Starting phenix.real_space_refine on Thu Jan 15 02:25:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opk_17063/01_2026/8opk_17063.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opk_17063/01_2026/8opk_17063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8opk_17063/01_2026/8opk_17063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opk_17063/01_2026/8opk_17063.map" model { file = "/net/cci-nas-00/data/ceres_data/8opk_17063/01_2026/8opk_17063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opk_17063/01_2026/8opk_17063.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 200 5.16 5 C 13736 2.51 5 N 3752 2.21 5 O 4096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21784 Number of models: 1 Model: "" Number of chains: 16 Chain: "Aa" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Ab" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ac" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Ad" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ae" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Af" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ag" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Ah" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ai" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Aj" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ak" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Al" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Am" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "An" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Chain: "Ao" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1353 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 157} Chain: "Ap" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 159} Time building chain proxies: 4.77, per 1000 atoms: 0.22 Number of scatterers: 21784 At special positions: 0 Unit cell: (181.662, 181.662, 87.132, 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 200 16.00 O 4096 8.00 N 3752 7.00 C 13736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 854.2 milliseconds 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 16 sheets defined 57.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUAa 72 " --> pdb=" O GLUAa 68 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 76 through 81 Processing helix chain 'Aa' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAa 99 " --> pdb=" O GLUAa 95 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAa 121 " --> pdb=" O VALAa 117 " (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 174 Processing helix chain 'Aa' and resid 182 through 187 Processing helix chain 'Aa' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGAa 197 " --> pdb=" O SERAa 194 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 210 through 221 removed outlier: 4.070A pdb=" N ILEAa 218 " --> pdb=" O ARGAa 214 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 66 through 71 Processing helix chain 'Ab' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAb 80 " --> pdb=" O GLNAb 76 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAb 92 " --> pdb=" O SERAb 88 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 107 through 122 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 Processing helix chain 'Ab' and resid 182 through 187 Processing helix chain 'Ab' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAb 197 " --> pdb=" O SERAb 194 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 210 through 221 Processing helix chain 'Ac' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUAc 72 " --> pdb=" O GLUAc 68 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 76 through 81 Processing helix chain 'Ac' and resid 86 through 101 removed outlier: 3.606A pdb=" N LEUAc 99 " --> pdb=" O GLUAc 95 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 107 through 122 removed outlier: 3.630A pdb=" N GLUAc 121 " --> pdb=" O VALAc 117 " (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 174 Processing helix chain 'Ac' and resid 182 through 187 Processing helix chain 'Ac' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGAc 197 " --> pdb=" O SERAc 194 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEAc 218 " --> pdb=" O ARGAc 214 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 66 through 71 Processing helix chain 'Ad' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAd 80 " --> pdb=" O GLNAd 76 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAd 92 " --> pdb=" O SERAd 88 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 107 through 122 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 Processing helix chain 'Ad' and resid 182 through 187 Processing helix chain 'Ad' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAd 197 " --> pdb=" O SERAd 194 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 210 through 221 Processing helix chain 'Ae' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUAe 72 " --> pdb=" O GLUAe 68 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 76 through 81 Processing helix chain 'Ae' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAe 99 " --> pdb=" O GLUAe 95 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAe 121 " --> pdb=" O VALAe 117 " (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 174 Processing helix chain 'Ae' and resid 182 through 187 Processing helix chain 'Ae' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGAe 197 " --> pdb=" O SERAe 194 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEAe 218 " --> pdb=" O ARGAe 214 " (cutoff:3.500A) Processing helix chain 'Af' and resid 66 through 71 Processing helix chain 'Af' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAf 80 " --> pdb=" O GLNAf 76 " (cutoff:3.500A) Processing helix chain 'Af' and resid 86 through 102 removed outlier: 3.661A pdb=" N THRAf 92 " --> pdb=" O SERAf 88 " (cutoff:3.500A) Processing helix chain 'Af' and resid 107 through 122 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 Processing helix chain 'Af' and resid 182 through 187 Processing helix chain 'Af' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAf 197 " --> pdb=" O SERAf 194 " (cutoff:3.500A) Processing helix chain 'Af' and resid 210 through 221 Processing helix chain 'Ag' and resid 66 through 72 removed outlier: 3.820A pdb=" N GLUAg 72 " --> pdb=" O GLUAg 68 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 76 through 81 Processing helix chain 'Ag' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAg 99 " --> pdb=" O GLUAg 95 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAg 121 " --> pdb=" O VALAg 117 " (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 174 Processing helix chain 'Ag' and resid 182 through 187 Processing helix chain 'Ag' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGAg 197 " --> pdb=" O SERAg 194 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEAg 218 " --> pdb=" O ARGAg 214 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 66 through 71 Processing helix chain 'Ah' and resid 76 through 81 removed outlier: 3.790A pdb=" N ILEAh 80 " --> pdb=" O GLNAh 76 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAh 92 " --> pdb=" O SERAh 88 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 107 through 122 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 Processing helix chain 'Ah' and resid 182 through 187 Processing helix chain 'Ah' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAh 197 " --> pdb=" O SERAh 194 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 210 through 221 Processing helix chain 'Ai' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUAi 72 " --> pdb=" O GLUAi 68 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 76 through 81 Processing helix chain 'Ai' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAi 99 " --> pdb=" O GLUAi 95 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 107 through 122 removed outlier: 3.630A pdb=" N GLUAi 121 " --> pdb=" O VALAi 117 " (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 174 Processing helix chain 'Ai' and resid 182 through 187 Processing helix chain 'Ai' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGAi 197 " --> pdb=" O SERAi 194 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEAi 218 " --> pdb=" O ARGAi 214 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 66 through 71 Processing helix chain 'Aj' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAj 80 " --> pdb=" O GLNAj 76 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAj 92 " --> pdb=" O SERAj 88 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 107 through 122 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 Processing helix chain 'Aj' and resid 182 through 187 Processing helix chain 'Aj' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAj 197 " --> pdb=" O SERAj 194 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 210 through 221 Processing helix chain 'Ak' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUAk 72 " --> pdb=" O GLUAk 68 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 76 through 81 Processing helix chain 'Ak' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAk 99 " --> pdb=" O GLUAk 95 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAk 121 " --> pdb=" O VALAk 117 " (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 174 Processing helix