Starting phenix.real_space_refine on Thu Apr 11 17:22:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opb_17047/04_2024/8opb_17047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opb_17047/04_2024/8opb_17047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opb_17047/04_2024/8opb_17047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opb_17047/04_2024/8opb_17047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opb_17047/04_2024/8opb_17047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opb_17047/04_2024/8opb_17047.pdb" } resolution = 3.58 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= 0.010 sd= 0.083 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 192 5.16 5 C 14736 2.51 5 N 4064 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Aa GLU 72": "OE1" <-> "OE2" Residue "Aa GLU 95": "OE1" <-> "OE2" Residue "Aa GLU 150": "OE1" <-> "OE2" Residue "Ab GLU 72": "OE1" <-> "OE2" Residue "Ab GLU 95": "OE1" <-> "OE2" Residue "Ab GLU 150": "OE1" <-> "OE2" Residue "Ac GLU 72": "OE1" <-> "OE2" Residue "Ac GLU 95": "OE1" <-> "OE2" Residue "Ac GLU 150": "OE1" <-> "OE2" Residue "Ad GLU 72": "OE1" <-> "OE2" Residue "Ad GLU 95": "OE1" <-> "OE2" Residue "Ad GLU 150": "OE1" <-> "OE2" Residue "Ae GLU 72": "OE1" <-> "OE2" Residue "Ae GLU 95": "OE1" <-> "OE2" Residue "Ae GLU 150": "OE1" <-> "OE2" Residue "Af GLU 72": "OE1" <-> "OE2" Residue "Af GLU 95": "OE1" <-> "OE2" Residue "Af GLU 150": "OE1" <-> "OE2" Residue "Ag GLU 72": "OE1" <-> "OE2" Residue "Ag GLU 95": "OE1" <-> "OE2" Residue "Ag GLU 150": "OE1" <-> "OE2" Residue "Ah GLU 72": "OE1" <-> "OE2" Residue "Ah GLU 95": "OE1" <-> "OE2" Residue "Ah GLU 150": "OE1" <-> "OE2" Residue "Ai GLU 72": "OE1" <-> "OE2" Residue "Ai GLU 95": "OE1" <-> "OE2" Residue "Ai GLU 150": "OE1" <-> "OE2" Residue "Aj GLU 72": "OE1" <-> "OE2" Residue "Aj GLU 95": "OE1" <-> "OE2" Residue "Aj GLU 150": "OE1" <-> "OE2" Residue "Ak GLU 72": "OE1" <-> "OE2" Residue "Ak GLU 95": "OE1" <-> "OE2" Residue "Ak GLU 150": "OE1" <-> "OE2" Residue "Al GLU 72": "OE1" <-> "OE2" Residue "Al GLU 95": "OE1" <-> "OE2" Residue "Al GLU 150": "OE1" <-> "OE2" Residue "Am GLU 72": "OE1" <-> "OE2" Residue "Am GLU 95": "OE1" <-> "OE2" Residue "Am GLU 150": "OE1" <-> "OE2" Residue "An GLU 72": "OE1" <-> "OE2" Residue "An GLU 95": "OE1" <-> "OE2" Residue "An GLU 150": "OE1" <-> "OE2" Residue "Ao GLU 72": "OE1" <-> "OE2" Residue "Ao GLU 95": "OE1" <-> "OE2" Residue "Ao GLU 150": "OE1" <-> "OE2" Residue "Ap GLU 72": "OE1" <-> "OE2" Residue "Ap GLU 95": "OE1" <-> "OE2" Residue "Ap GLU 150": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23328 Number of models: 1 Model: "" Number of chains: 16 Chain: "Aa" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ab" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ac" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ad" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ae" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Af" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ag" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ah" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ai" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Aj" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ak" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Al" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Am" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "An" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ao" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ap" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Time building chain proxies: 11.83, per 1000 atoms: 0.51 Number of scatterers: 23328 At special positions: 0 Unit cell: (129.2, 129.2, 173.85, 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 192 16.00 O 4336 8.00 N 4064 7.00 C 14736 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: 8.60 Conformation dependent library (CDL) restraints added in 4.3 seconds 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5536 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 16 sheets defined 50.8% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 71 Processing helix chain 'Aa' and resid 86 through 102 Processing helix chain 'Aa' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAa 117 " --> pdb=" O ASNAa 113 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 151 Processing helix chain 'Aa' and resid 155 through 161 Processing helix chain 'Aa' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAa 168 " --> pdb=" O SERAa 164 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALAAa 169 " --> pdb=" O ASPAa 165 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 182 through 187 Processing helix chain 'Aa' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAa 197 " --> pdb=" O SERAa 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAa 199 " --> pdb=" O ALAAa 196 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAa 217 " --> pdb=" O ALAAa 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAa 218 " --> pdb=" O ARGAa 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAa 219 " --> pdb=" O GLUAa 215 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 66 through 71 Processing helix chain 'Ab' and resid 86 through 102 Processing helix chain 'Ab' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAb 111 " --> pdb=" O GLUAb 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAb 117 " --> pdb=" O ASNAb 113 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 145 through 151 Processing helix chain 'Ab' and resid 155 through 161 Processing helix chain 'Ab' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAb 168 " --> pdb=" O SERAb 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAb 169 " --> pdb=" O ASPAb 165 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 182 through 187 Processing helix chain 'Ab' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAb 197 " --> pdb=" O SERAb 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAb 199 " --> pdb=" O ALAAb 196 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAb 217 " --> pdb=" O ALAAb 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAb 218 " --> pdb=" O ARGAb 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAb 219 " --> pdb=" O GLUAb 215 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 66 through 71 Processing helix chain 'Ac' and resid 86 through 102 Processing helix chain 'Ac' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAc 117 " --> pdb=" O ASNAc 113 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 151 Processing helix chain 'Ac' and resid 155 through 161 Processing helix chain 'Ac' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAc 168 " --> pdb=" O SERAc 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAc 169 " --> pdb=" O ASPAc 165 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 182 through 187 Processing helix chain 'Ac' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAc 197 " --> pdb=" O SERAc 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAc 199 " --> pdb=" O ALAAc 196 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAc 217 " --> pdb=" O ALAAc 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAc 218 " --> pdb=" O ARGAc 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAc 219 " --> pdb=" O GLUAc 215 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 66 through 71 Processing helix chain 'Ad' and resid 86 through 102 Processing helix chain 'Ad' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAd 111 " --> pdb=" O GLUAd 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAd 117 " --> pdb=" O ASNAd 113 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 145 through 151 Processing helix chain 'Ad' and resid 155 through 161 Processing helix chain 'Ad' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAd 168 " --> pdb=" O SERAd 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAd 169 " --> pdb=" O ASPAd 165 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 182 through 187 Processing helix chain 'Ad' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAd 197 " --> pdb=" O SERAd 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAd 199 " --> pdb=" O ALAAd 196 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAd 217 " --> pdb=" O ALAAd 213 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILEAd 218 " --> pdb=" O ARGAd 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAd 219 " --> pdb=" O GLUAd 215 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 66 through 71 Processing helix chain 'Ae' and resid 86 through 102 Processing helix chain 'Ae' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAe 117 " --> pdb=" O ASNAe 113 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 151 Processing helix chain 'Ae' and resid 155 through 161 Processing helix chain 'Ae' and resid 163 through 176 removed outlier: 3.856A pdb=" N GLUAe 168 " --> pdb=" O SERAe 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAe 169 " --> pdb=" O ASPAe 165 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 182 through 187 Processing helix chain 'Ae' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAe 197 " --> pdb=" O SERAe 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAe 199 " --> pdb=" O ALAAe 196 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAe 217 " --> pdb=" O ALAAe 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAe 218 " --> pdb=" O ARGAe 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAe 219 " --> pdb=" O GLUAe 215 " (cutoff:3.500A) Processing helix chain 'Af' and resid 66 through 71 Processing helix chain 'Af' and resid 86 through 102 Processing helix chain 'Af' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAf 111 " --> pdb=" O GLUAf 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAf 117 " --> pdb=" O ASNAf 113 " (cutoff:3.500A) Processing helix chain 'Af' and resid 145 through 151 Processing helix chain 'Af' and resid 155 through 161 Processing helix chain 'Af' and resid 163 through 176 removed outlier: 3.856A pdb=" N GLUAf 168 " --> pdb=" O SERAf 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAf 169 " --> pdb=" O ASPAf 165 " (cutoff:3.500A) Processing helix chain 'Af' and resid 182 through 187 Processing helix chain 'Af' and resid 193 through 199 removed outlier: 3.873A pdb=" N ARGAf 197 " --> pdb=" O SERAf 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAf 199 " --> pdb=" O ALAAf 196 " (cutoff:3.500A) Processing helix chain 'Af' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAf 217 " --> pdb=" O ALAAf 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAf 218 " --> pdb=" O ARGAf 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAf 219 " --> pdb=" O GLUAf 215 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 66 through 71 Processing helix chain 'Ag' and resid 86 through 102 Processing helix chain 'Ag' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAg 117 " --> pdb=" O ASNAg 113 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 151 Processing helix chain 'Ag' and resid 155 through 161 Processing helix chain 'Ag' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAg 168 " --> pdb=" O SERAg 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAg 169 " --> pdb=" O ASPAg 165 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 182 through 187 Processing helix chain 'Ag' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAg 197 " --> pdb=" O SERAg 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAg 199 " --> pdb=" O ALAAg 196 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 210 through 221 removed outlier: 3.724A pdb=" N HISAg 217 " --> pdb=" O ALAAg 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAg 218 " --> pdb=" O ARGAg 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAg 219 " --> pdb=" O GLUAg 215 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 66 through 71 Processing helix chain 'Ah' and resid 86 through 102 Processing helix chain 'Ah' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAh 111 " --> pdb=" O GLUAh 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAh 117 " --> pdb=" O ASNAh 113 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 145 through 151 Processing helix chain 'Ah' and resid 155 through 161 Processing helix chain 'Ah' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAh 168 " --> pdb=" O SERAh 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAh 169 " --> pdb=" O ASPAh 165 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 182 through 187 Processing helix chain 'Ah' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAh 197 " --> pdb=" O SERAh 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAh 199 " --> pdb=" O ALAAh 196 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAh 217 " --> pdb=" O ALAAh 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAh 218 " --> pdb=" O ARGAh 214 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLNAh 219 " --> pdb=" O GLUAh 215 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 66 through 71 Processing helix chain 'Ai' and resid 86 through 102 Processing helix chain 'Ai' and resid 107 through 122 removed outlier: 3.701A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAi 117 " --> pdb=" O ASNAi 113 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 151 Processing helix chain 'Ai' and resid 155 through 161 Processing helix chain 'Ai' and resid 163 through 176 removed outlier: 3.856A pdb=" N GLUAi 168 " --> pdb=" O SERAi 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAi 169 " --> pdb=" O ASPAi 165 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 182 through 187 Processing helix chain 'Ai' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAi 197 " --> pdb=" O SERAi 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAi 199 " --> pdb=" O ALAAi 196 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAi 217 " --> pdb=" O ALAAi 213 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILEAi 218 " --> pdb=" O ARGAi 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAi 219 " --> pdb=" O GLUAi 215 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 66 through 71 Processing helix chain 'Aj' and resid 86 through 102 Processing helix chain 'Aj' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAj 111 " --> pdb=" O GLUAj 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAj 117 " --> pdb=" O ASNAj 113 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 145 through 151 Processing helix chain 'Aj' and resid 155 through 161 Processing helix chain 'Aj' and resid 163 through 176 removed outlier: 3.856A pdb=" N GLUAj 168 " --> pdb=" O SERAj 164 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALAAj 169 " --> pdb=" O ASPAj 165 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 182 through 187 Processing helix chain 'Aj' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAj 197 " --> pdb=" O SERAj 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAj 199 " --> pdb=" O ALAAj 196 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAj 217 " --> pdb=" O ALAAj 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAj 218 " --> pdb=" O ARGAj 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAj 219 " --> pdb=" O GLUAj 215 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 66 through 71 Processing helix chain 'Ak' and resid 86 through 102 Processing helix chain 'Ak' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAk 117 " --> pdb=" O ASNAk 113 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 151 Processing helix chain 'Ak' and resid 155 through 161 Processing helix chain 'Ak' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAk 168 " --> pdb=" O SERAk 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAk 169 " --> pdb=" O ASPAk 165 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 182 through 187 Processing helix chain 'Ak' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAk 197 " --> pdb=" O SERAk 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAk 199 " --> pdb=" O ALAAk 196 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAk 217 " --> pdb=" O ALAAk 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAk 218 " --> pdb=" O ARGAk 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAk 219 " --> pdb=" O GLUAk 215 " (cutoff:3.500A) Processing helix chain 'Al' and resid 66 through 71 Processing helix chain 'Al' and resid 86 through 102 Processing helix chain 'Al' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAl 111 " --> pdb=" O GLUAl 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAl 117 " --> pdb=" O ASNAl 113 " (cutoff:3.500A) Processing helix chain 'Al' and resid 145 through 151 Processing helix chain 'Al' and resid 155 through 161 Processing helix chain 'Al' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAl 168 " --> pdb=" O SERAl 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAl 169 " --> pdb=" O ASPAl 165 " (cutoff:3.500A) Processing helix chain 'Al' and resid 182 through 187 Processing helix chain 'Al' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAl 197 " --> pdb=" O SERAl 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAl 199 " --> pdb=" O ALAAl 196 " (cutoff:3.500A) Processing helix chain 'Al' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAl 217 " --> pdb=" O ALAAl 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAl 218 " --> pdb=" O ARGAl 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAl 219 " --> pdb=" O GLUAl 215 " (cutoff:3.500A) Processing helix chain 'Am' and resid 66 through 71 Processing helix chain 'Am' and resid 86 through 102 Processing helix chain 'Am' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAm 117 " --> pdb=" O ASNAm 113 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 151 Processing helix chain 'Am' and resid 155 through 161 Processing helix chain 'Am' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAm 168 " --> pdb=" O SERAm 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAm 169 " --> pdb=" O ASPAm 165 " (cutoff:3.500A) Processing helix chain 'Am' and resid 182 through 187 Processing helix chain 'Am' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAm 197 " --> pdb=" O SERAm 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAm 199 " --> pdb=" O ALAAm 196 " (cutoff:3.500A) Processing helix chain 'Am' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAm 217 " --> pdb=" O ALAAm 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAm 218 " --> pdb=" O ARGAm 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAm 219 " --> pdb=" O GLUAm 215 " (cutoff:3.500A) Processing helix chain 'An' and resid 66 through 71 Processing helix chain 'An' and resid 86 through 102 Processing helix chain 'An' and resid 107 through 122 removed outlier: 3.701A pdb=" N VALAn 111 " --> pdb=" O GLUAn 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAn 117 " --> pdb=" O ASNAn 113 " (cutoff:3.500A) Processing helix chain 'An' and resid 145 through 151 Processing helix chain 'An' and resid 155 through 161 Processing helix chain 'An' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAn 168 " --> pdb=" O SERAn 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAn 169 " --> pdb=" O ASPAn 165 " (cutoff:3.500A) Processing helix chain 'An' and resid 182 through 187 Processing helix chain 'An' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAn 197 " --> pdb=" O SERAn 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAn 199 " --> pdb=" O ALAAn 196 " (cutoff:3.500A) Processing helix chain 'An' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAn 217 " --> pdb=" O ALAAn 213 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILEAn 218 " --> pdb=" O ARGAn 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAn 219 " --> pdb=" O GLUAn 215 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 66 through 71 Processing helix chain 'Ao' and resid 86 through 102 Processing helix chain 'Ao' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VALAo 117 " --> pdb=" O ASNAo 113 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 151 Processing helix chain 'Ao' and resid 155 through 161 Processing helix chain 'Ao' and resid 163 through 176 removed outlier: 3.856A pdb=" N GLUAo 168 " --> pdb=" O SERAo 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAo 169 " --> pdb=" O ASPAo 165 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 182 through 187 Processing helix chain 'Ao' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAo 197 " --> pdb=" O SERAo 194 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALAAo 199 " --> pdb=" O ALAAo 196 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 210 through 221 removed outlier: 3.722A pdb=" N HISAo 217 " --> pdb=" O ALAAo 213 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILEAo 218 " --> pdb=" O ARGAo 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAo 219 " --> pdb=" O GLUAo 215 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 66 through 71 Processing helix chain 'Ap' and resid 86 through 102 Processing helix chain 'Ap' and resid 107 through 122 removed outlier: 3.700A pdb=" N VALAp 111 " --> pdb=" O GLUAp 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VALAp 117 " --> pdb=" O ASNAp 113 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 145 through 151 Processing helix chain 'Ap' and resid 155 through 161 Processing helix chain 'Ap' and resid 163 through 176 removed outlier: 3.855A pdb=" N GLUAp 168 " --> pdb=" O SERAp 164 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAp 169 " --> pdb=" O ASPAp 165 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 182 through 187 Processing helix chain 'Ap' and resid 193 through 199 removed outlier: 3.874A pdb=" N ARGAp 197 " --> pdb=" O SERAp 194 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALAAp 199 " --> pdb=" O ALAAp 196 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 210 through 221 removed outlier: 3.723A pdb=" N HISAp 217 " --> pdb=" O ALAAp 213 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILEAp 218 " --> pdb=" O ARGAp 214 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLNAp 219 " --> pdb=" O GLUAp 215 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'Ab' and resid 131 through 133 Processing sheet with id=AA3, first strand: chain 'Ac' and resid 131 through 133 Processing sheet with id=AA4, first strand: chain 'Ad' and resid 131 through 133 Processing sheet with id=AA5, first strand: chain 'Ae' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'Af' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'Ag' and resid 131 through 133 Processing sheet with id=AA8, first strand: chain 'Ah' and resid 131 through 133 Processing sheet with id=AA9, first strand: chain 'Ai' and resid 131 through 133 Processing sheet with id=AB1, first strand: chain 'Aj' and resid 131 through 133 Processing sheet with id=AB2, first strand: chain 'Ak' and resid 131 through 133 Processing sheet with id=AB3, first strand: chain 'Al' and resid 131 through 133 Processing sheet with id=AB4, first strand: chain 'Am' and resid 131 through 133 Processing sheet with id=AB5, first strand: chain 'An' and resid 131 through 133 Processing sheet with id=AB6, first strand: chain 'Ao' and resid 131 through 133 Processing sheet with id=AB7, first strand: chain 'Ap' and resid 131 through 133 800 hydrogen bonds defined for protein. 2304 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: 5.60 Time building geometry restraints manager: 9.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4705 1.33 - 1.45: 5443 1.45 - 1.57: 13340 1.57 - 1.69: 0 1.69 - 1.81: 368 Bond restraints: 23856 Sorted by residual: bond pdb=" CA ASNAf 129 " pdb=" C ASNAf 129 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.23e-02 6.61e+03 2.06e+01 bond pdb=" CA ASNAk 129 " pdb=" C ASNAk 129 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.23e-02 6.61e+03 2.05e+01 bond pdb=" CA ASNAg 129 " pdb=" C ASNAg 129 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.23e-02 6.61e+03 2.05e+01 bond pdb=" CA ASNAb 129 " pdb=" C ASNAb 129 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.23e-02 6.61e+03 2.05e+01 bond pdb=" CA ASNAi 129 " pdb=" C ASNAi 129 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.23e-02 6.61e+03 2.05e+01 ... (remaining 23851 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.52: 928 106.52 - 113.40: 12559 113.40 - 120.28: 8617 120.28 - 127.16: 9944 127.16 - 134.05: 288 Bond angle restraints: 32336 Sorted by residual: angle pdb=" O VALAd 133 " pdb=" C VALAd 133 " pdb=" N METAd 134 " ideal model delta sigma weight residual 123.14 117.78 5.36 1.02e+00 9.61e-01 2.76e+01 angle pdb=" O VALAa 133 " pdb=" C VALAa 133 " pdb=" N METAa 134 " ideal model delta sigma weight residual 123.14 117.80 5.34 1.02e+00 9.61e-01 2.74e+01 angle pdb=" O VALAi 133 " pdb=" C VALAi 133 " pdb=" N METAi 134 " ideal model delta sigma weight residual 123.14 117.81 5.33 1.02e+00 9.61e-01 2.73e+01 angle pdb=" O VALAn 133 " pdb=" C VALAn 133 " pdb=" N METAn 134 " ideal model delta sigma weight residual 123.14 117.81 5.33 1.02e+00 9.61e-01 2.73e+01 angle pdb=" O VALAj 133 " pdb=" C VALAj 133 " pdb=" N METAj 134 " ideal model delta sigma weight residual 123.14 117.81 5.33 1.02e+00 9.61e-01 2.73e+01 ... (remaining 32331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 12565 16.93 - 33.86: 1691 33.86 - 50.79: 304 50.79 - 67.72: 48 67.72 - 84.65: 32 Dihedral angle restraints: 14640 sinusoidal: 6080 harmonic: 8560 Sorted by residual: dihedral pdb=" CA TRPAb 132 " pdb=" C TRPAb 132 " pdb=" N VALAb 133 " pdb=" CA VALAb 133 " ideal model delta harmonic sigma weight residual -180.00 -164.12 -15.88 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA TRPAl 132 " pdb=" C TRPAl 132 " pdb=" N VALAl 133 " pdb=" CA VALAl 133 " ideal model delta harmonic sigma weight residual -180.00 -164.14 -15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA TRPAj 132 " pdb=" C TRPAj 132 " pdb=" N VALAj 133 " pdb=" CA VALAj 133 " ideal model delta harmonic sigma weight residual -180.00 -164.18 -15.82 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 14637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1758 0.026 - 0.052: 987 0.052 - 0.077: 483 0.077 - 0.103: 228 0.103 - 0.129: 64 Chirality restraints: 3520 Sorted by residual: chirality pdb=" CA VALAf 187 " pdb=" N VALAf 187 " pdb=" C VALAf 187 " pdb=" CB VALAf 187 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA VALAe 187 " pdb=" N VALAe 187 " pdb=" C VALAe 187 " pdb=" CB VALAe 187 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA VALAk 187 " pdb=" N VALAk 187 " pdb=" C VALAk 187 " pdb=" CB VALAk 187 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 3517 not shown) Planarity restraints: 4192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALAb 44 " -0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PROAb 45 " 0.138 5.00e-02 4.00e+02 pdb=" CA PROAb 45 " -0.043 5.00e-02 4.00e+02 pdb=" CD PROAb 45 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALAf 44 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PROAf 45 " -0.138 5.00e-02 4.00e+02 pdb=" CA PROAf 45 " 0.043 5.00e-02 4.00e+02 pdb=" CD PROAf 45 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALAh 44 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PROAh 45 " -0.138 5.00e-02 4.00e+02 pdb=" CA PROAh 45 " 0.043 5.00e-02 4.00e+02 pdb=" CD PROAh 45 " 0.042 5.00e-02 4.00e+02 ... (remaining 4189 