Starting phenix.real_space_refine on Sun Aug 24 18:18:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opg_17052/08_2025/8opg_17052.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opg_17052/08_2025/8opg_17052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8opg_17052/08_2025/8opg_17052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opg_17052/08_2025/8opg_17052.map" model { file = "/net/cci-nas-00/data/ceres_data/8opg_17052/08_2025/8opg_17052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opg_17052/08_2025/8opg_17052.cif" } resolution = 3.2 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= 0.017 sd= 0.208 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 209 5.16 5 C 13984 2.51 5 N 3705 2.21 5 O 4161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22059 Number of models: 1 Model: "" Number of chains: 1 Chain: "Aa" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Restraints were copied for chains: Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As Time building chain proxies: 1.83, per 1000 atoms: 0.08 Number of scatterers: 22059 At special positions: 0 Unit cell: (135.85, 135.85, 158.65, 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 209 16.00 O 4161 8.00 N 3705 7.00 C 13984 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: 1.38 Conformation dependent library (CDL) restraints added in 776.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5244 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 38 sheets defined 43.4% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'Aa' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAa 95 " --> pdb=" O ASPAa 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUAa 99 " --> pdb=" O GLUAa 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAa 100 " --> pdb=" O ALAAa 96 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAa 112 " --> pdb=" O METAa 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAa 114 " --> pdb=" O THRAa 110 " (cutoff:3.500A) removed outlier: 3.764A 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 178 removed outlier: 3.525A pdb=" N ALAAa 169 " --> pdb=" O ASPAa 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAa 173 " --> pdb=" O ALAAa 169 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYSAa 177 " --> pdb=" O METAa 173 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAb 95 " --> pdb=" O ASPAb 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUAb 99 " --> pdb=" O GLUAb 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAb 100 " --> pdb=" O ALAAb 96 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAb 111 " --> pdb=" O GLUAb 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAb 112 " --> pdb=" O METAb 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAb 114 " --> pdb=" O THRAb 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAb 121 " --> pdb=" O VALAb 117 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 145 through 151 Processing helix chain 'Ab' and resid 155 through 161 Processing helix chain 'Ab' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAb 169 " --> pdb=" O ASPAb 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAb 173 " --> pdb=" O ALAAb 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAb 177 " --> pdb=" O METAb 173 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 86 through 102 removed outlier: 3.512A pdb=" N LEUAc 99 " --> pdb=" O GLUAc 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAc 100 " --> pdb=" O ALAAc 96 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAc 112 " --> pdb=" O METAc 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAc 114 " --> pdb=" O THRAc 110 " (cutoff:3.500A) removed outlier: 3.763A 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 178 removed outlier: 3.525A pdb=" N ALAAc 169 " --> pdb=" O ASPAc 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAc 173 " --> pdb=" O ALAAc 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAc 177 " --> pdb=" O METAc 173 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAd 99 " --> pdb=" O GLUAd 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAd 100 " --> pdb=" O ALAAd 96 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAd 111 " --> pdb=" O GLUAd 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAd 112 " --> pdb=" O METAd 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAd 114 " --> pdb=" O THRAd 110 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLUAd 121 " --> pdb=" O VALAd 117 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 145 through 151 Processing helix chain 'Ad' and resid 155 through 161 Processing helix chain 'Ad' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAd 169 " --> pdb=" O ASPAd 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAd 173 " --> pdb=" O ALAAd 169 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYSAd 177 " --> pdb=" O METAd 173 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 86 through 102 removed outlier: 3.501A pdb=" N GLUAe 95 " --> pdb=" O ASPAe 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUAe 99 " --> pdb=" O GLUAe 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAe 100 " --> pdb=" O ALAAe 96 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N METAe 112 " --> pdb=" O METAe 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAe 114 " --> pdb=" O THRAe 110 " (cutoff:3.500A) removed outlier: 3.763A 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 178 removed outlier: 3.524A pdb=" N ALAAe 169 " --> pdb=" O ASPAe 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAe 173 " --> pdb=" O ALAAe 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAe 177 " --> pdb=" O METAe 173 " (cutoff:3.500A) Processing helix chain 'Af' and resid 86 through 102 removed outlier: 3.501A pdb=" N GLUAf 95 " --> pdb=" O ASPAf 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUAf 99 " --> pdb=" O GLUAf 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAf 100 " --> pdb=" O ALAAf 96 " (cutoff:3.500A) Processing helix chain 'Af' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAf 111 " --> pdb=" O GLUAf 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAf 112 " --> pdb=" O METAf 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAf 114 " --> pdb=" O THRAf 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAf 121 " --> pdb=" O VALAf 117 " (cutoff:3.500A) Processing helix chain 'Af' and resid 145 through 151 Processing helix chain 'Af' and resid 155 through 161 Processing helix chain 'Af' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAf 169 " --> pdb=" O ASPAf 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAf 173 " --> pdb=" O ALAAf 169 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYSAf 177 " --> pdb=" O METAf 173 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAg 99 " --> pdb=" O GLUAg 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAg 100 " --> pdb=" O ALAAg 96 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAg 112 " --> pdb=" O METAg 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAg 114 " --> pdb=" O THRAg 110 " (cutoff:3.500A) removed outlier: 3.764A 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 178 removed outlier: 3.525A pdb=" N ALAAg 169 " --> pdb=" O ASPAg 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAg 173 " --> pdb=" O ALAAg 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAg 177 " --> pdb=" O METAg 173 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 86 through 102 removed outlier: 3.501A pdb=" N GLUAh 95 " --> pdb=" O ASPAh 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUAh 99 " --> pdb=" O GLUAh 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAh 100 " --> pdb=" O ALAAh 96 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAh 111 " --> pdb=" O GLUAh 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAh 112 " --> pdb=" O METAh 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLYAh 114 " --> pdb=" O THRAh 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAh 121 " --> pdb=" O VALAh 117 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 145 through 151 Processing helix chain 'Ah' and resid 155 through 161 Processing helix chain 'Ah' and resid 163 through 178 removed outlier: 3.524A pdb=" N ALAAh 169 " --> pdb=" O ASPAh 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAh 173 " --> pdb=" O ALAAh 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAh 177 " --> pdb=" O METAh 173 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAi 95 " --> pdb=" O ASPAi 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUAi 99 " --> pdb=" O GLUAi 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAi 100 " --> pdb=" O ALAAi 96 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAi 112 " --> pdb=" O METAi 108 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLYAi 114 " --> pdb=" O THRAi 110 " (cutoff:3.500A) removed outlier: 3.764A 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 178 removed outlier: 3.525A pdb=" N ALAAi 169 " --> pdb=" O ASPAi 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAi 173 " --> pdb=" O ALAAi 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAi 177 " --> pdb=" O METAi 173 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAj 99 " --> pdb=" O GLUAj 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAj 100 " --> pdb=" O ALAAj 96 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAj 111 " --> pdb=" O GLUAj 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N METAj 112 " --> pdb=" O METAj 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAj 114 " --> pdb=" O THRAj 110 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLUAj 121 " --> pdb=" O VALAj 117 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 145 through 151 Processing helix chain 'Aj' and resid 155 through 161 Processing helix chain 'Aj' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAj 169 " --> pdb=" O ASPAj 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAj 173 " --> pdb=" O ALAAj 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAj 177 " --> pdb=" O METAj 173 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAk 95 " --> pdb=" O ASPAk 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUAk 99 " --> pdb=" O GLUAk 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAk 100 " --> pdb=" O ALAAk 96 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAk 112 " --> pdb=" O METAk 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLYAk 114 " --> pdb=" O THRAk 110 " (cutoff:3.500A) removed outlier: 3.764A 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 178 removed outlier: 3.524A pdb=" N ALAAk 169 " --> pdb=" O ASPAk 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAk 173 " --> pdb=" O ALAAk 169 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYSAk 177 " --> pdb=" O METAk 173 " (cutoff:3.500A) Processing helix chain 'Al' and resid 86 through 102 removed outlier: 3.512A pdb=" N LEUAl 99 " --> pdb=" O GLUAl 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAl 100 " --> pdb=" O ALAAl 96 " (cutoff:3.500A) Processing helix chain 'Al' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAl 111 " --> pdb=" O GLUAl 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAl 112 " --> pdb=" O METAl 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLYAl 114 " --> pdb=" O THRAl 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAl 121 " --> pdb=" O VALAl 117 " (cutoff:3.500A) Processing helix chain 'Al' and resid 145 through 151 Processing helix chain 'Al' and resid 155 through 161 Processing helix chain 'Al' and resid 163 through 178 removed outlier: 3.524A pdb=" N ALAAl 169 " --> pdb=" O ASPAl 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAl 173 " --> pdb=" O ALAAl 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAl 177 " --> pdb=" O METAl 173 " (cutoff:3.500A) Processing helix chain 'Am' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAm 95 " --> pdb=" O ASPAm 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUAm 99 " --> pdb=" O GLUAm 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAm 100 " --> pdb=" O ALAAm 96 " (cutoff:3.500A) Processing helix chain 'Am' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAm 112 " --> pdb=" O METAm 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAm 114 " --> pdb=" O THRAm 110 " (cutoff:3.500A) removed outlier: 3.764A 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 178 removed outlier: 3.525A pdb=" N ALAAm 169 " --> pdb=" O ASPAm 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAm 173 " --> pdb=" O ALAAm 169 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYSAm 177 " --> pdb=" O METAm 173 " (cutoff:3.500A) Processing helix chain 'An' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAn 99 " --> pdb=" O GLUAn 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAn 100 " --> pdb=" O ALAAn 96 " (cutoff:3.500A) Processing helix chain 'An' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAn 111 " --> pdb=" O GLUAn 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAn 112 " --> pdb=" O METAn 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAn 114 " --> pdb=" O THRAn 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAn 121 " --> pdb=" O VALAn 117 " (cutoff:3.500A) Processing helix chain 'An' and resid 145 through 151 Processing helix chain 'An' and resid 155 through 161 Processing helix chain 'An' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAn 169 " --> pdb=" O ASPAn 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAn 173 " --> pdb=" O ALAAn 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAn 177 " --> pdb=" O METAn 173 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAo 99 " --> pdb=" O GLUAo 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAo 100 " --> pdb=" O ALAAo 96 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N METAo 112 " --> pdb=" O METAo 108 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLYAo 114 " --> pdb=" O THRAo 110 " (cutoff:3.500A) removed outlier: 3.763A 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 178 removed outlier: 3.525A pdb=" N ALAAo 169 " --> pdb=" O ASPAo 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAo 173 " --> pdb=" O ALAAo 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAo 177 " --> pdb=" O METAo 173 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAp 99 " --> pdb=" O GLUAp 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAp 100 " --> pdb=" O ALAAp 96 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAp 111 " --> pdb=" O GLUAp 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N METAp 112 " --> pdb=" O METAp 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAp 114 " --> pdb=" O THRAp 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAp 121 " --> pdb=" O VALAp 117 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 145 through 151 Processing helix chain 'Ap' and resid 155 through 161 Processing helix chain 'Ap' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAp 169 " --> pdb=" O ASPAp 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAp 173 " --> pdb=" O ALAAp 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAp 177 " --> pdb=" O METAp 173 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 86 through 102 removed outlier: 3.512A pdb=" N LEUAq 99 " --> pdb=" O GLUAq 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAq 100 " --> pdb=" O ALAAq 96 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAq 111 " --> pdb=" O GLUAq 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAq 112 " --> pdb=" O METAq 108 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLYAq 114 " --> pdb=" O THRAq 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAq 121 " --> pdb=" O VALAq 117 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 145 through 151 Processing helix chain 'Aq' and resid 155 through 161 Processing helix chain 'Aq' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAq 169 " --> pdb=" O ASPAq 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAq 173 " --> pdb=" O ALAAq 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAq 177 " --> pdb=" O METAq 173 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAr 95 " --> pdb=" O ASPAr 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUAr 99 " --> pdb=" O GLUAr 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAr 100 " --> pdb=" O ALAAr 96 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAr 111 " --> pdb=" O GLUAr 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N METAr 112 " --> pdb=" O METAr 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAr 114 " --> pdb=" O THRAr 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAr 121 " --> pdb=" O VALAr 117 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 145 through 151 Processing helix chain 'Ar' and resid 155 through 161 Processing helix chain 'Ar' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAr 169 " --> pdb=" O ASPAr 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAr 173 " --> pdb=" O ALAAr 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAr 177 " --> pdb=" O METAr 173 " (cutoff:3.500A) Processing helix chain 'As' and resid 86 through 102 removed outlier: 3.512A pdb=" N LEUAs 99 " --> pdb=" O GLUAs 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAs 100 " --> pdb=" O ALAAs 96 " (cutoff:3.500A) Processing helix chain 'As' and resid 107 through 122 removed outlier: 4.024A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAs 112 " --> pdb=" O METAs 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAs 114 " --> pdb=" O THRAs 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAs 121 " --> pdb=" O VALAs 117 " (cutoff:3.500A) Processing helix chain 'As' and resid 145 through 151 Processing helix chain 'As' and resid 155 through 161 Processing helix chain 'As' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAs 169 " --> pdb=" O ASPAs 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAs 173 " --> pdb=" O ALAAs 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAs 177 " --> pdb=" O METAs 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'Aa' and resid 131 through 133 Processing sheet with id=AA3, first strand: chain 'Ab' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'Ab' and resid 131 through 133 Processing sheet with id=AA5, first strand: chain 'Ac' and resid 58 through 59 Processing sheet with id=AA6, first strand: chain 'Ac' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'Ad' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'Ad' and resid 131 through 133 Processing sheet with id=AA9, first strand: chain 'Ae' and resid 58 through 59 Processing sheet with id=AB1, first strand: chain 'Ae' and resid 131 through 133 Processing sheet with id=AB2, first strand: chain 'Af' and resid 58 through 59 Processing sheet with id=AB3, first strand: chain 'Af' and resid 131 through 133 Processing sheet with id=AB4, first strand: chain 'Ag' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'Ag' and resid 131 through 133 Processing sheet with id=AB6, first strand: chain 'Ah' and resid 58 through 59 Processing sheet with id=AB7, first strand: chain 'Ah' and resid 131 through 133 Processing sheet with id=AB8, first strand: chain 'Ai' and resid 58 through 59 Processing sheet with id=AB9, first strand: chain 'Ai' and resid 131 through 133 Processing sheet with id=AC1, first strand: chain 'Aj' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'Aj' and resid 131 through 133 Processing sheet with id=AC3, first strand: chain 'Ak' and resid 58 through 59 Processing sheet with id=AC4, first strand: chain 'Ak' and resid 131 through 133 Processing sheet with id=AC5, first strand: chain 'Al' and resid 58 through 59 Processing sheet with id=AC6, first strand: chain 'Al' and resid 131 through 133 Processing sheet with id=AC7, first strand: chain 'Am' and resid 58 through 59 Processing sheet with id=AC8, first strand: chain 'Am' and resid 131 through 133 Processing sheet with id=AC9, first strand: chain 'An' and resid 58 through 59 Processing sheet with id=AD1, first strand: chain 'An' and resid 131 through 133 Processing sheet with id=AD2, first strand: chain 'Ao' and resid 58 through 59 Processing sheet with id=AD3, first strand: chain 'Ao' and resid 131 through 133 Processing sheet with id=AD4, first strand: chain 'Ap' and resid 58 through 59 Processing sheet with id=AD5, first strand: chain 'Ap' and resid 131 through 133 Processing sheet with id=AD6, first strand: chain 'Aq' and resid 58 through 59 Processing sheet with id=AD7, first strand: chain 'Aq' and resid 131 through 133 Processing sheet with id=AD8, first strand: chain 'Ar' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'Ar' and resid 131 through 133 Processing sheet with id=AE1, first strand: chain 'As' and resid 58 through 59 Processing sheet with id=AE2, first strand: chain 'As' and resid 131 through 133 713 hydrogen bonds defined for protein. 