chain 'Ak' and resid 182 through 187 Processing helix chain 'Ak' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGAk 197 " --> pdb=" O SERAk 194 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEAk 218 " --> pdb=" O ARGAk 214 " (cutoff:3.500A) Processing helix chain 'Al' and resid 66 through 71 Processing helix chain 'Al' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAl 80 " --> pdb=" O GLNAl 76 " (cutoff:3.500A) Processing helix chain 'Al' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAl 92 " --> pdb=" O SERAl 88 " (cutoff:3.500A) Processing helix chain 'Al' and resid 107 through 122 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 Processing helix chain 'Al' and resid 182 through 187 Processing helix chain 'Al' and resid 193 through 197 removed outlier: 4.115A pdb=" N ARGAl 197 " --> pdb=" O SERAl 194 " (cutoff:3.500A) Processing helix chain 'Al' and resid 210 through 221 Processing helix chain 'Am' and resid 66 through 72 removed outlier: 3.822A pdb=" N GLUAm 72 " --> pdb=" O GLUAm 68 " (cutoff:3.500A) Processing helix chain 'Am' and resid 76 through 81 Processing helix chain 'Am' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAm 99 " --> pdb=" O GLUAm 95 " (cutoff:3.500A) Processing helix chain 'Am' and resid 107 through 122 removed outlier: 3.631A pdb=" N GLUAm 121 " --> pdb=" O VALAm 117 " (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 174 Processing helix chain 'Am' and resid 182 through 187 Processing helix chain 'Am' and resid 192 through 199 removed outlier: 4.540A pdb=" N ARGAm 197 " --> pdb=" O SERAm 194 " (cutoff:3.500A) Processing helix chain 'Am' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEAm 218 " --> pdb=" O ARGAm 214 " (cutoff:3.500A) Processing helix chain 'An' and resid 66 through 71 Processing helix chain 'An' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAn 80 " --> pdb=" O GLNAn 76 " (cutoff:3.500A) Processing helix chain 'An' and resid 86 through 102 removed outlier: 3.661A pdb=" N THRAn 92 " --> pdb=" O SERAn 88 " (cutoff:3.500A) Processing helix chain 'An' and resid 107 through 122 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 Processing helix chain 'An' and resid 182 through 187 Processing helix chain 'An' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAn 197 " --> pdb=" O SERAn 194 " (cutoff:3.500A) Processing helix chain 'An' and resid 210 through 221 Processing helix chain 'Ao' and resid 66 through 72 removed outlier: 3.821A pdb=" N GLUAo 72 " --> pdb=" O GLUAo 68 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 76 through 81 Processing helix chain 'Ao' and resid 86 through 101 removed outlier: 3.607A pdb=" N LEUAo 99 " --> pdb=" O GLUAo 95 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 107 through 122 removed outlier: 3.630A pdb=" N GLUAo 121 " --> pdb=" O VALAo 117 " (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 174 Processing helix chain 'Ao' and resid 182 through 187 Processing helix chain 'Ao' and resid 192 through 199 removed outlier: 4.539A pdb=" N ARGAo 197 " --> pdb=" O SERAo 194 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 210 through 221 removed outlier: 4.069A pdb=" N ILEAo 218 " --> pdb=" O ARGAo 214 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 66 through 71 Processing helix chain 'Ap' and resid 76 through 81 removed outlier: 3.789A pdb=" N ILEAp 80 " --> pdb=" O GLNAp 76 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 86 through 102 removed outlier: 3.662A pdb=" N THRAp 92 " --> pdb=" O SERAp 88 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 107 through 122 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 Processing helix chain 'Ap' and resid 182 through 187 Processing helix chain 'Ap' and resid 193 through 197 removed outlier: 4.114A pdb=" N ARGAp 197 " --> pdb=" O SERAp 194 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 210 through 221 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUAa 139 " --> pdb=" O ASPAa 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Ab' and resid 131 through 134 Processing sheet with id=AA3, first strand: chain 'Ac' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUAc 139 " --> pdb=" O ASPAc 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Ad' and resid 131 through 134 Processing sheet with id=AA5, first strand: chain 'Ae' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUAe 139 " --> pdb=" O ASPAe 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Af' and resid 131 through 134 Processing sheet with id=AA7, first strand: chain 'Ag' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUAg 139 " --> pdb=" O ASPAg 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Ah' and resid 131 through 134 Processing sheet with id=AA9, first strand: chain 'Ai' and resid 131 through 136 removed outlier: 3.822A pdb=" N GLUAi 139 " --> pdb=" O ASPAi 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Aj' and resid 131 through 134 Processing sheet with id=AB2, first strand: chain 'Ak' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUAk 139 " --> pdb=" O ASPAk 136 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Al' and resid 131 through 134 Processing sheet with id=AB4, first strand: chain 'Am' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUAm 139 " --> pdb=" O ASPAm 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'An' and resid 131 through 134 Processing sheet with id=AB6, first strand: chain 'Ao' and resid 131 through 136 removed outlier: 3.823A pdb=" N GLUAo 139 " --> pdb=" O ASPAo 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ap' and resid 131 through 134 928 hydrogen bonds defined for protein. 2640 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: 3.49 Time building geometry restraints manager: 2.21 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: 4520 1.33 - 1.45: 5239 1.45 - 1.57: 12153 1.57 - 1.69: 0 1.69 - 1.81: 368 Bond restraints: 22280 Sorted by residual: bond pdb=" CA LYSAk 58 " pdb=" C LYSAk 58 " ideal model delta sigma weight residual 1.521 1.458 0.063 1.28e-02 6.10e+03 2.45e+01 bond pdb=" CA LYSAc 58 " pdb=" C LYSAc 58 " ideal model delta sigma weight residual 1.521 1.458 0.063 1.28e-02 6.10e+03 2.42e+01 bond pdb=" CA LYSAi 58 " pdb=" C LYSAi 58 " ideal model delta sigma weight residual 1.521 1.458 0.063 1.28e-02 6.10e+03 2.42e+01 bond pdb=" CA LYSAa 58 " pdb=" C LYSAa 58 " ideal model delta sigma weight residual 1.521 1.458 0.063 1.28e-02 6.10e+03 2.41e+01 bond pdb=" CA LYSAm 58 " pdb=" C LYSAm 58 " ideal model delta sigma weight residual 1.521 1.458 0.063 1.28e-02 6.10e+03 2.40e+01 ... (remaining 22275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 28968 1.82 - 3.64: 973 3.64 - 5.46: 171 5.46 - 7.28: 80 7.28 - 9.10: 24 Bond angle restraints: 30216 Sorted by residual: angle pdb=" N ASNAi 175 " pdb=" CA ASNAi 175 " pdb=" C ASNAi 175 " ideal model delta sigma weight residual 113.41 104.89 8.52 1.22e+00 6.72e-01 4.88e+01 angle pdb=" N ASNAo 175 " pdb=" CA ASNAo 175 " pdb=" C ASNAo 175 " ideal model delta sigma weight residual 113.41 104.91 8.50 1.22e+00 6.72e-01 4.86e+01 angle pdb=" N ASNAc 175 " pdb=" CA ASNAc 175 " pdb=" C ASNAc 175 " ideal model delta sigma weight residual 113.41 104.94 8.47 1.22e+00 6.72e-01 4.82e+01 angle pdb=" N ASNAk 175 " pdb=" CA ASNAk 175 " pdb=" C ASNAk 175 " ideal model delta sigma weight residual 113.41 104.95 8.46 1.22e+00 6.72e-01 4.81e+01 angle pdb=" N ASNAa 175 " pdb=" CA ASNAa 175 " pdb=" C ASNAa 175 " ideal model delta sigma weight residual 113.41 104.95 8.46 1.22e+00 6.72e-01 4.81e+01 ... (remaining 30211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 11807 17.30 - 34.60: 1193 34.60 - 51.89: 504 51.89 - 69.19: 72 69.19 - 86.49: 32 Dihedral angle restraints: 13608 sinusoidal: 5624 harmonic: 7984 Sorted by residual: dihedral pdb=" C ARGAo 191 " pdb=" N ARGAo 191 " pdb=" CA ARGAo 191 " pdb=" CB ARGAo 191 " ideal model delta harmonic sigma weight residual -122.60 -133.53 10.93 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C ARGAe 191 " pdb=" N ARGAe 191 " pdb=" CA ARGAe 191 " pdb=" CB ARGAe 191 " ideal model delta harmonic sigma weight residual -122.60 -133.49 10.89 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" C ARGAa 191 " pdb=" N ARGAa 191 " pdb=" CA ARGAa 191 " pdb=" CB ARGAa 191 " ideal model delta harmonic sigma weight residual -122.60 -133.45 10.85 0 2.50e+00 1.60e-01 1.88e+01 ... (remaining 13605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3019 0.085 - 0.171: 205 0.171 - 0.256: 16 0.256 - 0.342: 0 0.342 - 0.427: 8 Chirality restraints: 3248 Sorted by residual: chirality pdb=" CA ARGAe 191 " pdb=" N ARGAe 191 " pdb=" C ARGAe 191 " pdb=" CB ARGAe 191 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CA ARGAo 191 " pdb=" N ARGAo 191 " pdb=" C ARGAo 191 " pdb=" CB ARGAo 191 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CA ARGAa 191 " pdb=" N ARGAa 191 " pdb=" C ARGAa 191 " pdb=" CB ARGAa 191 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 3245 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARGAo 174 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C ARGAo 174 " -0.039 2.00e-02 2.50e+03 pdb=" O ARGAo 174 " 0.015 2.00e-02 2.50e+03 pdb=" N ASNAo 175 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARGAi 174 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C ARGAi 174 " -0.038 2.00e-02 2.50e+03 pdb=" O ARGAi 174 " 0.015 2.00e-02 2.50e+03 pdb=" N ASNAi 175 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARGAe 174 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C ARGAe 174 " -0.038 2.00e-02 2.50e+03 pdb=" O ARGAe 174 " 0.015 2.00e-02 2.50e+03 pdb=" N ASNAe 175 " 0.013 2.00e-02 2.50e+03 ... (remaining 3949 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7874 2.85 - 3.37: 21363 3.37 - 3.88: 36405 3.88 - 4.39: 44522 4.39 - 4.90: 70820 Nonbonded interactions: 180984 Sorted by model distance: nonbonded pdb=" OH TYRAj 101 " pdb=" O PROAj 144 " model vdw 2.342 3.040 nonbonded pdb=" OH TYRAn 101 " pdb=" O PROAn 144 " model vdw 2.342 3.040 nonbonded pdb=" OH TYRAl 101 " pdb=" O PROAl 144 " model vdw 2.343 3.040 nonbonded pdb=" OH TYRAd 101 " pdb=" O PROAd 144 " model vdw 2.343 3.040 nonbonded pdb=" OH TYRAb 101 " pdb=" O PROAb 144 " model vdw 2.343 3.040 ... (remaining 180979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ac' selection = chain 'Ae' selection = chain 'Ag' selection = chain 'Ai' selection = chain 'Ak' selection = chain 'Am' selection = chain 'Ao' } ncs_group { reference = chain 'Ab' selection = chain 'Ad' selection = chain 'Af' selection = chain 'Ah' selection = chain 'Aj' selection = chain 'Al' selection = chain 'An' 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 individual isotropic 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: 14.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 18.740 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 0.007 0.065 22280 Z= 0.481 Angle : 0.843 9.096 30216 Z= 0.529 Chirality : 0.050 0.427 3248 Planarity : 0.006 0.047 3952 Dihedral : 16.833 86.490 8456 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.68 % Allowed : 19.43 % Favored : 79.89 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.17), residues: 2672 helix: -1.43 (0.14), residues: 1328 sheet: -0.43 (0.35), residues: 176 loop : -0.74 (0.21), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAi 183 TYR 0.020 0.002 TYRAo 73 PHE 0.021 0.002 PHEAn 202 TRP 0.018 0.002 TRPAm 118 HIS 0.005 0.001 HISAd 69 Details of bonding type rmsd covalent geometry : bond 0.00679 (22280) covalent geometry : angle 0.84342 (30216) hydrogen bonds : bond 0.25207 ( 928) hydrogen bonds : angle 8.75175 ( 2640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 462 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 118 TRP cc_start: 0.8722 (t60) cc_final: 0.8455 (t60) REVERT: Ab 181 MET cc_start: 0.7566 (tpp) cc_final: 0.7071 (tpp) REVERT: Ac 160 MET cc_start: 0.8725 (mmp) cc_final: 0.8494 (mmp) REVERT: Ad 56 MET cc_start: 0.8173 (mmm) cc_final: 0.7693 (mmm) REVERT: Ad 108 MET cc_start: 0.7592 (tpp) cc_final: 0.7018 (tpp) REVERT: Ad 116 MET cc_start: 0.8549 (ttp) cc_final: 0.8191 (ttp) REVERT: Ad 181 MET cc_start: 0.7790 (tpp) cc_final: 0.7381 (tpp) REVERT: Af 56 MET cc_start: 0.7940 (mmm) cc_final: 0.7414 (mmm) REVERT: Af 90 PHE cc_start: 0.6562 (t80) cc_final: 0.6206 (t80) REVERT: Ag 134 MET cc_start: 0.7210 (ttt) cc_final: 0.6928 (ttm) REVERT: Ag 139 GLU cc_start: 0.7034 (tt0) cc_final: 0.6756 (tt0) REVERT: Ag 181 MET cc_start: 0.7838 (tpt) cc_final: 0.7503 (tpp) REVERT: Ah 90 PHE cc_start: 0.6577 (t80) cc_final: 0.6170 (t80) REVERT: Aj 56 MET cc_start: 0.8093 (mmm) cc_final: 0.7645 (mmm) REVERT: Aj 108 MET cc_start: 0.7692 (tpp) cc_final: 0.7116 (tpp) REVERT: Aj 164 SER cc_start: 0.8731 (t) cc_final: 0.8288 (m) REVERT: Ak 134 MET cc_start: 0.7890 (ttt) cc_final: 0.7682 (ttt) REVERT: Al 116 MET cc_start: 0.8537 (ttp) cc_final: 0.8260 (ttp) REVERT: Al 118 TRP cc_start: 0.8764 (t60) cc_final: 0.8481 (t60) REVERT: Am 94 TYR cc_start: 0.7504 (t80) cc_final: 0.7296 (t80) REVERT: Am 134 MET cc_start: 0.7268 (ttt) cc_final: 0.6992 (ttp) REVERT: Am 198 TYR cc_start: 0.8110 (m-80) cc_final: 0.7603 (m-80) REVERT: An 135 MET cc_start: 0.5885 (mmm) cc_final: 0.5654 (mmm) REVERT: Ao 134 MET cc_start: 0.7216 (ttt) cc_final: 0.6956 (ttm) REVERT: Ao 160 MET cc_start: 0.7947 (mmp) cc_final: 0.7636 (mmt) REVERT: Ao 208 ARG cc_start: 0.7466 (mtm110) cc_final: 0.6985 (mtm180) REVERT: Ap 90 PHE cc_start: 0.6690 (t80) cc_final: 0.6389 (t80) REVERT: Ap 135 MET cc_start: 0.5697 (mmm) cc_final: 0.5408 (mmm) outliers start: 16 outliers final: 5 residues processed: 476 average time/residue: 0.1574 time to fit residues: 115.6479 Evaluate side-chains 451 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 446 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 98 GLN Chi-restraints excluded: chain Af residue 98 GLN Chi-restraints excluded: chain Ah residue 98 GLN Chi-restraints excluded: chain Al residue 98 GLN Chi-restraints excluded: chain An residue 98 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 98 GLN ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 69 HIS Ab 151 ASN Ab 175 ASN ** Ac 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 69 HIS Ad 151 ASN Ad 175 ASN ** Ae 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 122 ASN Ah 122 ASN ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 140 GLN Aj 69 HIS Aj 175 ASN Ak 140 GLN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 69 HIS Al 151 ASN Al 175 ASN An 77 GLN An 122 ASN Ap 122 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.160772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132418 restraints weight = 30563.671| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.05 r_work: 0.3434 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 22280 Z= 0.305 Angle : 0.699 6.768 30216 Z= 0.368 Chirality : 0.046 0.150 3248 Planarity : 0.007 0.065 3952 Dihedral : 5.386 47.782 3023 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.91 % Allowed : 19.81 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.16), residues: 2672 helix: -1.22 (0.13), residues: 1400 sheet: 0.33 (0.33), residues: 176 loop : -0.67 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGAp 55 TYR 0.024 0.003 TYRAc 198 PHE 0.017 0.004 PHEAb 200 TRP 0.020 0.003 TRPAe 132 HIS 0.008 0.002 HISAi 217 Details of bonding type rmsd covalent geometry : bond 0.00717 (22280) covalent geometry : angle 0.69883 (30216) hydrogen bonds : bond 0.05165 ( 928) hydrogen bonds : angle 5.23391 ( 2640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 462 time to evaluate : 0.818 Fit side-chains REVERT: Aa 190 LEU cc_start: 0.8319 (tp) cc_final: 0.8027 (tt) REVERT: Ab 56 MET cc_start: 0.8583 (mmm) cc_final: 0.8033 (mmm) REVERT: Ab 121 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7396 (mt-10) REVERT: Ab 181 MET cc_start: 0.7684 (tpp) cc_final: 0.7254 (tpp) REVERT: Ad 56 MET cc_start: 0.8493 (mmm) cc_final: 0.7959 (mmm) REVERT: Ad 158 GLN cc_start: 0.8564 (mt0) cc_final: 0.8352 (mt0) REVERT: Ad 181 MET cc_start: 0.7975 (tpp) cc_final: 0.7619 (tpp) REVERT: Ad 220 MET cc_start: 0.8229 (mtm) cc_final: 0.8010 (mtm) REVERT: Ae 157 ARG cc_start: 0.7924 (ttp-110) cc_final: 0.7563 (ttp-110) REVERT: Af 56 MET cc_start: 0.8397 (mmm) cc_final: 0.7945 (mmm) REVERT: Ag 84 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6898 (ptt180) REVERT: Ag 124 THR cc_start: 0.7761 (OUTLIER) cc_final: 0.7531 (p) REVERT: Ag 220 MET cc_start: 0.6900 (mtp) cc_final: 0.6505 (mtp) REVERT: Ah 54 MET cc_start: 0.7908 (mtt) cc_final: 0.7707 (mtt) REVERT: Ah 70 LEU cc_start: 0.8342 (tp) cc_final: 0.8124 (tp) REVERT: Aj 56 MET cc_start: 0.8419 (mmm) cc_final: 0.7878 (mmm) REVERT: Al 56 MET cc_start: 0.8519 (mmm) cc_final: 0.7960 (mmm) REVERT: Al 98 GLN cc_start: 0.7985 (tt0) cc_final: 0.7779 (tt0) REVERT: Al 183 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7478 (mtp-110) REVERT: Am 124 THR cc_start: 0.7638 (OUTLIER) cc_final: 0.7380 (p) REVERT: Am 157 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7567 (ttp-110) REVERT: Am 220 MET cc_start: 0.6943 (mtp) cc_final: 0.6536 (mtp) REVERT: An 54 MET cc_start: 0.7764 (mtt) cc_final: 0.7482 (mtt) REVERT: Ao 112 MET cc_start: 0.8022 (mmp) cc_final: 0.7237 (mmm) REVERT: Ao 124 THR cc_start: 0.7698 (OUTLIER) cc_final: 0.7456 (p) REVERT: Ao 157 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7555 (ttp-110) REVERT: Ap 56 MET cc_start: 0.8433 (mmp) cc_final: 0.8217 (mmp) REVERT: Ap 135 MET cc_start: 0.6285 (mmm) cc_final: 0.5777 (mmm) outliers start: 45 outliers final: 20 residues processed: 496 average time/residue: 0.1708 time to fit residues: 127.6426 Evaluate side-chains 483 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 459 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 124 THR Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Ab residue 166 VAL Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ad residue 173 MET Chi-restraints excluded: chain Ad residue 175 ASN Chi-restraints excluded: chain Af residue 71 LEU Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Ag residue 84 ARG Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 166 VAL Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Aj residue 173 MET Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Al residue 166 VAL Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ap residue 98 GLN Chi-restraints excluded: chain Ap residue 124 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 256 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 250 optimal weight: 0.9980 chunk 251 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 141 