Conformation dependent library (CDL) restraints added in 5.6 seconds 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 24 sheets defined 55.8% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 71 Processing helix chain 'Aa' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAa 80 " --> pdb=" O GLNAa 77 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAa 97 " --> pdb=" O TRPAa 93 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAa 117 " --> pdb=" O ASNAa 113 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAa 151 " --> pdb=" O PROAa 147 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAa 162 " --> pdb=" O GLNAa 158 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAa 173 " --> pdb=" O ALAAa 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAa 177 " --> pdb=" O METAa 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAa 178 " --> pdb=" O ARGAa 174 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAa 188 " --> pdb=" O TYRAa 184 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAa 197 " --> pdb=" O SERAa 194 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAa 215 " --> pdb=" O VALAa 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAa 216 " --> pdb=" O ARGAa 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAa 217 " --> pdb=" O ALAAa 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAa 218 " --> pdb=" O ARGAa 214 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 66 through 71 Processing helix chain 'Ab' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAb 80 " --> pdb=" O GLNAb 77 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAb 97 " --> pdb=" O TRPAb 93 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAb 111 " --> pdb=" O GLUAb 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALAb 117 " --> pdb=" O ASNAb 113 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAb 151 " --> pdb=" O PROAb 147 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 155 through 162 removed outlier: 3.897A pdb=" N HISAb 162 " --> pdb=" O GLNAb 158 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAb 173 " --> pdb=" O ALAAb 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAb 177 " --> pdb=" O METAb 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAb 178 " --> pdb=" O ARGAb 174 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAb 188 " --> pdb=" O TYRAb 184 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAb 197 " --> pdb=" O SERAb 194 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAb 215 " --> pdb=" O VALAb 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAb 216 " --> pdb=" O ARGAb 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAb 217 " --> pdb=" O ALAAb 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAb 218 " --> pdb=" O ARGAb 214 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 66 through 71 Processing helix chain 'Ac' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAc 80 " --> pdb=" O GLNAc 77 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAc 97 " --> pdb=" O TRPAc 93 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAc 117 " --> pdb=" O ASNAc 113 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAc 151 " --> pdb=" O PROAc 147 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAc 162 " --> pdb=" O GLNAc 158 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAc 173 " --> pdb=" O ALAAc 169 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYSAc 177 " --> pdb=" O METAc 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAc 178 " --> pdb=" O ARGAc 174 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAc 188 " --> pdb=" O TYRAc 184 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAc 197 " --> pdb=" O SERAc 194 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAc 215 " --> pdb=" O VALAc 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAc 216 " --> pdb=" O ARGAc 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAc 217 " --> pdb=" O ALAAc 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAc 218 " --> pdb=" O ARGAc 214 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 66 through 71 Processing helix chain 'Ad' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAd 80 " --> pdb=" O GLNAd 77 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAd 97 " --> pdb=" O TRPAd 93 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAd 111 " --> pdb=" O GLUAd 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAd 117 " --> pdb=" O ASNAd 113 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAd 151 " --> pdb=" O PROAd 147 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAd 162 " --> pdb=" O GLNAd 158 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAd 173 " --> pdb=" O ALAAd 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAd 177 " --> pdb=" O METAd 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAd 178 " --> pdb=" O ARGAd 174 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAd 188 " --> pdb=" O TYRAd 184 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 194 through 199 removed outlier: 3.886A pdb=" N ARGAd 197 " --> pdb=" O SERAd 194 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAd 215 " --> pdb=" O VALAd 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAd 216 " --> pdb=" O ARGAd 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAd 217 " --> pdb=" O ALAAd 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAd 218 " --> pdb=" O ARGAd 214 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 66 through 71 Processing helix chain 'Ae' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAe 80 " --> pdb=" O GLNAe 77 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAe 97 " --> pdb=" O TRPAe 93 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAe 117 " --> pdb=" O ASNAe 113 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAe 151 " --> pdb=" O PROAe 147 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAe 162 " --> pdb=" O GLNAe 158 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAe 173 " --> pdb=" O ALAAe 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAe 177 " --> pdb=" O METAe 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAe 178 " --> pdb=" O ARGAe 174 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAe 188 " --> pdb=" O TYRAe 184 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 194 through 199 removed outlier: 3.886A pdb=" N ARGAe 197 " --> pdb=" O SERAe 194 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAe 215 " --> pdb=" O VALAe 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAe 216 " --> pdb=" O ARGAe 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAe 217 " --> pdb=" O ALAAe 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAe 218 " --> pdb=" O ARGAe 214 " (cutoff:3.500A) Processing helix chain 'Af' and resid 66 through 71 Processing helix chain 'Af' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAf 80 " --> pdb=" O GLNAf 77 " (cutoff:3.500A) Processing helix chain 'Af' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAf 97 " --> pdb=" O TRPAf 93 " (cutoff:3.500A) Processing helix chain 'Af' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAf 111 " --> pdb=" O GLUAf 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALAf 117 " --> pdb=" O ASNAf 113 " (cutoff:3.500A) Processing helix chain 'Af' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAf 151 " --> pdb=" O PROAf 147 " (cutoff:3.500A) Processing helix chain 'Af' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAf 162 " --> pdb=" O GLNAf 158 " (cutoff:3.500A) Processing helix chain 'Af' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAf 173 " --> pdb=" O ALAAf 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAf 177 " --> pdb=" O METAf 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAf 178 " --> pdb=" O ARGAf 174 " (cutoff:3.500A) Processing helix chain 'Af' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAf 188 " --> pdb=" O TYRAf 184 " (cutoff:3.500A) Processing helix chain 'Af' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAf 197 " --> pdb=" O SERAf 194 " (cutoff:3.500A) Processing helix chain 'Af' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAf 215 " --> pdb=" O VALAf 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAf 216 " --> pdb=" O ARGAf 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAf 217 " --> pdb=" O ALAAf 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAf 218 " --> pdb=" O ARGAf 214 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 66 through 71 Processing helix chain 'Ag' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAg 80 " --> pdb=" O GLNAg 77 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAg 97 " --> pdb=" O TRPAg 93 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAg 117 " --> pdb=" O ASNAg 113 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAg 151 " --> pdb=" O PROAg 147 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 155 through 162 removed outlier: 3.897A pdb=" N HISAg 162 " --> pdb=" O GLNAg 158 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAg 173 " --> pdb=" O ALAAg 169 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYSAg 177 " --> pdb=" O METAg 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAg 178 " --> pdb=" O ARGAg 174 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAg 188 " --> pdb=" O TYRAg 184 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAg 197 " --> pdb=" O SERAg 194 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAg 215 " --> pdb=" O VALAg 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAg 216 " --> pdb=" O ARGAg 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAg 217 " --> pdb=" O ALAAg 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAg 218 " --> pdb=" O ARGAg 214 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 66 through 71 Processing helix chain 'Ah' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAh 80 " --> pdb=" O GLNAh 77 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAh 97 " --> pdb=" O TRPAh 93 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAh 111 " --> pdb=" O GLUAh 107 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VALAh 117 " --> pdb=" O ASNAh 113 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAh 151 " --> pdb=" O PROAh 147 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAh 162 " --> pdb=" O GLNAh 158 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAh 173 " --> pdb=" O ALAAh 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAh 177 " --> pdb=" O METAh 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAh 178 " --> pdb=" O ARGAh 174 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAh 188 " --> pdb=" O TYRAh 184 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAh 197 " --> pdb=" O SERAh 194 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAh 215 " --> pdb=" O VALAh 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAh 216 " --> pdb=" O ARGAh 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAh 217 " --> pdb=" O ALAAh 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAh 218 " --> pdb=" O ARGAh 214 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 66 through 71 Processing helix chain 'Ai' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAi 80 " --> pdb=" O GLNAi 77 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAi 97 " --> pdb=" O TRPAi 93 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VALAi 117 " --> pdb=" O ASNAi 113 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAi 151 " --> pdb=" O PROAi 147 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAi 162 " --> pdb=" O GLNAi 158 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAi 173 " --> pdb=" O ALAAi 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAi 177 " --> pdb=" O METAi 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAi 178 " --> pdb=" O ARGAi 174 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAi 188 " --> pdb=" O TYRAi 184 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAi 197 " --> pdb=" O SERAi 194 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAi 215 " --> pdb=" O VALAi 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAi 216 " --> pdb=" O ARGAi 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAi 217 " --> pdb=" O ALAAi 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAi 218 " --> pdb=" O ARGAi 214 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 66 through 71 Processing helix chain 'Aj' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAj 80 " --> pdb=" O GLNAj 77 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 86 through 102 removed outlier: 3.605A pdb=" N VALAj 97 " --> pdb=" O TRPAj 93 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAj 111 " --> pdb=" O GLUAj 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAj 117 " --> pdb=" O ASNAj 113 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAj 151 " --> pdb=" O PROAj 147 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAj 162 " --> pdb=" O GLNAj 158 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAj 173 " --> pdb=" O ALAAj 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAj 177 " --> pdb=" O METAj 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAj 178 " --> pdb=" O ARGAj 174 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAj 188 " --> pdb=" O TYRAj 184 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAj 197 " --> pdb=" O SERAj 194 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAj 215 " --> pdb=" O VALAj 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAj 216 " --> pdb=" O ARGAj 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAj 217 " --> pdb=" O ALAAj 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAj 218 " --> pdb=" O ARGAj 214 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 66 through 71 Processing helix chain 'Ak' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAk 80 " --> pdb=" O GLNAk 77 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAk 97 " --> pdb=" O TRPAk 93 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 107 through 123 removed outlier: 3.570A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAk 117 " --> pdb=" O ASNAk 113 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAk 151 " --> pdb=" O PROAk 147 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 155 through 162 removed outlier: 3.895A pdb=" N HISAk 162 " --> pdb=" O GLNAk 158 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAk 173 " --> pdb=" O ALAAk 169 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSAk 177 " --> pdb=" O METAk 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAk 178 " --> pdb=" O ARGAk 174 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAk 188 " --> pdb=" O TYRAk 184 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAk 197 " --> pdb=" O SERAk 194 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 210 through 221 removed outlier: 3.692A pdb=" N GLUAk 215 " --> pdb=" O VALAk 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAk 216 " --> pdb=" O ARGAk 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAk 217 " --> pdb=" O ALAAk 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAk 218 " --> pdb=" O ARGAk 214 " (cutoff:3.500A) Processing helix chain 'Al' and resid 66 through 71 Processing helix chain 'Al' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAl 80 " --> pdb=" O GLNAl 77 " (cutoff:3.500A) Processing helix chain 'Al' and resid 86 through 102 removed outlier: 3.605A pdb=" N VALAl 97 " --> pdb=" O TRPAl 93 " (cutoff:3.500A) Processing helix chain 'Al' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAl 111 " --> pdb=" O GLUAl 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAl 117 " --> pdb=" O ASNAl 113 " (cutoff:3.500A) Processing helix chain 'Al' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAl 151 " --> pdb=" O PROAl 147 " (cutoff:3.500A) Processing helix chain 'Al' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAl 162 " --> pdb=" O GLNAl 158 " (cutoff:3.500A) Processing helix chain 'Al' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAl 173 " --> pdb=" O ALAAl 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAl 177 " --> pdb=" O METAl 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAl 178 " --> pdb=" O ARGAl 174 " (cutoff:3.500A) Processing helix chain 'Al' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAl 188 " --> pdb=" O TYRAl 184 " (cutoff:3.500A) Processing helix chain 'Al' and resid 194 through 199 removed outlier: 3.886A pdb=" N ARGAl 197 " --> pdb=" O SERAl 194 " (cutoff:3.500A) Processing helix chain 'Al' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAl 215 " --> pdb=" O VALAl 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAl 216 " --> pdb=" O ARGAl 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAl 217 " --> pdb=" O ALAAl 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAl 218 " --> pdb=" O ARGAl 214 " (cutoff:3.500A) Processing helix chain 'Am' and resid 66 through 71 Processing helix chain 'Am' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAm 80 " --> pdb=" O GLNAm 77 " (cutoff:3.500A) Processing helix chain 'Am' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAm 97 " --> pdb=" O TRPAm 93 " (cutoff:3.500A) Processing helix chain 'Am' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALAm 117 " --> pdb=" O ASNAm 113 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAm 151 " --> pdb=" O PROAm 147 " (cutoff:3.500A) Processing helix chain 'Am' and resid 155 through 162 removed outlier: 3.897A pdb=" N HISAm 162 " --> pdb=" O GLNAm 158 " (cutoff:3.500A) Processing helix chain 'Am' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAm 173 " --> pdb=" O ALAAm 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAm 177 " --> pdb=" O METAm 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAm 178 " --> pdb=" O ARGAm 174 " (cutoff:3.500A) Processing helix chain 'Am' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAm 188 " --> pdb=" O TYRAm 184 " (cutoff:3.500A) Processing helix chain 'Am' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAm 197 " --> pdb=" O SERAm 194 " (cutoff:3.500A) Processing helix chain 'Am' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAm 215 " --> pdb=" O VALAm 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAm 216 " --> pdb=" O ARGAm 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAm 217 " --> pdb=" O ALAAm 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAm 218 " --> pdb=" O ARGAm 214 " (cutoff:3.500A) Processing helix chain 'An' and resid 66 through 71 Processing helix chain 'An' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAn 80 " --> pdb=" O