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 8185 2.84 - 3.36: 22103 3.36 - 3.87: 35946 3.87 - 4.39: 40877 4.39 - 4.90: 67134 Nonbonded interactions: 174245 Sorted by model distance: nonbonded pdb=" O SERAo 125 " pdb=" OG SERAo 125 " model vdw 2.325 2.440 nonbonded pdb=" O SERAb 125 " pdb=" OG SERAb 125 " model vdw 2.325 2.440 nonbonded pdb=" O SERAk 125 " pdb=" OG SERAk 125 " model vdw 2.325 2.440 nonbonded pdb=" O SERAl 125 " pdb=" OG SERAl 125 " model vdw 2.325 2.440 nonbonded pdb=" O SERAj 125 " pdb=" OG SERAj 125 " model vdw 2.326 2.440 ... (remaining 174240 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' } 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: 1.740 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: 0.010 Extract box with map and model: 6.730 Check model and map are aligned: 0.370 Set scattering table: 0.200 Process input model: 55.830 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.004 0.056 23856 Z= 0.288 Angle : 0.887 8.535 32336 Z= 0.525 Chirality : 0.042 0.129 3520 Planarity : 0.007 0.080 4192 Dihedral : 15.409 84.650 9104 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.03 % Favored : 94.41 % Rotamer: Outliers : 0.63 % Allowed : 18.91 % Favored : 80.46 % 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: -1.65 (0.15), residues: 2864 helix: -1.08 (0.15), residues: 1184 sheet: -0.25 (0.44), residues: 160 loop : -1.14 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAj 132 HIS 0.011 0.003 HISAc 69 PHE 0.007 0.002 PHEAp 200 TYR 0.027 0.002 TYRAm 184 ARG 0.007 0.001 ARGAd 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 911 time to evaluate : 2.745 Fit side-chains revert: symmetry clash REVERT: Aa 69 HIS cc_start: 0.8679 (t-170) cc_final: 0.8428 (t-170) REVERT: Aa 127 ASN cc_start: 0.8607 (p0) cc_final: 0.8326 (p0) REVERT: Aa 183 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7028 (mpt180) REVERT: Aa 201 ASP cc_start: 0.8531 (t0) cc_final: 0.8303 (t0) REVERT: Ab 60 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8801 (mmtm) REVERT: Ab 73 TYR cc_start: 0.8610 (t80) cc_final: 0.7738 (t80) REVERT: Ab 78 ILE cc_start: 0.8890 (tp) cc_final: 0.8616 (tp) REVERT: Ab 127 ASN cc_start: 0.8648 (p0) cc_final: 0.8350 (p0) REVERT: Ab 129 ASN cc_start: 0.8481 (p0) cc_final: 0.8196 (p0) REVERT: Ab 165 ASP cc_start: 0.8025 (t0) cc_final: 0.7551 (t0) REVERT: Ac 69 HIS cc_start: 0.8632 (t-170) cc_final: 0.8345 (t-170) REVERT: Ac 127 ASN cc_start: 0.8541 (p0) cc_final: 0.8256 (p0) REVERT: Ad 55 ARG cc_start: 0.8684 (mtp85) cc_final: 0.8370 (mtp85) REVERT: Ad 69 HIS cc_start: 0.8723 (t-170) cc_final: 0.8378 (t-170) REVERT: Ad 73 TYR cc_start: 0.8632 (t80) cc_final: 0.8339 (t80) REVERT: Ad 76 GLN cc_start: 0.8423 (mp10) cc_final: 0.8178 (mp10) REVERT: Ad 127 ASN cc_start: 0.8529 (p0) cc_final: 0.8282 (p0) REVERT: Ad 158 GLN cc_start: 0.8743 (mt0) cc_final: 0.8456 (mt0) REVERT: Ad 165 ASP cc_start: 0.8061 (t0) cc_final: 0.7508 (t0) REVERT: Ae 76 GLN cc_start: 0.8560 (mp10) cc_final: 0.8320 (mp10) REVERT: Ae 102 ASP cc_start: 0.8793 (t0) cc_final: 0.8548 (t0) REVERT: Ae 158 GLN cc_start: 0.8858 (mt0) cc_final: 0.8511 (mt0) REVERT: Ae 165 ASP cc_start: 0.7899 (t0) cc_final: 0.7523 (t0) REVERT: Af 121 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8281 (mm-30) REVERT: Af 143 TYR cc_start: 0.9370 (m-80) cc_final: 0.8951 (m-80) REVERT: Af 165 ASP cc_start: 0.8029 (t0) cc_final: 0.7606 (t0) REVERT: Af 208 ARG cc_start: 0.7862 (mtm180) cc_final: 0.7619 (mtm180) REVERT: Ag 165 ASP cc_start: 0.7934 (t0) cc_final: 0.7411 (t0) REVERT: Ah 69 HIS cc_start: 0.8724 (t-170) cc_final: 0.8263 (t-170) REVERT: Ah 76 GLN cc_start: 0.8438 (mp10) cc_final: 0.8225 (mp10) REVERT: Ah 127 ASN cc_start: 0.8598 (p0) cc_final: 0.8336 (p0) REVERT: Ah 165 ASP cc_start: 0.7982 (t0) cc_final: 0.7415 (t0) REVERT: Ai 73 TYR cc_start: 0.8605 (t80) cc_final: 0.8187 (t80) REVERT: Ai 127 ASN cc_start: 0.8553 (p0) cc_final: 0.8316 (p0) REVERT: Ai 165 ASP cc_start: 0.8095 (t0) cc_final: 0.7472 (t0) REVERT: Aj 76 GLN cc_start: 0.8569 (mp10) cc_final: 0.8358 (mp10) REVERT: Aj 134 MET cc_start: 0.8684 (ttt) cc_final: 0.8473 (ttt) REVERT: Aj 165 ASP cc_start: 0.7998 (t0) cc_final: 0.7462 (t0) REVERT: Ak 69 HIS cc_start: 0.8801 (t-170) cc_final: 0.8497 (t-170) REVERT: Ak 73 TYR cc_start: 0.8751 (t80) cc_final: 0.8303 (t80) REVERT: Ak 76 GLN cc_start: 0.8501 (mp10) cc_final: 0.8251 (mp10) REVERT: Ak 91 ASP cc_start: 0.7688 (m-30) cc_final: 0.7445 (m-30) REVERT: Ak 165 ASP cc_start: 0.7904 (t0) cc_final: 0.7350 (t0) REVERT: Al 121 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8222 (mm-30) REVERT: Al 134 MET cc_start: 0.8774 (ttt) cc_final: 0.8545 (ttt) REVERT: Al 165 ASP cc_start: 0.7986 (t0) cc_final: 0.7697 (t0) REVERT: Al 181 MET cc_start: 0.9055 (tpp) cc_final: 0.8684 (tpp) REVERT: Am 69 HIS cc_start: 0.8759 (t-170) cc_final: 0.8481 (t-170) REVERT: Am 127 ASN cc_start: 0.8505 (p0) cc_final: 0.8269 (p0) REVERT: Am 157 ARG cc_start: 0.8947 (ttp80) cc_final: 0.8676 (ttt-90) REVERT: Am 165 ASP cc_start: 0.8088 (t0) cc_final: 0.7514 (t0) REVERT: An 69 HIS cc_start: 0.8713 (t-170) cc_final: 0.8488 (t-170) REVERT: An 73 TYR cc_start: 0.8688 (t80) cc_final: 0.8211 (t80) REVERT: An 127 ASN cc_start: 0.8556 (p0) cc_final: 0.8295 (p0) REVERT: Ao 76 GLN cc_start: 0.8488 (mp10) cc_final: 0.8256 (mp10) REVERT: Ao 127 ASN cc_start: 0.8565 (p0) cc_final: 0.8330 (p0) REVERT: Ao 134 MET cc_start: 0.8784 (ttt) cc_final: 0.8563 (ttt) REVERT: Ao 165 ASP cc_start: 0.7959 (t0) cc_final: 0.7430 (t0) REVERT: Ap 158 GLN cc_start: 0.8744 (mt0) cc_final: 0.8534 (mt0) REVERT: Ap 165 ASP cc_start: 0.7981 (t0) cc_final: 0.7439 (t0) outliers start: 16 outliers final: 0 residues processed: 911 average time/residue: 0.4353 time to fit residues: 570.1744 Evaluate side-chains 846 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 846 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 0.1980 chunk 74 optimal weight: 9.9990 chunk 147 optimal weight: 0.0980 chunk 116 optimal weight: 7.9990 chunk 225 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 151 ASN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 ASN Af 158 GLN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 151 ASN Ai 151 ASN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN An 151 ASN Ao 151 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23856 Z= 0.275 Angle : 0.677 8.992 32336 Z= 0.336 Chirality : 0.042 0.127 3520 Planarity : 0.006 0.055 4192 Dihedral : 4.363 15.480 3216 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.45 % Allowed : 20.09 % Favored : 77.45 % 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: -1.36 (0.15), residues: 2864 helix: -0.45 (0.14), residues: 1424 sheet: -0.08 (0.41), residues: 160 loop : -1.45 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAk 93 HIS 0.008 0.001 HISAj 69 PHE 0.010 0.002 PHEAk 200 TYR 0.023 0.002 TYRAl 198 ARG 0.006 0.001 ARGAk 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 838 time to evaluate : 2.710 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 127 ASN cc_start: 0.8683 (p0) cc_final: 0.8463 (p0) REVERT: Aa 136 ASP cc_start: 0.7646 (m-30) cc_final: 0.7149 (m-30) REVERT: Aa 181 MET cc_start: 0.8841 (tpp) cc_final: 0.8540 (tpp) REVERT: Aa 183 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7243 (mpt180) REVERT: Aa 201 ASP cc_start: 0.8785 (t0) cc_final: 0.8373 (t0) REVERT: Ab 54 MET cc_start: 0.7756 (ttp) cc_final: 0.7036 (ttp) REVERT: Ab 127 ASN cc_start: 0.8698 (p0) cc_final: 0.8452 (p0) REVERT: Ab 129 ASN cc_start: 0.8447 (p0) cc_final: 0.8120 (p0) REVERT: Ab 136 ASP cc_start: 0.7770 (m-30) cc_final: 0.7282 (m-30) REVERT: Ab 157 ARG cc_start: 0.8960 (ttp80) cc_final: 0.8556 (ttt90) REVERT: Ab 165 ASP cc_start: 0.7879 (t0) cc_final: 0.7563 (t0) REVERT: Ac 54 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7719 (ttp) REVERT: Ac 80 ILE cc_start: 0.8528 (pt) cc_final: 0.8296 (pt) REVERT: Ac 127 ASN cc_start: 0.8677 (p0) cc_final: 0.8416 (p0) REVERT: Ac 157 ARG cc_start: 0.8896 (ttp80) cc_final: 0.8641 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7847 (t0) cc_final: 0.7348 (t0) REVERT: Ad 102 ASP cc_start: 0.8918 (t0) cc_final: 0.8579 (t0) REVERT: Ad 127 ASN cc_start: 0.8627 (p0) cc_final: 0.8383 (p0) REVERT: Ad 165 ASP cc_start: 0.8018 (t0) cc_final: 0.7725 (t0) REVERT: Ae 54 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7557 (ttp) REVERT: Ae 77 GLN cc_start: 0.8600 (tp40) cc_final: 0.8223 (tp40) REVERT: Ae 102 ASP cc_start: 0.8904 (t0) cc_final: 0.8549 (t0) REVERT: Ae 127 ASN cc_start: 0.8655 (p0) cc_final: 0.8405 (p0) REVERT: Ae 129 ASN cc_start: 0.8343 (p0) cc_final: 0.8070 (p0) REVERT: Ae 158 GLN cc_start: 0.8892 (mt0) cc_final: 0.8624 (mt0) REVERT: Ae 165 ASP cc_start: 0.8035 (t0) cc_final: 0.7641 (t0) REVERT: Ae 181 MET cc_start: 0.8743 (tpp) cc_final: 0.8331 (tpp) REVERT: Af 127 ASN cc_start: 0.8668 (p0) cc_final: 0.8432 (p0) REVERT: Af 165 ASP cc_start: 0.7977 (t0) cc_final: 0.7628 (t0) REVERT: Ag 102 ASP cc_start: 0.8900 (t0) cc_final: 0.8615 (t0) REVERT: Ag 121 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7904 (mm-30) REVERT: Ag 165 ASP cc_start: 0.7953 (t0) cc_final: 0.7681 (t0) REVERT: Ag 188 ARG cc_start: 0.7168 (tpt170) cc_final: 0.6965 (tpt170) REVERT: Ag 208 ARG cc_start: 0.7907 (mtm180) cc_final: 0.7679 (mtm180) REVERT: Ah 54 MET cc_start: 0.7850 (ttp) cc_final: 0.6937 (ttp) REVERT: Ah 66 ASN cc_start: 0.7436 (t0) cc_final: 0.7185 (t0) REVERT: Ah 80 ILE cc_start: 0.8600 (pt) cc_final: 0.8380 (pt) REVERT: Ah 157 ARG cc_start: 0.8885 (ttp80) cc_final: 0.8621 (ttt-90) REVERT: Ai 73 TYR cc_start: 0.8982 (t80) cc_final: 0.8615 (t80) REVERT: Ai 127 ASN cc_start: 0.8632 (p0) cc_final: 0.8378 (p0) REVERT: Ai 136 ASP cc_start: 0.7622 (m-30) cc_final: 0.7227 (m-30) REVERT: Ai 157 ARG cc_start: 0.8990 (ttp80) cc_final: 0.8691 (ttt90) REVERT: Ai 165 ASP cc_start: 0.7973 (t0) cc_final: 0.7334 (t0) REVERT: Ai 201 ASP cc_start: 0.8580 (t0) cc_final: 0.8295 (t0) REVERT: Aj 56 MET cc_start: 0.8610 (mmp) cc_final: 0.8133 (mmp) REVERT: Aj 76 GLN cc_start: 0.8657 (mp10) cc_final: 0.8454 (mp10) REVERT: Aj 80 ILE cc_start: 0.8493 (pt) cc_final: 0.8180 (pt) REVERT: Aj 127 ASN cc_start: 0.8713 (p0) cc_final: 0.8487 (p0) REVERT: Aj 157 ARG cc_start: 0.8983 (ttp80) cc_final: 0.8723 (ttt-90) REVERT: Aj 165 ASP cc_start: 0.8111 (t0) cc_final: 0.7701 (t0) REVERT: Ak 73 TYR cc_start: 0.8958 (t80) cc_final: 0.8718 (t80) REVERT: Ak 77 GLN cc_start: 0.8448 (tp40) cc_final: 0.8245 (tp40) REVERT: Ak 136 ASP cc_start: 0.8056 (m-30) cc_final: 0.7614 (m-30) REVERT: Ak 165 ASP cc_start: 0.7884 (t0) cc_final: 0.7603 (t0) REVERT: Ak 174 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7370 (mmm-85) REVERT: Ak 201 ASP cc_start: 0.8655 (t0) cc_final: 0.8237 (t0) REVERT: Ak 204 GLU cc_start: 0.8306 (pp20) cc_final: 0.7944 (pp20) REVERT: Al 80 ILE cc_start: 0.8535 (pt) cc_final: 0.8291 (pt) REVERT: Al 127 ASN cc_start: 0.8752 (p0) cc_final: 0.8486 (p0) REVERT: Al 136 ASP cc_start: 0.8118 (m-30) cc_final: 0.7592 (m-30) REVERT: Al 157 ARG cc_start: 0.8966 (ttp80) cc_final: 0.8637 (ttt90) REVERT: Al 165 ASP cc_start: 0.7899 (t0) cc_final: 0.7618 (t0) REVERT: Al 204 GLU cc_start: 0.8181 (pp20) cc_final: 0.7907 (pp20) REVERT: Am 54 MET cc_start: 0.7798 (ttp) cc_final: 0.7036 (ttp) REVERT: Am 69 HIS cc_start: 0.8813 (t-170) cc_final: 0.8504 (t-170) REVERT: Am 127 ASN cc_start: 0.8594 (p0) cc_final: 0.8351 (p0) REVERT: Am 129 ASN cc_start: 0.8538 (p0) cc_final: 0.8170 (p0) REVERT: Am 165 ASP cc_start: 0.7973 (t0) cc_final: 0.7658 (t0) REVERT: An 69 HIS cc_start: 0.8718 (t-170) cc_final: 0.8504 (t-170) REVERT: An 73 TYR cc_start: 0.9006 (t80) cc_final: 0.8554 (t80) REVERT: An 127 ASN cc_start: 0.8655 (p0) cc_final: 0.8381 (p0) REVERT: An 165 ASP cc_start: 0.7783 (t0) cc_final: 0.7220 (t0) REVERT: An 174 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7306 (mmm-85) REVERT: Ao 127 ASN cc_start: 0.8649 (p0) cc_final: 0.8423 (p0) REVERT: Ap 127 ASN cc_start: 0.8644 (p0) cc_final: 0.8443 (p0) REVERT: Ap 129 ASN cc_start: 0.8413 (p0) cc_final: 0.8210 (p0) REVERT: Ap 165 ASP cc_start: 0.7967 (t0) cc_final: 0.7405 (t0) outliers start: 62 outliers final: 13 residues processed: 877 average time/residue: 0.4087 time to fit residues: 525.7252 Evaluate side-chains 834 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 819 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ac residue 54 MET Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ae residue 54 MET Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 205 VAL Chi-restraints excluded: chain Ap residue 78 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 1.9990 chunk 81 optimal weight: 0.0000 chunk 217 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 233 optimal weight: 30.0000 chunk 259 optimal weight: 0.8980 chunk 89 optimal weight: 30.0000 chunk 210 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 158 GLN Ab 140 GLN Ab 158 GLN Ad 151 ASN Ae 140 GLN Ae 158 GLN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 140 GLN Af 151 ASN Af 158 GLN Ag 151 ASN Ah 151 ASN Ai 140 GLN Ai 158 GLN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN Am 158 GLN An 151 ASN Ao 140 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23856 Z= 0.179 Angle : 0.632 9.405 32336 Z= 0.306 Chirality : 0.041 0.148 3520 Planarity : 0.006 0.062 4192 Dihedral : 4.237 17.142 3216 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.89 % Allowed : 19.30 % Favored : 77.81 % 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: -0.85 (0.16), residues: 2864 helix: -0.07 (0.14), residues: 1424 sheet: 1.01 (0.44), residues: 160 loop : -1.28 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAb 93 HIS 0.008 