optimal weight: 0.0060 chunk 67 optimal weight: 0.0870 chunk 155 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.2332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 175 ASN ** Ac 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 77 GLN Ae 98 GLN Ag 98 GLN ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 175 ASN Ak 98 GLN ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 175 ASN Am 98 GLN Ao 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134874 restraints weight = 30662.374| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.14 r_work: 0.3464 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22280 Z= 0.127 Angle : 0.560 10.392 30216 Z= 0.284 Chirality : 0.040 0.124 3248 Planarity : 0.006 0.056 3952 Dihedral : 4.365 19.039 3008 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.34 % Allowed : 20.54 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2672 helix: -0.85 (0.13), residues: 1432 sheet: 0.75 (0.32), residues: 176 loop : -0.15 (0.22), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAd 174 TYR 0.012 0.001 TYRAn 94 PHE 0.015 0.002 PHEAb 200 TRP 0.015 0.002 TRPAo 132 HIS 0.003 0.001 HISAi 217 Details of bonding type rmsd covalent geometry : bond 0.00297 (22280) covalent geometry : angle 0.55996 (30216) hydrogen bonds : bond 0.04000 ( 928) hydrogen bonds : angle 4.78301 ( 2640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 465 time to evaluate : 0.857 Fit side-chains REVERT: Aa 190 LEU cc_start: 0.8243 (tp) cc_final: 0.7979 (tt) REVERT: Ab 56 MET cc_start: 0.8521 (mmm) cc_final: 0.7929 (mmm) REVERT: Ab 121 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7390 (mt-10) REVERT: Ab 181 MET cc_start: 0.7691 (tpp) cc_final: 0.7296 (tpp) REVERT: Ac 124 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7636 (p) REVERT: Ad 56 MET cc_start: 0.8516 (mmm) cc_final: 0.7911 (mmm) REVERT: Ad 158 GLN cc_start: 0.8543 (mt0) cc_final: 0.8322 (mt0) REVERT: Ad 181 MET cc_start: 0.7929 (tpp) cc_final: 0.7563 (tpp) REVERT: Af 56 MET cc_start: 0.8369 (mmm) cc_final: 0.7737 (mmm) REVERT: Ag 84 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.6864 (ptt180) REVERT: Ag 124 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7526 (p) REVERT: Ag 220 MET cc_start: 0.6927 (mtp) cc_final: 0.6343 (mtp) REVERT: Ai 124 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7537 (p) REVERT: Aj 56 MET cc_start: 0.8343 (mmm) cc_final: 0.7770 (mmm) REVERT: Aj 183 ARG cc_start: 0.7723 (mtp-110) cc_final: 0.7354 (mtp-110) REVERT: Al 56 MET cc_start: 0.8472 (mmm) cc_final: 0.7874 (mmm) REVERT: Al 183 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7445 (mtp-110) REVERT: Am 157 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7571 (ttp-110) REVERT: Am 220 MET cc_start: 0.6907 (mtp) cc_final: 0.6364 (mtp) REVERT: An 55 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7522 (mtp180) REVERT: An 87 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7333 (mm-40) REVERT: Ao 112 MET cc_start: 0.8039 (mmp) cc_final: 0.7348 (mmm) REVERT: Ao 157 ARG cc_start: 0.7871 (ttp-110) cc_final: 0.7593 (ttp-110) REVERT: Ap 54 MET cc_start: 0.7687 (mtt) cc_final: 0.7380 (mtt) REVERT: Ap 73 TYR cc_start: 0.8030 (t80) cc_final: 0.7411 (t80) REVERT: Ap 135 MET cc_start: 0.6370 (mmm) cc_final: 0.5923 (mmm) outliers start: 55 outliers final: 21 residues processed: 502 average time/residue: 0.1682 time to fit residues: 127.3703 Evaluate side-chains 482 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 456 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ad residue 208 ARG Chi-restraints excluded: chain Ae residue 166 VAL Chi-restraints excluded: chain Af residue 71 LEU Chi-restraints excluded: chain Af residue 86 THR Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Ag residue 84 ARG Chi-restraints excluded: chain Ag residue 103 ILE Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ah residue 71 LEU Chi-restraints excluded: chain Ah residue 86 THR Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ai residue 124 THR Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Al residue 173 MET Chi-restraints excluded: chain Am residue 103 ILE Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 87 GLN Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain Ao residue 131 VAL Chi-restraints excluded: chain Ap residue 124 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 132 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 0.0980 chunk 216 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 211 optimal weight: 0.9980 chunk 78 optimal weight: 0.0870 chunk 240 optimal weight: 0.3980 chunk 66 optimal weight: 60.0000 chunk 171 optimal weight: 0.9990 chunk 16 optimal weight: 0.0020 overall best weight: 0.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 158 GLN Ab 175 ASN ** Ac 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 158 GLN Ad 77 GLN Ad 151 ASN ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 158 GLN Aj 175 ASN ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 140 GLN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 158 GLN Al 151 ASN Al 175 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.163821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.136350 restraints weight = 30695.228| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.16 r_work: 0.3483 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22280 Z= 0.104 Angle : 0.540 11.537 30216 Z= 0.268 Chirality : 0.039 0.121 3248 Planarity : 0.005 0.054 3952 Dihedral : 4.152 19.368 3008 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.96 % Allowed : 21.43 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2672 helix: -0.37 (0.14), residues: 1376 sheet: 0.86 (0.33), residues: 176 loop : 0.06 (0.22), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAj 174 TYR 0.011 0.001 TYRAo 94 PHE 0.016 0.002 PHEAj 200 TRP 0.014 0.001 TRPAg 132 HIS 0.003 0.001 HISAi 217 Details of bonding type rmsd covalent geometry : bond 0.00240 (22280) covalent geometry : angle 0.54012 (30216) hydrogen bonds : bond 0.03478 ( 928) hydrogen bonds : angle 4.56580 ( 2640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 448 time to evaluate : 0.843 Fit side-chains REVERT: Aa 70 LEU cc_start: 0.8154 (tp) cc_final: 0.7940 (mp) REVERT: Aa 190 LEU cc_start: 0.8194 (tp) cc_final: 0.7991 (tt) REVERT: Ab 217 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7735 (m-70) REVERT: Ac 124 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7615 (p) REVERT: Ad 56 MET cc_start: 0.8492 (mmm) cc_final: 0.7856 (mmm) REVERT: Ad 158 GLN cc_start: 0.8534 (mt0) cc_final: 0.8312 (mt0) REVERT: Ad 181 MET cc_start: 0.7916 (tpp) cc_final: 0.7561 (tpp) REVERT: Ae 198 TYR cc_start: 0.8303 (m-80) cc_final: 0.8034 (m-80) REVERT: Ae 220 MET cc_start: 0.7352 (mtm) cc_final: 0.7117 (mtm) REVERT: Af 56 MET cc_start: 0.8306 (mmm) cc_final: 0.7775 (mmp) REVERT: Ag 124 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7512 (p) REVERT: Ag 220 MET cc_start: 0.6862 (mtp) cc_final: 0.6361 (mtp) REVERT: Ah 220 MET cc_start: 0.7731 (mtm) cc_final: 0.7524 (mtt) REVERT: Ai 121 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7393 (mt-10) REVERT: Aj 56 MET cc_start: 0.8306 (mmm) cc_final: 0.7676 (mmm) REVERT: Aj 183 ARG cc_start: 0.7672 (mtp-110) cc_final: 0.7256 (mtp-110) REVERT: Al 56 MET cc_start: 0.8429 (mmm) cc_final: 0.7804 (mmm) REVERT: Al 183 ARG cc_start: 0.7726 (mtp-110) cc_final: 0.7335 (mtp-110) REVERT: Am 79 ASP cc_start: 0.6986 (m-30) cc_final: 0.6627 (m-30) REVERT: Am 124 THR cc_start: 0.7560 (OUTLIER) cc_final: 0.7284 (p) REVERT: Am 157 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7512 (ttp-110) REVERT: An 54 MET cc_start: 0.7497 (mtt) cc_final: 0.7180 (mtt) REVERT: An 55 ARG cc_start: 0.7601 (mtp180) cc_final: 0.7200 (mtp180) REVERT: Ao 112 MET cc_start: 0.8084 (mmp) cc_final: 0.7430 (mmm) REVERT: Ao 157 ARG cc_start: 0.7853 (ttp-110) cc_final: 0.7558 (ttp-110) REVERT: Ap 63 THR cc_start: 0.8300 (m) cc_final: 0.8085 (m) REVERT: Ap 135 MET cc_start: 0.6412 (mmm) cc_final: 0.6015 (mmm) outliers start: 46 outliers final: 23 residues processed: 476 average time/residue: 0.1629 time to fit residues: 118.1856 Evaluate side-chains 471 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 444 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 150 GLU Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Ab residue 217 HIS Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 159 ILE Chi-restraints excluded: chain Ad residue 208 ARG Chi-restraints excluded: chain Af residue 71 LEU Chi-restraints excluded: chain Af residue 86 THR Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Ag residue 56 MET Chi-restraints excluded: chain Ag residue 103 ILE Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ag residue 166 VAL Chi-restraints excluded: chain Ah residue 86 THR Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Al residue 173 MET Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain Ao residue 205 VAL Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 134 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 172 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 240 optimal weight: 0.0970 chunk 102 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 113 ASN Aa 158 GLN Ac 113 ASN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 158 GLN