2082 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: 3.18 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7144 1.34 - 1.46: 3921 1.46 - 1.58: 11108 1.58 - 1.69: 0 1.69 - 1.81: 399 Bond restraints: 22572 Sorted by residual: bond pdb=" C HISAh 69 " pdb=" N LEUAh 70 " ideal model delta sigma weight residual 1.335 1.275 0.060 1.36e-02 5.41e+03 1.91e+01 bond pdb=" C HISAp 69 " pdb=" N LEUAp 70 " ideal model delta sigma weight residual 1.335 1.276 0.059 1.36e-02 5.41e+03 1.90e+01 bond pdb=" C HISAq 69 " pdb=" N LEUAq 70 " ideal model delta sigma weight residual 1.335 1.276 0.059 1.36e-02 5.41e+03 1.90e+01 bond pdb=" C HISAg 69 " pdb=" N LEUAg 70 " ideal model delta sigma weight residual 1.335 1.276 0.059 1.36e-02 5.41e+03 1.90e+01 bond pdb=" C HISAe 69 " pdb=" N LEUAe 70 " ideal model delta sigma weight residual 1.335 1.276 0.059 1.36e-02 5.41e+03 1.89e+01 ... (remaining 22567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 29903 1.67 - 3.35: 573 3.35 - 5.02: 114 5.02 - 6.70: 19 6.70 - 8.37: 38 Bond angle restraints: 30647 Sorted by residual: angle pdb=" CA PROAp 109 " pdb=" N PROAp 109 " pdb=" CD PROAp 109 " ideal model delta sigma weight residual 112.00 107.73 4.27 1.40e+00 5.10e-01 9.30e+00 angle pdb=" CA PROAg 109 " pdb=" N PROAg 109 " pdb=" CD PROAg 109 " ideal model delta sigma weight residual 112.00 107.74 4.26 1.40e+00 5.10e-01 9.25e+00 angle pdb=" CA PROAe 109 " pdb=" N PROAe 109 " pdb=" CD PROAe 109 " ideal model delta sigma weight residual 112.00 107.75 4.25 1.40e+00 5.10e-01 9.23e+00 angle pdb=" CA PROAr 109 " pdb=" N PROAr 109 " pdb=" CD PROAr 109 " ideal model delta sigma weight residual 112.00 107.75 4.25 1.40e+00 5.10e-01 9.21e+00 angle pdb=" CA PROAb 109 " pdb=" N PROAb 109 " pdb=" CD PROAb 109 " ideal model delta sigma weight residual 112.00 107.76 4.24 1.40e+00 5.10e-01 9.19e+00 ... (remaining 30642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 11942 16.83 - 33.66: 1358 33.66 - 50.48: 399 50.48 - 67.31: 114 67.31 - 84.14: 38 Dihedral angle restraints: 13851 sinusoidal: 5738 harmonic: 8113 Sorted by residual: dihedral pdb=" CA METAs 135 " pdb=" C METAs 135 " pdb=" N ASPAs 136 " pdb=" CA ASPAs 136 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA METAi 135 " pdb=" C METAi 135 " pdb=" N ASPAi 136 " pdb=" CA ASPAi 136 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA METAe 135 " pdb=" C METAe 135 " pdb=" N ASPAe 136 " pdb=" CA ASPAe 136 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 13848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1783 0.025 - 0.051: 932 0.051 - 0.076: 484 0.076 - 0.101: 123 0.101 - 0.126: 41 Chirality restraints: 3363 Sorted by residual: chirality pdb=" CA PROAe 109 " pdb=" N PROAe 109 " pdb=" C PROAe 109 " pdb=" CB PROAe 109 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA PROAr 109 " pdb=" N PROAr 109 " pdb=" C PROAr 109 " pdb=" CB PROAr 109 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA PROAd 109 " pdb=" N PROAd 109 " pdb=" C PROAd 109 " pdb=" CB PROAd 109 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 3360 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C METAi 108 " -0.045 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PROAi 109 " 0.114 5.00e-02 4.00e+02 pdb=" CA PROAi 109 " -0.032 5.00e-02 4.00e+02 pdb=" CD PROAi 109 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C METAg 108 " -0.045 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PROAg 109 " 0.114 5.00e-02 4.00e+02 pdb=" CA PROAg 109 " -0.032 5.00e-02 4.00e+02 pdb=" CD PROAg 109 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C METAo 108 " -0.045 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PROAo 109 " 0.114 5.00e-02 4.00e+02 pdb=" CA PROAo 109 " -0.032 5.00e-02 4.00e+02 pdb=" CD PROAo 109 " -0.037 5.00e-02 4.00e+02 ... (remaining 3949 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 7415 2.84 - 3.36: 20233 3.36 - 3.87: 34832 3.87 - 4.39: 40205 4.39 - 4.90: 68634 Nonbonded interactions: 171319 Sorted by model distance: nonbonded pdb=" O PROAi 45 " pdb=" OH TYRAs 143 " model vdw 2.329 3.040 nonbonded pdb=" OH TYRAc 143 " pdb=" O PROAg 45 " model vdw 2.347 3.040 nonbonded pdb=" O PROAa 45 " pdb=" OH TYRAf 143 " model vdw 2.355 3.040 nonbonded pdb=" O PROAj 45 " pdb=" OH TYRAo 143 " model vdw 2.355 3.040 nonbonded pdb=" OH TYRAe 143 " pdb=" O PROAl 45 " model vdw 2.355 3.040 ... (remaining 171314 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: 0.04 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' } 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=0.00 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: 2.290 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 14.690 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22572 Z= 0.214 Angle : 0.645 8.372 30647 Z= 0.340 Chirality : 0.039 0.126 3363 Planarity : 0.007 0.066 3952 Dihedral : 16.696 84.139 8607 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.78 % Allowed : 19.53 % Favored : 79.69 % 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 aren not related in a simple way. whole: -2.73 (0.14), residues: 2717 helix: -1.77 (0.15), residues: 969 sheet: 0.07 (0.30), residues: 228 loop : -2.18 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAr 55 TYR 0.007 0.001 TYRAr 73 PHE 0.003 0.001 PHEAj 90 TRP 0.008 0.001 TRPAi 93 HIS 0.002 0.001 HISAg 42 Details of bonding type rmsd covalent geometry : bond 0.00390 (22572) covalent geometry : angle 0.64500 (30647) hydrogen bonds : bond 0.28545 ( 713) hydrogen bonds : angle 9.21184 ( 2082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 733 time to evaluate : 0.663 Fit side-chains REVERT: Aa 56 MET cc_start: 0.8579 (mmm) cc_final: 0.8370 (tpp) REVERT: Aa 77 GLN cc_start: 0.8383 (mt0) cc_final: 0.8100 (mp10) REVERT: Aa 107 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7894 (pt0) REVERT: Aa 108 MET cc_start: 0.8638 (tpt) cc_final: 0.8234 (tpt) REVERT: Ab 56 MET cc_start: 0.8533 (mmm) cc_final: 0.8149 (mmm) REVERT: Ac 150 GLU cc_start: 0.8341 (tt0) cc_final: 0.7898 (pt0) REVERT: Ad 46 ARG cc_start: 0.8983 (mtt90) cc_final: 0.8647 (mtt-85) REVERT: Ad 48 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8561 (mttp) REVERT: Ad 56 MET cc_start: 0.8588 (mmm) cc_final: 0.8161 (mmm) REVERT: Ad 77 GLN cc_start: 0.8404 (mt0) cc_final: 0.7987 (mp10) REVERT: Ae 76 GLN cc_start: 0.8076 (mp10) cc_final: 0.7718 (mp10) REVERT: Ae 107 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7978 (pt0) REVERT: Ae 160 MET cc_start: 0.9151 (mmt) cc_final: 0.8870 (mmm) REVERT: Af 55 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.6888 (mtm180) REVERT: Af 56 MET cc_start: 0.8603 (mmm) cc_final: 0.8283 (mmm) REVERT: Af 76 GLN cc_start: 0.8237 (mp10) cc_final: 0.8015 (mp10) REVERT: Af 150 GLU cc_start: 0.8282 (tt0) cc_final: 0.7942 (tt0) REVERT: Ag 76 GLN cc_start: 0.8129 (mp10) cc_final: 0.7802 (mp10) REVERT: Ag 150 GLU cc_start: 0.8230 (tt0) cc_final: 0.7911 (tt0) REVERT: Ag 160 MET cc_start: 0.9179 (mmt) cc_final: 0.8977 (mmm) REVERT: Ah 56 MET cc_start: 0.8515 (mmm) cc_final: 0.8271 (tpp) REVERT: Ah 150 GLU cc_start: 0.8348 (tt0) cc_final: 0.7978 (tt0) REVERT: Ai 56 MET cc_start: 0.8491 (mmm) cc_final: 0.8173 (mmm) REVERT: Ai 150 GLU cc_start: 0.8329 (tt0) cc_final: 0.7891 (pt0) REVERT: Aj 56 MET cc_start: 0.8570 (mmm) cc_final: 0.8360 (tpp) REVERT: Aj 58 LYS cc_start: 0.8576 (mttp) cc_final: 0.8276 (mtpt) REVERT: Aj 63 THR cc_start: 0.8439 (m) cc_final: 0.8225 (t) REVERT: Aj 108 MET cc_start: 0.8586 (tpt) cc_final: 0.8298 (tpt) REVERT: Aj 150 GLU cc_start: 0.8308 (tt0) cc_final: 0.7937 (tt0) REVERT: Ak 91 ASP cc_start: 0.8500 (m-30) cc_final: 0.8282 (m-30) REVERT: Ak 168 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8020 (mm-30) REVERT: Al 135 MET cc_start: 0.8515 (mmm) cc_final: 0.8193 (mmm) REVERT: Am 56 MET cc_start: 0.8705 (mmm) cc_final: 0.8263 (mmm) REVERT: Am 91 ASP cc_start: 0.8483 (m-30) cc_final: 0.8086 (m-30) REVERT: Am 107 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7949 (pt0) REVERT: An 56 MET cc_start: 0.8760 (mmm) cc_final: 0.8469 (tpp) REVERT: An 77 GLN cc_start: 0.8343 (mt0) cc_final: 0.8091 (mp10) REVERT: An 107 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7880 (pt0) REVERT: Ao 56 MET cc_start: 0.8575 (mmm) cc_final: 0.8217 (mmm) REVERT: Ao 77 GLN cc_start: 0.8444 (mt0) cc_final: 0.8134 (mp10) REVERT: Ao 91 ASP cc_start: 0.8500 (m-30) cc_final: 0.8297 (m-30) REVERT: Ap 58 LYS cc_start: 0.8608 (mttp) cc_final: 0.8396 (mttm) REVERT: Ap 66 ASN cc_start: 0.8585 (t0) cc_final: 0.7967 (t0) REVERT: Ap 135 MET cc_start: 0.8411 (mmm) cc_final: 0.8076 (mmm) REVERT: Ap 150 GLU cc_start: 0.8225 (tt0) cc_final: 0.7720 (pt0) REVERT: Aq 56 MET cc_start: 0.8589 (mmm) cc_final: 0.8330 (tpp) REVERT: Aq 150 GLU cc_start: 0.8318 (tt0) cc_final: 0.7892 (tt0) REVERT: Ar 56 MET cc_start: 0.8559 (mmm) cc_final: 0.8306 (mmm) REVERT: Ar 107 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7905 (pt0) REVERT: Ar 150 GLU cc_start: 0.8444 (tt0) cc_final: 0.8227 (tt0) REVERT: As 56 MET cc_start: 0.8565 (mmm) cc_final: 0.8271 (mmm) REVERT: As 77 GLN cc_start: 0.8369 (mt0) cc_final: 0.8110 (mp10) REVERT: As 91 ASP cc_start: 0.8516 (m-30) cc_final: 0.8278 (m-30) outliers start: 19 outliers final: 3 residues processed: 733 average time/residue: 0.1563 time to fit residues: 166.4787 Evaluate side-chains 615 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 611 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 48 LYS Chi-restraints excluded: chain Ad residue 48 LYS Chi-restraints excluded: chain Ae residue 48 LYS Chi-restraints excluded: chain Al residue 48 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 140 GLN Ad 69 HIS ** Ad 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 69 HIS ** Ae 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 140 GLN ** Ag 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 69 HIS ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 69 HIS Ah 113 ASN Ai 69 HIS ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS ** Aj 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 69 HIS ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 140 GLN Am 69 HIS ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 69 HIS ** An 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 69 HIS ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 69 HIS Ap 77 GLN ** Ap 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 140 GLN Aq 69 HIS Aq 77 GLN ** Aq 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 66 ASN ** As 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114204 restraints weight = 27831.426| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.92 r_work: 0.3128 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22572 Z= 0.125 Angle : 0.536 5.481 30647 Z= 0.272 Chirality : 0.040 0.124 3363 Planarity : 0.005 0.034 3952 Dihedral : 4.901 36.226 2999 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.56 % Allowed : 17.80 % Favored : 80.63 % 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 aren not related in a simple way. whole: -1.85 (0.15), residues: 2717 helix: -0.27 (0.15), residues: 1064 sheet: 0.12 (0.30), residues: 228 loop : -2.29 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAj 46 TYR 0.013 0.001 TYRAh 94 PHE 0.002 0.000 PHEAl 90 TRP 0.010 0.002 TRPAo 93 HIS 0.008 0.001 HISAk 69 Details of bonding type rmsd covalent geometry : bond 0.00302 (22572) covalent geometry : angle 0.53597 (30647) hydrogen bonds : bond 0.04359 ( 713) hydrogen bonds : angle 5.65436 ( 2082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 623 time to evaluate : 0.876 Fit side-chains REVERT: Aa 56 MET cc_start: 0.8698 (mmm) cc_final: 0.8433 (tpp) REVERT: Aa 77 GLN cc_start: 0.8656 (mt0) cc_final: 0.8220 (mp10) REVERT: Aa 107 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8050 (pt0) REVERT: Aa 173 MET cc_start: 0.7230 (tmm) cc_final: 0.6870 (tmm) REVERT: Ab 56 MET cc_start: 0.8603 (mmm) cc_final: 0.8333 (mmm) REVERT: Ab 95 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: Ab 181 MET cc_start: 0.6632 (tmm) cc_final: 0.6327 (tmm) REVERT: Ac 56 MET cc_start: 0.8772 (mmm) cc_final: 0.8515 (tpp) REVERT: Ac 95 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8323 (mm-30) REVERT: Ac 173 MET cc_start: 0.6950 (tmm) cc_final: 0.6718 (tmm) REVERT: Ad 56 MET cc_start: 0.8703 (mmm) cc_final: 0.8440 (tpp) REVERT: Ad 77 GLN cc_start: 0.8625 (mt0) cc_final: 0.8126 (mp10) REVERT: Ad 136 ASP cc_start: 0.8552 (t0) cc_final: 0.8251 (t0) REVERT: Ae 76 GLN cc_start: 0.8095 (mp10) cc_final: 0.7718 (mp10) REVERT: Ae 107 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8295 (pt0) REVERT: Ae 160 MET cc_start: 0.9148 (mmt) cc_final: 0.8939 (mmm) REVERT: Ae 181 MET cc_start: 0.6720 (tmm) cc_final: 0.6433 (tmm) REVERT: Af 55 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.7161 (mtm180) REVERT: Af 56 MET cc_start: 0.8666 (mmm) cc_final: 0.8440 (tpp) REVERT: Af 150 GLU cc_start: 0.8312 (tt0) cc_final: 0.8062 (pt0) REVERT: Ag 76 GLN cc_start: 0.8106 (mp10) cc_final: 0.7829 (mp10) REVERT: Ag 160 MET cc_start: 0.9198 (mmt) cc_final: 0.8993 (mmm) REVERT: Ah 56 MET cc_start: 0.8600 (mmm) cc_final: 0.8357 (tpp) REVERT: Ah 91 ASP cc_start: 0.8527 (m-30) cc_final: 0.8295 (m-30) REVERT: Ah 150 GLU cc_start: 0.8411 (tt0) cc_final: 0.8069 (pt0) REVERT: Ah 181 MET cc_start: 0.6840 (tmm) cc_final: 0.6579 (tmm) REVERT: Ai 56 MET cc_start: 0.8597 (mmm) cc_final: 0.8382 (mmm) REVERT: Ai 136 ASP cc_start: 0.8565 (t0) cc_final: 0.8346 (t0) REVERT: Aj 58 LYS cc_start: 0.8923 (mttp) cc_final: 0.8643 (mtpt) REVERT: Aj 95 GLU cc_start: 0.8750 (tp30) cc_final: 0.8202 (mm-30) REVERT: Aj 150 GLU cc_start: 0.8456 (tt0) cc_final: 0.8125 (pt0) REVERT: Ak 95 GLU cc_start: 0.8710 (tp30) cc_final: 0.8427 (mm-30) REVERT: Ak 150 GLU cc_start: 0.8344 (tt0) cc_final: 0.8075 (pt0) REVERT: Ak 160 MET cc_start: 0.9153 (mmt) cc_final: 0.8944 (mmm) REVERT: Al 108 MET cc_start: 0.8857 (tpt) cc_final: 0.8645 (tpt) REVERT: Al 135 MET cc_start: 0.8812 (mmm) cc_final: 0.8524 (mmm) REVERT: Al 150 GLU cc_start: 0.8391 (tt0) cc_final: 0.8123 (pt0) REVERT: Al 181 MET cc_start: 0.7353 (tpp) cc_final: 0.6892 (tmm) REVERT: Am 56 MET cc_start: 0.8830 (mmm) cc_final: 0.8604 (mmm) REVERT: Am 91 ASP cc_start: 0.8465 (m-30) cc_final: 0.8128 (m-30) REVERT: Am 95 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: An 56 MET cc_start: 0.8766 (mmm) cc_final: 0.8475 (tpp) REVERT: An 77 GLN cc_start: 0.8642 (mt0) cc_final: 0.8123 (mp10) REVERT: An 95 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8335 (mm-30) REVERT: An 107 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8112 (pt0) REVERT: An 150 GLU cc_start: 0.8691 (tt0) cc_final: 0.8341 (tt0) REVERT: An 181 MET cc_start: 0.7317 (tpp) cc_final: 0.6805 (tmm) REVERT: Ao 56 MET cc_start: 0.8667 (mmm) cc_final: 0.8435 (mmm) REVERT: Ao 58 LYS cc_start: 0.9035 (mttm) cc_final: 0.8823 (mttm) REVERT: Ao 77 GLN cc_start: 0.8714 (mt0) cc_final: 0.8231 (mp10) REVERT: Ao 173 MET cc_start: 0.7143 (tmm) cc_final: 0.6920 (tmm) REVERT: Ap 58 LYS cc_start: 0.8977 (mttp) cc_final: 0.8771 (mttm) REVERT: Ap 66 ASN cc_start: 0.8794 (t0) cc_final: 0.7916 (t0) REVERT: Ap 135 MET cc_start: 0.8811 (mmm) cc_final: 0.8553 (mmm) REVERT: Aq 56 MET cc_start: 0.8655 (mmm) cc_final: 0.8412 (tpp) REVERT: Aq 107 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: Aq 136 ASP cc_start: 0.8535 (t0) cc_final: 0.8205 (t0) REVERT: Ar 56 MET cc_start: 0.8727 (mmm) cc_final: 0.8494 (tpp) REVERT: Ar 95 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: As 56 MET cc_start: 0.8654 (mmm) cc_final: 0.8406 (tpp) REVERT: As 77 GLN cc_start: 0.8630 (mt0) cc_final: 0.8191 (mp10) REVERT: As 173 MET cc_start: 0.6975 (tmm) cc_final: 0.6761 (tmm) REVERT: As 181 MET cc_start: 0.6699 (tmm) cc_final: 0.6319 (tmm) outliers start: 38 outliers final: 21 residues processed: 648 average time/residue: 0.1618 time to fit residues: 153.8910 Evaluate side-chains 613 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 586 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 95 GLU Chi-restraints excluded: chain Ab residue 107 GLU Chi-restraints excluded: chain Ac residue 48 LYS Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 110 THR Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 110 THR Chi-restraints excluded: chain Af residue 110 THR Chi-restraints excluded: chain Ag residue 110 THR Chi-restraints excluded: chain Ah residue 110 THR Chi-restraints excluded: chain Ai residue 110 THR Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Aj residue 110 THR Chi-restraints excluded: chain Ak residue 107 GLU Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 107 GLU Chi-restraints excluded: chain Am residue 95 GLU Chi-restraints excluded: chain Am residue 110 THR Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 110 THR Chi-restraints excluded: chain Ao residue 103 ILE Chi-restraints excluded: chain Ap residue 77 GLN Chi-restraints excluded: chain Ap residue 107 GLU Chi-restraints excluded: chain Aq residue 77 GLN Chi-restraints excluded: chain Aq residue 107 GLU Chi-restraints excluded: chain Aq residue 110 THR Chi-restraints excluded: chain Ar residue 95 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 4 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 227 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 169 optimal weight: 0.0670 chunk 195 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 69 HIS ** Ab 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 151 ASN Ac 113 ASN Ad 69 HIS Ad 113 ASN Ae 69 HIS Ae 113 ASN Ae 151 ASN Af 69 HIS Af 113 ASN ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 69 HIS Ag 77 GLN Ag 113 ASN ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 151 ASN Ai 69 HIS ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS Aj 113 ASN ** Aj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 69 HIS Ak 113 ASN ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 113 ASN Am 69 HIS ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 66 ASN An 69 HIS An 113 ASN ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 69 HIS Ap 113 ASN Aq 69 HIS Aq 113 ASN ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 113 ASN ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 69 HIS As 113 ASN ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108077 restraints weight = 28093.859| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.86 r_work: 0.3074 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22572 Z= 0.163 Angle : 0.537 5.387 30647 Z= 0.269 Chirality : 0.041 0.125 3363 Planarity : 0.004 0.028 3952 Dihedral : 4.479 17.888 2983 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.30 % Allowed : 18.01 % Favored : 79.69 % 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 aren not related in a simple way. whole: -1.71 (0.15), residues: 2717 helix: 0.07 (0.15), residues: 1007 sheet: 0.43 (0.30), residues: 228 loop : -2.38 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAh 55 TYR 0.014 0.002 TYRAo 180 PHE 0.003 0.001 PHEAo 163 TRP 0.010 0.002 TRPAe 93 HIS 0.006 0.001 HISAf 69 Details of bonding type rmsd covalent geometry : bond 0.00400 (22572) covalent geometry : angle 