GLNAn 77 " (cutoff:3.500A) Processing helix chain 'An' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAn 97 " --> pdb=" O TRPAn 93 " (cutoff:3.500A) Processing helix chain 'An' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAn 111 " --> pdb=" O GLUAn 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAn 117 " --> pdb=" O ASNAn 113 " (cutoff:3.500A) Processing helix chain 'An' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAn 151 " --> pdb=" O PROAn 147 " (cutoff:3.500A) Processing helix chain 'An' and resid 155 through 162 removed outlier: 3.897A pdb=" N HISAn 162 " --> pdb=" O GLNAn 158 " (cutoff:3.500A) Processing helix chain 'An' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAn 173 " --> pdb=" O ALAAn 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAn 177 " --> pdb=" O METAn 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAn 178 " --> pdb=" O ARGAn 174 " (cutoff:3.500A) Processing helix chain 'An' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAn 188 " --> pdb=" O TYRAn 184 " (cutoff:3.500A) Processing helix chain 'An' and resid 194 through 199 removed outlier: 3.886A pdb=" N ARGAn 197 " --> pdb=" O SERAn 194 " (cutoff:3.500A) Processing helix chain 'An' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAn 215 " --> pdb=" O VALAn 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAn 216 " --> pdb=" O ARGAn 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAn 217 " --> pdb=" O ALAAn 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAn 218 " --> pdb=" O ARGAn 214 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 66 through 71 Processing helix chain 'Ao' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAo 80 " --> pdb=" O GLNAo 77 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAo 97 " --> pdb=" O TRPAo 93 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VALAo 117 " --> pdb=" O ASNAo 113 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAo 151 " --> pdb=" O PROAo 147 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 155 through 162 removed outlier: 3.897A pdb=" N HISAo 162 " --> pdb=" O GLNAo 158 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAo 173 " --> pdb=" O ALAAo 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAo 177 " --> pdb=" O METAo 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAo 178 " --> pdb=" O ARGAo 174 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAo 188 " --> pdb=" O TYRAo 184 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAo 197 " --> pdb=" O SERAo 194 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAo 215 " --> pdb=" O VALAo 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAo 216 " --> pdb=" O ARGAo 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAo 217 " --> pdb=" O ALAAo 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAo 218 " --> pdb=" O ARGAo 214 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 66 through 71 Processing helix chain 'Ap' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAp 80 " --> pdb=" O GLNAp 77 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 86 through 102 removed outlier: 3.605A pdb=" N VALAp 97 " --> pdb=" O TRPAp 93 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAp 111 " --> pdb=" O GLUAp 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAp 117 " --> pdb=" O ASNAp 113 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAp 151 " --> pdb=" O PROAp 147 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAp 162 " --> pdb=" O GLNAp 158 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAp 173 " --> pdb=" O ALAAp 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAp 177 " --> pdb=" O METAp 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAp 178 " --> pdb=" O ARGAp 174 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAp 188 " --> pdb=" O TYRAp 184 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 194 through 199 removed outlier: 3.886A pdb=" N ARGAp 197 " --> pdb=" O SERAp 194 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAp 215 " --> pdb=" O VALAp 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAp 216 " --> pdb=" O ARGAp 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAp 217 " --> pdb=" O ALAAp 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAp 218 " --> pdb=" O ARGAp 214 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 66 through 71 Processing helix chain 'Aq' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAq 80 " --> pdb=" O GLNAq 77 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAq 97 " --> pdb=" O TRPAq 93 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAq 111 " --> pdb=" O GLUAq 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAq 117 " --> pdb=" O ASNAq 113 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAq 151 " --> pdb=" O PROAq 147 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAq 162 " --> pdb=" O GLNAq 158 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAq 173 " --> pdb=" O ALAAq 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAq 177 " --> pdb=" O METAq 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAq 178 " --> pdb=" O ARGAq 174 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAq 188 " --> pdb=" O TYRAq 184 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAq 197 " --> pdb=" O SERAq 194 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAq 215 " --> pdb=" O VALAq 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAq 216 " --> pdb=" O ARGAq 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAq 217 " --> pdb=" O ALAAq 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAq 218 " --> pdb=" O ARGAq 214 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 66 through 71 Processing helix chain 'Ar' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAr 80 " --> pdb=" O GLNAr 77 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAr 97 " --> pdb=" O TRPAr 93 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAr 111 " --> pdb=" O GLUAr 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAr 117 " --> pdb=" O ASNAr 113 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAr 151 " --> pdb=" O PROAr 147 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAr 162 " --> pdb=" O GLNAr 158 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAr 173 " --> pdb=" O ALAAr 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAr 177 " --> pdb=" O METAr 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAr 178 " --> pdb=" O ARGAr 174 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAr 188 " --> pdb=" O TYRAr 184 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAr 197 " --> pdb=" O SERAr 194 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAr 215 " --> pdb=" O VALAr 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAr 216 " --> pdb=" O ARGAr 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAr 217 " --> pdb=" O ALAAr 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAr 218 " --> pdb=" O ARGAr 214 " (cutoff:3.500A) Processing helix chain 'As' and resid 66 through 71 Processing helix chain 'As' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAs 80 " --> pdb=" O GLNAs 77 " (cutoff:3.500A) Processing helix chain 'As' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAs 97 " --> pdb=" O TRPAs 93 " (cutoff:3.500A) Processing helix chain 'As' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAs 117 " --> pdb=" O ASNAs 113 " (cutoff:3.500A) Processing helix chain 'As' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAs 151 " --> pdb=" O PROAs 147 " (cutoff:3.500A) Processing helix chain 'As' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAs 162 " --> pdb=" O GLNAs 158 " (cutoff:3.500A) Processing helix chain 'As' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAs 173 " --> pdb=" O ALAAs 169 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSAs 177 " --> pdb=" O METAs 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAs 178 " --> pdb=" O ARGAs 174 " (cutoff:3.500A) Processing helix chain 'As' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAs 188 " --> pdb=" O TYRAs 184 " (cutoff:3.500A) Processing helix chain 'As' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAs 197 " --> pdb=" O SERAs 194 " (cutoff:3.500A) Processing helix chain 'As' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAs 215 " --> pdb=" O VALAs 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAs 216 " --> pdb=" O ARGAs 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAs 217 " --> pdb=" O ALAAs 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAs 218 " --> pdb=" O ARGAs 214 " (cutoff:3.500A) Processing helix chain 'At' and resid 66 through 71 Processing helix chain 'At' and resid 77 through 81 removed outlier: 3.816A pdb=" N ILEAt 80 " --> pdb=" O GLNAt 77 " (cutoff:3.500A) Processing helix chain 'At' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAt 97 " --> pdb=" O TRPAt 93 " (cutoff:3.500A) Processing helix chain 'At' and resid 107 through 123 removed outlier: 3.572A pdb=" N VALAt 111 " --> pdb=" O GLUAt 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAt 117 " --> pdb=" O ASNAt 113 " (cutoff:3.500A) Processing helix chain 'At' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAt 151 " --> pdb=" O PROAt 147 " (cutoff:3.500A) Processing helix chain 'At' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAt 162 " --> pdb=" O GLNAt 158 " (cutoff:3.500A) Processing helix chain 'At' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAt 173 " --> pdb=" O ALAAt 169 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSAt 177 " --> pdb=" O METAt 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAt 178 " --> pdb=" O ARGAt 174 " (cutoff:3.500A) Processing helix chain 'At' and resid 182 through 188 removed outlier: 3.525A pdb=" N ARGAt 188 " --> pdb=" O TYRAt 184 " (cutoff:3.500A) Processing helix chain 'At' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAt 197 " --> pdb=" O SERAt 194 " (cutoff:3.500A) Processing helix chain 'At' and resid 210 through 221 removed outlier: 3.694A pdb=" N GLUAt 215 " --> pdb=" O VALAt 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAt 216 " --> pdb=" O ARGAt 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAt 217 " --> pdb=" O ALAAt 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAt 218 " --> pdb=" O ARGAt 214 " (cutoff:3.500A) Processing helix chain 'Au' and resid 66 through 71 Processing helix chain 'Au' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAu 80 " --> pdb=" O GLNAu 77 " (cutoff:3.500A) Processing helix chain 'Au' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAu 97 " --> pdb=" O TRPAu 93 " (cutoff:3.500A) Processing helix chain 'Au' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAu 111 " --> pdb=" O GLUAu 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAu 117 " --> pdb=" O ASNAu 113 " (cutoff:3.500A) Processing helix chain 'Au' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAu 151 " --> pdb=" O PROAu 147 " (cutoff:3.500A) Processing helix chain 'Au' and resid 155 through 162 removed outlier: 3.895A pdb=" N HISAu 162 " --> pdb=" O GLNAu 158 " (cutoff:3.500A) Processing helix chain 'Au' and resid 163 through 178 removed outlier: 3.947A pdb=" N METAu 173 " --> pdb=" O ALAAu 169 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSAu 177 " --> pdb=" O METAu 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAu 178 " --> pdb=" O ARGAu 174 " (cutoff:3.500A) Processing helix chain 'Au' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAu 188 " --> pdb=" O TYRAu 184 " (cutoff:3.500A) Processing helix chain 'Au' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAu 197 " --> pdb=" O SERAu 194 " (cutoff:3.500A) Processing helix chain 'Au' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAu 215 " --> pdb=" O VALAu 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAu 216 " --> pdb=" O ARGAu 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAu 217 " --> pdb=" O ALAAu 213 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAu 218 " --> pdb=" O ARGAu 214 " (cutoff:3.500A) Processing helix chain 'Av' and resid 66 through 71 Processing helix chain 'Av' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAv 80 " --> pdb=" O GLNAv 77 " (cutoff:3.500A) Processing helix chain 'Av' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAv 97 " --> pdb=" O TRPAv 93 " (cutoff:3.500A) Processing helix chain 'Av' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAv 111 " --> pdb=" O GLUAv 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAv 117 " --> pdb=" O ASNAv 113 " (cutoff:3.500A) Processing helix chain 'Av' and resid 145 through 151 removed outlier: 3.677A pdb=" N ASNAv 151 " --> pdb=" O PROAv 147 " (cutoff:3.500A) Processing helix chain 'Av' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAv 162 " --> pdb=" O GLNAv 158 " (cutoff:3.500A) Processing helix chain 'Av' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAv 173 " --> pdb=" O ALAAv 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAv 177 " --> pdb=" O METAv 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAv 178 " --> pdb=" O ARGAv 174 " (cutoff:3.500A) Processing helix chain 'Av' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAv 188 " --> pdb=" O TYRAv 184 " (cutoff:3.500A) Processing helix chain 'Av' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAv 197 " --> pdb=" O SERAv 194 " (cutoff:3.500A) Processing helix chain 'Av' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAv 215 " --> pdb=" O VALAv 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAv 216 " --> pdb=" O ARGAv 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAv 217 " --> pdb=" O ALAAv 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAv 218 " --> pdb=" O ARGAv 214 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 66 through 71 Processing helix chain 'Aw' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAw 80 " --> pdb=" O GLNAw 77 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAw 97 " --> pdb=" O TRPAw 93 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAw 111 " --> pdb=" O GLUAw 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAw 117 " --> pdb=" O ASNAw 113 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAw 151 " --> pdb=" O PROAw 147 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAw 162 " --> pdb=" O GLNAw 158 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 163 through 178 removed outlier: 3.945A pdb=" N METAw 173 " --> pdb=" O ALAAw 169 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSAw 177 " --> pdb=" O METAw 173 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLUAw 178 " --> pdb=" O ARGAw 174 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAw 188 " --> pdb=" O TYRAw 184 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAw 197 " --> pdb=" O SERAw 194 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAw 215 " --> pdb=" O VALAw 211 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALAAw 216 " --> pdb=" O ARGAw 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HISAw 217 " --> pdb=" O ALAAw 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAw 218 " --> pdb=" O ARGAw 214 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 66 through 71 Processing helix chain 'Ax' and resid 77 through 81 removed outlier: 3.817A pdb=" N ILEAx 80 " --> pdb=" O GLNAx 77 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 86 through 102 removed outlier: 3.606A pdb=" N VALAx 97 " --> pdb=" O TRPAx 93 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 107 through 123 removed outlier: 3.571A pdb=" N VALAx 111 " --> pdb=" O GLUAx 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAx 117 " --> pdb=" O ASNAx 113 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 145 through 151 removed outlier: 3.678A pdb=" N ASNAx 151 " --> pdb=" O PROAx 147 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 155 through 162 removed outlier: 3.896A pdb=" N HISAx 162 " --> pdb=" O GLNAx 158 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 163 through 178 removed outlier: 3.946A pdb=" N METAx 173 " --> pdb=" O ALAAx 169 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYSAx 177 " --> pdb=" O METAx 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAx 178 " --> pdb=" O ARGAx 174 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 182 through 188 removed outlier: 3.524A pdb=" N ARGAx 188 " --> pdb=" O TYRAx 184 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 194 through 199 removed outlier: 3.885A pdb=" N ARGAx 197 " --> pdb=" O SERAx 194 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 210 through 221 removed outlier: 3.693A pdb=" N GLUAx 215 " --> pdb=" O VALAx 211 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALAAx 216 " --> pdb=" O ARGAx 212 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISAx 217 " --> pdb=" O ALAAx 213 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILEAx 218 " --> pdb=" O ARGAx 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAa 136 " --> pdb=" O GLUAa 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Ab' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAb 136 " --> pdb=" O GLUAb 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Ac' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAc 136 " --> pdb=" O GLUAc 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Ad' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAd 136 " --> pdb=" O GLUAd 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Ae' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAe 136 " --> pdb=" O GLUAe 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Af' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAf 136 " --> pdb=" O GLUAf 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Ag' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAg 136 " --> pdb=" O GLUAg 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Ah' and resid 131 through 136 removed outlier: 4.179A pdb=" N ASPAh 136 " --> pdb=" O GLUAh 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Ai' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAi 136 " --> pdb=" O GLUAi 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Aj' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAj 136 " --> pdb=" O GLUAj 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Ak' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAk 136 " --> pdb=" O GLUAk 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Al' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAl 136 " --> pdb=" O GLUAl 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Am' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAm 136 " --> pdb=" O GLUAm 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'An' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAn 136 " --> pdb=" O GLUAn 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Ao' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAo 136 " --> pdb=" O GLUAo 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ap' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAp 136 " --> pdb=" O GLUAp 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Aq' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAq 136 " --> pdb=" O GLUAq 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Ar' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAr 136 " --> pdb=" O GLUAr 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'As' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAs 136 " --> pdb=" O GLUAs 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'At' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAt 136 " --> pdb=" O GLUAt 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Au' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAu 136 " --> pdb=" O GLUAu 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Av' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAv 136 " --> pdb=" O GLUAv 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Aw' and resid 131 through 136 removed outlier: 4.177A pdb=" N ASPAw 136 " --> pdb=" O GLUAw 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Ax' and resid 131 through 136 removed outlier: 4.178A pdb=" N ASPAx 136 " --> pdb=" O GLUAx 139 " (cutoff:3.500A) 1272 hydrogen bonds defined for protein. 