Ai 113 ASN ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 158 GLN Ak 113 ASN Ak 158 GLN Al 175 ASN An 151 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.161275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133305 restraints weight = 30436.728| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.08 r_work: 0.3442 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22280 Z= 0.193 Angle : 0.585 12.983 30216 Z= 0.294 Chirality : 0.042 0.132 3248 Planarity : 0.005 0.058 3952 Dihedral : 4.341 20.399 3008 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.38 % Allowed : 20.83 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.17), residues: 2672 helix: -0.49 (0.14), residues: 1432 sheet: 1.17 (0.35), residues: 176 loop : 0.02 (0.22), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAb 55 TYR 0.023 0.002 TYRAf 73 PHE 0.023 0.003 PHEAb 200 TRP 0.019 0.002 TRPAg 132 HIS 0.004 0.001 HISAi 217 Details of bonding type rmsd covalent geometry : bond 0.00457 (22280) covalent geometry : angle 0.58485 (30216) hydrogen bonds : bond 0.04050 ( 928) hydrogen bonds : angle 4.64831 ( 2640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 442 time to evaluate : 0.866 Fit side-chains REVERT: Aa 190 LEU cc_start: 0.8249 (tp) cc_final: 0.7983 (tt) REVERT: Ab 121 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7394 (mt-10) REVERT: Ab 181 MET cc_start: 0.7698 (tpp) cc_final: 0.7272 (tpp) REVERT: Ab 191 ARG cc_start: 0.7636 (mtp180) cc_final: 0.7356 (mtp180) REVERT: Ab 217 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7787 (m-70) REVERT: Ab 220 MET cc_start: 0.8004 (mtm) cc_final: 0.7724 (mtm) REVERT: Ac 116 MET cc_start: 0.8712 (ttp) cc_final: 0.8461 (ttp) REVERT: Ad 56 MET cc_start: 0.8512 (mmm) cc_final: 0.7883 (mmm) REVERT: Ad 181 MET cc_start: 0.7956 (tpp) cc_final: 0.7610 (tpp) REVERT: Ad 217 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.7896 (m-70) REVERT: Ae 112 MET cc_start: 0.8176 (mmp) cc_final: 0.7430 (mmm) REVERT: Af 56 MET cc_start: 0.8359 (mmm) cc_final: 0.7860 (mmm) REVERT: Af 217 HIS cc_start: 0.7502 (OUTLIER) cc_final: 0.7098 (t-90) REVERT: Ag 84 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6924 (ptt180) REVERT: Ag 112 MET cc_start: 0.8189 (mmp) cc_final: 0.7428 (mmm) REVERT: Ag 124 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7503 (p) REVERT: Ag 220 MET cc_start: 0.6957 (mtp) cc_final: 0.6437 (mtp) REVERT: Aj 56 MET cc_start: 0.8379 (mmm) cc_final: 0.7782 (mmm) REVERT: Aj 183 ARG cc_start: 0.7810 (mtp-110) cc_final: 0.7390 (mtp-110) REVERT: Al 56 MET cc_start: 0.8499 (mmm) cc_final: 0.7894 (mmm) REVERT: Al 183 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7397 (mtp-110) REVERT: Al 217 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7935 (m-70) REVERT: Am 124 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7288 (p) REVERT: Am 157 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7552 (ttp-110) REVERT: An 220 MET cc_start: 0.7714 (mtm) cc_final: 0.7507 (mtt) REVERT: Ao 112 MET cc_start: 0.8080 (mmp) cc_final: 0.7398 (mmm) REVERT: Ao 157 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7602 (ttp-110) REVERT: Ap 135 MET cc_start: 0.6470 (mmm) cc_final: 0.6064 (mmm) outliers start: 56 outliers final: 33 residues processed: 473 average time/residue: 0.1651 time to fit residues: 118.6133 Evaluate side-chains 478 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 438 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Ab residue 217 HIS Chi-restraints excluded: chain Ac residue 70 LEU Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 159 ILE Chi-restraints excluded: chain Ad residue 208 ARG Chi-restraints excluded: chain Ad residue 217 HIS Chi-restraints excluded: chain Ae residue 135 MET Chi-restraints excluded: chain Ae residue 166 VAL Chi-restraints excluded: chain Af residue 71 LEU Chi-restraints excluded: chain Af residue 86 THR Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 217 HIS Chi-restraints excluded: chain Ag residue 84 ARG Chi-restraints excluded: chain Ag residue 103 ILE Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ag residue 166 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 86 THR Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 217 HIS Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 159 ILE Chi-restraints excluded: chain Al residue 173 MET Chi-restraints excluded: chain Al residue 175 ASN Chi-restraints excluded: chain Al residue 217 HIS Chi-restraints excluded: chain Am residue 103 ILE Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 166 VAL Chi-restraints excluded: chain Am residue 205 VAL Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain Ao residue 205 VAL Chi-restraints excluded: chain Ap residue 86 THR Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 134 MET Chi-restraints excluded: chain Ap residue 217 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 192 optimal weight: 0.1980 chunk 147 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 221 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 210 optimal weight: 0.9990 chunk 185 optimal weight: 0.0970 chunk 206 optimal weight: 1.9990 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 113 ASN Aa 158 GLN Ab 175 ASN Ac 113 ASN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 158 GLN Ah 151 ASN ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 158 GLN Ak 113 ASN Ak 158 GLN An 151 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.162723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134998 restraints weight = 30472.074| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.08 r_work: 0.3467 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22280 Z= 0.132 Angle : 0.547 14.055 30216 Z= 0.273 Chirality : 0.040 0.132 3248 Planarity : 0.005 0.054 3952 Dihedral : 4.190 20.204 3008 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.47 % Allowed : 20.83 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2672 helix: -0.28 (0.14), residues: 1424 sheet: 1.20 (0.35), residues: 176 loop : -0.01 (0.22), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAl 174 TYR 0.013 0.001 TYRAn 94 PHE 0.019 0.002 PHEAd 200 TRP 0.015 0.002 TRPAo 132 HIS 0.003 0.001 HISAi 217 Details of bonding type rmsd covalent geometry : bond 0.00314 (22280) covalent geometry : angle 0.54673 (30216) hydrogen bonds : bond 0.03593 ( 928) hydrogen bonds : angle 4.54222 ( 2640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 435 time to evaluate : 0.842 Fit side-chains REVERT: Aa 190 LEU cc_start: 0.8213 (tp) cc_final: 0.7974 (tt) REVERT: Ab 121 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7398 (mt-10) REVERT: Ab 181 MET cc_start: 0.7689 (tpp) cc_final: 0.7287 (tpp) REVERT: Ab 217 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7775 (m-70) REVERT: Ac 124 THR cc_start: 0.7894 (OUTLIER) cc_final: 0.7649 (p) REVERT: Ad 56 MET cc_start: 0.8497 (mmm) cc_final: 0.7860 (mmm) REVERT: Ad 158 GLN cc_start: 0.8507 (mt0) cc_final: 0.8207 (mt0) REVERT: Ad 181 MET cc_start: 0.7923 (tpp) cc_final: 0.7578 (tpp) REVERT: Ad 217 HIS cc_start: 0.8146 (OUTLIER) cc_final: 0.7878 (m-70) REVERT: Ae 56 MET cc_start: 0.5700 (mmp) cc_final: 0.5388 (mmp) REVERT: Ae 135 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6846 (mmp) REVERT: Af 54 MET cc_start: 0.7100 (mtt) cc_final: 0.6897 (mtt) REVERT: Af 56 MET cc_start: 0.8333 (mmm) cc_final: 0.7773 (mmm) REVERT: Ag 84 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.6847 (ptt180) REVERT: Ag 124 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.7499 (p) REVERT: Ag 220 MET cc_start: 0.6937 (mtp) cc_final: 0.6451 (mtp) REVERT: Ai 166 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8149 (t) REVERT: Aj 56 MET cc_start: 0.8333 (mmm) cc_final: 0.7611 (mmm) REVERT: Aj 183 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.7304 (mtp-110) REVERT: Aj 217 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7783 (m-70) REVERT: Al 56 MET cc_start: 0.8477 (mmm) cc_final: 0.7842 (mmm) REVERT: Al 183 ARG cc_start: 0.7727 (mtp-110) cc_final: 0.7325 (mtp-110) REVERT: Al 217 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7950 (m-70) REVERT: Am 124 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7270 (p) REVERT: Am 157 ARG cc_start: 0.7805 (ttp-110) cc_final: 0.7541 (ttp-110) REVERT: An 54 MET cc_start: 0.7506 (mtt) cc_final: 0.7192 (mtt) REVERT: An 55 ARG cc_start: 0.7565 (mtp180) cc_final: 0.7320 (mtp180) REVERT: An 220 MET cc_start: 0.7777 (mtm) cc_final: 0.7571 (mtt) REVERT: Ao 112 MET cc_start: 0.8053 (mmp) cc_final: 0.7432 (mmm) REVERT: Ao 157 ARG cc_start: 0.7891 (ttp-110) cc_final: 0.7594 (ttp-110) REVERT: Ap 135 MET cc_start: 0.6459 (mmm) cc_final: 0.6087 (mmm) outliers start: 58 outliers final: 37 residues processed: 469 average time/residue: 0.1664 time to fit residues: 118.5288 Evaluate side-chains 480 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 433 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Ab residue 71 LEU Chi-restraints excluded: chain Ab residue 175 ASN Chi-restraints excluded: chain Ab residue 208 ARG Chi-restraints excluded: chain Ab residue 217 HIS Chi-restraints excluded: chain Ac residue 70 LEU Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 150 GLU Chi-restraints excluded: chain Ac residue 159 ILE Chi-restraints excluded: chain Ad residue 208 