0.001 HISAe 69 PHE 0.006 0.001 PHEAa 200 TYR 0.026 0.001 TYRAc 198 ARG 0.006 0.001 ARGAg 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 904 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 80 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8044 (pt) REVERT: Aa 129 ASN cc_start: 0.8396 (p0) cc_final: 0.8123 (p0) REVERT: Aa 136 ASP cc_start: 0.7767 (m-30) cc_final: 0.7332 (m-30) REVERT: Aa 157 ARG cc_start: 0.8928 (ttp80) cc_final: 0.8682 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8888 (tpp) cc_final: 0.8474 (tpp) REVERT: Aa 183 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7034 (mpt180) REVERT: Aa 208 ARG cc_start: 0.7772 (mtm180) cc_final: 0.7527 (mtm180) REVERT: Ab 54 MET cc_start: 0.7909 (ttp) cc_final: 0.7159 (ttp) REVERT: Ab 69 HIS cc_start: 0.8778 (t-170) cc_final: 0.8517 (t-170) REVERT: Ab 80 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8191 (pt) REVERT: Ab 127 ASN cc_start: 0.8788 (p0) cc_final: 0.8520 (p0) REVERT: Ab 136 ASP cc_start: 0.7731 (m-30) cc_final: 0.7266 (m-30) REVERT: Ab 157 ARG cc_start: 0.8958 (ttp80) cc_final: 0.8562 (ttt90) REVERT: Ab 165 ASP cc_start: 0.7909 (t0) cc_final: 0.7493 (t0) REVERT: Ab 184 TYR cc_start: 0.7894 (t80) cc_final: 0.7569 (t80) REVERT: Ac 70 LEU cc_start: 0.9123 (tp) cc_final: 0.8896 (tp) REVERT: Ac 80 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8276 (pt) REVERT: Ac 127 ASN cc_start: 0.8687 (p0) cc_final: 0.8425 (p0) REVERT: Ac 157 ARG cc_start: 0.8871 (ttp80) cc_final: 0.8632 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7886 (t0) cc_final: 0.7363 (t0) REVERT: Ac 201 ASP cc_start: 0.8595 (t0) cc_final: 0.8255 (t0) REVERT: Ad 69 HIS cc_start: 0.8802 (t-170) cc_final: 0.8478 (t-170) REVERT: Ad 73 TYR cc_start: 0.8690 (t80) cc_final: 0.8069 (t80) REVERT: Ad 76 GLN cc_start: 0.8370 (mp10) cc_final: 0.8114 (mp10) REVERT: Ad 102 ASP cc_start: 0.8864 (t0) cc_final: 0.8498 (t0) REVERT: Ad 127 ASN cc_start: 0.8678 (p0) cc_final: 0.8402 (p0) REVERT: Ad 136 ASP cc_start: 0.7856 (m-30) cc_final: 0.7546 (m-30) REVERT: Ad 157 ARG cc_start: 0.8886 (ttp80) cc_final: 0.8649 (ttt-90) REVERT: Ad 165 ASP cc_start: 0.8017 (t0) cc_final: 0.7735 (t0) REVERT: Ae 76 GLN cc_start: 0.8445 (mp10) cc_final: 0.8038 (mp10) REVERT: Ae 102 ASP cc_start: 0.8874 (t0) cc_final: 0.8492 (t0) REVERT: Ae 127 ASN cc_start: 0.8722 (p0) cc_final: 0.8513 (p0) REVERT: Ae 129 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.8063 (p0) REVERT: Ae 157 ARG cc_start: 0.8934 (ttp80) cc_final: 0.8678 (ttt-90) REVERT: Ae 165 ASP cc_start: 0.8042 (t0) cc_final: 0.7759 (t0) REVERT: Ae 181 MET cc_start: 0.8777 (tpp) cc_final: 0.8457 (tpp) REVERT: Ae 204 GLU cc_start: 0.8236 (pp20) cc_final: 0.7765 (pp20) REVERT: Af 54 MET cc_start: 0.7880 (ttp) cc_final: 0.7232 (ttp) REVERT: Af 80 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8207 (pt) REVERT: Af 129 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8089 (p0) REVERT: Af 165 ASP cc_start: 0.7822 (t0) cc_final: 0.7558 (t0) REVERT: Ag 70 LEU cc_start: 0.9181 (tp) cc_final: 0.8922 (tp) REVERT: Ag 77 GLN cc_start: 0.8223 (tp40) cc_final: 0.8004 (tp40) REVERT: Ag 102 ASP cc_start: 0.8926 (t0) cc_final: 0.8620 (t0) REVERT: Ag 121 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7926 (mm-30) REVERT: Ag 136 ASP cc_start: 0.7662 (m-30) cc_final: 0.7140 (m-30) REVERT: Ag 165 ASP cc_start: 0.7975 (t0) cc_final: 0.7650 (t0) REVERT: Ag 208 ARG cc_start: 0.7898 (mtm180) cc_final: 0.7658 (mtm180) REVERT: Ah 54 MET cc_start: 0.7911 (ttp) cc_final: 0.7105 (ttp) REVERT: Ah 66 ASN cc_start: 0.7614 (t0) cc_final: 0.7141 (t0) REVERT: Ah 69 HIS cc_start: 0.8809 (t-170) cc_final: 0.8541 (t-170) REVERT: Ah 76 GLN cc_start: 0.8457 (mp10) cc_final: 0.8085 (mp10) REVERT: Ah 80 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8192 (pt) REVERT: Ah 157 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8567 (ttt90) REVERT: Ah 165 ASP cc_start: 0.7910 (t0) cc_final: 0.7680 (t0) REVERT: Ai 69 HIS cc_start: 0.8648 (t-170) cc_final: 0.8416 (t-170) REVERT: Ai 73 TYR cc_start: 0.8938 (t80) cc_final: 0.8534 (t80) REVERT: Ai 80 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8107 (pt) REVERT: Ai 127 ASN cc_start: 0.8687 (p0) cc_final: 0.8377 (p0) REVERT: Ai 136 ASP cc_start: 0.7727 (m-30) cc_final: 0.7216 (m-30) REVERT: Ai 157 ARG cc_start: 0.8925 (ttp80) cc_final: 0.8636 (ttt90) REVERT: Ai 165 ASP cc_start: 0.7960 (t0) cc_final: 0.7357 (t0) REVERT: Ai 201 ASP cc_start: 0.8646 (t0) cc_final: 0.8253 (t0) REVERT: Aj 56 MET cc_start: 0.8604 (mmp) cc_final: 0.8092 (mmp) REVERT: Aj 76 GLN cc_start: 0.8617 (mp10) cc_final: 0.8371 (mp10) REVERT: Aj 80 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8153 (pt) REVERT: Aj 127 ASN cc_start: 0.8741 (p0) cc_final: 0.8528 (p0) REVERT: Aj 129 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8004 (p0) REVERT: Aj 157 ARG cc_start: 0.8951 (ttp80) cc_final: 0.8732 (ttt-90) REVERT: Aj 165 ASP cc_start: 0.8139 (t0) cc_final: 0.7871 (t0) REVERT: Aj 204 GLU cc_start: 0.8245 (pp20) cc_final: 0.7578 (pp20) REVERT: Ak 69 HIS cc_start: 0.8794 (t-170) cc_final: 0.8582 (t-170) REVERT: Ak 73 TYR cc_start: 0.8942 (t80) cc_final: 0.8659 (t80) REVERT: Ak 129 ASN cc_start: 0.8603 (p0) cc_final: 0.8376 (p0) REVERT: Ak 136 ASP cc_start: 0.7780 (m-30) cc_final: 0.7365 (m-30) REVERT: Ak 157 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8667 (ttt-90) REVERT: Ak 165 ASP cc_start: 0.7811 (t0) cc_final: 0.7498 (t0) REVERT: Ak 201 ASP cc_start: 0.8649 (t0) cc_final: 0.8180 (t0) REVERT: Ak 204 GLU cc_start: 0.8201 (pp20) cc_final: 0.7889 (pp20) REVERT: Al 80 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8210 (pt) REVERT: Al 127 ASN cc_start: 0.8812 (p0) cc_final: 0.8598 (p0) REVERT: Al 136 ASP cc_start: 0.7902 (m-30) cc_final: 0.7344 (m-30) REVERT: Al 157 ARG cc_start: 0.8968 (ttp80) cc_final: 0.8644 (ttt90) REVERT: Al 165 ASP cc_start: 0.7842 (t0) cc_final: 0.7490 (t0) REVERT: Al 183 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7962 (ttp80) REVERT: Al 204 GLU cc_start: 0.8162 (pp20) cc_final: 0.7828 (pp20) REVERT: Am 54 MET cc_start: 0.7854 (ttp) cc_final: 0.6954 (ttp) REVERT: Am 69 HIS cc_start: 0.8776 (t-170) cc_final: 0.8444 (t-170) REVERT: Am 70 LEU cc_start: 0.9110 (tp) cc_final: 0.8852 (tp) REVERT: Am 127 ASN cc_start: 0.8725 (p0) cc_final: 0.8467 (p0) REVERT: Am 165 ASP cc_start: 0.7850 (t0) cc_final: 0.7395 (t0) REVERT: An 69 HIS cc_start: 0.8756 (t-170) cc_final: 0.8446 (t-170) REVERT: An 73 TYR cc_start: 0.9067 (t80) cc_final: 0.8540 (t80) REVERT: An 127 ASN cc_start: 0.8760 (p0) cc_final: 0.8497 (p0) REVERT: An 129 ASN cc_start: 0.8425 (p0) cc_final: 0.8026 (p0) REVERT: An 165 ASP cc_start: 0.7812 (t0) cc_final: 0.7140 (t0) REVERT: Ao 80 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8008 (pt) REVERT: Ao 102 ASP cc_start: 0.8801 (t0) cc_final: 0.8385 (t0) REVERT: Ao 127 ASN cc_start: 0.8709 (p0) cc_final: 0.8437 (p0) REVERT: Ao 157 ARG cc_start: 0.8946 (ttp80) cc_final: 0.8730 (ttt90) REVERT: Ao 165 ASP cc_start: 0.7899 (t0) cc_final: 0.7642 (t0) REVERT: Ap 127 ASN cc_start: 0.8722 (p0) cc_final: 0.8476 (p0) REVERT: Ap 129 ASN cc_start: 0.8428 (p0) cc_final: 0.8213 (p0) REVERT: Ap 165 ASP cc_start: 0.7950 (t0) cc_final: 0.7328 (t0) outliers start: 73 outliers final: 22 residues processed: 936 average time/residue: 0.4114 time to fit residues: 568.2374 Evaluate side-chains 866 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 832 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 80 ILE Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 80 ILE Chi-restraints excluded: chain Ac residue 80 ILE Chi-restraints excluded: chain Ac residue 129 ASN Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 151 ASN Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 80 ILE Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 129 ASN Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 80 ILE Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 80 ILE Chi-restraints excluded: chain Aj residue 78 ILE Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 129 ASN Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 129 ASN Chi-restraints excluded: chain Am residue 78 ILE Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 80 ILE Chi-restraints excluded: chain Ao residue 205 VAL Chi-restraints excluded: chain Ap residue 78 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.0980 chunk 196 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 175 optimal weight: 0.0570 chunk 262 optimal weight: 4.9990 chunk 278 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 140 GLN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 ASN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 151 ASN Aj 158 GLN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN Al 158 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23856 Z= 0.203 Angle : 0.640 10.083 32336 Z= 0.305 Chirality : 0.041 0.155 3520 Planarity : 0.006 0.063 4192 Dihedral : 4.094 16.148 3216 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.44 % Allowed : 22.03 % Favored : 74.53 % 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: -0.61 (0.16), residues: 2864 helix: 0.08 (0.14), residues: 1424 sheet: 1.49 (0.45), residues: 160 loop : -1.16 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAg 93 HIS 0.008 0.001 HISAa 69 PHE 0.008 0.001 PHEAn 200 TYR 0.024 0.001 TYRAb 198 ARG 0.006 0.001 ARGAb 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 901 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 78 ILE cc_start: 0.8379 (tp) cc_final: 0.8021 (pt) REVERT: Aa 136 ASP cc_start: 0.7307 (m-30) cc_final: 0.6925 (m-30) REVERT: Aa 157 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8653 (ttt-90) REVERT: Aa 183 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7096 (mpt180) REVERT: Aa 201 ASP cc_start: 0.8659 (t0) cc_final: 0.8154 (t0) REVERT: Ab 54 MET cc_start: 0.7808 (ttp) cc_final: 0.6894 (ttp) REVERT: Ab 69 HIS cc_start: 0.8771 (t-170) cc_final: 0.8460 (t-170) REVERT: Ab 127 ASN cc_start: 0.8830 (p0) cc_final: 0.8527 (p0) REVERT: Ab 136 ASP cc_start: 0.7287 (m-30) cc_final: 0.6681 (m-30) REVERT: Ab 157 ARG cc_start: 0.8946 (ttp80) cc_final: 0.8583 (ttt90) REVERT: Ab 165 ASP cc_start: 0.7978 (t0) cc_final: 0.7679 (t0) REVERT: Ab 184 TYR cc_start: 0.7994 (t80) cc_final: 0.7679 (t80) REVERT: Ac 127 ASN cc_start: 0.8727 (p0) cc_final: 0.8432 (p0) REVERT: Ac 135 MET cc_start: 0.8685 (mmm) cc_final: 0.8407 (mmm) REVERT: Ac 157 ARG cc_start: 0.8890 (ttp80) cc_final: 0.8614 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.7937 (t0) cc_final: 0.7310 (t0) REVERT: Ac 201 ASP cc_start: 0.8682 (t0) cc_final: 0.8258 (t0) REVERT: Ad 69 HIS cc_start: 0.8854 (t-170) cc_final: 0.8439 (t-170) REVERT: Ad 73 TYR cc_start: 0.8891 (t80) cc_final: 0.8467 (t80) REVERT: Ad 76 GLN cc_start: 0.8473 (mp10) cc_final: 0.8162 (mp10) REVERT: Ad 102 ASP cc_start: 0.8886 (t0) cc_final: 0.8500 (t0) REVERT: Ad 127 ASN cc_start: 0.8731 (p0) cc_final: 0.8409 (p0) REVERT: Ad 157 ARG cc_start: 0.8865 (ttp80) cc_final: 0.8629 (ttt-90) REVERT: Ad 165 ASP cc_start: 0.8052 (t0) cc_final: 0.7799 (t0) REVERT: Ae 102 ASP cc_start: 0.8908 (t0) cc_final: 0.8497 (t0) REVERT: Ae 127 ASN cc_start: 0.8758 (p0) cc_final: 0.8536 (p0) REVERT: Ae 129 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.8021 (p0) REVERT: Ae 136 ASP cc_start: 0.7304 (m-30) cc_final: 0.6650 (m-30) REVERT: Ae 165 ASP cc_start: 0.8005 (t0) cc_final: 0.7692 (t0) REVERT: Ae 181 MET cc_start: 0.8839 (tpp) cc_final: 0.8541 (tpp) REVERT: Ae 204 GLU cc_start: 0.8199 (pp20) cc_final: 0.7787 (pp20) REVERT: Af 54 MET cc_start: 0.7921 (ttp) cc_final: 0.7187 (ttp) REVERT: Af 73 TYR cc_start: 0.9005 (t80) cc_final: 0.8574 (t80) REVERT: Af 80 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8299 (pt) REVERT: Af 165 ASP cc_start: 0.7958 (t0) cc_final: 0.7640 (t0) REVERT: Ag 77 GLN cc_start: 0.8224 (tp40) cc_final: 0.7959 (tp40) REVERT: Ag 102 ASP cc_start: 0.8920 (t0) cc_final: 0.8632 (t0) REVERT: Ag 108 MET cc_start: 0.8368 (tpp) cc_final: 0.8112 (tpp) REVERT: Ag 136 ASP cc_start: 0.7108 (m-30) cc_final: 0.6606 (m-30) REVERT: Ag 165 ASP cc_start: 0.7976 (t0) cc_final: 0.7537 (t0) REVERT: Ah 54 MET cc_start: 0.7949 (ttp) cc_final: 0.7103 (ttp) REVERT: Ah 66 ASN cc_start: 0.7773 (t0) cc_final: 0.7256 (t0) REVERT: Ah 69 HIS cc_start: 0.8791 (t-170) cc_final: 0.8545 (t70) REVERT: Ah 76 GLN cc_start: 0.8438 (mp10) cc_final: 0.8071 (mp10) REVERT: Ah 80 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8431 (pt) REVERT: Ah 157 ARG cc_start: 0.8828 (ttp80) cc_final: 0.8605 (ttt-90) REVERT: Ah 165 ASP cc_start: 0.7981 (t0) cc_final: 0.7658 (t0) REVERT: Ai 69 HIS cc_start: 0.8670 (t-170) cc_final: 0.8390 (t-170) REVERT: Ai 73 TYR cc_start: 0.9086 (t80) cc_final: 0.8729 (t80) REVERT: Ai 80 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8227 (pt) REVERT: Ai 127 ASN cc_start: 0.8740 (p0) cc_final: 0.8455 (p0) REVERT: Ai 136 ASP cc_start: 0.7381 (m-30) cc_final: 0.6873 (m-30) REVERT: Ai 157 ARG cc_start: 0.8920 (ttp80) cc_final: 0.8651 (ttt90) REVERT: Ai 165 ASP cc_start: 0.8043 (t0) cc_final: 0.7396 (t0) REVERT: Ai 201 ASP cc_start: 0.8681 (t0) cc_final: 0.8259 (t0) REVERT: Aj 60 LYS cc_start: 0.9263 (mmtt) cc_final: 0.8985 (mmpt) REVERT: Aj 69 HIS cc_start: 0.8923 (t70) cc_final: 0.8712 (t-170) REVERT: Aj 80 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8436 (pt) REVERT: Aj 91 ASP cc_start: 0.8040 (m-30) cc_final: 0.7625 (m-30) REVERT: Aj 127 ASN cc_start: 0.8778 (p0) cc_final: 0.8529 (p0) REVERT: Aj 129 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7979 (p0) REVERT: Aj 157 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8755 (ttt-90) REVERT: Aj 165 ASP cc_start: 0.8136 (t0) cc_final: 0.7804 (t0) REVERT: Aj 204 GLU cc_start: 0.8166 (pp20) cc_final: 0.7652 (pp20) REVERT: Ak 69 HIS cc_start: 0.8782 (t-170) cc_final: 0.8579 (t-170) REVERT: Ak 73 TYR cc_start: 0.9083 (t80) cc_final: 0.8826 (t80) REVERT: Ak 136 ASP cc_start: 0.7862 (m-30) cc_final: 0.7560 (m-30) REVERT: Ak 140 GLN cc_start: 0.8262 (mt0) cc_final: 0.7736 (mt0) REVERT: Ak 157 ARG cc_start: 0.8921 (ttp80) cc_final: 0.8669 (ttt90) REVERT: Ak 165 ASP cc_start: 0.7883 (t0) cc_final: 0.7523 (t0) REVERT: Ak 201 ASP cc_start: 0.8712 (t0) cc_final: 0.8188 (t0) REVERT: Ak 204 GLU cc_start: 0.8169 (pp20) cc_final: 0.7931 (pp20) REVERT: Al 80 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8363 (pt) REVERT: Al 127 ASN cc_start: 0.8849 (p0) cc_final: 0.8612 (p0) REVERT: Al 129 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8191 (p0) REVERT: Al 136 ASP cc_start: 0.7778 (m-30) cc_final: 0.7332 (m-30) REVERT: Al 157 ARG cc_start: 0.8953 (ttp80) cc_final: 0.8654 (ttt90) REVERT: Al 165 ASP cc_start: 0.7899 (t0) cc_final: 0.7598 (t0) REVERT: Al 183 ARG cc_start: 0.8290 (ttp80) cc_final: 0.8076 (ttp80) REVERT: Al 204 GLU cc_start: 0.8147 (pp20) cc_final: 0.7759 (pp20) REVERT: Am 54 MET cc_start: 0.7954 (ttp) cc_final: 0.7073 (ttp) REVERT: Am 69 HIS cc_start: 0.8774 (t-170) cc_final: 0.8474 (t70) REVERT: Am 70 LEU cc_start: 0.9133 (tp) cc_final: 0.8894 (tp) REVERT: Am 80 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8408 (pt) REVERT: Am 127 ASN cc_start: 0.8759 (p0) cc_final: 0.8457 (p0) REVERT: Am 157 ARG cc_start: 0.8869 (ttt90) cc_final: 0.8599 (ttt90) REVERT: Am 165 ASP cc_start: 0.7892 (t0) cc_final: 0.7595 (t0) REVERT: Am 184 TYR cc_start: 0.7955 (t80) cc_final: 0.7372 (t80) REVERT: An 69 HIS cc_start: 0.8726 (t-170) cc_final: 0.8407 (t-170) REVERT: An 73 TYR cc_start: 0.9149 (t80) cc_final: 0.8535 (t80) REVERT: An 127 ASN cc_start: 0.8772 (p0) cc_final: 0.8475 (p0) REVERT: An 165 ASP cc_start: 0.7980 (t0) cc_final: 0.7239 (t0) REVERT: Ao 102 ASP cc_start: 0.8849 (t0) cc_final: 0.8365 (t0) REVERT: Ao 127 ASN cc_start: 0.8744 (p0) cc_final: 0.8446 (p0) REVERT: Ao 160 MET cc_start: 0.9097 (tpp) cc_final: 0.8526 (mmm) REVERT: Ao 165 ASP cc_start: 0.7803 (t0) cc_final: 0.7522 (t0) REVERT: Ao 204 GLU cc_start: 0.8181 (pp20) cc_final: 0.7468 (pp20) REVERT: Ap 127 ASN cc_start: 0.8762 (p0) cc_final: 0.8485 (p0) REVERT: Ap 129 ASN cc_start: 0.8424 (p0) cc_final: 0.8196 (p0) REVERT: Ap 165 ASP cc_start: 0.8019 (t0) cc_final: 0.7278 (t0) outliers start: 87 outliers final: 48 residues processed: 943 average time/residue: 0.4001 time to fit residues: 557.7334 Evaluate side-chains 937 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 880 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ab residue 155 THR Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 129 ASN Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 151 ASN Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 47 ILE Chi-restraints excluded: chain Af residue 80 ILE Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 149 VAL Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 80 ILE Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 80 ILE Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Aj residue 71 LEU Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 129 ASN Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 129 ASN Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Am residue 80 ILE Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain Am residue 155 THR Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 0.0170 chunk 158 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 129 ASN Af 140 GLN ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 158 GLN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 23856 Z= 0.421 Angle : 0.734 9.382 32336 Z= 0.357 Chirality : 0.045 0.158 3520 Planarity : 0.006 0.065 4192 Dihedral : 4.543 16.419 3216 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.84 % Allowed : 23.69 % Favored : 72.47 % 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: -0.83 (0.16), residues: 2864 helix: -0.10 (0.14), residues: 1424 sheet: 1.15 (0.42), residues: 160 loop : -1.22 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAl 93 HIS 0.009 0.001 HISAe 69 PHE 0.014 0.002 PHEAk 200 TYR 0.026 0.002 TYRAb 198 ARG 0.006 0.001 ARGAp 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 889 time to evaluate : 2.775 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 157 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8782 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8765 (tpp) cc_final: 0.8480 (tpp) REVERT: Aa 183 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7203 (mpt180) REVERT: Ab 54 MET cc_start: 0.8018 (ttp) cc_final: 0.7509 (ttp) REVERT: Ab 69 HIS cc_start: 0.8869 (t-170) cc_final: 0.8548 (t-170) REVERT: Ab 73 TYR cc_start: 0.9299 (t80) cc_final: 0.8902 (t80) REVERT: Ab 136 ASP cc_start: 0.7350 (m-30) cc_final: 0.6843 (m-30) REVERT: Ab 157 ARG cc_start: 0.9019 (ttp80) cc_final: 0.8644 (ttt90) REVERT: Ab 184 TYR cc_start: 0.8161 (t80) cc_final: 0.7890 (t80) REVERT: Ac 127 ASN cc_start: 0.8779 (p0) cc_final: 0.8390 (p0) REVERT: Ac 157 ARG cc_start: 0.8986 (ttp80) cc_final: 0.8706 (ttt-90) REVERT: Ac 165 ASP cc_start: 0.8075 (t0) cc_final: 0.7776 (t0) REVERT: Ac 201 ASP cc_start: 0.8851 (t0) cc_final: 0.8428 (t0) REVERT: Ad 102 ASP cc_start: 0.8912 (t0) cc_final: 0.8629 (t0) REVERT: Ad 127 ASN cc_start: 0.8765 (p0) cc_final: 0.8388 (p0) REVERT: Ad 129 ASN cc_start: 0.8509 (p0) cc_final: 0.8090 (p0) REVERT: Ad 157 ARG cc_start: 0.8912 (ttp80) cc_final: 0.8674 (ttt-90) REVERT: Ad 174 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.7367 (mmm-85) REVERT: Ae 91 ASP cc_start: 0.8152 (m-30) cc_final: 0.7947 (m-30) REVERT: Ae 102 ASP cc_start: 0.8934 (t0) cc_final: 0.8558 (t0) REVERT: Ae 127 ASN cc_start: 0.8833 (p0) cc_final: 0.8543 (p0) REVERT: Ae 129 ASN cc_start: 0.8334 (p0) cc_final: 0.7945 (p0) REVERT: Ae 136 ASP cc_start: 0.7381 (m-30) cc_final: 0.6727 (m-30) REVERT: Ae 158 GLN cc_start: 0.8786 (mt0) cc_final: 0.8559 (mt0) REVERT: Ae 165 ASP cc_start: 0.8192 (t0) cc_final: 0.7960 (t0) REVERT: Ae 181 MET cc_start: 0.8866 (tpp) cc_final: 0.8473 (tpp) REVERT: Ae 198 TYR cc_start: 0.8508 (m-10) cc_final: 0.8245 (m-10) REVERT: Ae 204 GLU cc_start: 0.8196 (pp20) cc_final: 0.7804 (pp20) REVERT: Af 54 MET cc_start: 0.8085 (ttp) cc_final: 0.7711 (ttp) REVERT: Af 73 TYR cc_start: 0.9246 (t80) cc_final: 0.8608 (t80) REVERT: Ag 102 ASP cc_start: 0.8964 (t0) cc_final: 0.8554 (t0) REVERT: Ag 135 MET cc_start: 0.8792 (mmm) cc_final: 0.8538 (mmm) REVERT: Ag 136 ASP cc_start: 0.7304 (m-30) cc_final: 0.6648 (m-30) REVERT: Ag 204 GLU cc_start: 0.8067 (pp20) cc_final: 0.7767 (pp20) REVERT: Ah 54 MET cc_start: 0.8117 (ttp) cc_final: 0.7564 (ttp) REVERT: Ah 66 ASN cc_start: 0.8053 (t0) cc_final: 0.7615 (t0) REVERT: Ah 69 HIS cc_start: 0.8913 (t-170) cc_final: 0.8677 (t70) REVERT: Ah 76 GLN cc_start: 0.8574 (mp10) cc_final: 0.8181 (mp10) REVERT: Ah 108 MET cc_start: 0.8790 (tpp) cc_final: 0.8542 (tpp) REVERT: Ah 157 ARG cc_start: 0.8917 (ttp80) cc_final: 0.8585 (ttt90) REVERT: Ai 69 HIS cc_start: 0.8801 (t-170) cc_final: 0.8443 (t-170) REVERT: Ai 127 ASN cc_start: 0.8777 (p0) cc_final: 0.8416 (p0) REVERT: Ai 129 ASN cc_start: 0.8415 (p0) cc_final: 0.7925 (p0) REVERT: Ai 136 ASP cc_start: 0.7525 (m-30) cc_final: 0.6943 (m-30) REVERT: Ai 157 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8712 (ttt90) REVERT: Ai 160 MET cc_start: 0.9075 (tpp) cc_final: 0.8411 (mmm) REVERT: Ai 201 ASP cc_start: 0.8838 (t0) cc_final: 0.8490 (t0) REVERT: Aj 60 LYS cc_start: 0.9347 (mmtt) cc_final: 0.9039 (mmpt) REVERT: Aj 80 ILE cc_start: 0.9228 (pt) cc_final: 0.9017 (pt) REVERT: Aj 91 ASP cc_start: 0.8076 (m-30) cc_final: 0.7698 (m-30) REVERT: Aj 127 ASN cc_start: 0.8837 (p0) cc_final: 0.8565 (p0) REVERT: Aj 129 ASN cc_start: 0.8362 (p0) cc_final: 0.7904 (p0) REVERT: Aj 204 GLU cc_start: 0.8173 (pp20) cc_final: 0.7680 (pp20) REVERT: Ak 136 ASP cc_start: 0.7946 (m-30) cc_final: 0.7616 (m-30) REVERT: Ak 157 ARG cc_start: 0.8996 (ttp80) cc_final: 0.8711 (ttt90) REVERT: Ak 201 ASP cc_start: 0.8882 (t0) cc_final: 0.8412 (t0) REVERT: Ak 204 GLU cc_start: 0.8234 (pp20) cc_final: 0.7920 (pp20) REVERT: Al 77 GLN cc_start: 0.8467 (tp40) cc_final: 0.8235 (tp40) REVERT: Al 127 ASN cc_start: 0.8847 (p0) cc_final: 0.8616 (p0) REVERT: Al 129 ASN cc_start: 0.8507 (p0) cc_final: 0.8131 (p0) REVERT: Al 136 ASP cc_start: 0.7851 (m-30) cc_final: 0.7411 (m-30) REVERT: Al 157 ARG cc_start: 0.8992 (ttp80) cc_final: 0.8705 (ttt90) REVERT: Al 204 GLU cc_start: 0.8235 (pp20) cc_final: 0.7827 (pp20) REVERT: Am 54 MET cc_start: 0.8195 (ttp) cc_final: 0.7573 (ttp) REVERT: Am 69 HIS cc_start: 0.8889 (t-170) cc_final: 0.8566 (t70) REVERT: Am 76 GLN cc_start: 0.8508 (mp10) cc_final: 0.8268 (mp10) REVERT: Am 78 ILE cc_start: 0.8746 (tp) cc_final: 0.8476 (tp) REVERT: Am 127 ASN cc_start: 0.8792 (p0) cc_final: 0.8465 (p0) REVERT: Am 157 ARG cc_start: 0.8898 (ttt90) cc_final: 0.8598 (ttt90) REVERT: Am 184 TYR cc_start: 0.8097 (t80) cc_final: 0.7630 (t80) REVERT: An 102 ASP cc_start: 0.8965 (t0) cc_final: 0.8556 (t0) REVERT: An 127 ASN cc_start: 0.8814 (p0) cc_final: 0.8482 (p0) REVERT: An 129 ASN cc_start: 0.8426 (p0) cc_final: 0.8051 (p0) REVERT: An 165 ASP cc_start: 0.8138 (t0) cc_final: 0.7836 (t0) REVERT: Ao 102 ASP cc_start: 0.8917 (t0) cc_final: 0.8492 (t0) REVERT: Ao 127 ASN cc_start: 0.8814 (p0) cc_final: 0.8390 (p0) REVERT: Ap 127 ASN cc_start: 0.8798 (p0) cc_final: 0.8479 (p0) REVERT: Ap 136 ASP cc_start: 0.7764 (m-30) cc_final: 0.7208 (t0) outliers start: 97 outliers final: 66 residues processed: 945 average time/residue: 0.4227 time to fit residues: 585.5597 Evaluate side-chains 921 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 855 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ab residue 195 LEU Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 133 VAL Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 151 ASN Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Ae residue 195 LEU Chi-restraints excluded: chain Af residue 129 ASN Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 149 VAL Chi-restraints excluded: chain Ag residue 159 ILE Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 159 ILE Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 47 ILE Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 50 ILE Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain Am residue 195 LEU Chi-restraints excluded: chain An residue 80 ILE Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 195 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 55 optimal weight: 0.4980 chunk 163 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 278 optimal weight: 0.0470 chunk 231 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 overall best weight: 2.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 158 GLN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 129 ASN Af 151 ASN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 158 GLN ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23856 Z= 0.250 Angle : 0.682 10.095 32336 Z= 0.326 Chirality : 0.043 0.158 3520 Planarity : 0.006 0.063 4192 Dihedral : 4.309 15.364 3216 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.72 % Allowed : 24.49 % Favored : 71.80 % 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: -0.64 (0.16), residues: 2864 helix: -0.05 (0.14), residues: 1424 sheet: 1.38 (0.42), residues: 192 loop : -1.07 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAg 93 HIS 0.011 0.001 HISAp 69 PHE 0.009 0.001 PHEAl 200 TYR 0.029 0.002 TYRAb 198 ARG 0.007 0.001 ARGAl 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 920 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 157 ARG cc_start: 0.8923 (ttp80) cc_final: 0.8715 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8740 (tpp) cc_final: 0.8430 (tpp) REVERT: Aa 183 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7216 (mpt180) REVERT: Ab 54 MET cc_start: 0.7966 (ttp) cc_final: 0.7433 (ttp) REVERT: Ab 69 HIS cc_start: 0.8762 (t-170) cc_final: 0.8446 (t-170) REVERT: Ab 73 TYR cc_start: 0.9248 (t80) cc_final: 0.8835 (t80) REVERT: Ab 127 ASN cc_start: 0.8872 (p0) cc_final: 0.8518 (p0) REVERT: Ab 136 ASP cc_start: 0.7201 (m-30) cc_final: 0.6568 (m-30) REVERT: Ab 184 TYR cc_start: 0.8202 (t80) cc_final: 0.7947 (t80) REVERT: Ac 127 ASN cc_start: 0.8826 (p0) cc_final: 0.8465 (p0) REVERT: Ac 135 MET cc_start: 0.8685 (mmm) cc_final: 0.8463 (mmm) REVERT: Ac 165 ASP cc_start: 0.8100 (t0) cc_final: 0.7734 (t0) REVERT: Ac 201 ASP cc_start: 0.8845 (t0) cc_final: 0.8390 (t0) REVERT: Ad 76 GLN cc_start: 0.8668 (mp10) cc_final: 0.8351 (mp10) REVERT: Ad 102 ASP cc_start: 0.8922 (t0) cc_final: 0.8614 (t0) REVERT: Ad 127 ASN cc_start: 0.8776 (p0) cc_final: 0.8436 (p0) REVERT: Ad 136 ASP cc_start: 0.7380 (m-30) cc_final: 0.7025 (m-30) REVERT: Ad 138 ASP cc_start: 0.7989 (t0) cc_final: 0.7711 (t0) REVERT: Ae 76 GLN cc_start: 0.8451 (mp10) cc_final: 0.8012 (mp10) REVERT: Ae 102 ASP cc_start: 0.8928 (t0) cc_final: 0.8566 (t0) REVERT: Ae 127 ASN cc_start: 0.8848 (p0) cc_final: 0.8560 (p0) REVERT: Ae 129 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7998 (p0) REVERT: Ae 136 ASP cc_start: 0.7300 (m-30) cc_final: 0.6682 (m-30) REVERT: Ae 158 GLN cc_start: 0.8778 (mt0) cc_final: 0.8551 (mt0) REVERT: Ae 165 ASP cc_start: 0.8153 (t0) cc_final: 0.7843 (t0) REVERT: Ae 181 MET cc_start: 0.8847 (tpp) cc_final: 0.8496 (tpp) REVERT: Ae 201 ASP cc_start: 0.8589 (t0) cc_final: 0.8099 (t0) REVERT: Ae 204 GLU cc_start: 0.8201 (pp20) cc_final: 0.7810 (pp20) REVERT: Af 54 MET cc_start: 0.7944 (ttp) cc_final: 0.7537 (ttp) REVERT: Af 73 TYR cc_start: 0.9198 (t80) cc_final: 0.8492 (t80) REVERT: Ag 77 GLN cc_start: 0.8234 (tp40) cc_final: 0.8006 (tp40) REVERT: Ag 102 ASP cc_start: 0.8945 (t0) cc_final: 0.8689 (t0) REVERT: Ag 135 MET cc_start: 0.8652 (mmm) cc_final: 0.8280 (mmm) REVERT: Ag 136 ASP cc_start: 0.7255 (m-30) cc_final: 0.6629 (m-30) REVERT: Ag 204 GLU cc_start: 0.8075 (pp20) cc_final: 0.7747 (pp20) REVERT: Ah 54 MET cc_start: 0.8215 (ttp) cc_final: 0.7568 (ttp) REVERT: Ah 66 ASN cc_start: 0.7909 (t0) cc_final: 0.7451 (t0) REVERT: Ah 69 HIS cc_start: 0.8847 (t-170) cc_final: 0.8603 (t-170) REVERT: Ah 76 GLN cc_start: 0.8635 (mp10) cc_final: 0.8212 (mp10) REVERT: Ah 136 ASP cc_start: 0.6696 (m-30) cc_final: 0.6125 (m-30) REVERT: Ah 157 ARG cc_start: 0.8881 (ttp80) cc_final: 0.8592 (ttt90) REVERT: Ai 80 ILE cc_start: 0.8852 (pt) cc_final: 0.8640 (pt) REVERT: Ai 127 ASN cc_start: 0.8805 (p0) cc_final: 0.8531 (p0) REVERT: Ai 129 ASN cc_start: 0.8384 (p0) cc_final: 0.8095 (p0) REVERT: Ai 136 ASP cc_start: 0.7467 (m-30) cc_final: 0.6819 (m-30) REVERT: Ai 160 MET cc_start: 0.8989 (tpp) cc_final: 0.8406 (mmm) REVERT: Aj 60 LYS cc_start: 0.9276 (mmtt) cc_final: 0.9008 (mmpt) REVERT: Aj 91 ASP cc_start: 0.8071 (m-30) cc_final: 0.7746 (m-30) REVERT: Aj 127 ASN cc_start: 0.8844 (p0) cc_final: 0.8592 (p0) REVERT: Aj 129 ASN cc_start: 0.8326 (p0) cc_final: 0.7928 (p0) REVERT: Aj 174 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7248 (mmm-85) REVERT: Aj 204 GLU cc_start: 0.8186 (pp20) cc_final: 0.7720 (pp20) REVERT: Ak 73 TYR cc_start: 0.8784 (t80) cc_final: 0.8509 (t80) REVERT: Ak 136 ASP cc_start: 0.7881 (m-30) cc_final: 0.7574 (m-30) REVERT: Ak 157 ARG cc_start: 0.8941 (ttp80) cc_final: 0.8664 (ttt90) REVERT: Ak 201 ASP cc_start: 0.8849 (t0) cc_final: 0.8339 (t0) REVERT: Ak 204 GLU cc_start: 0.8214 (pp20) cc_final: 0.7891 (pp20) REVERT: Al 129 ASN cc_start: 0.8493 (p0) cc_final: 0.8181 (p0) REVERT: Al 136 ASP cc_start: 0.7916 (m-30) cc_final: 0.7467 (m-30) REVERT: Al 157 ARG cc_start: 0.8957 (ttp80) cc_final: 0.8629 (ttt90) REVERT: Al 198 TYR cc_start: 0.8823 (m-10) cc_final: 0.8494 (m-10) REVERT: Al 204 GLU cc_start: 0.8240 (pp20) cc_final: 0.7814 (pp20) REVERT: Am 54 MET cc_start: 0.8158 (ttp) cc_final: 0.7713 (ttp) REVERT: Am 69 HIS cc_start: 0.8823 (t-170) cc_final: 0.8501 (t70) REVERT: Am 76 GLN cc_start: 0.8459 (mp10) cc_final: 0.8220 (mp10) REVERT: Am 78 ILE cc_start: 0.8688 (tp) cc_final: 0.8388 (tp) REVERT: Am 127 ASN cc_start: 0.8789 (p0) cc_final: 0.8457 (p0) REVERT: Am 129 ASN cc_start: 0.8484 (p0) cc_final: 0.8009 (p0) REVERT: Am 157 ARG cc_start: 0.8895 (ttt90) cc_final: 0.8607 (ttt90) REVERT: Am 184 TYR cc_start: 0.8134 (t80) cc_final: 0.7678 (t80) REVERT: An 102 ASP cc_start: 0.8945 (t0) cc_final: 0.8536 (t0) REVERT: An 127 ASN cc_start: 0.8834 (p0) cc_final: 0.8520 (p0) REVERT: An 129 ASN cc_start: 0.8439 (p0) cc_final: 0.7919 (p0) REVERT: An 136 ASP cc_start: 0.7642 (m-30) cc_final: 0.7163 (t0) REVERT: An 165 ASP cc_start: 0.8084 (t0) cc_final: 0.7753 (t0) REVERT: An 174 ARG cc_start: 0.7847 (mmm-85) cc_final: 0.7258 (mmm-85) REVERT: Ao 102 ASP cc_start: 0.8900 (t0) cc_final: 0.8489 (t0) REVERT: Ao 127 ASN cc_start: 0.8829 (p0) cc_final: 0.8422 (p0) REVERT: Ap 69 HIS cc_start: 0.8631 (t-170) cc_final: 0.8374 (t-170) REVERT: Ap 127 ASN cc_start: 0.8820 (p0) cc_final: 0.8468 (p0) REVERT: Ap 129 ASN cc_start: 0.8413 (p0) cc_final: 0.8144 (p0) REVERT: Ap 136 ASP cc_start: 0.7608 (m-30) cc_final: 0.7259 (t0) outliers start: 94 outliers final: 59 residues processed: 970 average time/residue: 0.4128 time to fit residues: 596.5443 Evaluate side-chains 949 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 889 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 71 LEU Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 47 ILE Chi-restraints excluded: chain Af residue 129 ASN Chi-restraints excluded: chain Af residue 133 VAL Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 187 VAL Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 50 ILE Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 187 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 8.9990 chunk 31 optimal weight: 0.0470 chunk 158 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 277 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 158 GLN ** Ac 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 151 ASN ** Ae 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 129 ASN Af 151 ASN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 151 ASN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23856 Z= 0.172 Angle : 0.664 10.591 32336 Z= 0.317 Chirality : 0.042 0.159 3520 Planarity : 0.006 0.062 4192 Dihedral : 4.148 16.034 3216 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.32 % Allowed : 25.63 % Favored : 71.04 % 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: -0.51 (0.16), residues: 2864 helix: 0.03 (0.14), residues: 1424 sheet: 2.37 (0.47), residues: 160 loop : -1.06 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAl 93 HIS 0.011 0.001 HISAp 69 PHE 0.005 0.001 PHEAf 202 TYR 0.033 0.001 TYRAb 198 ARG 0.007 0.001 ARGAp 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 932 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 58 LYS cc_start: 0.9119 (ptpt) cc_final: 0.8823 (ptpp) REVERT: Aa 76 GLN cc_start: 0.8189 (mp10) cc_final: 0.7979 (mp10) REVERT: Aa 116 MET cc_start: 0.8973 (tmm) cc_final: 0.8458 (ttt) REVERT: Aa 136 ASP cc_start: 0.7665 (m-30) cc_final: 0.7210 (m-30) REVERT: Aa 157 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8682 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8742 (tpp) cc_final: 0.8408 (tpp) REVERT: Aa 183 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7187 (mpt180) REVERT: Aa 184 TYR cc_start: 0.7746 (t80) cc_final: 0.7463 (t80) REVERT: Ab 54 MET cc_start: 0.7947 (ttp) cc_final: 0.7483 (ttp) REVERT: Ab 69 HIS cc_start: 0.8717 (t-170) cc_final: 0.8381 (t-170) REVERT: Ab 73 TYR cc_start: 0.9197 (t80) cc_final: 0.8731 (t80) REVERT: Ab 127 ASN cc_start: 0.8863 (p0) cc_final: 0.8513 (p0) REVERT: Ab 136 ASP cc_start: 0.7056 (m-30) cc_final: 0.6465 (m-30) REVERT: Ab 165 ASP cc_start: 0.8044 (t0) cc_final: 0.7778 (t0) REVERT: Ab 184 TYR cc_start: 0.8256 (t80) cc_final: 0.8029 (t80) REVERT: Ab 188 ARG cc_start: 0.7258 (tpt170) cc_final: 0.7029 (tpt170) REVERT: Ac 127 ASN cc_start: 0.8776 (p0) cc_final: 0.8464 (p0) REVERT: Ac 129 ASN cc_start: 0.8359 (p0) cc_final: 0.8079 (p0) REVERT: Ac 165 ASP cc_start: 0.8024 (t0) cc_final: 0.7594 (t0) REVERT: Ac 201 ASP cc_start: 0.8790 (t0) cc_final: 0.8281 (t0) REVERT: Ad 76 GLN cc_start: 0.8528 (mp10) cc_final: 0.8260 (mp10) REVERT: Ad 102 ASP cc_start: 0.8875 (t0) cc_final: 0.8516 (t0) REVERT: Ad 127 ASN cc_start: 0.8820 (p0) cc_final: 0.8479 (p0) REVERT: Ad 138 ASP cc_start: 0.7975 (t0) cc_final: 0.7720 (t0) REVERT: Ad 165 ASP cc_start: 0.8138 (t0) cc_final: 0.7885 (t0) REVERT: Ad 188 ARG cc_start: 0.7183 (tpt170) cc_final: 0.6874 (tpt170) REVERT: Ae 76 GLN cc_start: 0.8265 (mp10) cc_final: 0.7891 (mp10) REVERT: Ae 102 ASP cc_start: 0.8877 (t0) cc_final: 0.8521 (t0) REVERT: Ae 127 ASN cc_start: 0.8874 (p0) cc_final: 0.8582 (p0) REVERT: Ae 129 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8038 (p0) REVERT: Ae 136 ASP cc_start: 0.7259 (m-30) cc_final: 0.6645 (m-30) REVERT: Ae 165 ASP cc_start: 0.8067 (t0) cc_final: 0.7714 (t0) REVERT: Ae 181 MET cc_start: 0.8782 (tpp) cc_final: 0.8473 (tpp) REVERT: Ae 188 ARG cc_start: 0.7207 (tpt170) cc_final: 0.6960 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8158 (pp20) cc_final: 0.7760 (pp20) REVERT: Af 54 MET cc_start: 0.7875 (ttp) cc_final: 0.7433 (ttp) REVERT: Af 73 TYR cc_start: 0.9161 (t80) cc_final: 0.8285 (t80) REVERT: Af 80 ILE cc_start: 0.8269 (pt) cc_final: 0.8058 (pt) REVERT: Ag 77 GLN cc_start: 0.8152 (tp40) cc_final: 0.7938 (tp40) REVERT: Ag 102 ASP cc_start: 0.8880 (t0) cc_final: 0.8658 (t0) REVERT: Ag 136 ASP cc_start: 0.6640 (m-30) cc_final: 0.6060 (m-30) REVERT: Ag 165 ASP cc_start: 0.7985 (t0) cc_final: 0.7759 (t0) REVERT: Ag 204 GLU cc_start: 0.8110 (pp20) cc_final: 0.7778 (pp20) REVERT: Ah 54 MET cc_start: 0.8004 (ttp) cc_final: 0.7687 (ttp) REVERT: Ah 66 ASN cc_start: 0.7764 (t0) cc_final: 0.7241 (t0) REVERT: Ah 69 HIS cc_start: 0.8815 (t-170) cc_final: 0.8543 (t-170) REVERT: Ah 76 GLN cc_start: 0.8557 (mp10) cc_final: 0.8162 (mp10) REVERT: Ah 112 MET cc_start: 0.9027 (tpp) cc_final: 0.8819 (mmp) REVERT: Ah 136 ASP cc_start: 0.6628 (m-30) cc_final: 0.6067 (m-30) REVERT: Ah 157 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8562 (ttt90) REVERT: Ah 188 ARG cc_start: 0.7228 (tpt170) cc_final: 0.6987 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8367 (mp10) cc_final: 0.8039 (mp10) REVERT: Ai 127 ASN cc_start: 0.8830 (p0) cc_final: 0.8565 (p0) REVERT: Ai 136 ASP cc_start: 0.7502 (m-30) cc_final: 0.6960 (m-30) REVERT: Ai 160 MET cc_start: 0.8932 (tpp) cc_final: 0.8412 (mmm) REVERT: Ai 165 ASP cc_start: 0.7961 (t0) cc_final: 0.7522 (t0) REVERT: Ai 188 ARG cc_start: 0.7224 (tpt170) cc_final: 0.6978 (tpt170) REVERT: Aj 60 LYS cc_start: 0.9238 (mmtt) cc_final: 0.8979 (mmpt) REVERT: Aj 80 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8119 (pt) REVERT: Aj 91 ASP cc_start: 0.7999 (m-30) cc_final: 0.7770 (m-30) REVERT: Aj 127 ASN cc_start: 0.8847 (p0) cc_final: 0.8617 (p0) REVERT: Aj 136 ASP cc_start: 0.7716 (m-30) cc_final: 0.7185 (t0) REVERT: Aj 188 ARG cc_start: 0.7402 (tpt170) cc_final: 0.7119 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8197 (pp20) cc_final: 0.7739 (pp20) REVERT: Ak 73 TYR cc_start: 0.8689 (t80) cc_final: 0.8318 (t80) REVERT: Ak 157 ARG cc_start: 0.8936 (ttp80) cc_final: 0.8645 (ttt90) REVERT: Ak 165 ASP cc_start: 0.7819 (t0) cc_final: 0.7519 (t0) REVERT: Ak 201 ASP cc_start: 0.8796 (t0) cc_final: 0.8474 (t0) REVERT: Ak 204 GLU cc_start: 0.8204 (pp20) cc_final: 0.7888 (pp20) REVERT: Al 136 ASP cc_start: 0.7702 (m-30) cc_final: 0.7294 (m-30) REVERT: Al 157 ARG cc_start: 0.8930 (ttp80) cc_final: 0.8619 (ttt90) REVERT: Al 198 TYR cc_start: 0.8724 (m-80) cc_final: 0.8339 (m-10) REVERT: Al 204 GLU cc_start: 0.8165 (pp20) cc_final: 0.7740 (pp20) REVERT: Am 54 MET cc_start: 0.8055 (ttp) cc_final: 0.7572 (ttp) REVERT: Am 69 HIS cc_start: 0.8788 (t-170) cc_final: 0.8496 (t70) REVERT: Am 76 GLN cc_start: 0.8370 (mp10) cc_final: 0.8126 (mp10) REVERT: Am 127 ASN cc_start: 0.8802 (p0) cc_final: 0.8462 (p0) REVERT: Am 136 ASP cc_start: 0.7669 (m-30) cc_final: 0.7146 (t0) REVERT: Am 157 ARG cc_start: 0.8851 (ttt90) cc_final: 0.8518 (ttt90) REVERT: Am 165 ASP cc_start: 0.7905 (t0) cc_final: 0.7585 (t0) REVERT: Am 184 TYR cc_start: 0.8039 (t80) cc_final: 0.7670 (t80) REVERT: An 76 GLN cc_start: 0.8408 (mp10) cc_final: 0.7897 (mp10) REVERT: An 102 ASP cc_start: 0.8914 (t0) cc_final: 0.8487 (t0) REVERT: An 127 ASN cc_start: 0.8843 (p0) cc_final: 0.8549 (p0) REVERT: An 129 ASN cc_start: 0.8388 (p0) cc_final: 0.7928 (p0) REVERT: An 136 ASP cc_start: 0.7372 (m-30) cc_final: 0.7017 (t0) REVERT: An 201 ASP cc_start: 0.8367 (t0) cc_final: 0.7997 (t0) REVERT: Ao 102 ASP cc_start: 0.8901 (t0) cc_final: 0.8536 (t0) REVERT: Ao 127 ASN cc_start: 0.8798 (p0) cc_final: 0.8430 (p0) REVERT: Ao 129 ASN cc_start: 0.8478 (p0) cc_final: 0.8103 (p0) REVERT: Ao 174 ARG cc_start: 0.7812 (mmm-85) cc_final: 0.7003 (mmm-85) REVERT: Ao 188 ARG cc_start: 0.7286 (tpt170) cc_final: 0.6972 (tpt170) REVERT: Ao 204 GLU cc_start: 0.8016 (pp20) cc_final: 0.7422 (pp20) REVERT: Ap 127 ASN cc_start: 0.8849 (p0) cc_final: 0.8636 (p0) REVERT: Ap 129 ASN cc_start: 0.8427 (p0) cc_final: 0.8219 (p0) REVERT: Ap 188 ARG cc_start: 0.7250 (tpt170) cc_final: 0.6939 (tpt170) outliers start: 84 outliers final: 59 residues processed: 971 average time/residue: 0.4045 time to fit residues: 578.0303 Evaluate side-chains 969 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 908 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 155 THR Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 77 GLN Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ac residue 205 VAL Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 47 ILE Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 187 VAL Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 47 ILE Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 50 ILE Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain Am residue 155 THR Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 151 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 187 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.1980 chunk 110 optimal weight: 7.9990 chunk 165 optimal weight: 0.3980 chunk 83 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 189 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 218 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN ** Ac 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 158 GLN Af 151 ASN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 129 ASN Ah 158 GLN Ai 151 ASN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 129 ASN Ap 158 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23856 Z= 0.172 Angle : 0.666 10.259 32336 Z= 0.319 Chirality : 0.042 0.178 3520 Planarity : 0.006 0.063 4192 Dihedral : 4.004 19.538 3216 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.09 % Allowed : 26.34 % Favored : 70.57 % 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: -0.43 (0.16), residues: 2864 helix: 0.04 (0.14), residues: 1440 sheet: 2.53 (0.47), residues: 160 loop : -0.97 (0.18), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAl 93 HIS 0.011 0.001 HISAp 69 PHE 0.006 0.001 PHEAl 200 TYR 0.025 0.001 