3528 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: 10.16 Time building geometry restraints manager: 13.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7798 1.33 - 1.45: 7924 1.45 - 1.57: 19556 1.57 - 1.69: 2 1.69 - 1.81: 552 Bond restraints: 35832 Sorted by residual: bond pdb=" N GLNAo 158 " pdb=" CA GLNAo 158 " ideal model delta sigma weight residual 1.459 1.416 0.044 1.19e-02 7.06e+03 1.34e+01 bond pdb=" N GLNAd 158 " pdb=" CA GLNAd 158 " ideal model delta sigma weight residual 1.459 1.416 0.044 1.19e-02 7.06e+03 1.34e+01 bond pdb=" N GLNAu 158 " pdb=" CA GLNAu 158 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" N GLNAv 158 " pdb=" CA GLNAv 158 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.19e-02 7.06e+03 1.32e+01 bond pdb=" N GLNAx 158 " pdb=" CA GLNAx 158 " ideal model delta sigma weight residual 1.459 1.416 0.043 1.19e-02 7.06e+03 1.31e+01 ... (remaining 35827 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.05: 1056 104.05 - 111.55: 15656 111.55 - 119.04: 12815 119.04 - 126.54: 18425 126.54 - 134.04: 624 Bond angle restraints: 48576 Sorted by residual: angle pdb=" N VALAd 205 " pdb=" CA VALAd 205 " pdb=" C VALAd 205 " ideal model delta sigma weight residual 108.12 99.78 8.34 1.34e+00 5.57e-01 3.87e+01 angle pdb=" N VALAf 205 " pdb=" CA VALAf 205 " pdb=" C VALAf 205 " ideal model delta sigma weight residual 108.12 99.79 8.33 1.34e+00 5.57e-01 3.87e+01 angle pdb=" N VALAn 205 " pdb=" CA VALAn 205 " pdb=" C VALAn 205 " ideal model delta sigma weight residual 108.12 99.79 8.33 1.34e+00 5.57e-01 3.87e+01 angle pdb=" N VALAt 205 " pdb=" CA VALAt 205 " pdb=" C VALAt 205 " ideal model delta sigma weight residual 108.12 99.79 8.33 1.34e+00 5.57e-01 3.87e+01 angle pdb=" N VALAw 205 " pdb=" CA VALAw 205 " pdb=" C VALAw 205 " ideal model delta sigma weight residual 108.12 99.79 8.33 1.34e+00 5.57e-01 3.86e+01 ... (remaining 48571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 19147 17.50 - 34.99: 2477 34.99 - 52.49: 310 52.49 - 69.98: 26 69.98 - 87.48: 24 Dihedral angle restraints: 21984 sinusoidal: 9144 harmonic: 12840 Sorted by residual: dihedral pdb=" CA METAh 135 " pdb=" C METAh 135 " pdb=" N ASPAh 136 " pdb=" CA ASPAh 136 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA METAl 135 " pdb=" C METAl 135 " pdb=" N ASPAl 136 " pdb=" CA ASPAl 136 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA METAt 135 " pdb=" C METAt 135 " pdb=" N ASPAt 136 " pdb=" CA ASPAt 136 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 21981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3448 0.037 - 0.075: 1357 0.075 - 0.112: 389 0.112 - 0.149: 86 0.149 - 0.187: 24 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CA PROAf 210 " pdb=" N PROAf 210 " pdb=" C PROAf 210 " pdb=" CB PROAf 210 " both_signs ideal model delta sigma weight residual False 2.72 2.90 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA PROAj 210 " pdb=" N PROAj 210 " pdb=" C PROAj 210 " pdb=" CB PROAj 210 " both_signs ideal model delta sigma weight residual False 2.72 2.90 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA PROAs 210 " pdb=" N PROAs 210 " pdb=" C PROAs 210 " pdb=" CB PROAs 210 " both_signs ideal model delta sigma weight residual False 2.72 2.90 -0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 5301 not shown) Planarity restraints: 6288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C METAf 181 " 0.052 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PROAf 182 " -0.130 5.00e-02 4.00e+02 pdb=" CA PROAf 182 " 0.037 5.00e-02 4.00e+02 pdb=" CD PROAf 182 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C METAl 181 " -0.051 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PROAl 182 " 0.130 5.00e-02 4.00e+02 pdb=" CA PROAl 182 " -0.037 5.00e-02 4.00e+02 pdb=" CD PROAl 182 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C METAc 181 " -0.051 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PROAc 182 " 0.130 5.00e-02 4.00e+02 pdb=" CA PROAc 182 " -0.037 5.00e-02 4.00e+02 pdb=" CD PROAc 182 " -0.042 5.00e-02 4.00e+02 ... (remaining 6285 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 15375 2.88 - 3.38: 33690 3.38 - 3.89: 53397 3.89 - 4.39: 64316 4.39 - 4.90: 101744 Nonbonded interactions: 268522 Sorted by model distance: nonbonded pdb=" O PROAh 45 " pdb=" OH TYRAj 143 " model vdw 2.372 2.440 nonbonded pdb=" OH TYRAa 143 " pdb=" O PROAx 45 " model vdw 2.374 2.440 nonbonded pdb=" O PROAd 45 " pdb=" OH TYRAn 143 " model vdw 2.376 2.440 nonbonded pdb=" OH TYRAe 143 " pdb=" O PROAt 45 " model vdw 2.376 2.440 nonbonded pdb=" O PROAb 45 " pdb=" OH TYRAl 143 " model vdw 2.382 2.440 ... (remaining 268517 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 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 7.550 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 82.090 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.350 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: 0.020 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 0.078 35832 Z= 0.535 Angle : 0.963 8.540 48576 Z= 0.610 Chirality : 0.044 0.187 5304 Planarity : 0.008 0.075 6288 Dihedral : 14.435 87.480 13680 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 20.75 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -3.36 (0.11), residues: 4296 helix: -2.06 (0.10), residues: 1824 sheet: 0.80 (0.33), residues: 240 loop : -2.79 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPAj 132 HIS 0.003 0.001 HISAm 69 PHE 0.012 0.003 PHEAx 202 TYR 0.007 0.001 TYRAl 180 ARG 0.006 0.001 ARGAb 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 994 time to evaluate : 3.457 Fit side-chains REVERT: Aa 173 MET cc_start: 0.8521 (tmm) cc_final: 0.8251 (tmm) REVERT: Ab 112 MET cc_start: 0.9289 (mmt) cc_final: 0.8949 (mmt) REVERT: Ab 150 GLU cc_start: 0.8250 (tt0) cc_final: 0.7987 (tt0) REVERT: Ac 129 ASN cc_start: 0.8684 (m-40) cc_final: 0.8394 (m110) REVERT: Ac 173 MET cc_start: 0.8469 (tmm) cc_final: 0.8203 (tmm) REVERT: Ad 112 MET cc_start: 0.9286 (mmt) cc_final: 0.8945 (mmt) REVERT: Ad 150 GLU cc_start: 0.8244 (tt0) cc_final: 0.7978 (tt0) REVERT: Ae 173 MET cc_start: 0.8495 (tmm) cc_final: 0.8237 (tmm) REVERT: Af 112 MET cc_start: 0.9304 (mmt) cc_final: 0.8966 (mmt) REVERT: Af 150 GLU cc_start: 0.8245 (tt0) cc_final: 0.7982 (tt0) REVERT: Ag 173 MET cc_start: 0.8491 (tmm) cc_final: 0.8232 (tmm) REVERT: Ah 112 MET cc_start: 0.9285 (mmt) cc_final: 0.8956 (mmt) REVERT: Ah 150 GLU cc_start: 0.8252 (tt0) cc_final: 0.7991 (tt0) REVERT: Ai 102 ASP cc_start: 0.8405 (t0) cc_final: 0.8189 (t0) REVERT: Ai 157 ARG cc_start: 0.8414 (ptm160) cc_final: 0.8083 (ptm160) REVERT: Ai 173 MET cc_start: 0.8571 (tmm) cc_final: 0.8121 (tmm) REVERT: Aj 102 ASP cc_start: 0.8432 (t0) cc_final: 0.8203 (t0) REVERT: Aj 173 MET cc_start: 0.8445 (tmm) cc_final: 0.7988 (tmm) REVERT: Ak 102 ASP cc_start: 0.8414 (t0) cc_final: 0.8210 (t0) REVERT: Ak 173 MET cc_start: 0.8526 (tmm) cc_final: 0.8016 (tmm) REVERT: Al 102 ASP cc_start: 0.8429 (t0) cc_final: 0.8200 (t0) REVERT: Al 173 MET cc_start: 0.8442 (tmm) cc_final: 0.7976 (tmm) REVERT: Am 102 ASP cc_start: 0.8409 (t0) cc_final: 0.8197 (t0) REVERT: Am 173 MET cc_start: 0.8582 (tmm) cc_final: 0.8093 (tmm) REVERT: An 102 ASP cc_start: 0.8432 (t0) cc_final: 0.8204 (t0) REVERT: An 173 MET cc_start: 0.8439 (tmm) cc_final: 0.7990 (tmm) REVERT: Ao 102 ASP cc_start: 0.8416 (t0) cc_final: 0.8213 (t0) REVERT: Ao 173 MET cc_start: 0.8549 (tmm) cc_final: 0.8039 (tmm) REVERT: Ap 102 ASP cc_start: 0.8433 (t0) cc_final: 0.8211 (t0) REVERT: Ap 173 MET cc_start: 0.8447 (tmm) cc_final: 0.7995 (tmm) REVERT: Aq 72 GLU cc_start: 0.8543 (tt0) cc_final: 0.8247 (tt0) REVERT: Aq 101 TYR cc_start: 0.8520 (m-10) cc_final: 0.8249 (m-10) REVERT: Aq 139 GLU cc_start: 0.7698 (mt-10) cc_final: 0.6964 (pt0) REVERT: Aq 173 MET cc_start: 0.8360 (tmm) cc_final: 0.8074 (tmm) REVERT: Ar 72 GLU cc_start: 0.8628 (tt0) cc_final: 0.8344 (tt0) REVERT: Ar 112 MET cc_start: 0.9322 (mmt) cc_final: 0.8780 (mmt) REVERT: Ar 150 GLU cc_start: 0.8223 (tt0) cc_final: 0.7993 (tt0) REVERT: Ar 173 MET cc_start: 0.8490 (tmm) cc_final: 0.8153 (tmm) REVERT: Ar 201 ASP cc_start: 0.8568 (t0) cc_final: 0.8193 (t0) REVERT: As 72 GLU cc_start: 0.8587 (tt0) cc_final: 0.8288 (tt0) REVERT: As 101 TYR cc_start: 0.8529 (m-10) cc_final: 0.8253 (m-10) REVERT: As 139 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6899 (pt0) REVERT: At 72 GLU cc_start: 0.8628 (tt0) cc_final: 0.8343 (tt0) REVERT: At 112 MET cc_start: 0.9322 (mmt) cc_final: 0.8781 (mmt) REVERT: At 150 GLU cc_start: 0.8225 (tt0) cc_final: 0.7995 (tt0) REVERT: At 173 MET cc_start: 0.8486 (tmm) cc_final: 0.8148 (tmm) REVERT: At 201 ASP cc_start: 0.8572 (t0) cc_final: 0.8214 (t0) REVERT: Au 72 GLU cc_start: 0.8574 (tt0) cc_final: 0.8273 (tt0) REVERT: Au 101 TYR cc_start: 0.8557 (m-10) cc_final: 0.8213 (m-10) REVERT: Au 139 GLU cc_start: 0.7702 (mt-10) cc_final: 0.6912 (pt0) REVERT: Av 72 GLU cc_start: 0.8615 (tt0) cc_final: 0.8331 (tt0) REVERT: Av 112 MET cc_start: 0.9324 (mmt) cc_final: 0.8784 (mmt) REVERT: Av 150 GLU cc_start: 0.8223 (tt0) cc_final: 0.7991 (tt0) REVERT: Av 173 MET cc_start: 0.8495 (tmm) cc_final: 0.8156 (tmm) REVERT: Av 201 ASP cc_start: 0.8568 (t0) cc_final: 0.8207 (t0) REVERT: Aw 72 GLU cc_start: 0.8589 (tt0) cc_final: 0.8283 (tt0) REVERT: Aw 101 TYR cc_start: 0.8527 (m-10) cc_final: 0.8246 (m-10) REVERT: Aw 139 GLU cc_start: 0.7687 (mt-10) cc_final: 0.6898 (pt0) REVERT: Ax 72 GLU cc_start: 0.8613 (tt0) cc_final: 0.8324 (tt0) REVERT: Ax 112 MET cc_start: 0.9316 (mmt) cc_final: 0.8773 (mmt) REVERT: Ax 173 MET cc_start: 0.8497 (tmm) cc_final: 0.8163 (tmm) REVERT: Ax 201 ASP cc_start: 0.8564 (t0) cc_final: 0.8191 (t0) outliers start: 0 outliers final: 0 residues processed: 994 average time/residue: 0.5800 time to fit residues: 864.1286 Evaluate side-chains 940 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 940 time to evaluate : 4.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 3.9990 chunk 327 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 338 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 392 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Aa 158 GLN Ab 158 GLN Ac 69 HIS ** Ac 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 158 GLN Ad 158 GLN Ae 69 HIS Ae 158 GLN Af 158 GLN Ag 69 HIS Ag 158 GLN Ah 158 GLN Ai 69 HIS Ai 151 ASN Ai 158 GLN Aj 69 HIS Aj 158 GLN Ak 69 HIS Ak 151 ASN Ak 158 GLN Al 69 HIS Al 158 GLN Am 69 HIS Am 151 ASN Am 158 GLN An 69 HIS An 158 GLN Ao 69 HIS Ao 151 ASN Ao 158 GLN Ap 69 HIS Ap 158 GLN Aq 158 GLN ** Ar 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 158 GLN As 158 GLN ** At 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 158 GLN Au 158 GLN ** Av 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 158 GLN Aw 158 GLN ** Ax 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 158 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35832 Z= 0.309 Angle : 0.624 5.250 48576 Z= 0.324 Chirality : 0.040 0.138 5304 Planarity : 0.006 0.060 6288 Dihedral : 4.574 21.661 4824 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.11 % Allowed : 16.54 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 4296 helix: -0.59 (0.12), residues: 1800 sheet: -0.61 (0.32), residues: 288 loop : -1.79 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAh 132 HIS 0.002 0.001 HISAu 162 PHE 0.015 0.003 PHEAr 202 TYR 0.011 0.002 TYRAn 180 ARG 0.006 0.001 ARGAc 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 980 time to evaluate : 3.944 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: Aa 108 MET cc_start: 0.9106 (tpt) cc_final: 0.8766 (tpp) REVERT: Aa 201 ASP cc_start: 0.8823 (t0) cc_final: 0.8417 (t0) REVERT: Ab 77 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7552 (tm-30) REVERT: Ab 150 GLU cc_start: 0.8056 (tt0) cc_final: 0.7801 (tt0) REVERT: Ab 181 MET cc_start: 0.8111 (tpp) cc_final: 0.7709 (tpp) REVERT: Ab 201 ASP cc_start: 0.8827 (t0) cc_final: 0.8261 (t0) REVERT: Ac 77 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8188 (tm-30) REVERT: Ac 201 ASP cc_start: 0.8817 (t0) cc_final: 0.8426 (t0) REVERT: Ad 150 GLU cc_start: 0.8056 (tt0) cc_final: 0.7804 (tt0) REVERT: Ad 181 MET cc_start: 0.8106 (tpp) cc_final: 0.7708 (tpp) REVERT: Ad 201 ASP cc_start: 0.8829 (t0) cc_final: 0.8264 (t0) REVERT: Ae 77 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8164 (tm-30) REVERT: Ae 108 MET cc_start: 0.9115 (tpt) cc_final: 0.8773 (tpp) REVERT: Ae 201 ASP cc_start: 0.8822 (t0) cc_final: 0.8422 (t0) REVERT: Af 150 GLU cc_start: 0.8062 (tt0) cc_final: 0.7806 (tt0) REVERT: Af 181 MET cc_start: 0.8147 (tpp) cc_final: 0.7797 (tpp) REVERT: Af 201 ASP cc_start: 0.8831 (t0) cc_final: 0.8260 (t0) REVERT: Ag 77 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8202 (tm-30) REVERT: Ag 108 MET cc_start: 0.9099 (tpt) cc_final: 0.8750 (tpp) REVERT: Ag 201 ASP cc_start: 0.8821 (t0) cc_final: 0.8431 (t0) REVERT: Ah 150 GLU cc_start: 0.8066 (tt0) cc_final: 0.7814 (tt0) REVERT: Ah 181 MET cc_start: 0.8104 (tpp) cc_final: 0.7703 (tpp) REVERT: Ah 201 ASP cc_start: 0.8829 (t0) cc_final: 0.8257 (t0) REVERT: Ai 72 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: Ai 80 ILE cc_start: 0.8726 (pt) cc_final: 0.8393 (pt) REVERT: Ai 173 MET cc_start: 0.8360 (tmm) cc_final: 0.7840 (tmm) REVERT: Aj 72 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: Aj 77 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7904 (tm-30) REVERT: Aj 102 ASP cc_start: 0.8301 (t0) cc_final: 0.8020 (t0) REVERT: Aj 151 ASN cc_start: 0.8897 (m-40) cc_final: 0.8465 (m-40) REVERT: Aj 173 MET cc_start: 0.8213 (tmm) cc_final: 0.7692 (tmm) REVERT: Aj 201 ASP cc_start: 0.8781 (t0) cc_final: 0.8498 (t0) REVERT: Ak 72 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: Ak 77 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8005 (tm-30) REVERT: Ak 79 ASP cc_start: 0.7178 (m-30) cc_final: 0.6930 (m-30) REVERT: Ak 173 MET cc_start: 0.8326 (tmm) cc_final: 0.7819 (tmm) REVERT: Ak 220 MET cc_start: 0.5090 (mmm) cc_final: 0.4886 (mmm) REVERT: Al 72 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: Al 77 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7906 (tm-30) REVERT: Al 102 ASP cc_start: 0.8326 (t0) cc_final: 0.8042 (t0) REVERT: Al 151 ASN cc_start: 0.8889 (m-40) cc_final: 0.8457 (m-40) REVERT: Al 173 MET cc_start: 0.8228 (tmm) cc_final: 0.7707 (tmm) REVERT: Al 201 ASP cc_start: 0.8785 (t0) cc_final: 0.8501 (t0) REVERT: Am 72 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: Am 80 ILE cc_start: 0.8733 (pt) cc_final: 0.8402 (pt) REVERT: Am 173 MET cc_start: 0.8345 (tmm) cc_final: 0.7819 (tmm) REVERT: An 72 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: An 77 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7903 (tm-30) REVERT: An 102 ASP cc_start: 0.8302 (t0) cc_final: 0.8018 (t0) REVERT: An 151 ASN cc_start: 0.8891 (m-40) cc_final: 0.8461 (m-40) REVERT: An 173 MET cc_start: 0.8218 (tmm) cc_final: 0.7693 (tmm) REVERT: An 201 ASP cc_start: 0.8804 (t0) cc_final: 0.8522 (t0) REVERT: Ao 72 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: Ao 80 ILE cc_start: 0.8730 (pt) cc_final: 0.8400 (pt) REVERT: Ao 173 MET cc_start: 0.8333 (tmm) cc_final: 0.7823 (tmm) REVERT: Ap 72 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: Ap 77 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7899 (tm-30) REVERT: Ap 102 ASP cc_start: 0.8303 (t0) cc_final: 0.8022 (t0) REVERT: Ap 151 ASN cc_start: 0.8864 (m-40) cc_final: 0.8441 (m-40) REVERT: Ap 173 MET cc_start: 0.8215 (tmm) cc_final: 0.7697 (tmm) REVERT: Ap 201 ASP cc_start: 0.8782 (t0) cc_final: 0.8498 (t0) REVERT: Aq 72 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: Aq 73 TYR cc_start: 0.8663 (t80) cc_final: 0.8372 (t80) REVERT: Aq 77 GLN cc_start: 0.8418 (tm-30) cc_final: 0.7748 (tm-30) REVERT: Aq 101 TYR cc_start: 0.8189 (m-10) cc_final: 0.7803 (m-10) REVERT: Aq 181 MET cc_start: 0.8209 (tpp) cc_final: 0.7816 (tpp) REVERT: Aq 201 ASP cc_start: 0.8758 (t0) cc_final: 0.8347 (t0) REVERT: Ar 72 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: Ar 77 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8076 (tm-30) REVERT: Ar 129 ASN cc_start: 0.8734 (m-40) cc_final: 0.8457 (m-40) REVERT: Ar 173 MET cc_start: 0.8372 (tmm) cc_final: 0.8159 (tmm) REVERT: Ar 181 MET cc_start: 0.8134 (tpp) cc_final: 0.7817 (tpp) REVERT: Ar 201 ASP cc_start: 0.8753 (t0) cc_final: 0.8338 (t0) REVERT: As 72 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: As 73 TYR cc_start: 0.8652 (t80) cc_final: 0.8362 (t80) REVERT: As 77 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7759 (tm-30) REVERT: As 101 TYR cc_start: 0.8159 (m-10) cc_final: 0.7786 (m-10) REVERT: As 201 ASP cc_start: 0.8758 (t0) cc_final: 0.8349 (t0) REVERT: At 72 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: At 129 ASN cc_start: 0.8733 (m-40) cc_final: 0.8459 (m-40) REVERT: At 181 MET cc_start: 0.8181 (tpp) cc_final: 0.7869 (tpp) REVERT: At 201 ASP cc_start: 0.8728 (t0) cc_final: 0.8311 (t0) REVERT: Au 72 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: Au 73 TYR cc_start: 0.8655 (t80) cc_final: 0.8383 (t80) REVERT: Au 77 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7743 (tm-30) REVERT: Au 101 TYR cc_start: 0.8183 (m-10) cc_final: 0.7796 (m-10) REVERT: Au 181 MET cc_start: 0.8183 (tpp) cc_final: 0.7663 (tpp) REVERT: Au 201 ASP cc_start: 0.8760 (t0) cc_final: 0.8345 (t0) REVERT: Av 72 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: Av 77 GLN cc_start: 0.8282 (tm-30) cc_final: 0.8076 (tm-30) REVERT: Av 129 ASN cc_start: 0.8737 (m-40) cc_final: 0.8461 (m-40) REVERT: Av 181 MET cc_start: 0.8186 (tpp) cc_final: 0.7876 (tpp) REVERT: Av 201 ASP cc_start: 0.8756 (t0) cc_final: 0.8341 (t0) REVERT: Aw 72 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: Aw 73 TYR cc_start: 0.8655 (t80) cc_final: 0.8366 (t80) REVERT: Aw 77 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7758 (tm-30) REVERT: Aw 101 TYR cc_start: 0.8174 (m-10) cc_final: 0.7800 (m-10) REVERT: Aw 201 ASP cc_start: 0.8756 (t0) cc_final: 0.8348 (t0) REVERT: Ax 72 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: Ax 129 ASN cc_start: 0.8730 (m-40) cc_final: 0.8455 (m-40) REVERT: Ax 181 MET cc_start: 0.8132 (tpp) cc_final: 0.7817 (tpp) REVERT: Ax 201 ASP cc_start: 0.8724 (t0) cc_final: 0.8309 (t0) outliers start: 157 outliers final: 52 residues processed: 1048 average time/residue: 0.4827 time to fit residues: 818.6360 Evaluate side-chains 1032 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 964 time to evaluate : 4.