ARG Chi-restraints excluded: chain Ad residue 217 HIS Chi-restraints excluded: chain Ae residue 135 MET Chi-restraints excluded: chain Ae residue 166 VAL Chi-restraints excluded: chain Af residue 71 LEU Chi-restraints excluded: chain Af residue 86 THR Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Ag residue 84 ARG Chi-restraints excluded: chain Ag residue 103 ILE Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 166 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 86 THR Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 217 HIS Chi-restraints excluded: chain Ai residue 134 MET Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 166 VAL Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Aj residue 217 HIS Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 159 ILE Chi-restraints excluded: chain Al residue 173 MET Chi-restraints excluded: chain Al residue 217 HIS Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 135 MET Chi-restraints excluded: chain Am residue 166 VAL Chi-restraints excluded: chain Am residue 205 VAL Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain Ao residue 205 VAL Chi-restraints excluded: chain Ap residue 86 THR Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 134 MET Chi-restraints excluded: chain Ap residue 217 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 127 optimal weight: 0.1980 chunk 217 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 56 optimal weight: 0.0870 chunk 192 optimal weight: 0.2980 chunk 202 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 210 optimal weight: 0.0980 chunk 97 optimal weight: 0.3980 chunk 108 optimal weight: 0.4980 chunk 140 optimal weight: 0.7980 overall best weight: 0.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 113 ASN Aa 158 GLN ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 175 ASN Ac 113 ASN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 158 GLN Ah 151 ASN ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 158 GLN Ak 113 ASN Ak 140 GLN Ak 158 GLN Al 77 GLN An 151 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.163711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.136487 restraints weight = 30573.932| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.02 r_work: 0.3483 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22280 Z= 0.115 Angle : 0.541 14.090 30216 Z= 0.268 Chirality : 0.040 0.135 3248 Planarity : 0.005 0.053 3952 Dihedral : 4.107 20.019 3008 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.21 % Allowed : 21.39 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2672 helix: 0.05 (0.14), residues: 1384 sheet: 1.25 (0.36), residues: 176 loop : -0.06 (0.21), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAb 174 TYR 0.013 0.001 TYRAn 94 PHE 0.018 0.002 PHEAb 200 TRP 0.013 0.001 TRPAg 132 HIS 0.003 0.001 HISAi 217 Details of bonding type rmsd covalent geometry : bond 0.00272 (22280) covalent geometry : angle 0.54133 (30216) hydrogen bonds : bond 0.03420 ( 928) hydrogen bonds : angle 4.43998 ( 2640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 437 time to evaluate : 0.784 Fit side-chains REVERT: Aa 190 LEU cc_start: 0.8173 (tp) cc_final: 0.7966 (tt) REVERT: Ab 181 MET cc_start: 0.7605 (tpp) cc_final: 0.7209 (tpp) REVERT: Ab 217 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7823 (m-70) REVERT: Ac 116 MET cc_start: 0.8745 (ttp) cc_final: 0.8470 (ttp) REVERT: Ac 124 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7621 (p) REVERT: Ad 56 MET cc_start: 0.8469 (mmm) cc_final: 0.7814 (mmm) REVERT: Ad 158 GLN cc_start: 0.8497 (mt0) cc_final: 0.8190 (mt0) REVERT: Ad 181 MET cc_start: 0.7907 (tpp) cc_final: 0.7577 (tpp) REVERT: Ad 217 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7926 (m-70) REVERT: Ae 56 MET cc_start: 0.5646 (mmp) cc_final: 0.5326 (mmp) REVERT: Ae 108 MET cc_start: 0.7296 (tpt) cc_final: 0.7064 (tpt) REVERT: Ae 112 MET cc_start: 0.8172 (mmp) cc_final: 0.7547 (mmt) REVERT: Ae 135 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6826 (mmp) REVERT: Ae 157 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.7412 (ttp-110) REVERT: Af 55 ARG cc_start: 0.7479 (mtp180) cc_final: 0.7264 (mtp180) REVERT: Af 56 MET cc_start: 0.8270 (mmm) cc_final: 0.7735 (mmm) REVERT: Af 217 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6894 (t-90) REVERT: Ag 84 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6723 (ptt180) REVERT: Ag 112 MET cc_start: 0.8145 (mmp) cc_final: 0.7434 (mmm) REVERT: Ag 124 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7467 (p) REVERT: Ag 220 MET cc_start: 0.6917 (mtp) cc_final: 0.6459 (mtp) REVERT: Ai 121 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7424 (mm-30) REVERT: Ai 124 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7432 (p) REVERT: Ai 166 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8141 (t) REVERT: Ai 173 MET cc_start: 0.7737 (mmt) cc_final: 0.7500 (mmp) REVERT: Aj 56 MET cc_start: 0.8276 (mmm) cc_final: 0.7501 (mmm) REVERT: Aj 183 ARG cc_start: 0.7699 (mtp-110) cc_final: 0.7268 (mtp-110) REVERT: Aj 217 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7898 (m-70) REVERT: Ak 172 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7200 (tm-30) REVERT: Al 56 MET cc_start: 0.8417 (mmm) cc_final: 0.7783 (mmm) REVERT: Al 183 ARG cc_start: 0.7665 (mtp-110) cc_final: 0.7282 (mtp-110) REVERT: Al 217 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.8003 (m-70) REVERT: Am 124 THR cc_start: 0.7529 (OUTLIER) cc_final: 0.7245 (p) REVERT: Am 157 ARG cc_start: 0.7782 (ttp-110) cc_final: 0.7505 (ttp-110) REVERT: An 54 MET cc_start: 0.7418 (mtt) cc_final: 0.7102 (mtt) REVERT: An 112 MET cc_start: 0.7091 (mmm) cc_final: 0.6856 (mmm) REVERT: An 160 MET cc_start: 0.8160 (mmm) cc_final: 0.7949 (mmm) REVERT: An 220 MET cc_start: 0.7790 (mtm) cc_final: 0.7584 (mtt) REVERT: Ao 112 MET cc_start: 0.8026 (mmp) cc_final: 0.7443 (mmm) REVERT: Ao 157 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7622 (ttp-110) REVERT: Ap 135 MET cc_start: 0.6428 (mmm) cc_final: 0.6105 (mmm) outliers start: 52 outliers final: 34 residues processed: 470 average time/residue: 0.1623 time to fit residues: 115.4851 Evaluate side-chains 483 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 437 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 150 GLU Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Ab residue 71 LEU Chi-restraints excluded: chain Ab residue 175 ASN Chi-restraints excluded: chain Ab residue 208 ARG Chi-restraints excluded: chain Ab residue 217 HIS Chi-restraints excluded: chain Ac residue 70 LEU Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 150 GLU Chi-restraints excluded: chain Ac residue 159 ILE Chi-restraints excluded: chain Ad residue 208 ARG Chi-restraints excluded: chain Ad residue 217 HIS Chi-restraints excluded: chain Ae residue 135 MET Chi-restraints excluded: chain Ae residue 166 VAL Chi-restraints excluded: chain Af residue 71 LEU Chi-restraints excluded: chain Af residue 86 THR Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 217 HIS Chi-restraints excluded: chain Ag residue 84 ARG Chi-restraints excluded: chain Ag residue 103 ILE Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 166 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 86 THR Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 217 HIS Chi-restraints excluded: chain Ai residue 124 THR Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 166 VAL Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Aj residue 217 HIS Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 159 ILE Chi-restraints excluded: chain Al residue 173 MET Chi-restraints excluded: chain Al residue 217 HIS Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 166 VAL Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain Ao residue 205 VAL Chi-restraints excluded: chain Ap residue 86 THR Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 134 MET Chi-restraints excluded: chain Ap residue 217 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 242 optimal weight: 0.9980 chunk 201 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 66 optimal weight: 50.0000 chunk 103 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 239 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 113 ASN Aa 158 GLN ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 113 ASN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 158 GLN ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 158 GLN Ak 113 ASN Ak 158 GLN Al 151 ASN Al 175 ASN An 151 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.161871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134230 restraints weight = 30287.477| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.06 r_work: 0.3446 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22280 Z= 0.187 Angle : 0.588 13.782 30216 Z= 0.293 Chirality : 0.042 0.145 3248 Planarity : 0.005 0.056 3952 Dihedral : 4.279 20.567 3008 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.30 % Allowed : 21.22 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2672 helix: -0.22 (0.14), residues: 1432 sheet: 1.35 (0.37), residues: 176 loop : 0.03 (0.22), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAj 55 TYR 0.018 0.002 TYRAn 94 PHE 0.022 0.003 PHEAb 200 TRP 0.017 0.002 TRPAm 132 HIS 0.004 0.001 HISAi 217 Details