TYRAb 198 ARG 0.008 0.001 ARGAf 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 940 time to evaluate : 2.714 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 136 ASP cc_start: 0.7623 (m-30) cc_final: 0.7170 (m-30) REVERT: Aa 157 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8661 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8798 (tpp) cc_final: 0.8477 (tpp) REVERT: Aa 183 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7158 (mpt180) REVERT: Aa 184 TYR cc_start: 0.7729 (t80) cc_final: 0.7439 (t80) REVERT: Ab 73 TYR cc_start: 0.9192 (t80) cc_final: 0.8860 (t80) REVERT: Ab 127 ASN cc_start: 0.8878 (p0) cc_final: 0.8569 (p0) REVERT: Ab 165 ASP cc_start: 0.7979 (t0) cc_final: 0.7600 (t0) REVERT: Ab 184 TYR cc_start: 0.8239 (t80) cc_final: 0.7981 (t80) REVERT: Ac 127 ASN cc_start: 0.8811 (p0) cc_final: 0.8495 (p0) REVERT: Ac 129 ASN cc_start: 0.8335 (p0) cc_final: 0.8085 (p0) REVERT: Ac 138 ASP cc_start: 0.7809 (t0) cc_final: 0.7515 (t0) REVERT: Ac 201 ASP cc_start: 0.8756 (t0) cc_final: 0.8212 (t0) REVERT: Ad 73 TYR cc_start: 0.8703 (t80) cc_final: 0.8384 (t80) REVERT: Ad 76 GLN cc_start: 0.8251 (mp10) cc_final: 0.7797 (mp10) REVERT: Ad 102 ASP cc_start: 0.8850 (t0) cc_final: 0.8500 (t0) REVERT: Ad 116 MET cc_start: 0.8847 (tmm) cc_final: 0.8420 (ttt) REVERT: Ad 127 ASN cc_start: 0.8846 (p0) cc_final: 0.8541 (p0) REVERT: Ad 136 ASP cc_start: 0.6956 (m-30) cc_final: 0.6646 (m-30) REVERT: Ad 138 ASP cc_start: 0.7983 (t0) cc_final: 0.7722 (t0) REVERT: Ad 165 ASP cc_start: 0.8092 (t0) cc_final: 0.7867 (t0) REVERT: Ad 188 ARG cc_start: 0.7185 (tpt170) cc_final: 0.6935 (tpt170) REVERT: Ad 204 GLU cc_start: 0.7907 (pp20) cc_final: 0.7315 (pp20) REVERT: Ae 73 TYR cc_start: 0.8464 (t80) cc_final: 0.7311 (t80) REVERT: Ae 76 GLN cc_start: 0.8175 (mp10) cc_final: 0.7837 (mp10) REVERT: Ae 102 ASP cc_start: 0.8848 (t0) cc_final: 0.8494 (t0) REVERT: Ae 127 ASN cc_start: 0.8861 (p0) cc_final: 0.8521 (p0) REVERT: Ae 129 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.8006 (p0) REVERT: Ae 136 ASP cc_start: 0.7163 (m-30) cc_final: 0.6760 (m-30) REVERT: Ae 165 ASP cc_start: 0.7981 (t0) cc_final: 0.7634 (t0) REVERT: Ae 181 MET cc_start: 0.8791 (tpp) cc_final: 0.8566 (tpp) REVERT: Ae 188 ARG cc_start: 0.7247 (tpt170) cc_final: 0.7030 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8155 (pp20) cc_final: 0.7803 (pp20) REVERT: Af 54 MET cc_start: 0.7939 (ttp) cc_final: 0.7546 (ttp) REVERT: Af 73 TYR cc_start: 0.9132 (t80) cc_final: 0.8243 (t80) REVERT: Af 165 ASP cc_start: 0.7963 (t0) cc_final: 0.7703 (t0) REVERT: Af 188 ARG cc_start: 0.7366 (tpt170) cc_final: 0.7145 (tpt170) REVERT: Ag 76 GLN cc_start: 0.8252 (mp10) cc_final: 0.8049 (mp10) REVERT: Ag 102 ASP cc_start: 0.8831 (t0) cc_final: 0.8603 (t0) REVERT: Ag 124 THR cc_start: 0.8755 (p) cc_final: 0.8532 (p) REVERT: Ag 135 MET cc_start: 0.8422 (mmm) cc_final: 0.8088 (mmm) REVERT: Ag 165 ASP cc_start: 0.7893 (t0) cc_final: 0.7640 (t0) REVERT: Ag 204 GLU cc_start: 0.8077 (pp20) cc_final: 0.7703 (pp20) REVERT: Ah 66 ASN cc_start: 0.7675 (t0) cc_final: 0.7203 (t0) REVERT: Ah 69 HIS cc_start: 0.8798 (t-170) cc_final: 0.8550 (t-170) REVERT: Ah 116 MET cc_start: 0.8893 (tmm) cc_final: 0.8678 (ttt) REVERT: Ah 136 ASP cc_start: 0.6434 (m-30) cc_final: 0.5921 (m-30) REVERT: Ah 165 ASP cc_start: 0.7927 (t0) cc_final: 0.7619 (t0) REVERT: Ah 188 ARG cc_start: 0.7275 (tpt170) cc_final: 0.7070 (tpt170) REVERT: Ai 60 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8690 (mmpt) REVERT: Ai 76 GLN cc_start: 0.8246 (mp10) cc_final: 0.7550 (mp10) REVERT: Ai 116 MET cc_start: 0.9059 (tmm) cc_final: 0.8375 (ttt) REVERT: Ai 127 ASN cc_start: 0.8848 (p0) cc_final: 0.8600 (p0) REVERT: Ai 136 ASP cc_start: 0.6964 (m-30) cc_final: 0.6593 (m-30) REVERT: Ai 183 ARG cc_start: 0.8227 (mtp-110) cc_final: 0.7827 (ttm-80) REVERT: Ai 188 ARG cc_start: 0.7242 (tpt170) cc_final: 0.6813 (tpt170) REVERT: Aj 60 LYS cc_start: 0.9261 (mmtt) cc_final: 0.8993 (mmpt) REVERT: Aj 80 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7943 (pt) REVERT: Aj 91 ASP cc_start: 0.8024 (m-30) cc_final: 0.7592 (m-30) REVERT: Aj 127 ASN cc_start: 0.8873 (p0) cc_final: 0.8637 (p0) REVERT: Aj 188 ARG cc_start: 0.7399 (tpt170) cc_final: 0.7121 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8148 (pp20) cc_final: 0.7712 (pp20) REVERT: Ak 70 LEU cc_start: 0.8908 (tp) cc_final: 0.8645 (mt) REVERT: Ak 73 TYR cc_start: 0.8662 (t80) cc_final: 0.8377 (t80) REVERT: Ak 124 THR cc_start: 0.8839 (p) cc_final: 0.7952 (p) REVERT: Ak 165 ASP cc_start: 0.7768 (t0) cc_final: 0.7452 (t0) REVERT: Ak 201 ASP cc_start: 0.8742 (t0) cc_final: 0.8381 (t0) REVERT: Ak 204 GLU cc_start: 0.8192 (pp20) cc_final: 0.7869 (pp20) REVERT: Al 136 ASP cc_start: 0.7823 (m-30) cc_final: 0.7405 (m-30) REVERT: Al 157 ARG cc_start: 0.8934 (ttp80) cc_final: 0.8646 (ttt90) REVERT: Al 173 MET cc_start: 0.8627 (tmm) cc_final: 0.8370 (tmm) REVERT: Al 188 ARG cc_start: 0.7401 (tpt170) cc_final: 0.7166 (tpt170) REVERT: Al 204 GLU cc_start: 0.8137 (pp20) cc_final: 0.7650 (pp20) REVERT: Am 54 MET cc_start: 0.7887 (ttp) cc_final: 0.7460 (ttp) REVERT: Am 69 HIS cc_start: 0.8813 (t-170) cc_final: 0.8510 (t-170) REVERT: Am 76 GLN cc_start: 0.8271 (mp10) cc_final: 0.8046 (mp10) REVERT: Am 127 ASN cc_start: 0.8818 (p0) cc_final: 0.8474 (p0) REVERT: Am 136 ASP cc_start: 0.7463 (m-30) cc_final: 0.7192 (t0) REVERT: Am 157 ARG cc_start: 0.8864 (ttt90) cc_final: 0.8542 (ttt90) REVERT: Am 165 ASP cc_start: 0.7819 (t0) cc_final: 0.7375 (t0) REVERT: Am 184 TYR cc_start: 0.8157 (t80) cc_final: 0.7835 (t80) REVERT: Am 188 ARG cc_start: 0.7308 (tpt170) cc_final: 0.7104 (tpt170) REVERT: An 76 GLN cc_start: 0.8309 (mp10) cc_final: 0.7771 (mp10) REVERT: An 102 ASP cc_start: 0.8880 (t0) cc_final: 0.8478 (t0) REVERT: An 127 ASN cc_start: 0.8833 (p0) cc_final: 0.8529 (p0) REVERT: An 129 ASN cc_start: 0.8362 (p0) cc_final: 0.8005 (p0) REVERT: An 136 ASP cc_start: 0.7503 (m-30) cc_final: 0.7095 (t0) REVERT: An 188 ARG cc_start: 0.7235 (tpt170) cc_final: 0.6849 (tpt170) REVERT: An 197 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7967 (mtp-110) REVERT: Ao 102 ASP cc_start: 0.8855 (t0) cc_final: 0.8500 (t0) REVERT: Ao 127 ASN cc_start: 0.8814 (p0) cc_final: 0.8449 (p0) REVERT: Ao 129 ASN cc_start: 0.8469 (p0) cc_final: 0.8112 (p0) REVERT: Ao 183 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7896 (ttm-80) REVERT: Ao 188 ARG cc_start: 0.7254 (tpt170) cc_final: 0.6994 (tpt170) REVERT: Ao 204 GLU cc_start: 0.8006 (pp20) cc_final: 0.7479 (pp20) REVERT: Ap 127 ASN cc_start: 0.8868 (p0) cc_final: 0.8647 (p0) REVERT: Ap 136 ASP cc_start: 0.6815 (t0) cc_final: 0.5982 (t0) REVERT: Ap 165 ASP cc_start: 0.8027 (t0) cc_final: 0.7725 (t0) REVERT: Ap 188 ARG cc_start: 0.7282 (tpt170) cc_final: 0.7063 (tpt170) outliers start: 78 outliers final: 58 residues processed: 979 average time/residue: 0.3993 time to fit residues: 575.6435 Evaluate side-chains 972 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 912 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 77 GLN Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 71 LEU Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 47 ILE Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 187 VAL Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 47 ILE Chi-restraints excluded: chain Ak residue 58 LYS Chi-restraints excluded: chain Ak residue 78 ILE Chi-restraints excluded: chain Ak residue 129 ASN Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 50 ILE Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 129 ASN Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 155 THR Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 47 ILE Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain Am residue 155 THR Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 151 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Chi-restraints excluded: chain Ap residue 187 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 242 optimal weight: 8.9990 chunk 258 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 158 GLN ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** An 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23856 Z= 0.310 Angle : 0.721 9.793 32336 Z= 0.353 Chirality : 0.044 0.166 3520 Planarity : 0.006 0.065 4192 Dihedral : 4.270 17.986 3216 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.16 % Allowed : 26.86 % Favored : 69.98 % 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: -0.49 (0.16), residues: 2864 helix: 0.04 (0.14), residues: 1424 sheet: 2.48 (0.47), residues: 160 loop : -1.05 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPAb 93 HIS 0.015 0.002 HISAd 69 PHE 0.014 0.002 PHEAl 200 TYR 0.058 0.002 TYRAl 198 ARG 0.009 0.001 ARGAf 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 899 time to evaluate : 2.747 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 116 MET cc_start: 0.8908 (tmm) cc_final: 0.8514 (ttt) REVERT: Aa 157 ARG cc_start: 0.8969 (ttp80) cc_final: 0.8763 (ttt-90) REVERT: Aa 181 MET cc_start: 0.8784 (tpp) cc_final: 0.8434 (tpp) REVERT: Aa 183 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7169 (mpt180) REVERT: Aa 184 TYR cc_start: 0.7815 (t80) cc_final: 0.7548 (t80) REVERT: Aa 201 ASP cc_start: 0.8953 (t0) cc_final: 0.8674 (t0) REVERT: Ab 69 HIS cc_start: 0.8637 (t-170) cc_final: 0.8343 (t-170) REVERT: Ab 73 TYR cc_start: 0.9254 (t80) cc_final: 0.8989 (t80) REVERT: Ab 127 ASN cc_start: 0.8910 (p0) cc_final: 0.8532 (p0) REVERT: Ab 157 ARG cc_start: 0.8931 (ttp80) cc_final: 0.8620 (ttt90) REVERT: Ab 184 TYR cc_start: 0.8245 (t80) cc_final: 0.8019 (t80) REVERT: Ac 76 GLN cc_start: 0.8474 (mp10) cc_final: 0.7902 (mp10) REVERT: Ac 127 ASN cc_start: 0.8833 (p0) cc_final: 0.8457 (p0) REVERT: Ac 129 ASN cc_start: 0.8390 (p0) cc_final: 0.8013 (p0) REVERT: Ac 201 ASP cc_start: 0.8852 (t0) cc_final: 0.8596 (t0) REVERT: Ad 76 GLN cc_start: 0.8418 (mp10) cc_final: 0.7925 (mp10) REVERT: Ad 102 ASP cc_start: 0.8888 (t0) cc_final: 0.8523 (t0) REVERT: Ad 116 MET cc_start: 0.8908 (tmm) cc_final: 0.8603 (ttt) REVERT: Ad 127 ASN cc_start: 0.8843 (p0) cc_final: 0.8495 (p0) REVERT: Ad 138 ASP cc_start: 0.8122 (t0) cc_final: 0.7884 (t0) REVERT: Ad 188 ARG cc_start: 0.7255 (tpt170) cc_final: 0.6826 (tpt170) REVERT: Ad 197 ARG cc_start: 0.8618 (mtp-110) cc_final: 0.8125 (mtp-110) REVERT: Ad 204 GLU cc_start: 0.7917 (pp20) cc_final: 0.7298 (pp20) REVERT: Ae 56 MET cc_start: 0.8893 (mmp) cc_final: 0.8582 (mmp) REVERT: Ae 73 TYR cc_start: 0.8459 (t80) cc_final: 0.8249 (t80) REVERT: Ae 76 GLN cc_start: 0.8330 (mp10) cc_final: 0.8112 (mp10) REVERT: Ae 102 ASP cc_start: 0.8880 (t0) cc_final: 0.8529 (t0) REVERT: Ae 127 ASN cc_start: 0.8886 (p0) cc_final: 0.8575 (p0) REVERT: Ae 129 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8075 (p0) REVERT: Ae 165 ASP cc_start: 0.8009 (t0) cc_final: 0.7693 (t0) REVERT: Ae 181 MET cc_start: 0.8911 (tpp) cc_final: 0.8609 (tpp) REVERT: Ae 188 ARG cc_start: 0.7259 (tpt170) cc_final: 0.6868 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8157 (pp20) cc_final: 0.7759 (pp20) REVERT: Af 73 TYR cc_start: 0.9216 (t80) cc_final: 0.8716 (t80) REVERT: Af 108 MET cc_start: 0.8492 (ttt) cc_final: 0.8254 (tpp) REVERT: Af 165 ASP cc_start: 0.8218 (t0) cc_final: 0.7883 (t0) REVERT: Ag 102 ASP cc_start: 0.8895 (t0) cc_final: 0.8647 (t0) REVERT: Ag 157 ARG cc_start: 0.9183 (ptm-80) cc_final: 0.8863 (ptm-80) REVERT: Ag 204 GLU cc_start: 0.8075 (pp20) cc_final: 0.7708 (pp20) REVERT: Ah 66 ASN cc_start: 0.7887 (t0) cc_final: 0.7429 (t0) REVERT: Ah 69 HIS cc_start: 0.8884 (t-170) cc_final: 0.8585 (t-170) REVERT: Ah 77 GLN cc_start: 0.8054 (tp-100) cc_final: 0.7848 (tp40) REVERT: Ah 116 MET cc_start: 0.9029 (tmm) cc_final: 0.8697 (ttt) REVERT: Ah 136 ASP cc_start: 0.6646 (m-30) cc_final: 0.6093 (m-30) REVERT: Ah 188 ARG cc_start: 0.7310 (tpt170) cc_final: 0.6947 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8448 (mp10) cc_final: 0.7753 (mp10) REVERT: Ai 80 ILE cc_start: 0.8797 (pt) cc_final: 0.8568 (pt) REVERT: Ai 116 MET cc_start: 0.9114 (tmm) cc_final: 0.8516 (ttt) REVERT: Ai 127 ASN cc_start: 0.8860 (p0) cc_final: 0.8572 (p0) REVERT: Ai 136 ASP cc_start: 0.7077 (m-30) cc_final: 0.6765 (m-30) REVERT: Ai 188 ARG cc_start: 0.7266 (tpt170) cc_final: 0.6867 (tpt170) REVERT: Aj 60 LYS cc_start: 0.9328 (mmtt) cc_final: 0.9061 (mmpt) REVERT: Aj 127 ASN cc_start: 0.8901 (p0) cc_final: 0.8628 (p0) REVERT: Aj 129 ASN cc_start: 0.8370 (p0) cc_final: 0.7981 (p0) REVERT: Aj 174 ARG cc_start: 0.7725 (mmm-85) cc_final: 0.7319 (mmm-85) REVERT: Aj 188 ARG cc_start: 0.7428 (tpt170) cc_final: 0.7017 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8225 (pp20) cc_final: 0.7765 (pp20) REVERT: Ak 151 ASN cc_start: 0.8742 (t0) cc_final: 0.8507 (t0) REVERT: Ak 188 ARG cc_start: 0.7162 (tpt170) cc_final: 0.6758 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8862 (t0) cc_final: 0.8464 (t0) REVERT: Ak 204 GLU cc_start: 0.8213 (pp20) cc_final: 0.7892 (pp20) REVERT: Al 136 ASP cc_start: 0.7775 (m-30) cc_final: 0.7332 (m-30) REVERT: Al 157 ARG cc_start: 0.8951 (ttp80) cc_final: 0.8698 (ttt90) REVERT: Al 173 MET cc_start: 0.8683 (tmm) cc_final: 0.8415 (tmm) REVERT: Al 188 ARG cc_start: 0.7510 (tpt170) cc_final: 0.7208 (tpt170) REVERT: Al 204 GLU cc_start: 0.8145 (pp20) cc_final: 0.7661 (pp20) REVERT: Am 54 MET cc_start: 0.7834 (ttp) cc_final: 0.7626 (ttp) REVERT: Am 69 HIS cc_start: 0.8835 (t-170) cc_final: 0.8533 (t70) REVERT: Am 76 GLN cc_start: 0.8467 (mp10) cc_final: 0.8205 (mp10) REVERT: Am 127 ASN cc_start: 0.8828 (p0) cc_final: 0.8463 (p0) REVERT: Am 129 ASN cc_start: 0.8417 (p0) cc_final: 0.7930 (p0) REVERT: Am 136 ASP cc_start: 