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 127 ASN Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 127 ASN Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 127 ASN Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 127 ASN Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 127 ASN Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 127 ASN Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 127 ASN Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 127 ASN Chi-restraints excluded: chain Aj residue 63 THR Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 108 MET Chi-restraints excluded: chain Aj residue 127 ASN Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 127 ASN Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Al residue 63 THR Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 108 MET Chi-restraints excluded: chain Al residue 127 ASN Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 127 ASN Chi-restraints excluded: chain An residue 63 THR Chi-restraints excluded: chain An residue 72 GLU Chi-restraints excluded: chain An residue 108 MET Chi-restraints excluded: chain An residue 127 ASN Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 127 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 63 THR Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 108 MET Chi-restraints excluded: chain Ap residue 127 ASN Chi-restraints excluded: chain Aq residue 63 THR Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 80 ILE Chi-restraints excluded: chain As residue 63 THR Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain Au residue 63 THR Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 80 ILE Chi-restraints excluded: chain Aw residue 63 THR Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 80 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 0.0870 chunk 121 optimal weight: 8.9990 chunk 326 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 393 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 chunk 350 optimal weight: 0.0970 chunk 389 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 315 optimal weight: 0.7980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 69 HIS Ac 69 HIS ** Ac 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 69 HIS Ae 69 HIS ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 69 HIS Ag 69 HIS ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 69 HIS Aj 69 HIS Al 69 HIS An 69 HIS Ap 69 HIS Aq 127 ASN Aq 151 ASN ** Ar 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 151 ASN As 127 ASN As 151 ASN ** At 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 151 ASN Au 127 ASN Au 151 ASN ** Av 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 127 ASN Aw 151 ASN ** Ax 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35832 Z= 0.171 Angle : 0.538 8.095 48576 Z= 0.271 Chirality : 0.037 0.125 5304 Planarity : 0.006 0.060 6288 Dihedral : 4.371 23.829 4824 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.51 % Allowed : 16.85 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4296 helix: 0.20 (0.12), residues: 1800 sheet: -0.41 (0.29), residues: 288 loop : -1.42 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAb 132 HIS 0.002 0.000 HISAt 217 PHE 0.008 0.002 PHEAs 202 TYR 0.008 0.001 TYRAa 180 ARG 0.005 0.000 ARGAx 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 968 time to evaluate : 3.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 201 ASP cc_start: 0.8867 (t0) cc_final: 0.8422 (t0) REVERT: Ab 54 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7395 (ptt) REVERT: Ab 77 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7625 (tm-30) REVERT: Ab 108 MET cc_start: 0.8695 (tpp) cc_final: 0.8443 (tpp) REVERT: Ab 150 GLU cc_start: 0.8118 (tt0) cc_final: 0.7788 (tt0) REVERT: Ab 181 MET cc_start: 0.8138 (tpp) cc_final: 0.7746 (tpp) REVERT: Ab 201 ASP cc_start: 0.8786 (t0) cc_final: 0.8309 (t0) REVERT: Ac 54 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7113 (ptt) REVERT: Ac 201 ASP cc_start: 0.8863 (t0) cc_final: 0.8441 (t0) REVERT: Ad 54 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7378 (ptt) REVERT: Ad 77 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7673 (tm-30) REVERT: Ad 108 MET cc_start: 0.8670 (tpp) cc_final: 0.8418 (tpp) REVERT: Ad 150 GLU cc_start: 0.8122 (tt0) cc_final: 0.7790 (tt0) REVERT: Ad 181 MET cc_start: 0.8043 (tpp) cc_final: 0.7645 (tpp) REVERT: Ad 201 ASP cc_start: 0.8782 (t0) cc_final: 0.8303 (t0) REVERT: Ae 77 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8098 (tm-30) REVERT: Ae 201 ASP cc_start: 0.8869 (t0) cc_final: 0.8428 (t0) REVERT: Af 54 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7332 (ptt) REVERT: Af 77 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7673 (tm-30) REVERT: Af 108 MET cc_start: 0.8679 (tpp) cc_final: 0.8432 (tpp) REVERT: Af 150 GLU cc_start: 0.8130 (tt0) cc_final: 0.7797 (tt0) REVERT: Af 201 ASP cc_start: 0.8786 (t0) cc_final: 0.8315 (t0) REVERT: Ag 54 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7167 (ptt) REVERT: Ag 201 ASP cc_start: 0.8864 (t0) cc_final: 0.8423 (t0) REVERT: Ah 77 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7542 (tm-30) REVERT: Ah 108 MET cc_start: 0.8677 (tpp) cc_final: 0.8420 (tpp) REVERT: Ah 150 GLU cc_start: 0.8135 (tt0) cc_final: 0.7801 (tt0) REVERT: Ah 181 MET cc_start: 0.8041 (tpp) cc_final: 0.7642 (tpp) REVERT: Ah 201 ASP cc_start: 0.8782 (t0) cc_final: 0.8304 (t0) REVERT: Ai 77 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8189 (tp40) REVERT: Ai 80 ILE cc_start: 0.8651 (pt) cc_final: 0.8444 (pt) REVERT: Ai 151 ASN cc_start: 0.8651 (m110) cc_final: 0.8191 (m110) REVERT: Ai 173 MET cc_start: 0.8282 (tmm) cc_final: 0.7798 (tmm) REVERT: Aj 77 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7892 (tm-30) REVERT: Aj 112 MET cc_start: 0.9268 (mmm) cc_final: 0.9060 (mmm) REVERT: Aj 151 ASN cc_start: 0.8756 (m-40) cc_final: 0.8260 (m-40) REVERT: Aj 173 MET cc_start: 0.8150 (tmm) cc_final: 0.7651 (tmm) REVERT: Aj 201 ASP cc_start: 0.8858 (t0) cc_final: 0.8435 (t0) REVERT: Ak 151 ASN cc_start: 0.8684 (m110) cc_final: 0.8259 (m110) REVERT: Ak 173 MET cc_start: 0.8282 (tmm) cc_final: 0.7788 (tmm) REVERT: Al 77 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7911 (tm-30) REVERT: Al 112 MET cc_start: 0.9263 (mmm) cc_final: 0.9054 (mmm) REVERT: Al 151 ASN cc_start: 0.8755 (m-40) cc_final: 0.8257 (m-40) REVERT: Al 173 MET cc_start: 0.8213 (tmm) cc_final: 0.7690 (tmm) REVERT: Al 201 ASP cc_start: 0.8857 (t0) cc_final: 0.8437 (t0) REVERT: Am 77 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8186 (tp40) REVERT: Am 80 ILE cc_start: 0.8655 (pt) cc_final: 0.8449 (pt) REVERT: Am 151 ASN cc_start: 0.8686 (m110) cc_final: 0.8232 (m110) REVERT: Am 173 MET cc_start: 0.8283 (tmm) cc_final: 0.7796 (tmm) REVERT: Am 201 ASP cc_start: 0.8918 (t0) cc_final: 0.8446 (t0) REVERT: An 77 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7894 (tm-30) REVERT: An 112 MET cc_start: 0.9241 (mmm) cc_final: 0.9019 (mmm) REVERT: An 151 ASN cc_start: 0.8759 (m-40) cc_final: 0.8271 (m-40) REVERT: An 173 MET cc_start: 0.8214 (tmm) cc_final: 0.7694 (tmm) REVERT: An 201 ASP cc_start: 0.8859 (t0) cc_final: 0.8455 (t0) REVERT: Ao 77 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8179 (tp40) REVERT: Ao 151 ASN cc_start: 0.8695 (m110) cc_final: 0.8267 (m110) REVERT: Ao 173 MET cc_start: 0.8292 (tmm) cc_final: 0.7794 (tmm) REVERT: Ao 201 ASP cc_start: 0.8928 (t0) cc_final: 0.8414 (t0) REVERT: Ap 72 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: Ap 77 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7912 (tm-30) REVERT: Ap 112 MET cc_start: 0.9240 (mmm) cc_final: 0.9025 (mmm) REVERT: Ap 151 ASN cc_start: 0.8758 (m-40) cc_final: 0.8263 (m-40) REVERT: Ap 173 MET cc_start: 0.8158 (tmm) cc_final: 0.7655 (tmm) REVERT: Ap 201 ASP cc_start: 0.8856 (t0) cc_final: 0.8434 (t0) REVERT: Aq 72 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: Aq 77 GLN cc_start: 0.8407 (tm-30) cc_final: 0.7918 (tm-30) REVERT: Aq 101 TYR cc_start: 0.8136 (m-10) cc_final: 0.7800 (m-10) REVERT: Aq 142 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: Aq 181 MET cc_start: 0.8190 (tpp) cc_final: 0.7730 (tpp) REVERT: Aq 201 ASP cc_start: 0.8802 (t0) cc_final: 0.8326 (t0) REVERT: Ar 72 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: Ar 129 ASN cc_start: 0.8687 (m-40) cc_final: 0.8378 (m-40) REVERT: Ar 142 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: Ar 201 ASP cc_start: 0.8806 (t0) cc_final: 0.8347 (t0) REVERT: As 72 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: As 77 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7937 (tm-30) REVERT: As 101 TYR cc_start: 0.8119 (m-10) cc_final: 0.7788 (m-10) REVERT: As 142 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: As 201 ASP cc_start: 0.8803 (t0) cc_final: 0.8330 (t0) REVERT: At 72 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: At 129 ASN cc_start: 0.8689 (m-40) cc_final: 0.8381 (m-40) REVERT: At 142 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: At 201 ASP cc_start: 0.8811 (t0) cc_final: 0.8360 (t0) REVERT: Au 72 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: Au 77 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7920 (tm-30) REVERT: Au 101 TYR cc_start: 0.8128 (m-10) cc_final: 0.7853 (m-10) REVERT: Au 142 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: Au 181 MET cc_start: 0.8107 (tpp) cc_final: 0.7583 (tpp) REVERT: Au 201 ASP cc_start: 0.8807 (t0) cc_final: 0.8300 (t0) REVERT: Av 72 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: Av 129 ASN cc_start: 0.8690 (m-40) cc_final: 0.8380 (m-40) REVERT: Av 142 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: Av 151 ASN cc_start: 0.8487 (m110) cc_final: 0.8051 (m-40) REVERT: Av 201 ASP cc_start: 0.8808 (t0) cc_final: 0.8345 (t0) REVERT: Aw 72 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: Aw 77 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7937 (tm-30) REVERT: Aw 101 TYR cc_start: 0.8095 (m-10) cc_final: 0.7750 (m-10) REVERT: Aw 142 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: Aw 201 ASP cc_start: 0.8801 (t0) cc_final: 0.8326 (t0) REVERT: Ax 72 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: Ax 129 ASN cc_start: 0.8702 (m-40) cc_final: 0.8399 (m-40) REVERT: Ax 142 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: Ax 151 ASN cc_start: 0.8418 (m110) cc_final: 0.8066 (m-40) REVERT: Ax 201 ASP cc_start: 0.8808 (t0) cc_final: 0.8360 (t0) outliers start: 172 outliers final: 55 residues processed: 1063 average time/residue: 0.4632 time to fit residues: 789.8184 Evaluate side-chains 1037 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 960 time to evaluate : 3.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 63 THR Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Al residue 63 THR Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 108 MET Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 155 THR Chi-restraints excluded: chain An residue 63 THR Chi-restraints excluded: chain An residue 108 MET Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 63 THR Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Aq residue 63 THR Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 142 GLU Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain As residue 63 THR Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 142 GLU Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 142 GLU Chi-restraints excluded: chain Au residue 63 THR Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 142 GLU Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 142 GLU Chi-restraints excluded: chain Aw residue 63 THR Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 142 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 394 optimal weight: 2.9990 chunk 417 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 373 optimal weight: 0.1980 chunk 112 optimal weight: 5.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Aa 127 ASN Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 69 HIS ** Ac 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 69 HIS ** Ad 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 69 HIS Ae 127 ASN Af 69 HIS ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 69 HIS Ag 127 ASN Ah 69 HIS ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS Aj 127 ASN Al 69 HIS Al 127 ASN An 69 HIS An 127 ASN Ap 69 HIS Ap 127 ASN Aq 151 ASN As 151 ASN Au 151 ASN ** Av 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 151 ASN ** Ax 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35832 Z= 0.228 Angle : 0.563 5.901 48576 Z= 0.281 Chirality : 0.038 0.123 5304 Planarity : 0.006 0.059 6288 Dihedral : 4.303 27.959 4824 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.30 % Allowed : 18.61 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 4296 helix: 0.83 (0.13), residues: 1656 sheet: 0.03 (0.28), residues: 288 loop : -1.08 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAs 132 HIS 0.002 0.001 HISAd 217 PHE 0.012 0.002 PHEAc 163 TYR 0.018 0.001 TYRAi 73 ARG 0.006 0.000 ARGAr 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 985 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 201 ASP cc_start: 0.8878 (t0) cc_final: 0.8525 (t0) REVERT: Ab 54 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6949 (ptt) REVERT: Ab 77 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7754 (tm-30) REVERT: Ab 181 MET cc_start: 0.8241 (tpp) cc_final: 0.7800 (tpp) REVERT: Ab 201 ASP cc_start: 0.8797 (t0) cc_final: 0.8279 (t0) REVERT: Ac 54 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6946 (ptt) REVERT: Ac 112 MET cc_start: 0.9126 (mmt) cc_final: 0.8801 (mmt) REVERT: Ac 201 ASP cc_start: 0.8892 (t0) cc_final: 0.8511 (t0) REVERT: Ad 54 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6954 (ptt) REVERT: Ad 77 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7750 (tm-30) REVERT: Ad 181 MET cc_start: 0.8097 (tpp) cc_final: 0.7660 (tpp) REVERT: Ad 201 ASP cc_start: 0.8795 (t0) cc_final: 0.8273 (t0) REVERT: Ae 77 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8123 (tm-30) REVERT: Ae 201 ASP cc_start: 0.8900 (t0) cc_final: 0.8518 (t0) REVERT: Af 54 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6908 (ptt) REVERT: Af 77 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7750 (tm-30) REVERT: Af 201 ASP cc_start: 0.8797 (t0) cc_final: 0.8277 (t0) REVERT: Ag 54 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6827 (ptt) REVERT: Ag 77 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8109 (tm-30) REVERT: Ag 201 ASP cc_start: 0.8900 (t0) cc_final: 0.8520 (t0) REVERT: Ah 77 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7666 (tm-30) REVERT: Ah 181 MET cc_start: 0.8098 (tpp) cc_final: 0.7824 (tpp) REVERT: Ah 201 ASP cc_start: 0.8796 (t0) cc_final: 0.8279 (t0) REVERT: Ai 56 MET cc_start: 0.8165 (mmt) cc_final: 0.7881 (mmt) REVERT: Ai 72 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8312 (tt0) REVERT: Ai 77 GLN cc_start: 0.8519 (tm-30) cc_final: 0.7822 (tp-100) REVERT: Ai 151 ASN cc_start: 0.8657 (m110) cc_final: 0.8215 (m110) REVERT: Ai 173 MET cc_start: 0.8463 (tmm) cc_final: 0.8024 (tmm) REVERT: Ai 201 ASP cc_start: 0.8995 (t0) cc_final: 0.8494 (t0) REVERT: Aj 77 GLN cc_start: 0.8376 (tm-30) cc_final: 0.7523 (tm-30) REVERT: Aj 134 MET cc_start: 0.8131 (ttp) cc_final: 0.7722 (ttp) REVERT: Aj 136 ASP cc_start: 0.8312 (t0) cc_final: 0.8095 (t0) REVERT: Aj 151 ASN cc_start: 0.8720 (m-40) cc_final: 0.8368 (m-40) REVERT: Aj 173 MET cc_start: 0.8321 (tmm) cc_final: 0.7894 (tmm) REVERT: Aj 201 ASP cc_start: 0.8930 (t0) cc_final: 0.8498 (t0) REVERT: Ak 56 MET cc_start: 0.8133 (mmt) cc_final: 0.7850 (mmt) REVERT: Ak 72 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: Ak 151 ASN cc_start: 0.8693 (m110) cc_final: 0.8288 (m-40) REVERT: Ak 173 MET cc_start: 0.8466 (tmm) cc_final: 0.7997 (tmm) REVERT: Al 72 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: Al 77 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7573 (tm-30) REVERT: Al 134 MET cc_start: 0.8145 (ttp) cc_final: 0.7790 (ttp) REVERT: Al 136 ASP cc_start: 0.8346 (t0) cc_final: 0.8115 (t0) REVERT: Al 151 ASN cc_start: 0.8713 (m-40) cc_final: 0.8361 (m-40) REVERT: Al 173 MET cc_start: 0.8328 (tmm) cc_final: 0.7896 (tmm) REVERT: Al 201 ASP cc_start: 0.8931 (t0) cc_final: 0.8501 (t0) REVERT: Am 56 MET cc_start: 0.8131 (mmt) cc_final: 0.7840 (mmt) REVERT: Am 72 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: Am 77 GLN cc_start: 0.8531 (tm-30) cc_final: 0.7844 (tp-100) REVERT: Am 151 ASN cc_start: 0.8658 (m110) cc_final: 0.8221 (m110) REVERT: Am 173 MET cc_start: 0.8474 (tmm) cc_final: 0.8010 (tmm) REVERT: An 72 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: An 77 GLN cc_start: 0.8386 (tm-30) cc_final: 0.7505 (tm-30) REVERT: An 134 MET cc_start: 0.8145 (ttp) cc_final: 0.7759 (ttp) REVERT: An 136 ASP cc_start: 0.8319 (t0) cc_final: 0.8104 (t0) REVERT: An 151 ASN cc_start: 0.8719 (m-40) cc_final: 0.8358 (m-40) REVERT: An 173 MET cc_start: 0.8320 (tmm) cc_final: 0.7897 (tmm) REVERT: An 201 ASP cc_start: 0.8931 (t0) cc_final: 0.8502 (t0) REVERT: Ao 56 MET cc_start: 0.8128 (mmt) cc_final: 0.7837 (mmt) REVERT: Ao 72 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: Ao 77 GLN cc_start: 0.8522 (tm-30) cc_final: 0.7811 (tp-100) REVERT: Ao 151 ASN cc_start: 0.8667 (m110) cc_final: 0.8260 (m-40) REVERT: Ao 173 MET cc_start: 0.8475 (tmm) cc_final: 0.8003 (tmm) REVERT: Ao 201 ASP cc_start: 0.8971 (t0) cc_final: 0.8537 (t0) REVERT: Ap 72 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: Ap 77 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7530 (tm-30) REVERT: Ap 134 MET cc_start: 0.8151 (ttp) cc_final: 0.7762 (ttp) REVERT: Ap 136 ASP cc_start: 0.8324 (t0) cc_final: 0.8109 (t0) REVERT: Ap 151 ASN cc_start: 0.8720 (m-40) cc_final: 0.8371 (m-40) REVERT: Ap 173 MET cc_start: 0.8321 (tmm) cc_final: 0.7901 (tmm) REVERT: Ap 201 ASP cc_start: 0.8925 (t0) cc_final: 0.8493 (t0) REVERT: Aq 72 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: Aq 101 TYR cc_start: 0.8288 (m-10) cc_final: 0.7972 (m-10) REVERT: Aq 142 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: Aq 181 MET cc_start: 0.8165 (tpp) cc_final: 0.7557 (tpp) REVERT: Aq 201 ASP cc_start: 0.8821 (t0) cc_final: 0.8338 (t0) REVERT: Ar 72 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: Ar 142 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: Ar 201 ASP cc_start: 0.8805 (t0) cc_final: 0.8433 (t0) REVERT: As 72 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: As 99 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7493 (tp) REVERT: As 101 TYR cc_start: 0.8213 (m-10) cc_final: 0.7929 (m-10) REVERT: As 142 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: As 201 ASP cc_start: 0.8822 (t0) cc_final: 0.8336 (t0) REVERT: At 72 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: At 142 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: At 201 ASP cc_start: 0.8799 (t0) cc_final: 0.8428 (t0) REVERT: Au 72 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: Au 101 TYR cc_start: 0.8284 (m-10) cc_final: 0.7970 (m-10) REVERT: Au 142 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: Au 181 MET cc_start: 0.8201 (tpp) cc_final: 0.7590 (tpp) REVERT: Au 201 ASP cc_start: 0.8825 (t0) cc_final: 0.8339 (t0) REVERT: Av 72 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: Av 142 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: Av 181 MET cc_start: 0.7931 (tpp) cc_final: 0.7552 (tpp) REVERT: Av 201 ASP cc_start: 0.8795 (t0) cc_final: 0.8418 (t0) REVERT: Aw 72 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: Aw 99 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7492 (tp) REVERT: Aw 101 TYR cc_start: 0.8210 (m-10) cc_final: 0.7923 (m-10) REVERT: Aw 142 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: Aw 201 ASP cc_start: 0.8820 (t0) cc_final: 0.8333 (t0) REVERT: Ax 72 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: Ax 142 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: Ax 201 ASP cc_start: 0.8807 (t0) cc_final: 0.8441 (t0) outliers start: 126 outliers final: 67 residues processed: 1030 average time/residue: 0.4486 time to fit residues: 732.8402 Evaluate side-chains 1076 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 979 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 133 VAL Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 108 MET Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 108 MET Chi-restraints excluded: chain Al residue 121 GLU Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 72 GLU Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 108 MET Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 108 MET Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 142 GLU Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 142 GLU Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 142 GLU Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 142 GLU Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 142 GLU Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 99 LEU Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 142 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 310 optimal weight: 0.0020 chunk 172 optimal weight: 4.9990 chunk 356 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 374 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Ab 69 HIS Ac 69 HIS Ad 69 HIS Ae 69 HIS Af 69 HIS Ag 69 HIS Ah 69 HIS Aj 69 HIS Al 69 HIS An 69 HIS Ap 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 35832 Z= 0.376 Angle : 0.622 5.386 48576 Z= 0.315 Chirality : 0.040 0.124 5304 Planarity : 0.006 0.058 6288 Dihedral : 4.535 27.774 4824 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.85 % Allowed : 19.44 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4296 helix: 0.59 (0.13), residues: 1656 sheet: -0.05 (0.29), residues: 288 loop : -1.07 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPAh 93 HIS 0.002 0.001 HISAf 217 PHE 0.017 0.003 PHEAf 163 TYR 0.017 0.002 TYRAo 73 ARG 0.005 0.001 ARGAx 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1101 time to evaluate : 4.201 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: Aa 77 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8388 (tp40) REVERT: Aa 201 ASP cc_start: 0.8922 (t0) cc_final: 0.8562 (t0) REVERT: Ab 54 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6839 (ptt) REVERT: Ab 99 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7472 (tp) REVERT: Ab 181 MET cc_start: 0.8255 (tpp) cc_final: 0.7860 (tpp) REVERT: Ab 201 ASP cc_start: 0.8878 (t0) cc_final: 0.8371 (t0) REVERT: Ac 54 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6756 (ptt) REVERT: Ac 77 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8227 (tm-30) REVERT: Ac 201 ASP cc_start: 0.8948 (t0) cc_final: 0.8579 (t0) REVERT: Ad 54 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6825 (ptt) REVERT: Ad 99 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7467 (tp) REVERT: Ad 181 MET cc_start: 0.8175 (tpp) cc_final: 0.7882 (tpp) REVERT: Ad 201 ASP cc_start: 0.8876 (t0) cc_final: 0.8381 (t0) REVERT: Ae 77 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8231 (tm-30) REVERT: Ae 201 ASP cc_start: 0.8922 (t0) cc_final: 0.8564 (t0) REVERT: Af 54 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6862 (ptt) REVERT: Af 99 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7448 (tp) REVERT: Af 201 ASP cc_start: 0.8879 (t0) cc_final: 0.8380 (t0) REVERT: Ag 54 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6769 (ptt) REVERT: Ag 77 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8245 (tm-30) REVERT: Ag 201 ASP cc_start: 0.8919 (t0) cc_final: 0.8566 (t0) REVERT: Ah 99 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7467 (tp) REVERT: Ah 181 MET cc_start: 0.8187 (tpp) cc_final: 0.7886 (tpp) REVERT: Ah 201 ASP cc_start: 0.8874 (t0) cc_final: 0.8371 (t0) REVERT: Ai 72 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: Ai 121 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: Ai 173 MET cc_start: 0.8624 (tmm) cc_final: 0.8307 (tmm) REVERT: Aj 72 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: Aj 151 ASN cc_start: 0.8530 (m-40) cc_final: 0.8329 (m-40) REVERT: Aj 173 MET cc_start: 0.8528 (tmm) cc_final: 0.8241 (tmm) REVERT: Aj 201 ASP cc_start: 0.8883 (t0) cc_final: 0.8555 (t0) REVERT: Ak 72 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: Ak 77 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8397 (tm-30) REVERT: Ak 121 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: Ak 173 MET cc_start: 0.8644 (tmm) cc_final: 0.8284 (tmm) REVERT: Al 72 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: Al 151 ASN cc_start: 0.8529 (m-40) cc_final: 0.8326 (m-40) REVERT: Al 173 MET cc_start: 0.8527 (tmm) cc_final: 0.8236 (tmm) REVERT: Al 201 ASP cc_start: 0.8884 (t0) cc_final: 0.8556 (t0) REVERT: Am 72 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: Am 121 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: Am 151 ASN cc_start: 0.8666 (m110) cc_final: 0.8260 (m-40) REVERT: Am 173 MET cc_start: 0.8629 (tmm) cc_final: 0.8269 (tmm) REVERT: An 72 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: An 151 ASN cc_start: 0.8530 (m-40) cc_final: 0.8325 (m-40) REVERT: An 173 MET cc_start: 0.8528 (tmm) cc_final: 0.8238 (tmm) REVERT: An 201 ASP cc_start: 0.8882 (t0) cc_final: 0.8556 (t0) REVERT: Ao 72 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: Ao 121 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: Ao 173 MET cc_start: 0.8643 (tmm) cc_final: 0.8283 (tmm) REVERT: Ap 72 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: Ap 173 MET cc_start: 0.8529 (tmm) cc_final: 0.8243 (tmm) REVERT: Ap 201 ASP cc_start: 0.8880 (t0) cc_final: 0.8551 (t0) REVERT: Aq 72 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: Aq 77 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8345 (tm-30) REVERT: Aq 99 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7513 (tp) REVERT: Aq 101 TYR cc_start: 0.8388 (m-10) cc_final: 0.8047 (m-10) REVERT: Aq 139 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6358 (pt0) REVERT: Aq 142 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: Aq 151 ASN cc_start: 0.8452 (m110) cc_final: 0.7993 (m-40) REVERT: Aq 172 GLU cc_start: 0.8041 (tt0) cc_final: 0.7791 (tt0) REVERT: Aq 181 MET cc_start: 0.8183 (tpp) cc_final: 0.7646 (tpp) REVERT: Aq 201 ASP cc_start: 0.8832 (t0) cc_final: 0.8370 (t0) REVERT: Ar 72 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: Ar 77 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8300 (tm-30) REVERT: Ar 99 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7348 (tp) REVERT: Ar 129 ASN cc_start: 0.8674 (m-40) cc_final: 0.8402 (m-40) REVERT: Ar 142 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: Ar 201 ASP cc_start: 0.8788 (t0) cc_final: 0.8544 (t0) REVERT: As 72 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: As 77 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8337 (tm-30) REVERT: As 101 TYR cc_start: 0.8358 (m-10) cc_final: 0.8017 (m-10) REVERT: As 139 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6363 (pt0) REVERT: As 142 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: As 151 ASN cc_start: 0.8465 (m110) cc_final: 0.8006 (m-40) REVERT: As 172 GLU cc_start: 0.8007 (tt0) cc_final: 0.7771 (tt0) REVERT: As 201 ASP cc_start: 0.8854 (t0) cc_final: 0.8384 (t0) REVERT: At 72 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: At 77 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8285 (tm-30) REVERT: At 99 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7343 (tp) REVERT: At 129 ASN cc_start: 0.8674 (m-40) cc_final: 0.8400 (m-40) REVERT: At 142 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: At 197 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7709 (ptm160) REVERT: At 201 ASP cc_start: 0.8781 (t0) cc_final: 0.8532 (t0) REVERT: Au 72 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: Au 77 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8354 (tm-30) REVERT: Au 99 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7507 (tp) REVERT: Au 101 TYR cc_start: 0.8363 (m-10) cc_final: 0.7961 (m-10) REVERT: Au 139 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6362 (pt0) REVERT: Au 142 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: Au 151 ASN cc_start: 0.8516 (m110) cc_final: 0.8047 (m-40) REVERT: Au 172 GLU cc_start: 0.8036 (tt0) cc_final: 0.7784 (tt0) REVERT: Au 181 MET cc_start: 0.8217 (tpp) cc_final: 0.7721 (tpp) REVERT: Au 201 ASP cc_start: 0.8832 (t0) cc_final: 0.8369 (t0) REVERT: Av 72 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: Av 77 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8297 (tm-30) REVERT: Av 99 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7332 (tp) REVERT: Av 142 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: Av 201 ASP cc_start: 0.8782 (t0) cc_final: 0.8533 (t0) REVERT: Aw 72 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: Aw 77 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8328 (tm-30) REVERT: Aw 101 TYR cc_start: 0.8381 (m-10) cc_final: 0.8043 (m-10) REVERT: Aw 139 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6363 (pt0) REVERT: Aw 142 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: Aw 151 ASN cc_start: 0.8464 (m110) cc_final: 0.8009 (m-40) REVERT: Aw 172 GLU cc_start: 0.8002 (tt0) cc_final: 0.7767 (tt0) REVERT: Aw 201 ASP cc_start: 0.8852 (t0) cc_final: 0.8380 (t0) REVERT: Ax 72 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: Ax 77 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8280 (tm-30) REVERT: Ax 99 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7336 (tp) REVERT: Ax 142 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: Ax 197 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7712 (ptm160) REVERT: Ax 201 ASP cc_start: 0.8789 (t0) cc_final: 0.8546 (t0) outliers start: 147 outliers final: 84 residues processed: 1160 average time/residue: 0.4954 time to fit residues: 907.7063 Evaluate side-chains 1218 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1091 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ab residue 142 GLU Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 80 ILE Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 142 GLU Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 99 LEU Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Ad residue 121 GLU Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ad residue 142 GLU Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 142 GLU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 142 GLU Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 142 GLU Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 106 THR Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 142 GLU Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 121 GLU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 108 MET Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 121 GLU Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 108 MET Chi-restraints excluded: chain Al residue 121 GLU Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 121 GLU Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 72 GLU Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 108 MET Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 121 GLU Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 108 MET Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 121 GLU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 142 GLU Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 121 GLU Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 142 GLU Chi-restraints excluded: chain As residue 175 ASN Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 99 LEU Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 142 GLU Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 121 GLU Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 142 GLU Chi-restraints excluded: chain Au residue 175 ASN Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 99 LEU Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 142 GLU Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 121 GLU Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Aw residue 175 ASN Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 99 LEU Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 142 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 4.9990 chunk 376 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 245 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 417 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 34 optimal weight: 0.3980 chunk 138 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Ac 69 HIS Ae 69 HIS Ag 69 HIS ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 175 ASN Aj 69 HIS ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 175 ASN Al 69 HIS Am 175 ASN An 69 HIS ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 175 ASN Ap 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 151 ASN At 175 ASN Au 151 ASN Av 175 ASN Aw 151 ASN Ax 175 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35832 Z= 0.195 Angle : 0.551 8.913 48576 Z= 0.272 Chirality : 0.037 0.126 5304 Planarity : 0.006 0.059 6288 Dihedral : 4.324 26.082 4824 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.77 % Allowed : 20.34 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 4296 helix: 0.81 (0.13), residues: 1656 sheet: 0.28 (0.28), residues: 288 loop : -0.89 (0.14), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAf 132 HIS 0.002 0.000 HISAd 217 PHE 0.009 0.002 PHEAs 202 TYR 0.018 0.001 TYRAm 73 ARG 0.006 0.000 ARGAt 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1049 time to evaluate : 3.694 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: Aa 54 MET cc_start: 0.6592 (ptt) cc_final: 0.5994 (ptt) REVERT: Aa 77 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8322 (tp40) REVERT: Aa 99 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7470 (tp) REVERT: Aa 112 MET cc_start: 0.9235 (mmt) cc_final: 0.8807 (mmt) REVERT: Aa 151 ASN cc_start: 0.7992 (m-40) cc_final: 0.7682 (m-40) REVERT: Aa 190 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7279 (tt) REVERT: Aa 201 ASP cc_start: 0.8909 (t0) cc_final: 0.8502 (t0) REVERT: Ab 54 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6724 (ptt) REVERT: Ab 77 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8189 (tm-30) REVERT: Ab 99 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7473 (tp) REVERT: Ab 181 MET cc_start: 0.8186 (tpp) cc_final: 0.7779 (tpp) REVERT: Ab 201 ASP cc_start: 0.8891 (t0) cc_final: 0.8383 (t0) REVERT: Ac 54 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6448 (ptt) REVERT: Ac 112 MET cc_start: 0.9214 (mmt) cc_final: 0.8807 (mmt) REVERT: Ac 190 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7273 (tt) REVERT: Ac 201 ASP cc_start: 0.8899 (t0) cc_final: 0.8519 (t0) REVERT: Ad 54 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6719 (ptt) REVERT: Ad 77 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8191 (tm-30) REVERT: Ad 99 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7462 (tp) REVERT: Ad 181 MET cc_start: 0.8096 (tpp) cc_final: 0.7824 (tpp) REVERT: Ad 201 ASP cc_start: 0.8895 (t0) cc_final: 0.8390 (t0) REVERT: Ae 54 MET cc_start: 0.6506 (ptt) cc_final: 0.5905 (ptt) REVERT: Ae 76 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8180 (mm-40) REVERT: Ae 99 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7420 (tp) REVERT: Ae 112 MET cc_start: 0.9235 (mmt) cc_final: 0.8797 (mmt) REVERT: Ae 151 ASN cc_start: 0.7997 (m-40) cc_final: 0.7686 (m-40) REVERT: Ae 190 