of bonding type rmsd covalent geometry : bond 0.00444 (22280) covalent geometry : angle 0.58841 (30216) hydrogen bonds : bond 0.03918 ( 928) hydrogen bonds : angle 4.55363 ( 2640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 436 time to evaluate : 0.857 Fit side-chains REVERT: Aa 190 LEU cc_start: 0.8223 (tp) cc_final: 0.7958 (tt) REVERT: Ab 56 MET cc_start: 0.8567 (mmm) cc_final: 0.7905 (mmm) REVERT: Ab 181 MET cc_start: 0.7731 (tpp) cc_final: 0.7305 (tpp) REVERT: Ab 217 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7790 (m-70) REVERT: Ab 220 MET cc_start: 0.8003 (mtm) cc_final: 0.7748 (mtm) REVERT: Ad 55 ARG cc_start: 0.8214 (mtp180) cc_final: 0.7006 (mtp180) REVERT: Ad 56 MET cc_start: 0.8532 (mmm) cc_final: 0.7894 (mmm) REVERT: Ad 158 GLN cc_start: 0.8522 (mt0) cc_final: 0.8220 (mt0) REVERT: Ad 181 MET cc_start: 0.7963 (tpp) cc_final: 0.7635 (tpp) REVERT: Ad 217 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7899 (m-70) REVERT: Ae 56 MET cc_start: 0.5629 (mmp) cc_final: 0.5345 (mmp) REVERT: Ae 135 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6762 (mmp) REVERT: Ae 157 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7413 (ttp-110) REVERT: Af 56 MET cc_start: 0.8357 (mmm) cc_final: 0.7891 (mmm) REVERT: Af 135 MET cc_start: 0.5892 (mmm) cc_final: 0.5009 (mmm) REVERT: Af 217 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.7061 (t-90) REVERT: Ag 84 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6988 (ptt180) REVERT: Ag 112 MET cc_start: 0.8115 (mmp) cc_final: 0.7360 (mmm) REVERT: Ag 124 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7540 (p) REVERT: Ag 220 MET cc_start: 0.7007 (mtp) cc_final: 0.6502 (mtp) REVERT: Ah 160 MET cc_start: 0.8286 (mmm) cc_final: 0.8053 (mmm) REVERT: Ai 166 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8140 (t) REVERT: Aj 56 MET cc_start: 0.8334 (mmm) cc_final: 0.7622 (mmm) REVERT: Aj 183 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.7344 (mtp-110) REVERT: Aj 217 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7854 (m-70) REVERT: Al 56 MET cc_start: 0.8509 (mmm) cc_final: 0.7884 (mmm) REVERT: Al 183 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7350 (mtp-110) REVERT: Al 217 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7943 (m-70) REVERT: Am 124 THR cc_start: 0.7559 (OUTLIER) cc_final: 0.7278 (p) REVERT: Am 157 ARG cc_start: 0.7817 (ttp-110) cc_final: 0.7536 (ttp-110) REVERT: An 54 MET cc_start: 0.7502 (mtt) cc_final: 0.7265 (mtt) REVERT: An 112 MET cc_start: 0.7158 (mmm) cc_final: 0.6904 (mmm) REVERT: Ao 112 MET cc_start: 0.8073 (mmp) cc_final: 0.7445 (mmm) REVERT: Ao 157 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7623 (ttp-110) REVERT: Ap 135 MET cc_start: 0.6458 (mmm) cc_final: 0.6138 (mmm) outliers start: 54 outliers final: 35 residues processed: 468 average time/residue: 0.1611 time to fit residues: 114.8027 Evaluate side-chains 479 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 434 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Ab residue 208 ARG Chi-restraints excluded: chain Ab residue 217 HIS Chi-restraints excluded: chain Ac residue 70 LEU Chi-restraints excluded: chain Ac residue 84 ARG Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 159 ILE Chi-restraints excluded: chain Ad residue 208 ARG Chi-restraints excluded: chain Ad residue 217 HIS Chi-restraints excluded: chain Ae residue 135 MET Chi-restraints excluded: chain Ae residue 166 VAL Chi-restraints excluded: chain Af residue 71 LEU Chi-restraints excluded: chain Af residue 86 THR Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 217 HIS Chi-restraints excluded: chain Ag residue 84 ARG Chi-restraints excluded: chain Ag residue 103 ILE Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ag residue 166 VAL Chi-restraints excluded: chain Ag residue 205 VAL Chi-restraints excluded: chain Ah residue 86 THR Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 217 HIS Chi-restraints excluded: chain Ai residue 134 MET Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 166 VAL Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Aj residue 217 HIS Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 159 ILE Chi-restraints excluded: chain Ak residue 173 MET Chi-restraints excluded: chain Al residue 173 MET Chi-restraints excluded: chain Al residue 217 HIS Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 166 VAL Chi-restraints excluded: chain Am residue 205 VAL Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain Ao residue 205 VAL Chi-restraints excluded: chain Ap residue 86 THR Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 217 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 166 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 236 optimal weight: 0.5980 chunk 254 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 249 optimal weight: 0.3980 chunk 262 optimal weight: 0.7980 chunk 81 optimal weight: 0.4980 chunk 177 optimal weight: 0.3980 chunk 96 optimal weight: 0.5980 chunk 144 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 158 GLN Ac 113 ASN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 113 ASN Al 175 ASN An 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.162334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134526 restraints weight = 30430.480| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.08 r_work: 0.3447 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22280 Z= 0.186 Angle : 0.603 15.188 30216 Z= 0.298 Chirality : 0.042 0.171 3248 Planarity : 0.005 0.056 3952 Dihedral : 4.329 20.880 3008 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.21 % Allowed : 21.68 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2672 helix: -0.10 (0.14), residues: 1384 sheet: 1.34 (0.37), residues: 176 loop : -0.11 (0.21), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAj 55 TYR 0.021 0.002 TYRAf 94 PHE 0.022 0.003 PHEAb 200 TRP 0.018 0.002 TRPAo 132 HIS 0.004 0.001 HISAi 217 Details of bonding type rmsd covalent geometry : bond 0.00444 (22280) covalent geometry : angle 0.60319 (30216) hydrogen bonds : bond 0.03881 ( 928) hydrogen bonds : angle 4.58962 ( 2640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 439 time to evaluate : 0.892 Fit side-chains REVERT: Aa 190 LEU cc_start: 0.8237 (tp) cc_final: 0.7944 (tt) REVERT: Ab 56 MET cc_start: 0.8540 (mmm) cc_final: 0.7871 (mmm) REVERT: Ab 181 MET cc_start: 0.7733 (tpp) cc_final: 0.7274 (tpp) REVERT: Ab 217 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.7771 (m-70) REVERT: Ab 220 MET cc_start: 0.7988 (mtm) cc_final: 0.7744 (mtm) REVERT: Ad 56 MET cc_start: 0.8508 (mmm) cc_final: 0.7880 (mmm) REVERT: Ad 158 GLN cc_start: 0.8513 (mt0) cc_final: 0.8219 (mt0) REVERT: Ad 181 MET cc_start: 0.7980 (tpp) cc_final: 0.7616 (tpp) REVERT: Ad 217 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7868 (m-70) REVERT: Ad 220 MET cc_start: 0.7993 (mtm) cc_final: 0.7785 (mtm) REVERT: Ae 56 MET cc_start: 0.5599 (mmp) cc_final: 0.5255 (mmp) REVERT: Ae 135 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6750 (mmp) REVERT: Ae 157 ARG cc_start: 0.7924 (ttp-110) cc_final: 0.7526 (ttp-110) REVERT: Af 56 MET cc_start: 0.8363 (mmm) cc_final: 0.7900 (mmm) REVERT: Af 135 MET cc_start: 0.5968 (mmm) cc_final: 0.5108 (mmm) REVERT: Af 217 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.7079 (t-90) REVERT: Ag 84 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7048 (ptt180) REVERT: Ag 112 MET cc_start: 0.8119 (mmp) cc_final: 0.7418 (mmm) REVERT: Ag 124 THR cc_start: 0.7786 (OUTLIER) cc_final: 0.7541 (p) REVERT: Ag 220 MET cc_start: 0.7034 (mtp) cc_final: 0.6519 (mtp) REVERT: Ai 121 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7422 (mm-30) REVERT: Ai 166 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8129 (t) REVERT: Aj 56 MET cc_start: 0.8337 (mmm) cc_final: 0.7632 (mmm) REVERT: Aj 183 ARG cc_start: 0.7736 (mtp-110) cc_final: 0.7302 (mtp-110) REVERT: Aj 217 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7772 (m-70) REVERT: Al 56 MET cc_start: 0.8456 (mmm) cc_final: 0.7852 (mmm) REVERT: Al 183 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7331 (mtp-110) REVERT: Al 217 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7946 (m-70) REVERT: Am 124 THR cc_start: 0.7554 (OUTLIER) cc_final: 0.7275 (p) REVERT: Am 157 ARG cc_start: 0.7810 (ttp-110) cc_final: 0.7531 (ttp-110) REVERT: An 54 MET cc_start: 0.7360 (mtt) cc_final: 0.7035 (mtt) REVERT: Ao 112 MET cc_start: 0.8073 (mmp) cc_final: 0.7432 (mmm) REVERT: Ao 157 ARG cc_start: 0.7932 (ttp-110) cc_final: 0.7631 (ttp-110) REVERT: Ap 135 MET cc_start: 0.6490 (mmm) cc_final: 0.6183 (mmm) REVERT: Ap 160 MET cc_start: 0.8213 (mmm) cc_final: 0.7958 (mmm) outliers start: 52 outliers final: 36 residues processed: 468 average time/residue: 0.1645 time to fit residues: 117.8279 Evaluate side-chains 484 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 438 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Ab residue 173 MET Chi-restraints excluded: chain Ab residue 208 ARG Chi-restraints excluded: chain Ab residue 217 HIS Chi-restraints excluded: chain Ac residue 70 LEU Chi-restraints excluded: chain Ac residue 84 ARG Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 159 ILE Chi-restraints excluded: chain Ad residue 166 VAL Chi-restraints excluded: chain Ad