0.53700 (30647) hydrogen bonds : bond 0.04368 ( 713) hydrogen bonds : angle 5.21197 ( 2082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 589 time to evaluate : 0.882 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8684 (mt0) cc_final: 0.8187 (mp10) REVERT: Aa 173 MET cc_start: 0.7399 (tmm) cc_final: 0.7048 (tmm) REVERT: Aa 181 MET cc_start: 0.7250 (tpp) cc_final: 0.6605 (tmm) REVERT: Ab 56 MET cc_start: 0.8598 (mmm) cc_final: 0.8267 (mmm) REVERT: Ab 66 ASN cc_start: 0.8799 (t0) cc_final: 0.8154 (t0) REVERT: Ab 173 MET cc_start: 0.7303 (tmm) cc_final: 0.6972 (tmm) REVERT: Ab 181 MET cc_start: 0.6605 (tmm) cc_final: 0.6282 (tmm) REVERT: Ac 95 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8297 (mm-30) REVERT: Ac 142 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8334 (mt-10) REVERT: Ac 150 GLU cc_start: 0.8487 (tt0) cc_final: 0.8105 (pt0) REVERT: Ac 173 MET cc_start: 0.7093 (tmm) cc_final: 0.6755 (tmm) REVERT: Ac 181 MET cc_start: 0.7375 (tpp) cc_final: 0.6826 (tmm) REVERT: Ad 136 ASP cc_start: 0.8625 (t0) cc_final: 0.8310 (t0) REVERT: Ad 181 MET cc_start: 0.7176 (tpp) cc_final: 0.6560 (tmm) REVERT: Ae 76 GLN cc_start: 0.8042 (mp10) cc_final: 0.7669 (mp10) REVERT: Ae 181 MET cc_start: 0.6769 (tmm) cc_final: 0.6467 (tmm) REVERT: Af 55 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7065 (mtm180) REVERT: Af 56 MET cc_start: 0.8753 (mmm) cc_final: 0.8443 (mmm) REVERT: Af 67 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8744 (tt) REVERT: Af 181 MET cc_start: 0.7203 (tpp) cc_final: 0.6654 (tmm) REVERT: Ag 76 GLN cc_start: 0.8102 (mp10) cc_final: 0.7878 (mp10) REVERT: Ag 181 MET cc_start: 0.7109 (tpp) cc_final: 0.6499 (tmm) REVERT: Ah 56 MET cc_start: 0.8722 (mmm) cc_final: 0.8374 (tpp) REVERT: Ah 91 ASP cc_start: 0.8579 (m-30) cc_final: 0.8327 (m-30) REVERT: Ah 181 MET cc_start: 0.6771 (tmm) cc_final: 0.6461 (tmm) REVERT: Ai 56 MET cc_start: 0.8597 (mmm) cc_final: 0.8340 (mmm) REVERT: Ai 136 ASP cc_start: 0.8547 (t0) cc_final: 0.8268 (t0) REVERT: Ai 181 MET cc_start: 0.7210 (tpp) cc_final: 0.6615 (tmm) REVERT: Aj 58 LYS cc_start: 0.8964 (mttp) cc_final: 0.8655 (mtpt) REVERT: Aj 181 MET cc_start: 0.7346 (tpp) cc_final: 0.6767 (tmm) REVERT: Ak 56 MET cc_start: 0.8500 (mmm) cc_final: 0.8140 (tpp) REVERT: Ak 95 GLU cc_start: 0.8715 (tp30) cc_final: 0.8418 (mm-30) REVERT: Ak 150 GLU cc_start: 0.8441 (tt0) cc_final: 0.8079 (pt0) REVERT: Ak 160 MET cc_start: 0.9146 (mmt) cc_final: 0.8931 (mmm) REVERT: Ak 181 MET cc_start: 0.7172 (tpp) cc_final: 0.6676 (tmm) REVERT: Al 136 ASP cc_start: 0.8524 (t0) cc_final: 0.8304 (t0) REVERT: Al 173 MET cc_start: 0.7314 (tmm) cc_final: 0.6807 (tmm) REVERT: Al 181 MET cc_start: 0.7276 (tpp) cc_final: 0.6829 (tmm) REVERT: Am 56 MET cc_start: 0.8889 (mmm) cc_final: 0.8506 (mmm) REVERT: Am 91 ASP cc_start: 0.8542 (m-30) cc_final: 0.8304 (m-30) REVERT: Am 181 MET cc_start: 0.6705 (tmm) cc_final: 0.6374 (tmm) REVERT: An 56 MET cc_start: 0.8718 (mmm) cc_final: 0.8340 (tpp) REVERT: An 77 GLN cc_start: 0.8649 (mt0) cc_final: 0.8185 (mp10) REVERT: An 95 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8412 (mm-30) REVERT: An 173 MET cc_start: 0.7153 (tmm) cc_final: 0.6744 (tmm) REVERT: An 181 MET cc_start: 0.7236 (tpp) cc_final: 0.6728 (tmm) REVERT: Ao 77 GLN cc_start: 0.8724 (mt0) cc_final: 0.8221 (mp10) REVERT: Ao 142 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8272 (mt-10) REVERT: Ao 150 GLU cc_start: 0.8534 (tt0) cc_final: 0.8237 (tt0) REVERT: Ao 173 MET cc_start: 0.7208 (tmm) cc_final: 0.6911 (tmm) REVERT: Ao 181 MET cc_start: 0.7147 (tpp) cc_final: 0.6607 (tmm) REVERT: Ap 66 ASN cc_start: 0.8873 (t0) cc_final: 0.8485 (t0) REVERT: Ap 136 ASP cc_start: 0.8598 (t0) cc_final: 0.8373 (t0) REVERT: Ap 173 MET cc_start: 0.7293 (tmm) cc_final: 0.7032 (tmm) REVERT: Ap 181 MET cc_start: 0.7187 (tpp) cc_final: 0.6527 (tmm) REVERT: Aq 56 MET cc_start: 0.8698 (mmm) cc_final: 0.8305 (tpp) REVERT: Aq 136 ASP cc_start: 0.8620 (t0) cc_final: 0.8244 (t0) REVERT: Aq 160 MET cc_start: 0.9294 (mmp) cc_final: 0.9015 (mmm) REVERT: Aq 181 MET cc_start: 0.7260 (tpp) cc_final: 0.6687 (tmm) REVERT: Ar 66 ASN cc_start: 0.8733 (t0) cc_final: 0.8495 (t0) REVERT: Ar 107 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7978 (pt0) REVERT: Ar 150 GLU cc_start: 0.8617 (tt0) cc_final: 0.8247 (pt0) REVERT: Ar 181 MET cc_start: 0.7121 (tpp) cc_final: 0.6701 (tmm) REVERT: As 56 MET cc_start: 0.8655 (mmm) cc_final: 0.8275 (tpp) REVERT: As 77 GLN cc_start: 0.8688 (mt0) cc_final: 0.8180 (mp10) REVERT: As 121 GLU cc_start: 0.7308 (mp0) cc_final: 0.6892 (mp0) REVERT: As 173 MET cc_start: 0.7145 (tmm) cc_final: 0.6843 (tmm) REVERT: As 181 MET cc_start: 0.6657 (tmm) cc_final: 0.6299 (tmm) outliers start: 56 outliers final: 28 residues processed: 615 average time/residue: 0.1712 time to fit residues: 156.0238 Evaluate side-chains 579 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 548 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 110 THR Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Af residue 67 LEU Chi-restraints excluded: chain Af residue 77 GLN Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 110 THR Chi-restraints excluded: chain Ag residue 77 GLN Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 110 THR Chi-restraints excluded: chain Ah residue 110 THR Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Aj residue 103 ILE Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Aj residue 110 THR Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 110 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 103 ILE Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Aq residue 77 GLN Chi-restraints excluded: chain As residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 185 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** Ab 69 HIS ** Ab 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 69 HIS ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 69 HIS ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS ** Aj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 69 HIS ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 66 ASN ** An 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104002 restraints weight = 28364.487| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.85 r_work: 0.3006 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 22572 Z= 0.289 Angle : 0.638 7.451 30647 Z= 0.315 Chirality : 0.045 0.136 3363 Planarity : 0.004 0.031 3952 Dihedral : 4.734 21.334 2983 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.55 % Allowed : 16.00 % Favored : 81.46 % 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 aren not related in a simple way. whole: -1.58 (0.16), residues: 2717 helix: 0.11 (0.15), residues: 1083 sheet: 0.63 (0.31), residues: 228 loop : -2.39 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAa 55 TYR 0.014 0.002 TYRAd 180 PHE 0.009 0.001 PHEAo 163 TRP 0.013 0.003 TRPAr 93 HIS 0.005 0.001 HISAs 69 Details of bonding type rmsd covalent geometry : bond 0.00707 (22572) covalent geometry : angle 0.63782 (30647) hydrogen bonds : bond 0.04843 ( 713) hydrogen bonds : angle 5.24476 ( 2082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 538 time to evaluate : 0.713 Fit side-chains REVERT: Aa 66 ASN cc_start: 0.9022 (t0) cc_final: 0.8639 (t0) REVERT: Aa 173 MET cc_start: 0.7476 (tmm) cc_final: 0.6936 (tmm) REVERT: Aa 181 MET cc_start: 0.7228 (tpp) cc_final: 0.6530 (tmm) REVERT: Ab 56 MET cc_start: 0.8667 (mmm) cc_final: 0.8343 (mmm) REVERT: Ab 173 MET cc_start: 0.7412 (tmm) cc_final: 0.7056 (tmm) REVERT: Ab 181 MET cc_start: 0.6584 (tmm) cc_final: 0.6239 (tmm) REVERT: Ac 56 MET cc_start: 0.8832 (mmm) cc_final: 0.8504 (mmm) REVERT: Ac 66 ASN cc_start: 0.9022 (t0) cc_final: 0.8381 (t0) REVERT: Ac 134 MET cc_start: 0.8772 (ttp) cc_final: 0.8509 (ttp) REVERT: Ac 173 MET cc_start: 0.7320 (tmm) cc_final: 0.6792 (tmm) REVERT: Ac 181 MET cc_start: 0.7277 (tpp) cc_final: 0.6613 (tmm) REVERT: Ad 76 GLN cc_start: 0.8039 (mp10) cc_final: 0.7656 (mp10) REVERT: Ad 121 GLU cc_start: 0.7670 (mp0) cc_final: 0.7464 (mp0) REVERT: Ad 136 ASP cc_start: 0.8675 (t0) cc_final: 0.8369 (t0) REVERT: Ad 181 MET cc_start: 0.7239 (tpp) cc_final: 0.6665 (tmm) REVERT: Ae 76 GLN cc_start: 0.8063 (mp10) cc_final: 0.7644 (mp10) REVERT: Ae 181 MET cc_start: 0.6718 (tmm) cc_final: 0.6418 (tmm) REVERT: Af 55 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.7000 (mtm180) REVERT: Af 56 MET cc_start: 0.8809 (mmm) cc_final: 0.8485 (mmm) REVERT: Af 67 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8785 (tt) REVERT: Af 181 MET cc_start: 0.7094 (tpp) cc_final: 0.6521 (tmm) REVERT: Ag 56 MET cc_start: 0.8731 (tpp) cc_final: 0.8522 (tpp) REVERT: Ag 76 GLN cc_start: 0.7985 (mp10) cc_final: 0.7649 (mp10) REVERT: Ag 181 MET cc_start: 0.7234 (tpp) cc_final: 0.6536 (tmm) REVERT: Ah 76 GLN cc_start: 0.8085 (mp10) cc_final: 0.7701 (mp10) REVERT: Ah 91 ASP cc_start: 0.8550 (m-30) cc_final: 0.8179 (m-30) REVERT: Ah 95 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: Ah 136 ASP cc_start: 0.8691 (t0) cc_final: 0.8451 (t0) REVERT: Ah 181 MET cc_start: 0.6775 (tmm) cc_final: 0.6388 (tmm) REVERT: Ai 56 MET cc_start: 0.8650 (mmm) cc_final: 0.8444 (mmm) REVERT: Ai 136 ASP cc_start: 0.8608 (t0) cc_final: 0.8333 (t0) REVERT: Ai 181 MET cc_start: 0.7217 (tpp) cc_final: 0.6709 (tmm) REVERT: Aj 58 LYS cc_start: 0.8984 (mttp) cc_final: 0.8665 (mtpt) REVERT: Aj 66 ASN cc_start: 0.8829 (t0) cc_final: 0.8436 (t0) REVERT: Aj 181 MET cc_start: 0.7362 (tpp) cc_final: 0.6803 (tmm) REVERT: Ak 160 MET cc_start: 0.9194 (mmt) cc_final: 0.8973 (mmm) REVERT: Ak 181 MET cc_start: 0.7255 (tpp) cc_final: 0.6671 (tmm) REVERT: Al 136 ASP cc_start: 0.8657 (t0) cc_final: 0.8416 (t0) REVERT: Al 173 MET cc_start: 0.7389 (tmm) cc_final: 0.6981 (tmm) REVERT: Al 181 MET cc_start: 0.7235 (tpp) cc_final: 0.6828 (tmm) REVERT: Am 91 ASP cc_start: 0.8559 (m-30) cc_final: 0.8343 (m-30) REVERT: Am 181 MET cc_start: 0.6716 (tmm) cc_final: 0.6368 (tmm) REVERT: An 56 MET