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7278 (tt) REVERT: Ae 201 ASP cc_start: 0.8910 (t0) cc_final: 0.8527 (t0) REVERT: Af 54 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6745 (ptt) REVERT: Af 77 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8165 (tm-30) REVERT: Af 99 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7461 (tp) REVERT: Af 201 ASP cc_start: 0.8899 (t0) cc_final: 0.8397 (t0) REVERT: Ag 54 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6447 (ptt) REVERT: Ag 99 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7477 (tp) REVERT: Ag 112 MET cc_start: 0.9234 (mmt) cc_final: 0.8804 (mmt) REVERT: Ag 151 ASN cc_start: 0.7994 (m-40) cc_final: 0.7690 (m-40) REVERT: Ag 190 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7277 (tt) REVERT: Ag 201 ASP cc_start: 0.8909 (t0) cc_final: 0.8511 (t0) REVERT: Ah 77 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7892 (tm-30) REVERT: Ah 99 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7465 (tp) REVERT: Ah 135 MET cc_start: 0.7390 (mtt) cc_final: 0.7122 (mtp) REVERT: Ah 181 MET cc_start: 0.8092 (tpp) cc_final: 0.7824 (tpp) REVERT: Ah 201 ASP cc_start: 0.8894 (t0) cc_final: 0.8389 (t0) REVERT: Ai 72 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: Ai 173 MET cc_start: 0.8539 (tmm) cc_final: 0.8202 (tmm) REVERT: Aj 72 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: Aj 77 GLN cc_start: 0.8435 (tm-30) cc_final: 0.7738 (tm-30) REVERT: Aj 151 ASN cc_start: 0.8491 (m-40) cc_final: 0.8194 (m-40) REVERT: Aj 173 MET cc_start: 0.8423 (tmm) cc_final: 0.8101 (tmm) REVERT: Aj 201 ASP cc_start: 0.8873 (t0) cc_final: 0.8502 (t0) REVERT: Ak 72 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: Ak 77 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8428 (tp40) REVERT: Ak 173 MET cc_start: 0.8529 (tmm) cc_final: 0.8114 (tmm) REVERT: Al 72 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: Al 77 GLN cc_start: 0.8443 (tm-30) cc_final: 0.7736 (tm-30) REVERT: Al 151 ASN cc_start: 0.8490 (m-40) cc_final: 0.8192 (m-40) REVERT: Al 173 MET cc_start: 0.8406 (tmm) cc_final: 0.8059 (tmm) REVERT: Al 201 ASP cc_start: 0.8876 (t0) cc_final: 0.8486 (t0) REVERT: Am 72 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: Am 151 ASN cc_start: 0.8691 (m110) cc_final: 0.8243 (m110) REVERT: Am 173 MET cc_start: 0.8525 (tmm) cc_final: 0.8118 (tmm) REVERT: An 72 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: An 77 GLN cc_start: 0.8443 (tm-30) cc_final: 0.7736 (tm-30) REVERT: An 151 ASN cc_start: 0.8491 (m-40) cc_final: 0.8192 (m-40) REVERT: An 173 MET cc_start: 0.8424 (tmm) cc_final: 0.8089 (tmm) REVERT: An 201 ASP cc_start: 0.8900 (t0) cc_final: 0.8498 (t0) REVERT: Ao 72 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: Ao 173 MET cc_start: 0.8531 (tmm) cc_final: 0.8115 (tmm) REVERT: Ap 72 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: Ap 77 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7746 (tm-30) REVERT: Ap 173 MET cc_start: 0.8427 (tmm) cc_final: 0.8091 (tmm) REVERT: Ap 201 ASP cc_start: 0.8871 (t0) cc_final: 0.8500 (t0) REVERT: Aq 72 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: Aq 99 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7498 (tp) REVERT: Aq 139 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5986 (pt0) REVERT: Aq 142 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: Aq 151 ASN cc_start: 0.8340 (m110) cc_final: 0.7960 (m-40) REVERT: Aq 181 MET cc_start: 0.8079 (tpp) cc_final: 0.7560 (tpp) REVERT: Aq 201 ASP cc_start: 0.8867 (t0) cc_final: 0.8363 (t0) REVERT: Ar 72 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: Ar 129 ASN cc_start: 0.8634 (m-40) cc_final: 0.8216 (m-40) REVERT: Ar 134 MET cc_start: 0.6969 (ttp) cc_final: 0.6512 (ttp) REVERT: Ar 142 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: Ar 190 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7424 (tt) REVERT: Ar 201 ASP cc_start: 0.8821 (t0) cc_final: 0.8586 (t0) REVERT: As 72 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: As 99 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7503 (tp) REVERT: As 139 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6055 (pt0) REVERT: As 142 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: As 151 ASN cc_start: 0.8301 (m-40) cc_final: 0.7985 (m-40) REVERT: As 201 ASP cc_start: 0.8868 (t0) cc_final: 0.8361 (t0) REVERT: At 72 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: At 129 ASN cc_start: 0.8637 (m-40) cc_final: 0.8218 (m-40) REVERT: At 134 MET cc_start: 0.6958 (ttp) cc_final: 0.6496 (ttp) REVERT: At 190 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7464 (tt) REVERT: At 201 ASP cc_start: 0.8820 (t0) cc_final: 0.8583 (t0) REVERT: Au 72 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: Au 99 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7524 (tp) REVERT: Au 142 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: Au 151 ASN cc_start: 0.8297 (m-40) cc_final: 0.7983 (m-40) REVERT: Au 181 MET cc_start: 0.8109 (tpp) cc_final: 0.7582 (tpp) REVERT: Au 201 ASP cc_start: 0.8868 (t0) cc_final: 0.8363 (t0) REVERT: Av 72 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: Av 142 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: Av 190 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7349 (tt) REVERT: Av 201 ASP cc_start: 0.8830 (t0) cc_final: 0.8573 (t0) REVERT: Aw 72 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: Aw 99 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7523 (tp) REVERT: Aw 142 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: Aw 151 ASN cc_start: 0.8302 (m-40) cc_final: 0.7991 (m-40) REVERT: Aw 201 ASP cc_start: 0.8866 (t0) cc_final: 0.8360 (t0) REVERT: Ax 72 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: Ax 190 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7461 (tt) REVERT: Ax 201 ASP cc_start: 0.8843 (t0) cc_final: 0.8613 (t0) outliers start: 144 outliers final: 70 residues processed: 1111 average time/residue: 0.4865 time to fit residues: 859.1855 Evaluate side-chains 1166 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1048 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 190 LEU Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ab residue 206 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 121 GLU Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 190 LEU Chi-restraints excluded: chain Ac residue 206 THR Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 99 LEU Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ad residue 206 THR Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 190 LEU Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 206 THR Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ag residue 190 LEU Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 206 THR Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 175 ASN Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 108 MET Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 175 ASN Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 108 MET Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 175 ASN Chi-restraints excluded: chain An residue 72 GLU Chi-restraints excluded: chain An residue 108 MET Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 175 ASN Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 108 MET Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 139 GLU Chi-restraints excluded: chain Aq residue 142 GLU Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain Ar residue 190 LEU Chi-restraints excluded: chain As residue 63 THR Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 110 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 139 GLU Chi-restraints excluded: chain As residue 142 GLU Chi-restraints excluded: chain As residue 175 ASN Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 175 ASN Chi-restraints excluded: chain At residue 190 LEU Chi-restraints excluded: chain Au residue 63 THR Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 142 GLU Chi-restraints excluded: chain Au residue 175 ASN Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 142 GLU Chi-restraints excluded: chain Av residue 175 ASN Chi-restraints excluded: chain Av residue 190 LEU Chi-restraints excluded: chain Aw residue 63 THR Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 99 LEU Chi-restraints excluded: chain Aw residue 110 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Aw residue 175 ASN Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 175 ASN Chi-restraints excluded: chain Ax residue 190 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 238 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 351 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 416 optimal weight: 0.0050 chunk 260 optimal weight: 6.9990 chunk 253 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ai 175 ASN Ak 76 GLN Ak 175 ASN Al 69 HIS Am 175 ASN Ao 175 ASN Aq 151 ASN Ar 175 ASN At 175 ASN Av 175 ASN Ax 175 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 35832 Z= 0.193 Angle : 0.564 9.647 48576 Z= 0.276 Chirality : 0.037 0.125 5304 Planarity : 0.006 0.058 6288 Dihedral : 4.317 25.609 4824 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.80 % Allowed : 21.02 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 4296 helix: 0.42 (0.12), residues: 1800 sheet: 0.51 (0.28), residues: 288 loop : -0.90 (0.15), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAf 132 HIS 0.001 0.000 HISAu 217 PHE 0.008 0.002 PHEAh 163 TYR 0.019 0.001 TYRAp 73 ARG 0.007 0.000 ARGAw 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1029 time to evaluate : 3.695 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: Aa 54 MET cc_start: 0.6817 (ptt) cc_final: 0.6260 (ptt) REVERT: Aa 99 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7394 (tp) REVERT: Aa 112 MET cc_start: 0.9173 (mmt) cc_final: 0.8696 (mmt) REVERT: Aa 151 ASN cc_start: 0.8023 (m-40) cc_final: 0.7744 (m-40) REVERT: Aa 201 ASP cc_start: 0.8902 (t0) cc_final: 0.8496 (t0) REVERT: Ab 54 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6519 (ptt) REVERT: Ab 77 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8186 (tm-30) REVERT: Ab 99 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7512 (tp) REVERT: Ab 108 MET cc_start: 0.8842 (tpp) cc_final: 0.8560 (tpp) REVERT: Ab 181 MET cc_start: 0.8187 (tpp) cc_final: 0.7776 (tpp) REVERT: Ab 201 ASP cc_start: 0.8864 (t0) cc_final: 0.8374 (t0) REVERT: Ac 54 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6388 (ptt) REVERT: Ac 76 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8422 (mm-40) REVERT: Ac 201 ASP cc_start: 0.8894 (t0) cc_final: 0.8502 (t0) REVERT: Ad 54 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6520 (ptt) REVERT: Ad 99 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7485 (tp) REVERT: Ad 181 MET cc_start: 0.8197 (tpp) cc_final: 0.7715 (tpp) REVERT: Ad 201 ASP cc_start: 0.8872 (t0) cc_final: 0.8381 (t0) REVERT: Ae 54 MET cc_start: 0.6631 (ptt) cc_final: 0.5983 (ptt) REVERT: Ae 99 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7397 (tp) REVERT: Ae 112 MET cc_start: 0.9207 (mmt) cc_final: 0.8730 (mmt) REVERT: Ae 151 ASN cc_start: 0.8034 (m-40) cc_final: 0.7751 (m-40) REVERT: Ae 201 ASP cc_start: 0.8899 (t0) cc_final: 0.8499 (t0) REVERT: Af 54 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6673 (ptt) REVERT: Af 99 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7504 (tp) REVERT: Af 108 MET cc_start: 0.8839 (tpp) cc_final: 0.8551 (tpp) REVERT: Af 201 ASP cc_start: 0.8870 (t0) cc_final: 0.8388 (t0) REVERT: Ag 54 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6395 (ptt) REVERT: Ag 76 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8430 (mm-40) REVERT: Ag 99 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7403 (tp) REVERT: Ag 112 MET cc_start: 0.9207 (mmt) cc_final: 0.8733 (mmt) REVERT: Ag 151 ASN cc_start: 0.8026 (m-40) cc_final: 0.7752 (m-40) REVERT: Ag 201 ASP cc_start: 0.8901 (t0) cc_final: 0.8510 (t0) REVERT: Ah 77 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7885 (tm-30) REVERT: Ah 99 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7502 (tp) REVERT: Ah 108 MET cc_start: 0.8846 (tpp) cc_final: 0.8560 (tpp) REVERT: Ah 181 MET cc_start: 0.8199 (tpp) cc_final: 0.7718 (tpp) REVERT: Ah 201 ASP cc_start: 0.8872 (t0) cc_final: 0.8384 (t0) REVERT: Ai 60 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8789 (mmtm) REVERT: Ai 72 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: Ai 173 MET cc_start: 0.8465 (tmm) cc_final: 0.8058 (tmm) REVERT: Aj 72 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: Aj 77 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7771 (tm-30) REVERT: Aj 151 ASN cc_start: 0.8445 (m-40) cc_final: 0.8123 (m-40) REVERT: Aj 173 MET cc_start: 0.8380 (tmm) cc_final: 0.8023 (tmm) REVERT: Aj 201 ASP cc_start: 0.8898 (t0) cc_final: 0.8469 (t0) REVERT: Ak 60 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8794 (mmtm) REVERT: Ak 72 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: Ak 99 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7465 (tp) REVERT: Ak 173 MET cc_start: 0.8467 (tmm) cc_final: 0.8002 (tmm) REVERT: Al 72 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: Al 77 GLN cc_start: 0.8512 (tm-30) cc_final: 0.7974 (tm-30) REVERT: Al 151 ASN cc_start: 0.8444 (m-40) cc_final: 0.8120 (m-40) REVERT: Al 173 MET cc_start: 0.8394 (tmm) cc_final: 0.8010 (tmm) REVERT: Al 201 ASP cc_start: 0.8902 (t0) cc_final: 0.8496 (t0) REVERT: Am 60 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8777 (mmtm) REVERT: Am 72 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: Am 151 ASN cc_start: 0.8690 (m110) cc_final: 0.8218 (m110) REVERT: Am 173 MET cc_start: 0.8499 (tmm) cc_final: 0.8039 (tmm) REVERT: An 72 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: An 77 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7774 (tm-30) REVERT: An 151 ASN cc_start: 0.8447 (m-40) cc_final: 0.8124 (m-40) REVERT: An 173 MET cc_start: 0.8397 (tmm) cc_final: 0.8025 (tmm) REVERT: An 201 ASP cc_start: 0.8902 (t0) cc_final: 0.8484 (t0) REVERT: Ao 60 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8789 (mmtm) REVERT: Ao 72 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: Ao 173 MET cc_start: 0.8429 (tmm) cc_final: 0.7976 (tmm) REVERT: Ap 72 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: Ap 77 GLN cc_start: 0.8579 (tm-30) cc_final: 0.7942 (tm-30) REVERT: Ap 173 MET cc_start: 0.8398 (tmm) cc_final: 0.8027 (tmm) REVERT: Ap 201 ASP cc_start: 0.8860 (t0) cc_final: 0.8460 (t0) REVERT: Aq 72 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: Aq 99 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7476 (tp) REVERT: Aq 139 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5956 (pt0) REVERT: Aq 181 MET cc_start: 0.8177 (tpp) cc_final: 0.7545 (tpp) REVERT: Aq 201 ASP cc_start: 0.8872 (t0) cc_final: 0.8386 (t0) REVERT: Ar 72 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: Ar 129 ASN cc_start: 0.8644 (m-40) cc_final: 0.8237 (m-40) REVERT: Ar 134 MET cc_start: 0.6999 (ttp) cc_final: 0.6570 (ttp) REVERT: Ar 181 MET cc_start: 0.8049 (tpp) cc_final: 0.7784 (tpp) REVERT: Ar 201 ASP cc_start: 0.8837 (t0) cc_final: 0.8594 (t0) REVERT: As 72 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: As 99 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7465 (tp) REVERT: As 139 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.5959 (pt0) REVERT: As 142 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: As 201 ASP cc_start: 0.8877 (t0) cc_final: 0.8397 (t0) REVERT: At 72 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: At 134 MET cc_start: 0.7005 (ttp) cc_final: 0.6570 (ttp) REVERT: At 181 MET cc_start: 0.8048 (tpp) cc_final: 0.7821 (tpp) REVERT: At 190 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7393 (tt) REVERT: At 201 ASP cc_start: 0.8901 (t0) cc_final: 0.8668 (t0) REVERT: Au 72 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: Au 99 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7470 (tp) REVERT: Au 139 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.5946 (pt0) REVERT: Au 142 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: Au 181 MET cc_start: 0.8205 (tpp) cc_final: 0.7573 (tpp) REVERT: Au 201 ASP cc_start: 0.8878 (t0) cc_final: 0.8387 (t0) REVERT: Av 72 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: Av 190 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7438 (tt) REVERT: Av 201 ASP cc_start: 0.8902 (t0) cc_final: 0.8670 (t0) REVERT: Aw 72 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: Aw 99 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7457 (tp) REVERT: Aw 139 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.5961 (pt0) REVERT: Aw 142 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: Aw 201 ASP cc_start: 0.8877 (t0) cc_final: 0.8395 (t0) REVERT: Ax 72 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: Ax 77 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8288 (tp40) REVERT: Ax 181 MET cc_start: 0.8048 (tpp) cc_final: 0.7822 (tpp) REVERT: Ax 190 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7388 (tt) REVERT: Ax 201 ASP cc_start: 0.8907 (t0) cc_final: 0.8671 (t0) outliers start: 145 outliers final: 70 residues processed: 1094 average time/residue: 0.4919 time to fit residues: 852.5086 Evaluate side-chains 1140 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1027 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 80 ILE Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ab residue 206 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 80 ILE Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 80 ILE Chi-restraints excluded: chain Ad residue 99 LEU Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ad residue 206 THR Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 206 THR Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 80 ILE Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 206 THR Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 206 THR Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 175 ASN Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 108 MET Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 175 ASN Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 108 MET Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 175 ASN Chi-restraints excluded: chain An residue 72 GLU Chi-restraints excluded: chain An residue 108 MET Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 175 ASN Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 108 MET Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 