residue 208 ARG Chi-restraints excluded: chain Ad residue 217 HIS Chi-restraints excluded: chain Ae residue 135 MET Chi-restraints excluded: chain Ae residue 166 VAL Chi-restraints excluded: chain Af residue 71 LEU Chi-restraints excluded: chain Af residue 86 THR Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 217 HIS Chi-restraints excluded: chain Ag residue 84 ARG Chi-restraints excluded: chain Ag residue 103 ILE Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ag residue 166 VAL Chi-restraints excluded: chain Ah residue 86 THR Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 217 HIS Chi-restraints excluded: chain Ai residue 134 MET Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 166 VAL Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Aj residue 217 HIS Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 159 ILE Chi-restraints excluded: chain Al residue 173 MET Chi-restraints excluded: chain Al residue 175 ASN Chi-restraints excluded: chain Al residue 217 HIS Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 166 VAL Chi-restraints excluded: chain Am residue 205 VAL Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain Ao residue 205 VAL Chi-restraints excluded: chain Ap residue 86 THR Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 217 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 18 optimal weight: 0.6980 chunk 224 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 175 optimal weight: 0.0870 chunk 235 optimal weight: 0.5980 chunk 183 optimal weight: 0.3980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 158 GLN Ac 113 ASN Ac 158 GLN Ak 113 ASN Ak 158 GLN Al 175 ASN An 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.161021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.133763 restraints weight = 30534.410| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.04 r_work: 0.3449 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22280 Z= 0.188 Angle : 0.607 15.285 30216 Z= 0.301 Chirality : 0.042 0.190 3248 Planarity : 0.005 0.056 3952 Dihedral : 4.334 21.302 3008 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.08 % Allowed : 22.15 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2672 helix: -0.10 (0.14), residues: 1384 sheet: 1.32 (0.37), residues: 176 loop : -0.10 (0.21), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAp 55 TYR 0.021 0.002 TYRAn 94 PHE 0.021 0.003 PHEAj 200 TRP 0.018 0.002 TRPAo 132 HIS 0.004 0.001 HISAi 217 Details of bonding type rmsd covalent geometry : bond 0.00447 (22280) covalent geometry : angle 0.60703 (30216) hydrogen bonds : bond 0.03904 ( 928) hydrogen bonds : angle 4.61682 ( 2640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5344 Ramachandran restraints generated. 2672 Oldfield, 0 Emsley, 2672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 429 time to evaluate : 0.841 Fit side-chains REVERT: Aa 190 LEU cc_start: 0.8226 (tp) cc_final: 0.7960 (tt) REVERT: Ab 56 MET cc_start: 0.8516 (mmm) cc_final: 0.7844 (mmm) REVERT: Ab 181 MET cc_start: 0.7695 (tpp) cc_final: 0.7227 (tpp) REVERT: Ab 217 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7832 (m-70) REVERT: Ab 220 MET cc_start: 0.8038 (mtm) cc_final: 0.7806 (mtm) REVERT: Ac 116 MET cc_start: 0.8673 (ttp) cc_final: 0.8454 (ttp) REVERT: Ad 56 MET cc_start: 0.8480 (mmm) cc_final: 0.7857 (mmm) REVERT: Ad 158 GLN cc_start: 0.8513 (mt0) cc_final: 0.8209 (mt0) REVERT: Ad 181 MET cc_start: 0.7969 (tpp) cc_final: 0.7612 (tpp) REVERT: Ad 217 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7923 (m-70) REVERT: Ae 56 MET cc_start: 0.5585 (mmp) cc_final: 0.5245 (mmp) REVERT: Ae 135 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6707 (mmp) REVERT: Ae 157 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7547 (ttp-110) REVERT: Af 56 MET cc_start: 0.8345 (mmm) cc_final: 0.7862 (mmm) REVERT: Af 135 MET cc_start: 0.5961 (mmm) cc_final: 0.5168 (mmm) REVERT: Af 217 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.7066 (t-90) REVERT: Ag 84 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7054 (ptt180) REVERT: Ag 112 MET cc_start: 0.8086 (mmp) cc_final: 0.7386 (mmm) REVERT: Ag 124 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7505 (p) REVERT: Ag 220 MET cc_start: 0.7040 (mtp) cc_final: 0.6536 (mtp) REVERT: Ai 166 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8093 (t) REVERT: Aj 55 ARG cc_start: 0.8316 (mtp85) cc_final: 0.8021 (mtm110) REVERT: Aj 56 MET cc_start: 0.8266 (mmm) cc_final: 0.7615 (mmm) REVERT: Aj 183 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7338 (mtp-110) REVERT: Aj 217 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7796 (m-70) REVERT: Al 55 ARG cc_start: 0.8497 (mtp-110) cc_final: 0.8111 (mtp180) REVERT: Al 56 MET cc_start: 0.8441 (mmm) cc_final: 0.7884 (mmm) REVERT: Al 183 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7369 (mtp-110) REVERT: Al 217 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7952 (m-70) REVERT: Am 124 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7265 (p) REVERT: Am 157 ARG cc_start: 0.7808 (ttp-110) cc_final: 0.7532 (ttp-110) REVERT: An 54 MET cc_start: 0.7396 (mtt) cc_final: 0.7147 (mtt) REVERT: Ao 112 MET cc_start: 0.8038 (mmp) cc_final: 0.7386 (mmm) REVERT: Ao 157 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7632 (ttp-110) REVERT: Ap 135 MET cc_start: 0.6490 (mmm) cc_final: 0.6226 (mmm) outliers start: 49 outliers final: 38 residues processed: 458 average time/residue: 0.1602 time to fit residues: 112.6233 Evaluate side-chains 477 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 429 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Ab residue 173 MET Chi-restraints excluded: chain Ab residue 208 ARG Chi-restraints excluded: chain Ab residue 217 HIS Chi-restraints excluded: chain Ac residue 70 LEU Chi-restraints excluded: chain Ac residue 84 ARG Chi-restraints excluded: chain Ac residue 124 THR Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 159 ILE Chi-restraints excluded: chain Ad residue 166 VAL Chi-restraints excluded: chain Ad residue 208 ARG Chi-restraints excluded: chain Ad residue 217 HIS Chi-restraints excluded: chain Ae residue 135 MET Chi-restraints excluded: chain Ae residue 166 VAL Chi-restraints excluded: chain Af residue 71 LEU Chi-restraints excluded: chain Af residue 86 THR Chi-restraints excluded: chain Af residue 124 THR Chi-restraints excluded: chain Af residue 217 HIS Chi-restraints excluded: chain Ag residue 84 ARG Chi-restraints excluded: chain Ag residue 103 ILE Chi-restraints excluded: chain Ag residue 124 THR Chi-restraints excluded: chain Ag residue 131 VAL Chi-restraints excluded: chain Ag residue 166 VAL Chi-restraints excluded: chain Ah residue 86 THR Chi-restraints excluded: chain Ah residue 124 THR Chi-restraints excluded: chain Ah residue 217 HIS Chi-restraints excluded: chain Ai residue 134 MET Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 166 VAL Chi-restraints excluded: chain Ai residue 173 MET Chi-restraints excluded: chain Aj residue 217 HIS Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 159 ILE Chi-restraints excluded: chain Ak residue 173 MET Chi-restraints excluded: chain Al residue 173 MET Chi-restraints excluded: chain Al residue 175 ASN Chi-restraints excluded: chain Al residue 217 HIS Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 166 VAL Chi-restraints excluded: chain Am residue 205 VAL Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain Ao residue 205 VAL Chi-restraints excluded: chain Ap residue 86 THR Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 217 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 229 optimal weight: 0.4980 chunk 203 optimal weight: 0.2980 chunk 166 optimal weight: 0.9980 chunk 152 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 228 optimal weight: 0.6980 chunk 109 optimal weight: 0.0870 chunk 252 optimal weight: 0.0870 chunk 211 optimal weight: 0.4980 chunk 96 optimal weight: 0.1980 chunk 156 optimal weight: 0.2980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 158 GLN Ac 113 ASN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 151 ASN ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 113 ASN Ak 158 GLN Al 98 GLN Al 175 ASN Ap 77 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.163470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.136199 restraints weight = 30536.737| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.01 r_work: 0.3479 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22280 Z= 0.115 Angle : 0.574 15.386 30216 Z= 0.279 Chirality : 0.040 0.186 3248 Planarity : 0.005 0.054 3952 Dihedral : 4.119 19.987 3008 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.96 % Allowed : 22.41 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2672 helix: 0.19 (0.14), residues: 1376 sheet: 1.28 (0.37), residues: 176 loop : -0.12 (0.21), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAb 55 TYR 0.017 0.001 TYRAn 94 PHE 0.015 0.002 PHEAj 200 TRP 0.016 0.002 TRPAp 93 HIS 0.003 0.001 HISAi 217 Details of bonding type rmsd covalent geometry : bond 0.00275 (22280) covalent geometry : angle 0.57412 (30216) hydrogen bonds : bond 0.03375 ( 928) hydrogen bonds : angle 4.46049 ( 2640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6638.57 seconds wall clock time: 114 minutes 0.85 seconds (6840.85 seconds total)