cc_start: 0.8721 (mmm) cc_final: 0.8302 (mmm) REVERT: An 77 GLN cc_start: 0.8745 (mt0) cc_final: 0.8209 (mp10) REVERT: An 95 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8461 (mm-30) REVERT: An 181 MET cc_start: 0.7229 (tpp) cc_final: 0.6705 (tmm) REVERT: Ao 77 GLN cc_start: 0.8754 (mt0) cc_final: 0.8232 (mp10) REVERT: Ao 136 ASP cc_start: 0.8575 (t0) cc_final: 0.8321 (t0) REVERT: Ao 181 MET cc_start: 0.7178 (tpp) cc_final: 0.6680 (tmm) REVERT: Ap 66 ASN cc_start: 0.8876 (t0) cc_final: 0.8526 (t0) REVERT: Ap 173 MET cc_start: 0.7398 (tmm) cc_final: 0.7066 (tmm) REVERT: Ap 181 MET cc_start: 0.7394 (tpp) cc_final: 0.6626 (tmm) REVERT: Aq 56 MET cc_start: 0.8745 (mmm) cc_final: 0.8348 (tpp) REVERT: Aq 181 MET cc_start: 0.7278 (tpp) cc_final: 0.6691 (tmm) REVERT: Ar 95 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: Ar 136 ASP cc_start: 0.8552 (t0) cc_final: 0.8283 (t0) REVERT: Ar 181 MET cc_start: 0.7128 (tpp) cc_final: 0.6560 (tmm) REVERT: As 173 MET cc_start: 0.7336 (tmm) cc_final: 0.6799 (tmm) REVERT: As 181 MET cc_start: 0.6698 (tmm) cc_final: 0.6332 (tmm) outliers start: 62 outliers final: 54 residues processed: 562 average time/residue: 0.1627 time to fit residues: 136.3683 Evaluate side-chains 587 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 529 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ac residue 103 ILE Chi-restraints excluded: chain Ac residue 110 THR Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 103 ILE Chi-restraints excluded: chain Ae residue 110 THR Chi-restraints excluded: chain Af residue 67 LEU Chi-restraints excluded: chain Af residue 77 GLN Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 103 ILE Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Af residue 110 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ag residue 110 THR Chi-restraints excluded: chain Ah residue 92 THR Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 106 THR Chi-restraints excluded: chain Ah residue 110 THR Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Ai residue 110 THR Chi-restraints excluded: chain Aj residue 103 ILE Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Aj residue 110 THR Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 110 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 110 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 103 ILE Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ao residue 119 CYS Chi-restraints excluded: chain Ap residue 103 ILE Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Aq residue 77 GLN Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 106 THR Chi-restraints excluded: chain As residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 255 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 249 optimal weight: 0.0170 chunk 59 optimal weight: 0.0980 chunk 240 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- 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** Ab 69 HIS Ab 113 ASN Ab 151 ASN Af 151 ASN Ag 151 ASN Ai 69 HIS ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS ** Aj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 69 HIS Al 66 ASN ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 151 ASN ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 151 ASN As 66 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.140242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111926 restraints weight = 27925.089| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.88 r_work: 0.3100 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22572 Z= 0.099 Angle : 0.506 8.604 30647 Z= 0.247 Chirality : 0.039 0.119 3363 Planarity : 0.003 0.025 3952 Dihedral : 4.449 21.692 2983 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.36 % Allowed : 17.56 % Favored : 81.09 % 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 aren not related in a simple way. whole: -1.06 (0.16), residues: 2717 helix: 0.74 (0.16), residues: 1026 sheet: 0.90 (0.33), residues: 228 loop : -2.16 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAd 55 TYR 0.016 0.001 TYRAe 180 PHE 0.002 0.000 PHEAg 163 TRP 0.013 0.002 TRPAf 132 HIS 0.004 0.001 HISAb 69 Details of bonding type rmsd covalent geometry : bond 0.00251 (22572) covalent geometry : angle 0.50624 (30647) hydrogen bonds : bond 0.03194 ( 713) hydrogen bonds : angle 4.90471 ( 2082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 564 time to evaluate : 0.679 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8643 (mt0) cc_final: 0.8129 (mp10) REVERT: Aa 107 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8088 (pt0) REVERT: Aa 173 MET cc_start: 0.7440 (tmm) cc_final: 0.7015 (tmm) REVERT: Aa 181 MET cc_start: 0.7180 (tpp) cc_final: 0.6543 (tmm) REVERT: Ab 56 MET cc_start: 0.8585 (mmm) cc_final: 0.8215 (mmm) REVERT: Ab 173 MET cc_start: 0.7304 (tmm) cc_final: 0.6926 (tmm) REVERT: Ab 181 MET cc_start: 0.6592 (tmm) cc_final: 0.6234 (tmm) REVERT: Ac 66 ASN cc_start: 0.8983 (t0) cc_final: 0.8393 (t0) REVERT: Ac 173 MET cc_start: 0.7135 (tmm) cc_final: 0.6728 (tmm) REVERT: Ac 181 MET cc_start: 0.7252 (tpp) cc_final: 0.6796 (tmm) REVERT: Ad 56 MET cc_start: 0.8642 (mmm) cc_final: 0.8374 (tpp) REVERT: Ad 76 GLN cc_start: 0.8013 (mp10) cc_final: 0.7804 (mp10) REVERT: Ad 181 MET cc_start: 0.7268 (tpp) cc_final: 0.6687 (tmm) REVERT: Ae 76 GLN cc_start: 0.7979 (mp10) cc_final: 0.7664 (mp10) REVERT: Ae 107 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8153 (pt0) REVERT: Ae 121 GLU cc_start: 0.7404 (mp0) cc_final: 0.6990 (mt-10) REVERT: Ae 181 MET cc_start: 0.6717 (tmm) cc_final: 0.6401 (tmm) REVERT: Af 55 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.7053 (mtm180) REVERT: Af 56 MET cc_start: 0.8775 (mmm) cc_final: 0.8434 (mmm) REVERT: Af 116 MET cc_start: 0.8824 (ttp) cc_final: 0.8609 (ttp) REVERT: Af 181 MET cc_start: 0.7103 (tpp) cc_final: 0.6571 (tmm) REVERT: Ag 76 GLN cc_start: 0.7980 (mp10) cc_final: 0.7770 (mp10) REVERT: Ag 150 GLU cc_start: 0.8542 (tt0) cc_final: 0.8260 (tt0) REVERT: Ag 181 MET cc_start: 0.7204 (tpp) cc_final: 0.6606 (tmm) REVERT: Ah 76 GLN cc_start: 0.8039 (mp10) cc_final: 0.7745 (mp10) REVERT: Ah 91 ASP cc_start: 0.8509 (m-30) cc_final: 0.8128 (m-30) REVERT: Ah 95 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: Ah 112 MET cc_start: 0.8975 (mmp) cc_final: 0.8703 (mmp) REVERT: Ah 181 MET cc_start: 0.6713 (tmm) cc_final: 0.6353 (tmm) REVERT: Ai 56 MET cc_start: 0.8601 (mmm) cc_final: 0.8373 (mmm) REVERT: Ai 121 GLU cc_start: 0.7362 (mp0) cc_final: 0.7075 (mp0) REVERT: Ai 134 MET cc_start: 0.8668 (ttp) cc_final: 0.8210 (ttp) REVERT: Ai 181 MET cc_start: 0.7138 (tpp) cc_final: 0.6743 (tmm) REVERT: Aj 58 LYS cc_start: 0.8979 (mttp) cc_final: 0.8715 (mtpt) REVERT: Aj 181 MET cc_start: 0.7397 (tpp) cc_final: 0.6792 (tmm) REVERT: Ak 181 MET cc_start: 0.7182 (tpp) cc_final: 0.6692 (tmm) REVERT: Al 173 MET cc_start: 0.7270 (tmm) cc_final: 0.6803 (tmm) REVERT: Al 181 MET cc_start: 0.7174 (tpp) cc_final: 0.6824 (tmm) REVERT: Am 56 MET cc_start: 0.8865 (mmm) cc_final: 0.8595 (mmm) REVERT: Am 181 MET cc_start: 0.6666 (tmm) cc_final: 0.6340 (tmm) REVERT: An 56 MET cc_start: 0.8703 (mmm) cc_final: 0.8292 (tpp) REVERT: An 77 GLN cc_start: 0.8577 (mt0) cc_final: 0.8060 (mp10) REVERT: An 107 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: An 181 MET cc_start: 0.7211 (tpp) cc_final: 0.6741 (tmm) REVERT: Ao 77 GLN cc_start: 0.8680 (mt0) cc_final: 0.8116 (mp10) REVERT: Ao 173 MET cc_start: 0.7190 (tmm) cc_final: 0.6836 (tmm) REVERT: Ao 181 MET cc_start: 0.7162 (tpp) cc_final: 0.6657 (tmm) REVERT: Ap 66 ASN cc_start: 0.8834 (t0) cc_final: 0.8536 (t0) REVERT: Ap 121 GLU cc_start: 0.7475 (mp0) cc_final: 0.7196 (mp0) REVERT: Ap 173 MET cc_start: 0.7368 (tmm) cc_final: 0.7014 (tmm) REVERT: Ap 181 MET cc_start: 0.7365 (tpp) cc_final: 0.6658 (tmm) REVERT: Aq 56 MET cc_start: 0.8642 (mmm) cc_final: 0.8334 (tpp) REVERT: Aq 136 ASP cc_start: 0.8667 (t0) cc_final: 0.8329 (t0) REVERT: Aq 160 MET cc_start: 0.9271 (mmp) cc_final: 0.8991 (mmm) REVERT: Aq 181 MET cc_start: 0.7302 (tpp) cc_final: 0.6713 (tmm) REVERT: Ar 56 MET cc_start: 0.8734 (mmm) cc_final: 0.8492 (tpp) REVERT: Ar 136 ASP cc_start: 0.8509 (t0) cc_final: 0.8258 (t0) REVERT: Ar 181 MET cc_start: 0.7104 (tpp) cc_final: 0.6726 (tmm) REVERT: As 56 MET cc_start: 0.8655 (mmm) cc_final: 0.8384 (mmm) REVERT: As 77 GLN cc_start: 0.8612 (mt0) cc_final: 0.8104 (mp10) REVERT: As 173 MET cc_start: 0.7179 (tmm) cc_final: 0.6789 (tmm) REVERT: As 181 MET cc_start: 0.6620 (tmm) cc_final: 0.6286 (tmm) outliers start: 33 outliers final: 22 residues processed: 573 average time/residue: 0.1693 time to fit residues: 142.4348 Evaluate side-chains 564 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 539 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ac residue 48 LYS Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 106 THR Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Ak residue 119 CYS Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain As residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 229 optimal weight: 6.9990 chunk 261 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 234 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 ASN Ag 151 ASN Ah 151 ASN Ai 69 HIS ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS Aj 151 ASN Ak 69 HIS Ak 151 ASN Al 66 ASN ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 151 ASN ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 69 HIS ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 69 HIS Aq 151 ASN As 66 ASN As 151 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112851 restraints weight = 28063.984| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.88 r_work: 0.3107 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22572 Z= 0.104 Angle : 0.503 9.116 30647 Z= 0.245 Chirality : 0.039 0.120 3363 Planarity : 0.003 0.031 3952 Dihedral : 4.323 22.398 2983 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.73 % Allowed : 18.01 % Favored : 80.26 % 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 