139 GLU Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 175 ASN Chi-restraints excluded: chain As residue 63 THR Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 139 GLU Chi-restraints excluded: chain As residue 142 GLU Chi-restraints excluded: chain As residue 175 ASN Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 175 ASN Chi-restraints excluded: chain At residue 190 LEU Chi-restraints excluded: chain Au residue 63 THR Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 110 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 139 GLU Chi-restraints excluded: chain Au residue 142 GLU Chi-restraints excluded: chain Au residue 175 ASN Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 175 ASN Chi-restraints excluded: chain Av residue 190 LEU Chi-restraints excluded: chain Aw residue 63 THR Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 99 LEU Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 139 GLU Chi-restraints excluded: chain Aw residue 142 GLU Chi-restraints excluded: chain Aw residue 175 ASN Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 175 ASN Chi-restraints excluded: chain Ax residue 190 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 327 optimal weight: 0.1980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 175 ASN Ak 76 GLN Ak 175 ASN Al 69 HIS Am 175 ASN Ao 175 ASN At 175 ASN Av 175 ASN Ax 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35832 Z= 0.200 Angle : 0.574 10.799 48576 Z= 0.281 Chirality : 0.037 0.124 5304 Planarity : 0.006 0.058 6288 Dihedral : 4.295 24.279 4824 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.88 % Allowed : 21.46 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.13), residues: 4296 helix: 0.49 (0.12), residues: 1800 sheet: 0.61 (0.28), residues: 288 loop : -0.86 (0.15), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPAf 132 HIS 0.001 0.000 HISAf 217 PHE 0.008 0.002 PHEAh 163 TYR 0.020 0.001 TYRAd 73 ARG 0.008 0.000 ARGAa 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1029 time to evaluate : 3.832 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: Aa 54 MET cc_start: 0.6899 (ptt) cc_final: 0.6302 (ptt) REVERT: Aa 77 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8244 (tp40) REVERT: Aa 99 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7394 (tp) REVERT: Aa 112 MET cc_start: 0.9153 (mmt) cc_final: 0.8715 (mmt) REVERT: Aa 201 ASP cc_start: 0.8897 (t0) cc_final: 0.8488 (t0) REVERT: Ab 54 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6653 (ptt) REVERT: Ab 77 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8178 (tm-30) REVERT: Ab 99 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7512 (tp) REVERT: Ab 181 MET cc_start: 0.8324 (tpp) cc_final: 0.7858 (tpp) REVERT: Ab 201 ASP cc_start: 0.8868 (t0) cc_final: 0.8385 (t0) REVERT: Ac 54 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6367 (ptt) REVERT: Ac 112 MET cc_start: 0.9153 (mmt) cc_final: 0.8832 (mmt) REVERT: Ac 201 ASP cc_start: 0.8892 (t0) cc_final: 0.8491 (t0) REVERT: Ad 54 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6649 (ptt) REVERT: Ad 99 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7510 (tp) REVERT: Ad 181 MET cc_start: 0.8262 (tpp) cc_final: 0.7786 (tpp) REVERT: Ad 201 ASP cc_start: 0.8874 (t0) cc_final: 0.8385 (t0) REVERT: Ae 54 MET cc_start: 0.6836 (ptt) cc_final: 0.6263 (ptt) REVERT: Ae 99 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7391 (tp) REVERT: Ae 112 MET cc_start: 0.9149 (mmt) cc_final: 0.8684 (mmt) REVERT: Ae 201 ASP cc_start: 0.8896 (t0) cc_final: 0.8492 (t0) REVERT: Af 54 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6524 (ptt) REVERT: Af 99 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7505 (tp) REVERT: Af 201 ASP cc_start: 0.8869 (t0) cc_final: 0.8397 (t0) REVERT: Ag 54 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6356 (ptt) REVERT: Ag 99 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7397 (tp) REVERT: Ag 112 MET cc_start: 0.9148 (mmt) cc_final: 0.8694 (mmt) REVERT: Ag 201 ASP cc_start: 0.8900 (t0) cc_final: 0.8502 (t0) REVERT: Ah 77 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7913 (tm-30) REVERT: Ah 99 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7505 (tp) REVERT: Ah 181 MET cc_start: 0.8263 (tpp) cc_final: 0.7774 (tpp) REVERT: Ah 201 ASP cc_start: 0.8874 (t0) cc_final: 0.8393 (t0) REVERT: Ai 56 MET cc_start: 0.7724 (mmt) cc_final: 0.7326 (mmt) REVERT: Ai 60 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8790 (mmtm) REVERT: Ai 72 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: Ai 77 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8251 (tp-100) REVERT: Ai 99 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7462 (tp) REVERT: Ai 173 MET cc_start: 0.8496 (tmm) cc_final: 0.8172 (tmm) REVERT: Ai 201 ASP cc_start: 0.8942 (t0) cc_final: 0.8533 (t0) REVERT: Aj 56 MET cc_start: 0.7786 (mmt) cc_final: 0.7212 (mmt) REVERT: Aj 72 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: Aj 77 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7988 (tm-30) REVERT: Aj 151 ASN cc_start: 0.8435 (m-40) cc_final: 0.8120 (m-40) REVERT: Aj 173 MET cc_start: 0.8398 (tmm) cc_final: 0.8012 (tmm) REVERT: Aj 201 ASP cc_start: 0.8853 (t0) cc_final: 0.8442 (t0) REVERT: Ak 56 MET cc_start: 0.7827 (mmt) cc_final: 0.7374 (mmt) REVERT: Ak 60 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8799 (mmtm) REVERT: Ak 72 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: Ak 173 MET cc_start: 0.8500 (tmm) cc_final: 0.8147 (tmm) REVERT: Al 72 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: Al 77 GLN cc_start: 0.8567 (tm-30) cc_final: 0.7798 (tm-30) REVERT: Al 151 ASN cc_start: 0.8429 (m-40) cc_final: 0.8111 (m-40) REVERT: Al 173 MET cc_start: 0.8386 (tmm) cc_final: 0.7977 (tmm) REVERT: Al 201 ASP cc_start: 0.8865 (t0) cc_final: 0.8435 (t0) REVERT: Am 56 MET cc_start: 0.7831 (mmt) cc_final: 0.7376 (mmt) REVERT: Am 60 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8797 (mmtm) REVERT: Am 72 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: Am 99 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7425 (tp) REVERT: Am 151 ASN cc_start: 0.8693 (m110) cc_final: 0.8227 (m110) REVERT: Am 173 MET cc_start: 0.8488 (tmm) cc_final: 0.8137 (tmm) REVERT: Am 201 ASP cc_start: 0.8903 (t0) cc_final: 0.8510 (t0) REVERT: An 72 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: An 77 GLN cc_start: 0.8557 (tm-30) cc_final: 0.7992 (tm-30) REVERT: An 151 ASN cc_start: 0.8434 (m-40) cc_final: 0.8114 (m-40) REVERT: An 173 MET cc_start: 0.8394 (tmm) cc_final: 0.8003 (tmm) REVERT: An 201 ASP cc_start: 0.8875 (t0) cc_final: 0.8465 (t0) REVERT: Ao 56 MET cc_start: 0.7830 (mmt) cc_final: 0.7376 (mmt) REVERT: Ao 60 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8794 (mmtm) REVERT: Ao 72 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: Ao 99 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7468 (tp) REVERT: Ao 173 MET cc_start: 0.8503 (tmm) cc_final: 0.8149 (tmm) REVERT: Ao 201 ASP cc_start: 0.8927 (t0) cc_final: 0.8510 (t0) REVERT: Ap 72 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: Ap 77 GLN cc_start: 0.8572 (tm-30) cc_final: 0.7705 (tm-30) REVERT: Ap 173 MET cc_start: 0.8388 (tmm) cc_final: 0.7991 (tmm) REVERT: Ap 201 ASP cc_start: 0.8859 (t0) cc_final: 0.8425 (t0) REVERT: Aq 72 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: Aq 99 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7453 (tp) REVERT: Aq 139 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.5934 (pt0) REVERT: Aq 160 MET cc_start: 0.9229 (mmm) cc_final: 0.8862 (mmp) REVERT: Aq 181 MET cc_start: 0.8189 (tpp) cc_final: 0.7570 (tpp) REVERT: Aq 201 ASP cc_start: 0.8876 (t0) cc_final: 0.8398 (t0) REVERT: Ar 72 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: Ar 99 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7422 (tp) REVERT: Ar 190 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7323 (tt) REVERT: Ar 201 ASP cc_start: 0.8877 (t0) cc_final: 0.8647 (t0) REVERT: As 72 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: As 99 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7444 (tp) REVERT: As 139 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.5966 (pt0) REVERT: As 160 MET cc_start: 0.9228 (mmm) cc_final: 0.8873 (mmp) REVERT: As 201 ASP cc_start: 0.8942 (t0) cc_final: 0.8447 (t0) REVERT: At 72 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: At 99 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7412 (tp) REVERT: At 201 ASP cc_start: 0.8881 (t0) cc_final: 0.8645 (t0) REVERT: Au 72 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: Au 99 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7446 (tp) REVERT: Au 139 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5950 (pt0) REVERT: Au 181 MET cc_start: 0.8254 (tpp) cc_final: 0.7537 (tpp) REVERT: Au 201 ASP cc_start: 0.8876 (t0) cc_final: 0.8403 (t0) REVERT: Av 72 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: Av 99 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7413 (tp) REVERT: Av 181 MET cc_start: 0.8083 (tpp) cc_final: 0.7832 (tpp) REVERT: Av 201 ASP cc_start: 0.8885 (t0) cc_final: 0.8647 (t0) REVERT: Aw 72 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: Aw 99 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7436 (tp) REVERT: Aw 139 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.5945 (pt0) REVERT: Aw 160 MET cc_start: 0.9231 (mmm) cc_final: 0.8874 (mmp) REVERT: Aw 201 ASP cc_start: 0.8940 (t0) cc_final: 0.8444 (t0) REVERT: Ax 72 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: Ax 77 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8291 (tp40) REVERT: Ax 99 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7414 (tp) REVERT: Ax 201 ASP cc_start: 0.8886 (t0) cc_final: 0.8662 (t0) outliers start: 148 outliers final: 74 residues processed: 1091 average time/residue: 0.4974 time to fit residues: 865.3960 Evaluate side-chains 1145 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1027 time to evaluate : 3.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 80 ILE Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ab residue 206 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 121 GLU Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 80 ILE Chi-restraints excluded: chain Ad residue 99 LEU Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ad residue 206 THR Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 80 ILE Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 206 THR Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 206 THR Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 175 ASN Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 108 MET Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 175 ASN Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 108 MET Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 175 ASN Chi-restraints excluded: chain An residue 72 GLU Chi-restraints excluded: chain An residue 108 MET Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 175 ASN Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 108 MET Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 139 GLU Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 190 LEU Chi-restraints excluded: chain As residue 63 THR Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 110 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 139 GLU Chi-restraints excluded: chain As residue 175 ASN Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 99 LEU Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 175 ASN Chi-restraints excluded: chain Au residue 63 THR Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 110 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 139 GLU Chi-restraints excluded: chain Au residue 175 ASN Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 99 LEU Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 175 ASN Chi-restraints excluded: chain Aw residue 63 THR Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 99 LEU Chi-restraints excluded: chain Aw residue 110 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 139 GLU Chi-restraints excluded: chain Aw residue 175 ASN Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 99 LEU Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 175 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 8.9990 chunk 398 optimal weight: 4.9990 chunk 363 optimal weight: 1.9990 chunk 388 optimal weight: 0.7980 chunk 233 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 304 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 350 optimal weight: 0.0670 chunk 366 optimal weight: 4.9990 chunk 386 optimal weight: 3.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 76 GLN Af 76 GLN Ah 76 GLN Ai 175 ASN Ak 175 ASN Al 69 HIS Am 175 ASN Ao 175 ASN Ar 175 ASN At 175 ASN Av 175 ASN Ax 175 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 35832 Z= 0.181 Angle : 0.577 11.435 48576 Z= 0.282 Chirality : 0.037 0.123 5304 Planarity : 0.006 0.058 6288 Dihedral : 4.276 25.678 4824 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.38 % Allowed : 22.27 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 4296 helix: 0.54 (0.12), residues: 1800 sheet: 0.74 (0.28), residues: 288 loop : -0.83 (0.15), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAt 93 HIS 0.002 0.000 HISAh 217 PHE 0.007 0.001 PHEAa 202 TYR 0.023 0.001 TYRAd 73 ARG 0.009 0.000 ARGAa 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1019 time to evaluate : 3.923 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: Aa 54 MET cc_start: 0.6946 (ptt) cc_final: 0.6381 (ptt) REVERT: Aa 76 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8301 (mm-40) REVERT: Aa 112 MET cc_start: 0.9162 (mmt) cc_final: 0.8720 (mmt) REVERT: Aa 201 ASP cc_start: 0.8891 (t0) cc_final: 0.8487 (t0) REVERT: Ab 54 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6658 (ptt) REVERT: Ab 99 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7464 (tp) REVERT: Ab 181 MET cc_start: 0.8306 (tpp) cc_final: 0.7821 (tpp) REVERT: Ab 201 ASP cc_start: 0.8869 (t0) cc_final: 0.8383 (t0) REVERT: Ac 54 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6365 (ptt) REVERT: Ac 112 MET cc_start: 0.9136 (mmt) cc_final: 0.8814 (mmt) REVERT: Ac 177 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7843 (tptt) REVERT: Ac 201 ASP cc_start: 0.8886 (t0) cc_final: 0.8485 (t0) REVERT: Ad 54 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6654 (ptt) REVERT: Ad 99 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7494 (tp) REVERT: Ad 181 MET cc_start: 0.8230 (tpp) cc_final: 0.7730 (tpp) REVERT: Ad 201 ASP cc_start: 0.8875 (t0) cc_final: 0.8387 (t0) REVERT: Ae 54 MET cc_start: 0.6932 (ptt) cc_final: 0.6364 (ptt) REVERT: Ae 112 MET cc_start: 0.9170 (mmt) cc_final: 0.8710 (mmt) REVERT: Ae 201 ASP cc_start: 0.8885 (t0) cc_final: 0.8489 (t0) REVERT: Af 54 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6693 (ptt) REVERT: Af 99 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7491 (tp) REVERT: Af 201 ASP cc_start: 0.8872 (t0) cc_final: 0.8398 (t0) REVERT: Ag 54 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6301 (ptt) REVERT: Ag 99 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7385 (tp) REVERT: Ag 112 MET cc_start: 0.9169 (mmt) cc_final: 0.8711 (mmt) REVERT: Ag 201 ASP cc_start: 0.8889 (t0) cc_final: 0.8496 (t0) REVERT: Ah 77 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8169 (tm-30) REVERT: Ah 99 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7492 (tp) REVERT: Ah 181 MET cc_start: 0.8220 (tpp) cc_final: 0.7714 (tpp) REVERT: Ah 201 ASP cc_start: 0.8878 (t0) cc_final: 0.8395 (t0) REVERT: Ai 56 MET cc_start: 0.7828 (mmt) cc_final: 0.7401 (mmt) REVERT: Ai 60 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8770 (mmtm) REVERT: Ai 72 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: Ai 99 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7445 (tp) REVERT: Ai 173 MET cc_start: 0.8455 (tmm) cc_final: 0.8076 (tmm) REVERT: Ai 201 ASP cc_start: 0.8937 (t0) cc_final: 0.8526 (t0) REVERT: Aj 56 MET cc_start: 0.7731 (mmt) cc_final: 0.7087 (mmt) REVERT: Aj 72 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: Aj 77 GLN cc_start: 0.8543 (tm-30) cc_final: 0.7744 (tm-30) REVERT: Aj 151 ASN cc_start: 0.8433 (m-40) cc_final: 0.8075 (m-40) REVERT: Aj 173 MET cc_start: 0.8357 (tmm) cc_final: 0.7943 (tmm) REVERT: Aj 201 ASP cc_start: 0.8858 (t0) cc_final: 0.8420 (t0) REVERT: Ak 56 MET cc_start: 0.7849 (mmt) cc_final: 0.7299 (mmt) REVERT: Ak 60 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8782 (mmtm) REVERT: Ak 72 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: Ak 76 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8468 (mm-40) REVERT: Ak 99 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7466 (tp) REVERT: Ak 173 MET cc_start: 0.8432 (tmm) cc_final: 0.7983 (tmm) REVERT: Al 56 MET cc_start: 0.7387 (mmt) cc_final: 0.6814 (mmp) REVERT: Al 72 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: Al 77 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7740 (tm-30) REVERT: Al 151 ASN cc_start: 0.8425 (m-40) cc_final: 0.8062 (m-40) REVERT: Al 173 MET cc_start: 0.8376 (tmm) cc_final: 0.7953 (tmm) REVERT: Al 201 ASP cc_start: 0.8882 (t0) cc_final: 0.8475 (t0) REVERT: Am 56 MET cc_start: 0.7837 (mmt) cc_final: 0.7279 (mmt) REVERT: Am 72 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: Am 99 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7480 (tp) REVERT: Am 151 ASN cc_start: 0.8659 (m110) cc_final: 0.8169 (m110) REVERT: Am 173 MET cc_start: 0.8432 (tmm) cc_final: 0.7994 (tmm) REVERT: Am 201 ASP cc_start: 0.8944 (t0) cc_final: 0.8525 (t0) REVERT: An 56 MET cc_start: 0.7404 (mmt) cc_final: 0.6849 (mmp) REVERT: An 77 GLN cc_start: 0.8551 (tm-30) cc_final: 0.7740 (tm-30) REVERT: An 151 ASN cc_start: 0.8471 (m-40) cc_final: 0.8091 (m-40) REVERT: An 173 MET cc_start: 0.8381 (tmm) cc_final: 0.7957 (tmm) REVERT: An 201 ASP cc_start: 0.8862 (t0) cc_final: 0.8428 (t0) REVERT: Ao 56 MET cc_start: 0.7847 (mmt) cc_final: 0.7297 (mmt) REVERT: Ao 60 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8790 (mmtm) REVERT: Ao 72 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: Ao 99 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7437 (tp) REVERT: Ao 173 MET cc_start: 0.8435 (tmm) cc_final: 0.7986 (tmm) REVERT: Ao 201 ASP cc_start: 0.8934 (t0) cc_final: 0.8509 (t0) REVERT: Ap 56 MET cc_start: 0.7376 (mmt) cc_final: 0.6789 (mmp) REVERT: Ap 72 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: Ap 77 GLN cc_start: 0.8563 (tm-30) cc_final: 0.7721 (tm-30) REVERT: Ap 135 MET cc_start: 0.8233 (mmm) cc_final: 0.8030 (mmm) REVERT: Ap 173 MET cc_start: 0.8377 (tmm) cc_final: 0.7959 (tmm) REVERT: Ap 201 ASP cc_start: 0.8858 (t0) cc_final: 0.8420 (t0) REVERT: Aq 72 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: Aq 99 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7413 (tp) REVERT: Aq 181 MET cc_start: 0.8148 (tpp) cc_final: 0.7529 (tpp) REVERT: Aq 201 ASP cc_start: 0.8920 (t0) cc_final: 0.8393 (t0) REVERT: Ar 72 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8086 (tt0) REVERT: Ar 99 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7395 (tp) REVERT: Ar 181 MET cc_start: 0.8117 (tpp) cc_final: 0.7885 (tpp) REVERT: Ar 190 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7346 (tt) REVERT: As 72 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: As 99 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7409 (tp) REVERT: As 201 ASP cc_start: 0.8959 (t0) cc_final: 0.8470 (t0) REVERT: At 72 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: At 76 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8343 (mm110) REVERT: At 99 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7329 (tp) REVERT: At 181 MET cc_start: 0.8055 (tpp) cc_final: 0.7820 (tpp) REVERT: At 190 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7400 (tt) REVERT: At 201 ASP cc_start: 0.8908 (t0) cc_final: 0.8673 (t0) REVERT: Au 72 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: Au 99 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7408 (tp) REVERT: Au 139 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.5871 (pt0) REVERT: Au 181 MET cc_start: 0.8239 (tpp) cc_final: 0.7531 (tpp) REVERT: Au 201 ASP cc_start: 0.8937 (t0) cc_final: 0.8404 (t0) REVERT: Av 72 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: Av 99 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7332 (tp) REVERT: Av 181 MET cc_start: 0.8097 (tpp) cc_final: 0.7854 (tpp) REVERT: Av 190 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7357 (tt) REVERT: Av 201 ASP cc_start: 0.8892 (t0) cc_final: 0.8661 (t0) REVERT: Aw 72 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: Aw 99 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7401 (tp) REVERT: Aw 139 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5873 (pt0) REVERT: Aw 201 ASP cc_start: 0.8959 (t0) cc_final: 0.8464 (t0) REVERT: Ax 72 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: Ax 77 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8403 (tp40) REVERT: Ax 99 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7331 (tp) REVERT: Ax 181 MET cc_start: 0.8072 (tpp) cc_final: 0.7837 (tpp) REVERT: Ax 190 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7366 (tt) REVERT: Ax 201 ASP cc_start: 0.8912 (t0) cc_final: 0.8691 (t0) outliers start: 129 outliers final: 67 residues processed: 1066 average time/residue: 0.3984 time to fit residues: 675.7274 Evaluate side-chains 1123 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1012 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 54 MET Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ab residue 206 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 177 LYS Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 99 LEU Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 206 THR Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 175 ASN Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 108 MET Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 175 ASN Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 108 MET Chi-restraints excluded: chain Al residue 135 MET Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 175 ASN Chi-restraints excluded: chain An residue 108 MET Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 72 GLU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 175 ASN Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 72 GLU Chi-restraints excluded: chain Ap residue 108 MET Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 175 ASN Chi-restraints excluded: chain Ar residue 190 LEU Chi-restraints excluded: chain As residue 63 THR Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 110 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 175 ASN Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 99 LEU Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 175 ASN Chi-restraints excluded: chain At residue 190 LEU Chi-restraints excluded: chain Au residue 63 THR Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 110 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 139 GLU Chi-restraints excluded: chain Au residue 175 ASN Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 99 LEU Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 175 ASN Chi-restraints excluded: chain Av residue 190 LEU Chi-restraints excluded: chain Aw residue 63 THR Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 99 LEU Chi-restraints excluded: chain Aw residue 110 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 139 GLU Chi-restraints excluded: chain Aw residue 175 ASN Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 99 LEU Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 175 ASN Chi-restraints excluded: chain Ax residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 7.9990 chunk 410 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 430 optimal weight: 5.9990 chunk 396 optimal weight: 0.8980 chunk 342 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 chunk 210 optimal weight: 0.8980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 76 GLN Ag 76 GLN Ai 175 ASN ** Aj 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 69 HIS Am 76 GLN ** Ap 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 175 ASN At 175 ASN Av 175 ASN ** Ax 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 35832 Z= 0.328 Angle : 0.654 11.815 48576 Z= 0.319 Chirality : 0.039 0.132 5304 Planarity : 0.006 0.058 6288 Dihedral : 4.427 26.375 4824 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.04 % Allowed : 22.54 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4296 helix: 0.35 (0.12), residues: 1800 sheet: 0.48 (0.28), residues: 288 loop : -0.84 (0.15), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRPAp 93 HIS 0.001 0.001 HISAb 217 PHE 0.015 0.003 PHEAb 163 TYR 0.021 0.002 TYRAh 73 ARG 0.009 0.001 ARGAe 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1026 time to evaluate : 4.003 Fit side-chains revert: symmetry clash REVERT: Aa 54 MET cc_start: 0.6873 (ptt) cc_final: 0.6289 (ptt) REVERT: Aa 112 MET cc_start: 0.9235 (mmt) cc_final: 0.8666 (mmt) REVERT: Aa 201 ASP cc_start: 0.8889 (t0) cc_final: 0.8474 (t0) REVERT: Ab 54 MET cc_start: 0.7066 (ptt) cc_final: 0.6401 (ptt) REVERT: Ab 99 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7538 (tp) REVERT: Ab 108 MET cc_start: 0.8932 (tpt) cc_final: 0.8688 (tpp) REVERT: Ab 181 MET cc_start: 0.8402 (tpp) cc_final: 0.7908 (tpp) REVERT: Ab 201 ASP cc_start: 0.8873 (t0) cc_final: 0.8381 (t0) REVERT: Ac 54 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6446 (ptt) REVERT: Ac 112 MET cc_start: 0.9199 (mmt) cc_final: 0.8888 (mmt) REVERT: Ac 201 ASP cc_start: 0.8885 (t0) cc_final: 0.8479 (t0) REVERT: Ad 54 MET cc_start: 0.7064 (ptt) cc_final: 0.6401 (ptt) REVERT: Ad 99 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7505 (tp) REVERT: Ad 135 MET cc_start: 0.8140 (mtt) cc_final: 0.7804 (mtt) REVERT: Ad 181 MET cc_start: 0.8328 (tpp) cc_final: 0.7831 (tpp) REVERT: Ad 201 ASP cc_start: 0.8878 (t0) cc_final: 0.8381 (t0) REVERT: Ae 54 MET cc_start: 0.6962 (ptt) cc_final: 0.6367 (ptt) REVERT: Ae 99 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7427 (tp) REVERT: Ae 112 MET cc_start: 0.9229 (mmt) cc_final: 0.8645 (mmt) REVERT: Ae 201 ASP cc_start: 0.8877 (t0) cc_final: 0.8477 (t0) REVERT: Af 54 MET cc_start: 0.7025 (ptt) cc_final: 0.6602 (ptt) REVERT: Af 99 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7519 (tp) REVERT: Af 108 MET cc_start: 0.8928 (tpt) cc_final: 0.8694 (tpp) REVERT: Af 201 ASP cc_start: 0.8874 (t0) cc_final: 0.8388 (t0) REVERT: Ag 54 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6543 (ptt) REVERT: Ag 99 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7405 (tp) REVERT: Ag 112 MET cc_start: 0.9226 (mmt) cc_final: 0.8649 (mmt) REVERT: Ag 201 ASP cc_start: 0.8887 (t0) cc_final: 0.8483 (t0) REVERT: Ah 99 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7534 (tp) REVERT: Ah 108 MET cc_start: 0.8934 (tpt) cc_final: 0.8686 (tpp) REVERT: Ah 181 MET cc_start: 0.8312 (tpp) cc_final: 0.7818 (tpp) REVERT: Ah 201 ASP cc_start: 0.8876 (t0) cc_final: 0.8385 (t0) REVERT: Ai 72 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: Ai 77 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8114 (tp-100) REVERT: Ai 99 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7495 (tp) REVERT: Ai 173 MET cc_start: 0.8577 (tmm) cc_final: 0.8281 (tmm) REVERT: Aj 72 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: Aj 77 GLN cc_start: 0.8597 (tm-30) cc_final: 0.7684 (tm-30) REVERT: Aj 151 ASN cc_start: 0.8499 (m-40) cc_final: 0.8253 (m-40) REVERT: Aj 173 MET cc_start: 0.8436 (tmm) cc_final: 0.8066 (tmm) REVERT: Aj 201 ASP cc_start: 0.8862 (t0) cc_final: 0.8406 (t0) REVERT: Ak 72 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: Ak 76 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8466 (mm-40) REVERT: Ak 99 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7508 (tp) REVERT: Ak 173 MET cc_start: 0.8591 (tmm) cc_final: 0.8234 (tmm) REVERT: Al 72 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: Al 77 GLN cc_start: 0.8615 (tm-30) cc_final: 0.7753 (tm-30) REVERT: Al 151 ASN cc_start: 0.8494 (m-40) cc_final: 0.8248 (m-40) REVERT: Al 173 MET cc_start: 0.8438 (tmm) cc_final: 0.8066 (tmm) REVERT: Al 201 ASP cc_start: 0.8876 (t0) cc_final: 0.8471 (t0) REVERT: Am 72 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: Am 77 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8235 (tp-100) REVERT: Am 151 ASN cc_start: 0.8721 (m110) cc_final: 0.8253 (m110) REVERT: Am 173 MET cc_start: 0.8588 (tmm) cc_final: 0.8241 (tmm) REVERT: An 72 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: An 77 GLN cc_start: 0.8612 (tm-30) cc_final: 0.7693 (tm-30) REVERT: An 151 ASN cc_start: 0.8496 (m-40) cc_final: 0.8247 (m-40) REVERT: An 173 MET cc_start: 0.8441 (tmm) cc_final: 0.8072 (tmm) REVERT: An 201 ASP cc_start: 0.8856 (t0) cc_final: 0.8433 (t0) REVERT: Ao 77 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8103 (tp-100) REVERT: Ao 99 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7465 (tp) REVERT: Ao 173 MET cc_start: 0.8577 (tmm) cc_final: 0.8213 (tmm) REVERT: Ap 77 GLN cc_start: 0.8610 (tm-30) cc_final: 0.7765 (tm-30) REVERT: Ap 99 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7789 (tp) REVERT: Ap 135 MET cc_start: 0.8319 (mmm) cc_final: 0.8111 (mmm) REVERT: Ap 173 MET cc_start: 0.8436 (tmm) cc_final: 0.8072 (tmm) REVERT: Ap 201 ASP cc_start: 0.8863 (t0) cc_final: 0.8408 (t0) REVERT: Aq 72 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: Aq 99 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7511 (tp) REVERT: Aq 139 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6065 (pt0) REVERT: Aq 181 MET cc_start: 0.8258 (tpp) cc_final: 0.7512 (tpp) REVERT: Aq 201 ASP cc_start: 0.8893 (t0) cc_final: 0.8388 (t0) REVERT: Ar 72 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: Ar 99 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7384 (tp) REVERT: Ar 190 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7228 (tt) REVERT: As 72 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: As 99 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7507 (tp) REVERT: As 139 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6075 (pt0) REVERT: As 201 ASP cc_start: 0.8955 (t0) cc_final: 0.8466 (t0) REVERT: At 72 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: At 99 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7370 (tp) REVERT: At 190 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7248 (tt) REVERT: At 201 ASP cc_start: 0.8919 (t0) cc_final: 0.8718 (t0) REVERT: Au 72 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: Au 99 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7512 (tp) REVERT: Au 139 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6076 (pt0) REVERT: Au 181 MET cc_start: 0.8324 (tpp) cc_final: 0.7609 (tpp) REVERT: Au 201 ASP cc_start: 0.8896 (t0) cc_final: 0.8384 (t0) REVERT: Av 72 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: Av 99 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7372 (tp) REVERT: Av 190 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7251 (tt) REVERT: Aw 72 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: Aw 99 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7501 (tp) REVERT: Aw 139 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6063 (pt0) REVERT: Aw 201 ASP cc_start: 0.8953 (t0) cc_final: 0.8460 (t0) REVERT: Ax 72 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: Ax 99 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7378 (tp) REVERT: Ax 190 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7247 (tt) outliers start: 116 outliers final: 66 residues processed: 1064 average time/residue: 0.5382 time to fit residues: 918.3861 Evaluate side-chains 1123 residues out of total 3816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1015 time to evaluate : 4.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 63 THR Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 133 VAL Chi-restraints excluded: chain Ab residue 206 THR Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 63 THR Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 99 LEU Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ad residue 206 THR Chi-restraints excluded: chain Ae residue 63 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Ag residue 54 MET Chi-restraints excluded: chain Ag residue 63 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 155 THR Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 206 THR Chi-restraints excluded: chain Ai residue 63 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 72 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 108 MET Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 175 ASN Chi-restraints excluded: chain Aj residue 72 GLU Chi-restraints excluded: chain Aj residue 108 MET Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 63 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 72 GLU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 108 MET Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Al residue 72 GLU Chi-restraints excluded: chain Al residue 108 MET Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 63 THR Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 72 GLU Chi-restraints excluded: chain Am residue 108 MET Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 72 GLU Chi-restraints excluded: chain An residue 108 MET Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 63 THR Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 99 LEU Chi-restraints excluded: chain Ao residue 108 MET Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 63 THR Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 108 MET Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 151 ASN Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 72 GLU Chi-restraints excluded: chain Aq residue 99 LEU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 139 GLU Chi-restraints excluded: chain Ar residue 63 THR Chi-restraints excluded: chain Ar residue 72 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 190 LEU Chi-restraints excluded: chain As residue 63 THR Chi-restraints excluded: chain As residue 72 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 110 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 139 GLU Chi-restraints excluded: chain As residue 175 ASN Chi-restraints excluded: chain At residue 63 THR Chi-restraints excluded: chain At residue 72 GLU Chi-restraints excluded: chain At residue 99 LEU Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 190 LEU Chi-restraints excluded: chain Au residue 63 THR Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 99 LEU Chi-restraints excluded: chain Au residue 110 THR Chi-restraints excluded: chain Au residue 133 VAL Chi-restraints excluded: chain Au residue 139 GLU Chi-restraints excluded: chain Au residue 175 ASN Chi-restraints excluded: chain Av residue 63 THR Chi-restraints excluded: chain Av residue 72 GLU Chi-restraints excluded: chain Av residue 99 LEU Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 190 LEU Chi-restraints excluded: chain Aw residue 63 THR Chi-restraints excluded: chain Aw residue 72 GLU Chi-restraints excluded: chain Aw residue 99 LEU Chi-restraints excluded: chain Aw residue 110 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 139 GLU Chi-restraints excluded: chain Aw residue 175 ASN Chi-restraints excluded: chain Ax residue 63 THR Chi-restraints excluded: chain Ax residue 72 GLU Chi-restraints excluded: chain Ax residue 99 LEU Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 190 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 0.3980 chunk 365 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 316 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 352 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 76 GLN Ac 76 GLN Ag 76 GLN Ai 175 ASN ** Aj 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 175 ASN Al 69 HIS Am 76 GLN Am 175 ASN Ao 175 ASN ** Ap 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.135439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.111668 restraints weight = 46227.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.116271 restraints weight = 22932.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.119465 restraints weight = 14223.783| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35832 Z= 0.197 Angle : 0.608 12.239 48576 Z= 0.292 Chirality : 0.037 0.124 5304 Planarity : 0.006 0.058 6288 Dihedral : 4.302 24.802 4824 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.83 % Allowed : 22.59 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 4296 helix: 0.50 (0.12), residues: 1800 sheet: 0.68 (0.28), residues: 288 loop : -0.79 (0.15), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAs 93 HIS 0.001 0.000 HISAb 217 PHE 0.008 0.002 PHEAa 202 TYR 0.023 0.001 TYRAp 73 ARG 0.009 0.000 ARGAg 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11225.01 seconds wall clock time: 211 minutes 19.60 seconds (12679.60 seconds total)