0.7601 (m-30) cc_final: 0.7180 (t0) REVERT: Am 157 ARG cc_start: 0.8874 (ttt90) cc_final: 0.8540 (ttt90) REVERT: Am 184 TYR cc_start: 0.8148 (t80) cc_final: 0.7904 (t80) REVERT: An 76 GLN cc_start: 0.8522 (mp10) cc_final: 0.7913 (mp10) REVERT: An 102 ASP cc_start: 0.8940 (t0) cc_final: 0.8509 (t0) REVERT: An 127 ASN cc_start: 0.8883 (p0) cc_final: 0.8543 (p0) REVERT: An 129 ASN cc_start: 0.8423 (p0) cc_final: 0.7995 (p0) REVERT: An 136 ASP cc_start: 0.7486 (m-30) cc_final: 0.7077 (t0) REVERT: An 174 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7156 (mmm-85) REVERT: An 183 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7607 (ttm-80) REVERT: An 188 ARG cc_start: 0.7332 (tpt170) cc_final: 0.6963 (tpt170) REVERT: Ao 77 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8179 (tm-30) REVERT: Ao 102 ASP cc_start: 0.8906 (t0) cc_final: 0.8553 (t0) REVERT: Ao 127 ASN cc_start: 0.8839 (p0) cc_final: 0.8427 (p0) REVERT: Ao 188 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6885 (tpt170) REVERT: Ao 204 GLU cc_start: 0.8001 (pp20) cc_final: 0.7405 (pp20) REVERT: Ap 127 ASN cc_start: 0.8905 (p0) cc_final: 0.8647 (p0) REVERT: Ap 129 ASN cc_start: 0.8429 (p0) cc_final: 0.8048 (p0) REVERT: Ap 136 ASP cc_start: 0.6964 (t0) cc_final: 0.6270 (t0) REVERT: Ap 188 ARG cc_start: 0.7343 (tpt170) cc_final: 0.7139 (tpt170) outliers start: 80 outliers final: 65 residues processed: 944 average time/residue: 0.4141 time to fit residues: 571.1849 Evaluate side-chains 956 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 890 time to evaluate : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 129 ASN Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 80 ILE Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 71 LEU Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 149 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 50 ILE Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Aj residue 149 VAL Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 47 ILE Chi-restraints excluded: chain Ak residue 58 LYS Chi-restraints excluded: chain Ak residue 78 ILE Chi-restraints excluded: chain Ak residue 129 ASN Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 50 ILE Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 129 ASN Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 47 ILE Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain Am residue 155 THR Chi-restraints excluded: chain An residue 47 ILE Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 151 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 286 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 158 GLN Al 129 ASN ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 158 GLN ** Ao 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23856 Z= 0.323 Angle : 0.737 9.798 32336 Z= 0.360 Chirality : 0.045 0.168 3520 Planarity : 0.006 0.063 4192 Dihedral : 4.382 18.227 3216 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.69 % Allowed : 27.69 % Favored : 69.62 % 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: -0.59 (0.16), residues: 2864 helix: -0.08 (0.14), residues: 1424 sheet: 1.83 (0.43), residues: 192 loop : -1.03 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPAg 93 HIS 0.016 0.001 HISAd 69 PHE 0.013 0.002 PHEAa 200 TYR 0.043 0.002 TYRAa 198 ARG 0.008 0.001 ARGAf 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5728 Ramachandran restraints generated. 2864 Oldfield, 0 Emsley, 2864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 914 time to evaluate : 2.571 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 116 MET cc_start: 0.8874 (tmm) cc_final: 0.8514 (ttt) REVERT: Aa 181 MET cc_start: 0.8771 (tpp) cc_final: 0.8441 (tpp) REVERT: Aa 183 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7218 (mpt180) REVERT: Aa 184 TYR cc_start: 0.7842 (t80) cc_final: 0.7553 (t80) REVERT: Ab 73 TYR cc_start: 0.9272 (t80) cc_final: 0.9032 (t80) REVERT: Ab 127 ASN cc_start: 0.8917 (p0) cc_final: 0.8559 (p0) REVERT: Ab 157 ARG cc_start: 0.8940 (ttp80) cc_final: 0.8617 (ttt90) REVERT: Ab 184 TYR cc_start: 0.8275 (t80) cc_final: 0.8010 (t80) REVERT: Ab 188 ARG cc_start: 0.7384 (tpt170) cc_final: 0.7014 (tpt170) REVERT: Ac 127 ASN cc_start: 0.8831 (p0) cc_final: 0.8452 (p0) REVERT: Ac 201 ASP cc_start: 0.8861 (t0) cc_final: 0.8640 (t0) REVERT: Ad 58 LYS cc_start: 0.9209 (ptpt) cc_final: 0.8992 (ptpt) REVERT: Ad 76 GLN cc_start: 0.8365 (mp10) cc_final: 0.7907 (mp10) REVERT: Ad 77 GLN cc_start: 0.8035 (tp40) cc_final: 0.7462 (mm-40) REVERT: Ad 102 ASP cc_start: 0.8925 (t0) cc_final: 0.8525 (t0) REVERT: Ad 116 MET cc_start: 0.8889 (tmm) cc_final: 0.8244 (ttt) REVERT: Ad 127 ASN cc_start: 0.8849 (p0) cc_final: 0.8480 (p0) REVERT: Ad 129 ASN cc_start: 0.8511 (p0) cc_final: 0.8078 (p0) REVERT: Ad 138 ASP cc_start: 0.8189 (t0) cc_final: 0.7935 (t0) REVERT: Ad 165 ASP cc_start: 0.8158 (t0) cc_final: 0.7904 (t0) REVERT: Ad 188 ARG cc_start: 0.7296 (tpt170) cc_final: 0.6883 (tpt170) REVERT: Ad 197 ARG cc_start: 0.8605 (mtp-110) cc_final: 0.8126 (mtp-110) REVERT: Ae 73 TYR cc_start: 0.8497 (t80) cc_final: 0.8270 (t80) REVERT: Ae 76 GLN cc_start: 0.8330 (mp10) cc_final: 0.7938 (mp10) REVERT: Ae 102 ASP cc_start: 0.8906 (t0) cc_final: 0.8553 (t0) REVERT: Ae 127 ASN cc_start: 0.8894 (p0) cc_final: 0.8568 (p0) REVERT: Ae 129 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8072 (p0) REVERT: Ae 165 ASP cc_start: 0.8089 (t0) cc_final: 0.7759 (t0) REVERT: Ae 181 MET cc_start: 0.8924 (tpp) cc_final: 0.8565 (tpp) REVERT: Ae 188 ARG cc_start: 0.7253 (tpt170) cc_final: 0.6833 (tpt170) REVERT: Ae 204 GLU cc_start: 0.8132 (pp20) cc_final: 0.7718 (pp20) REVERT: Af 73 TYR cc_start: 0.9203 (t80) cc_final: 0.8630 (t80) REVERT: Af 165 ASP cc_start: 0.8121 (t0) cc_final: 0.7749 (t0) REVERT: Af 188 ARG cc_start: 0.7303 (tpt170) cc_final: 0.6961 (tpt170) REVERT: Ag 135 MET cc_start: 0.8442 (mmm) cc_final: 0.8071 (mmm) REVERT: Ag 157 ARG cc_start: 0.9166 (ptm-80) cc_final: 0.8829 (ptm-80) REVERT: Ag 184 TYR cc_start: 0.7961 (t80) cc_final: 0.7510 (t80) REVERT: Ag 204 GLU cc_start: 0.8136 (pp20) cc_final: 0.7819 (pp20) REVERT: Ah 66 ASN cc_start: 0.8015 (t0) cc_final: 0.7582 (t0) REVERT: Ah 69 HIS cc_start: 0.8889 (t-170) cc_final: 0.8590 (t-170) REVERT: Ah 116 MET cc_start: 0.8993 (tmm) cc_final: 0.8722 (ttt) REVERT: Ah 136 ASP cc_start: 0.6826 (m-30) cc_final: 0.6467 (m-30) REVERT: Ah 188 ARG cc_start: 0.7349 (tpt170) cc_final: 0.6974 (tpt170) REVERT: Ai 76 GLN cc_start: 0.8467 (mp10) cc_final: 0.7796 (mp10) REVERT: Ai 80 ILE cc_start: 0.8881 (pt) cc_final: 0.8655 (pt) REVERT: Ai 116 MET cc_start: 0.9078 (tmm) cc_final: 0.8550 (ttt) REVERT: Ai 127 ASN cc_start: 0.8865 (p0) cc_final: 0.8569 (p0) REVERT: Ai 129 ASN cc_start: 0.8445 (p0) cc_final: 0.7985 (p0) REVERT: Ai 160 MET cc_start: 0.8964 (tpp) cc_final: 0.8416 (mmm) REVERT: Ai 188 ARG cc_start: 0.7322 (tpt170) cc_final: 0.6942 (tpt170) REVERT: Ai 197 ARG cc_start: 0.8900 (mtm110) cc_final: 0.8486 (ptm-80) REVERT: Aj 60 LYS cc_start: 0.9326 (mmtt) cc_final: 0.9067 (mmpt) REVERT: Aj 127 ASN cc_start: 0.8916 (p0) cc_final: 0.8629 (p0) REVERT: Aj 188 ARG cc_start: 0.7446 (tpt170) cc_final: 0.7019 (tpt170) REVERT: Aj 204 GLU cc_start: 0.8185 (pp20) cc_final: 0.7719 (pp20) REVERT: Ak 151 ASN cc_start: 0.8789 (t0) cc_final: 0.8506 (t0) REVERT: Ak 188 ARG cc_start: 0.7205 (tpt170) cc_final: 0.6900 (tpt170) REVERT: Ak 201 ASP cc_start: 0.8888 (t0) cc_final: 0.8366 (t0) REVERT: Ak 204 GLU cc_start: 0.8238 (pp20) cc_final: 0.7915 (pp20) REVERT: Al 136 ASP cc_start: 0.7822 (m-30) cc_final: 0.7369 (m-30) REVERT: Al 157 ARG cc_start: 0.8958 (ttp80) cc_final: 0.8722 (ttt90) REVERT: Al 158 GLN cc_start: 0.8759 (mt0) cc_final: 0.8555 (mt0) REVERT: Al 188 ARG cc_start: 0.7485 (tpt170) cc_final: 0.7054 (tpt170) REVERT: Al 204 GLU cc_start: 0.8161 (pp20) cc_final: 0.7610 (pp20) REVERT: Am 54 MET cc_start: 0.7856 (ttp) cc_final: 0.7644 (ttp) REVERT: Am 58 LYS cc_start: 0.9214 (ptpt) cc_final: 0.8984 (ptpp) REVERT: Am 69 HIS cc_start: 0.8822 (t-170) cc_final: 0.8543 (t70) REVERT: Am 76 GLN cc_start: 0.8511 (mp10) cc_final: 0.8261 (mp10) REVERT: Am 78 ILE cc_start: 0.8628 (tp) cc_final: 0.8310 (tp) REVERT: Am 127 ASN cc_start: 0.8818 (p0) cc_final: 0.8465 (p0) REVERT: Am 129 ASN cc_start: 0.8428 (p0) cc_final: 0.7930 (p0) REVERT: Am 136 ASP cc_start: 0.7752 (m-30) cc_final: 0.7536 (t0) REVERT: Am 157 ARG cc_start: 0.8855 (ttt90) cc_final: 0.8531 (ttt90) REVERT: Am 184 TYR cc_start: 0.8192 (t80) cc_final: 0.7975 (t80) REVERT: Am 188 ARG cc_start: 0.7376 (tpt170) cc_final: 0.7055 (tpt170) REVERT: An 76 GLN cc_start: 0.8475 (mp10) cc_final: 0.7884 (mp10) REVERT: An 102 ASP cc_start: 0.8929 (t0) cc_final: 0.8519 (t0) REVERT: An 127 ASN cc_start: 0.8846 (p0) cc_final: 0.8507 (p0) REVERT: An 129 ASN cc_start: 0.8420 (p0) cc_final: 0.7897 (p0) REVERT: An 136 ASP cc_start: 0.7571 (m-30) cc_final: 0.7200 (t0) REVERT: An 183 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7663 (ttm-80) REVERT: An 188 ARG cc_start: 0.7480 (tpt170) cc_final: 0.7087 (tpt170) REVERT: Ao 77 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8181 (tm-30) REVERT: Ao 102 ASP cc_start: 0.8900 (t0) cc_final: 0.8542 (t0) REVERT: Ao 127 ASN cc_start: 0.8848 (p0) cc_final: 0.8425 (p0) REVERT: Ao 188 ARG cc_start: 0.7369 (tpt170) cc_final: 0.6979 (tpt170) REVERT: Ao 204 GLU cc_start: 0.8117 (pp20) cc_final: 0.7520 (pp20) REVERT: Ap 127 ASN cc_start: 0.8900 (p0) cc_final: 0.8642 (p0) REVERT: Ap 129 ASN cc_start: 0.8444 (p0) cc_final: 0.8044 (p0) REVERT: Ap 136 ASP cc_start: 0.6947 (t0) cc_final: 0.6318 (t70) outliers start: 68 outliers final: 57 residues processed: 952 average time/residue: 0.4108 time to fit residues: 575.0192 Evaluate side-chains 956 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 898 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Aa residue 149 VAL Chi-restraints excluded: chain Aa residue 187 VAL Chi-restraints excluded: chain Ab residue 47 ILE Chi-restraints excluded: chain Ab residue 80 ILE Chi-restraints excluded: chain Ab residue 149 VAL Chi-restraints excluded: chain Ac residue 47 ILE Chi-restraints excluded: chain Ac residue 149 VAL Chi-restraints excluded: chain Ac residue 155 THR Chi-restraints excluded: chain Ad residue 149 VAL Chi-restraints excluded: chain Ad residue 155 THR Chi-restraints excluded: chain Ae residue 129 ASN Chi-restraints excluded: chain Ae residue 149 VAL Chi-restraints excluded: chain Ae residue 155 THR Chi-restraints excluded: chain Ae residue 187 VAL Chi-restraints excluded: chain Af residue 149 VAL Chi-restraints excluded: chain Af residue 155 THR Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 50 ILE Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 129 ASN Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 47 ILE Chi-restraints excluded: chain Ah residue 133 VAL Chi-restraints excluded: chain Ah residue 149 VAL Chi-restraints excluded: chain Ah residue 155 THR Chi-restraints excluded: chain Ah residue 205 VAL Chi-restraints excluded: chain Ai residue 77 GLN Chi-restraints excluded: chain Ai residue 149 VAL Chi-restraints excluded: chain Ai residue 155 THR Chi-restraints excluded: chain Aj residue 149 VAL Chi-restraints excluded: chain Aj residue 155 THR Chi-restraints excluded: chain Ak residue 47 ILE Chi-restraints excluded: chain Ak residue 78 ILE Chi-restraints excluded: chain Ak residue 129 ASN Chi-restraints excluded: chain Ak residue 155 THR Chi-restraints excluded: chain Ak residue 187 VAL Chi-restraints excluded: chain Ak residue 205 VAL Chi-restraints excluded: chain Al residue 50 ILE Chi-restraints excluded: chain Al residue 129 ASN Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 149 VAL Chi-restraints excluded: chain Al residue 187 VAL Chi-restraints excluded: chain Am residue 47 ILE Chi-restraints excluded: chain Am residue 149 VAL Chi-restraints excluded: chain An residue 47 ILE Chi-restraints excluded: chain An residue 149 VAL Chi-restraints excluded: chain An residue 155 THR Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain An residue 205 VAL Chi-restraints excluded: chain Ao residue 47 ILE Chi-restraints excluded: chain Ao residue 151 ASN Chi-restraints excluded: chain Ao residue 155 THR Chi-restraints excluded: chain Ap residue 47 ILE Chi-restraints excluded: chain Ap residue 78 ILE Chi-restraints excluded: chain Ap residue 149 VAL Chi-restraints excluded: chain Ap residue 155 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 129 ASN ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 ASN ** Ag 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 129 ASN ** Al 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Al 129 ASN ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104673 restraints weight = 39421.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107667 restraints weight = 25746.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109718 restraints weight = 19646.233| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23856 Z= 0.198 Angle : 0.711 10.290 32336 Z= 0.345 Chirality : 0.043 0.161 3520 Planarity : 0.006 0.063 4192 Dihedral : 4.264 19.938 3216 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.45 % Allowed : 27.85 % Favored : 69.70 % 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: -0.06 (0.17), residues: 2864 helix: 0.34 (0.15), residues: 1328 sheet: 2.64 (0.46), residues: 160 loop : -0.69 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPAg 93 HIS 0.018 0.002 HISAd 69 PHE 0.008 0.001 PHEAl 200 TYR 0.039 0.001 TYRAa 198 ARG 0.008 0.001 ARGAf 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7939.06 seconds wall clock time: 143 minutes 1.61 seconds (8581.61 seconds total)