aren not related in a simple way. whole: -0.73 (0.16), residues: 2717 helix: 1.12 (0.17), residues: 1026 sheet: 0.95 (0.33), residues: 228 loop : -2.03 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAa 46 TYR 0.014 0.001 TYRAd 180 PHE 0.003 0.000 PHEAo 163 TRP 0.010 0.002 TRPAh 132 HIS 0.005 0.001 HISAb 69 Details of bonding type rmsd covalent geometry : bond 0.00265 (22572) covalent geometry : angle 0.50259 (30647) hydrogen bonds : bond 0.03172 ( 713) hydrogen bonds : angle 4.74117 ( 2082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 533 time to evaluate : 0.675 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8612 (mt0) cc_final: 0.8135 (mp10) REVERT: Aa 107 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8075 (pt0) REVERT: Aa 173 MET cc_start: 0.7475 (tmm) cc_final: 0.7087 (tmm) REVERT: Aa 181 MET cc_start: 0.7245 (tpp) cc_final: 0.6619 (tmm) REVERT: Ab 56 MET cc_start: 0.8575 (mmm) cc_final: 0.8186 (mmm) REVERT: Ab 173 MET cc_start: 0.7259 (tmm) cc_final: 0.6844 (tmm) REVERT: Ab 181 MET cc_start: 0.6631 (tmm) cc_final: 0.6267 (tmm) REVERT: Ac 66 ASN cc_start: 0.8997 (t0) cc_final: 0.8477 (t0) REVERT: Ac 173 MET cc_start: 0.7120 (tmm) cc_final: 0.6748 (tmm) REVERT: Ac 181 MET cc_start: 0.7245 (tpp) cc_final: 0.6848 (tmm) REVERT: Ad 56 MET cc_start: 0.8648 (mmm) cc_final: 0.8371 (tpp) REVERT: Ad 76 GLN cc_start: 0.8017 (mp10) cc_final: 0.7796 (mp10) REVERT: Ad 181 MET cc_start: 0.7244 (tpp) cc_final: 0.6710 (tmm) REVERT: Ae 76 GLN cc_start: 0.7959 (mp10) cc_final: 0.7683 (mp10) REVERT: Ae 107 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8118 (pt0) REVERT: Ae 121 GLU cc_start: 0.7357 (mp0) cc_final: 0.7046 (mp0) REVERT: Ae 181 MET cc_start: 0.6716 (tmm) cc_final: 0.6418 (tmm) REVERT: Af 55 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.7131 (mtm180) REVERT: Af 116 MET cc_start: 0.8829 (ttp) cc_final: 0.8609 (ttp) REVERT: Af 181 MET cc_start: 0.7192 (tpp) cc_final: 0.6597 (tmm) REVERT: Ag 181 MET cc_start: 0.7208 (tpp) cc_final: 0.6633 (tmm) REVERT: Ah 76 GLN cc_start: 0.8076 (mp10) cc_final: 0.7797 (mp10) REVERT: Ah 91 ASP cc_start: 0.8474 (m-30) cc_final: 0.8179 (m-30) REVERT: Ah 112 MET cc_start: 0.8990 (mmp) cc_final: 0.8790 (mmp) REVERT: Ah 135 MET cc_start: 0.8727 (mmm) cc_final: 0.8448 (mmt) REVERT: Ah 136 ASP cc_start: 0.8631 (t0) cc_final: 0.8426 (t0) REVERT: Ah 173 MET cc_start: 0.7237 (tmm) cc_final: 0.6730 (tmm) REVERT: Ah 181 MET cc_start: 0.6732 (tmm) cc_final: 0.6367 (tmm) REVERT: Ai 56 MET cc_start: 0.8557 (mmm) cc_final: 0.8324 (mmm) REVERT: Ai 121 GLU cc_start: 0.7324 (mp0) cc_final: 0.7014 (mp0) REVERT: Ai 134 MET cc_start: 0.8708 (ttp) cc_final: 0.8336 (ttp) REVERT: Ai 181 MET cc_start: 0.7131 (tpp) cc_final: 0.6716 (tmm) REVERT: Aj 58 LYS cc_start: 0.8993 (mttp) cc_final: 0.8743 (mtpt) REVERT: Aj 181 MET cc_start: 0.7376 (tpp) cc_final: 0.6820 (tmm) REVERT: Ak 181 MET cc_start: 0.7325 (tpp) cc_final: 0.6770 (tmm) REVERT: Al 173 MET cc_start: 0.7219 (tmm) cc_final: 0.6759 (tmm) REVERT: Al 181 MET cc_start: 0.7223 (tpp) cc_final: 0.6842 (tmm) REVERT: Am 107 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: Am 181 MET cc_start: 0.6722 (tmm) cc_final: 0.6390 (tmm) REVERT: An 56 MET cc_start: 0.8667 (mmm) cc_final: 0.8247 (tpp) REVERT: An 77 GLN cc_start: 0.8583 (mt0) cc_final: 0.8079 (mp10) REVERT: An 107 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: An 181 MET cc_start: 0.7194 (tpp) cc_final: 0.6753 (tmm) REVERT: Ao 77 GLN cc_start: 0.8634 (mt0) cc_final: 0.8114 (mp10) REVERT: Ao 173 MET cc_start: 0.7192 (tmm) cc_final: 0.6860 (tmm) REVERT: Ao 181 MET cc_start: 0.7177 (tpp) cc_final: 0.6669 (tmm) REVERT: Ap 121 GLU cc_start: 0.7486 (mp0) cc_final: 0.7247 (mp0) REVERT: Ap 173 MET cc_start: 0.7309 (tmm) cc_final: 0.6961 (tmm) REVERT: Ap 181 MET cc_start: 0.7454 (tpp) cc_final: 0.6828 (tmm) REVERT: Aq 56 MET cc_start: 0.8619 (mmm) cc_final: 0.8279 (tpp) REVERT: Aq 136 ASP cc_start: 0.8624 (t0) cc_final: 0.8379 (t0) REVERT: Aq 160 MET cc_start: 0.9279 (mmp) cc_final: 0.9003 (mmm) REVERT: Aq 181 MET cc_start: 0.7296 (tpp) cc_final: 0.6725 (tmm) REVERT: Ar 56 MET cc_start: 0.8715 (mmm) cc_final: 0.8456 (tpp) REVERT: Ar 181 MET cc_start: 0.7085 (tpp) cc_final: 0.6702 (tmm) REVERT: As 56 MET cc_start: 0.8644 (mmm) cc_final: 0.8366 (mmm) REVERT: As 77 GLN cc_start: 0.8594 (mt0) cc_final: 0.8110 (mp10) REVERT: As 173 MET cc_start: 0.7104 (tmm) cc_final: 0.6790 (tmm) REVERT: As 181 MET cc_start: 0.6669 (tmm) cc_final: 0.6354 (tmm) outliers start: 42 outliers final: 30 residues processed: 547 average time/residue: 0.1466 time to fit residues: 119.0973 Evaluate side-chains 555 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 522 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Ab residue 60 LYS Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ac residue 103 ILE Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ah residue 106 THR Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Ak residue 119 CYS Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 119 CYS Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Aq residue 77 GLN Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 48 LYS Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 241 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 261 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 95 optimal weight: 0.0370 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 151 ASN Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 151 ASN Ae 151 ASN Ag 77 GLN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 69 HIS ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS Aj 151 ASN Ak 69 HIS ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 151 ASN ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 69 HIS Ar 151 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112890 restraints weight = 28039.661| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.88 r_work: 0.3112 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22572 Z= 0.109 Angle : 0.509 7.484 30647 Z= 0.248 Chirality : 0.039 0.117 3363 Planarity : 0.003 0.031 3952 Dihedral : 4.261 20.223 2983 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.93 % Allowed : 18.26 % Favored : 79.81 % 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 aren not related in a simple way. whole: -0.59 (0.16), residues: 2717 helix: 1.30 (0.16), residues: 1026 sheet: 0.94 (0.33), residues: 228 loop : -1.98 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAm 55 TYR 0.014 0.001 TYRAe 180 PHE 0.003 0.000 PHEAo 163 TRP 0.010 0.002 TRPAf 132 HIS 0.005 0.001 HISAb 69 Details of bonding type rmsd covalent geometry : bond 0.00277 (22572) covalent geometry : angle 0.50928 (30647) hydrogen bonds : bond 0.03127 ( 713) hydrogen bonds : angle 4.70564 ( 2082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 519 time to evaluate : 0.784 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8577 (mt0) cc_final: 0.8017 (mp10) REVERT: Aa 107 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8066 (pt0) REVERT: Aa 173 MET cc_start: 0.7489 (tmm) cc_final: 0.7111 (tmm) REVERT: Aa 181 MET cc_start: 0.7227 (tpp) cc_final: 0.6635 (tmm) REVERT: Ab 173 MET cc_start: 0.7278 (tmm) cc_final: 0.6840 (tmm) REVERT: Ab 181 MET cc_start: 0.6551 (tmm) cc_final: 0.6175 (tmm) REVERT: Ac 66 ASN cc_start: 0.8993 (t0) cc_final: 0.8473 (t0) REVERT: Ac 95 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: Ac 173 MET cc_start: 0.7111 (tmm) cc_final: 0.6737 (tmm) REVERT: Ac 181 MET cc_start: 0.7197 (tpp) cc_final: 0.6748 (tmm) REVERT: Ad 56 MET cc_start: 0.8613 (mmm) cc_final: 0.8331 (tpp) REVERT: Ad 76 GLN cc_start: 0.8039 (mp10) cc_final: 0.7805 (mp10) REVERT: Ad 181 MET cc_start: 0.7301 (tpp) cc_final: 0.6756 (tmm) REVERT: Ae 76 GLN cc_start: 0.7943 (mp10) cc_final: 0.7666 (mp10) REVERT: Ae 107 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8095 (pt0) REVERT: Ae 121 GLU cc_start: 0.7235 (mp0) cc_final: 0.7030 (mp0) REVERT: Ae 151 ASN cc_start: 0.8199 (t160) cc_final: 0.7939 (t0) REVERT: Ae 181 MET cc_start: 0.6732 (tmm) cc_final: 0.6422 (tmm) REVERT: Af 55 ARG cc_start: 0.8466 (mmm-85) cc_final: 0.7165 (mtm180) REVERT: Af 60 LYS cc_start: 0.8869 (mttm) cc_final: 0.8569 (mttp) REVERT: Af 116 MET cc_start: 0.8792 (ttp) cc_final: 0.8569 (ttp) REVERT: Af 151 ASN cc_start: 0.8263 (t160) cc_final: 0.8056 (t0) REVERT: Af 181 MET cc_start: 0.7153 (tpp) cc_final: 0.6584 (tmm) REVERT: Ag 181 MET cc_start: 0.7230 (tpp) cc_final: 0.6671 (tmm) REVERT: Ah 112 MET cc_start: 0.8984 (mmp) cc_final: 0.8782 (mmp) REVERT: Ah 135 MET cc_start: 0.8738 (mmm) cc_final: 0.8499 (mmt) REVERT: Ah 173 MET cc_start: 0.7218 (tmm) cc_final: 0.6715 (tmm) REVERT: Ah 181 MET cc_start: 0.6762 (tmm) cc_final: 0.6392 (tmm) REVERT: Ai 56 MET cc_start: 0.8533 (mmm) cc_final: 0.8296 (mmm) REVERT: Ai 134 MET cc_start: 0.8701 (ttp) cc_final: 0.8373 (ttp) REVERT: Ai 181 MET cc_start: 0.7209 (tpp) cc_final: 0.6764 (tmm) REVERT: Aj 58 LYS cc_start: 0.9005 (mttp) cc_final: 0.8748 (mtpt) REVERT: Aj 181 MET cc_start: 0.7412 (tpp) cc_final: 0.6800 (tmm) REVERT: Ak 66 ASN cc_start: 0.8840 (t0) cc_final: 0.8635 (t0) REVERT: Ak 95 GLU cc_start: 0.8667 (tp30) cc_final: 0.8358 (mm-30) REVERT: Ak 150 GLU cc_start: 0.8459 (tt0) cc_final: 0.8126 (pt0) REVERT: Ak 181 MET cc_start: 0.7294 (tpp) cc_final: 0.6682 (tmm) REVERT: Al 173 MET cc_start: 0.7230 (tmm) cc_final: 0.6740 (tmm) REVERT: Al 181 MET cc_start: 0.7143 (tpp) cc_final: 0.6814 (tmm) REVERT: Am 56 MET cc_start: 0.8756 (mmm) cc_final: 0.8404 (mmm) REVERT: Am 107 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7871 (pt0) REVERT: Am 181 MET cc_start: 0.6715 (tmm) cc_final: 0.6419 (tmm) REVERT: An 56 MET cc_start: 0.8653 (mmm) cc_final: 0.8218 (tpp) REVERT: An 77 GLN cc_start: 0.8592 (mt0) cc_final: 0.8078 (mp10) REVERT: An 107 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: An 173 MET cc_start: 0.6999 (tmm) cc_final: 0.6544 (tmm) REVERT: An 181 MET cc_start: 0.7191 (tpp) cc_final: 0.6735 (tmm) REVERT: Ao 136 ASP cc_start: 0.8459 (t0) cc_final: 0.8245 (t0) REVERT: Ao 173 MET cc_start: 0.7171 (tmm) cc_final: 0.6839 (tmm) REVERT: Ao 181 MET cc_start: 0.7161 (tpp) cc_final: 0.6667 (tmm) REVERT: Ap 173 MET cc_start: 0.7369 (tmm) cc_final: 0.6978 (tmm) REVERT: Ap 181 MET cc_start: 0.7468 (tpp) cc_final: 0.6786 (tmm) REVERT: Aq 56 MET cc_start: 0.8610 (mmm) cc_final: 0.8214 (tpp) REVERT: Aq 136 ASP cc_start: 0.8655 (t0) cc_final: 0.8426 (t0) REVERT: Aq 160 MET cc_start: 0.9276 (mmp) cc_final: 0.9008 (mmm) REVERT: Aq 181 MET cc_start: 0.7274 (tpp) cc_final: 0.6730 (tmm) REVERT: Ar 56 MET cc_start: 0.8694 (mmm) cc_final: 0.8415 (tpp) REVERT: Ar 107 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: Ar 181 MET cc_start: 0.7132 (tpp) cc_final: 0.6764 (tmm) REVERT: As 56 MET cc_start: 0.8630 (mmm) cc_final: 0.8332 (mmm) REVERT: As 77 GLN cc_start: 0.8622 (mt0) cc_final: 0.8141 (mp10) REVERT: As 173 MET cc_start: 0.7100 (tmm) cc_final: 0.6774 (tmm) REVERT: As 181 MET cc_start: 0.6696 (tmm) cc_final: 0.6387 (tmm) outliers start: 47 outliers final: 33 residues processed: 538 average time/residue: 0.1559 time to fit residues: 123.9270 Evaluate side-chains 552 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 514 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Ab residue 60 LYS Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Ad residue 119 CYS Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Ag residue 77 GLN Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Ak residue 119 CYS Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 119 CYS Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Ap residue 119 CYS Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 77 GLN Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain Ar residue 107 GLU Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 205 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 151 ASN Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 151 ASN Ag 151 ASN Ah 151 ASN Ai 69 HIS ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS Aj 151 ASN Ak 69 HIS ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN Am 69 HIS ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 151 ASN ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 151 ASN ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 151 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113833 restraints weight = 27869.181| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.88 r_work: 0.3125 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22572 Z= 0.100 Angle : 0.518 10.246 30647 Z= 0.250 Chirality : 0.039 0.116 3363 Planarity : 0.003 0.031 3952 Dihedral : 4.247 21.576 2983 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.64 % Allowed : 18.91 % Favored : 79.44 % 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 aren not related in a simple way. whole: -0.58 (0.16), residues: 2717 helix: 1.39 (0.16), residues: 1007 sheet: 0.96 (0.33), residues: 228 loop : -2.01 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAm 55 TYR 0.013 0.001 TYRAe 180 PHE 0.004 0.000 PHEAg 163 TRP 0.010 0.001 TRPAf 132 HIS 0.006 0.001 HISAb 69 Details of bonding type rmsd covalent geometry : bond 0.00256 (22572) covalent geometry : angle 0.51817 (30647) hydrogen bonds : bond 0.02996 ( 713) hydrogen bonds : angle 4.72703 ( 2082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 513 time to evaluate : 0.912 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8570 (mt0) cc_final: 0.8017 (mp10) REVERT: Aa 107 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: Aa 151 ASN cc_start: 0.8231 (t160) cc_final: 0.7728 (t0) REVERT: Aa 173 MET cc_start: 0.7446 (tmm) cc_final: 0.7094 (tmm) REVERT: Aa 181 MET cc_start: 0.7256 (tpp) cc_final: 0.6667 (tmm) REVERT: Ab 48 LYS cc_start: 0.8813 (mptt) cc_final: 0.8604 (mptt) REVERT: Ab 173 MET cc_start: 0.7215 (tmm) cc_final: 0.6796 (tmm) REVERT: Ab 181 MET cc_start: 0.6545 (tmm) cc_final: 0.6170 (tmm) REVERT: Ac 56 MET cc_start: 0.8664 (mmm) cc_final: 0.8325 (mmm) REVERT: Ac 173 MET cc_start: 0.7148 (tmm) cc_final: 0.6771 (tmm) REVERT: Ac 181 MET cc_start: 0.7197 (tpp) cc_final: 0.6759 (tmm) REVERT: Ad 56 MET cc_start: 0.8609 (mmm) cc_final: 0.8325 (tpp) REVERT: Ad 181 MET cc_start: 0.7285 (tpp) cc_final: 0.6753 (tmm) REVERT: Ae 121 GLU cc_start: 0.7212 (mp0) cc_final: 0.6994 (mp0) REVERT: Ae 142 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8353 (mt-10) REVERT: Ae 181 MET cc_start: 0.6736 (tmm) cc_final: 0.6424 (tmm) REVERT: Af 55 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.7176 (mtm180) REVERT: Af 60 LYS cc_start: 0.8898 (mttm) cc_final: 0.8598 (mttp) REVERT: Af 116 MET cc_start: 0.8789 (ttp) cc_final: 0.8547 (ttp) REVERT: Af 181 MET cc_start: 0.7135 (tpp) cc_final: 0.6577 (tmm) REVERT: Ag 181 MET cc_start: 0.7270 (tpp) cc_final: 0.6685 (tmm) REVERT: Ah 135 MET cc_start: 0.8681 (mmm) cc_final: 0.8474 (mmt) REVERT: Ah 173 MET cc_start: 0.7205 (tmm) cc_final: 0.6725 (tmm) REVERT: Ah 181 MET cc_start: 0.6730 (tmm) cc_final: 0.6369 (tmm) REVERT: Ai 56 MET cc_start: 0.8488 (mmm) cc_final: 0.8243 (mmm) REVERT: Ai 121 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7090 (mt-10) REVERT: Ai 134 MET cc_start: 0.8731 (ttp) cc_final: 0.8389 (ttp) REVERT: Ai 181 MET cc_start: 0.7209 (tpp) cc_final: 0.6775 (tmm) REVERT: Aj 58 LYS cc_start: 0.8999 (mttp) cc_final: 0.8737 (mtpt) REVERT: Aj 181 MET cc_start: 0.7484 (tpp) cc_final: 0.6838 (tmm) REVERT: Ak 95 GLU cc_start: 0.8612 (tp30) cc_final: 0.8121 (mm-30) REVERT: Ak 150 GLU cc_start: 0.8457 (tt0) cc_final: 0.8142 (pt0) REVERT: Ak 181 MET cc_start: 0.7291 (tpp) cc_final: 0.6709 (tmm) REVERT: Al 173 MET cc_start: 0.7213 (tmm) cc_final: 0.6733 (tmm) REVERT: Al 181 MET cc_start: 0.7167 (tpp) cc_final: 0.6814 (tmm) REVERT: Am 56 MET cc_start: 0.8783 (mmm) cc_final: 0.8580 (mmm) REVERT: Am 181 MET cc_start: 0.6743 (tmm) cc_final: 0.6447 (tmm) REVERT: An 56 MET cc_start: 0.8642 (mmm) cc_final: 0.8197 (tpp) REVERT: An 77 GLN cc_start: 0.8604 (mt0) cc_final: 0.8072 (mp10) REVERT: An 107 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: An 173 MET cc_start: 0.6971 (tmm) cc_final: 0.6518 (tmm) REVERT: An 181 MET cc_start: 0.7188 (tpp) cc_final: 0.6735 (tmm) REVERT: Ao 136 ASP cc_start: 0.8470 (t0) cc_final: 0.8228 (t0) REVERT: Ao 151 ASN cc_start: 0.8347 (t160) cc_final: 0.8137 (t0) REVERT: Ao 173 MET cc_start: 0.7165 (tmm) cc_final: 0.6839 (tmm) REVERT: Ao 181 MET cc_start: 0.7181 (tpp) cc_final: 0.6680 (tmm) REVERT: Ap 150 GLU cc_start: 0.8458 (tt0) cc_final: 0.8239 (pt0) REVERT: Ap 173 MET cc_start: 0.7357 (tmm) cc_final: 0.6974 (tmm) REVERT: Ap 181 MET cc_start: 0.7405 (tpp) cc_final: 0.6708 (tmm) REVERT: Aq 56 MET cc_start: 0.8587 (mmm) cc_final: 0.8191 (tpp) REVERT: Aq 160 MET cc_start: 0.9268 (mmp) cc_final: 0.9002 (mmm) REVERT: Aq 181 MET cc_start: 0.7272 (tpp) cc_final: 0.6710 (tmm) REVERT: Ar 56 MET cc_start: 0.8676 (mmm) cc_final: 0.8394 (tpp) REVERT: Ar 107 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: Ar 181 MET cc_start: 0.7140 (tpp) cc_final: 0.6786 (tmm) REVERT: As 56 MET cc_start: 0.8616 (mmm) cc_final: 0.8322 (mmm) REVERT: As 77 GLN cc_start: 0.8617 (mt0) cc_final: 0.8145 (mp10) REVERT: As 173 MET cc_start: 0.7127 (tmm) cc_final: 0.6797 (tmm) REVERT: As 181 MET cc_start: 0.6702 (tmm) cc_final: 0.6398 (tmm) outliers start: 40 outliers final: 28 residues processed: 532 average time/residue: 0.1555 time to fit residues: 122.4764 Evaluate side-chains 540 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 509 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ac residue 48 LYS Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Ag residue 77 GLN Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Ak residue 119 CYS Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain An residue 44 VAL Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Ap residue 119 CYS Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 77 GLN Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain Ar residue 107 GLU Chi-restraints excluded: chain As residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 39 optimal weight: 6.9990 chunk 238 optimal weight: 0.2980 chunk 159 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 151 ASN Af 151 ASN Ag 151 ASN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 151 ASN Aj 69 HIS Ak 69 HIS ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 151 ASN ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109907 restraints weight = 28138.103| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.89 r_work: 0.3076 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22572 Z= 0.159 Angle : 0.573 14.603 30647 Z= 0.275 Chirality : 0.041 0.124 3363 Planarity : 0.004 0.035 3952 Dihedral : 4.373 21.202 2983 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.73 % Allowed : 19.24 % Favored : 79.03 % 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 aren not related in a simple way. whole: -0.78 (0.16), residues: 2717 helix: 1.12 (0.16), residues: 1007 sheet: 0.88 (0.33), residues: 228 loop : -2.05 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAc 55 TYR 0.012 0.002 TYRAe 180 PHE 0.006 0.001 PHEAo 163 TRP 0.009 0.002 TRPAf 132 HIS 0.006 0.001 HISAb 69 Details of bonding type rmsd covalent geometry : bond 0.00395 (22572) covalent geometry : angle 0.57347 (30647) hydrogen bonds : bond 0.03667 ( 713) hydrogen bonds : angle 4.93256 ( 2082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 539 time to evaluate : 0.812 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8619 (mt0) cc_final: 0.8054 (mp10) REVERT: Aa 107 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8126 (pt0) REVERT: Aa 173 MET cc_start: 0.7524 (tmm) cc_final: 0.7132 (tmm) REVERT: Aa 181 MET cc_start: 0.7269 (tpp) cc_final: 0.6676 (tmm) REVERT: Ab 95 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8553 (mm-30) REVERT: Ab 173 MET cc_start: 0.7307 (tmm) cc_final: 0.6899 (tmm) REVERT: Ab 181 MET cc_start: 0.6443 (tmm) cc_final: 0.5996 (tmm) REVERT: Ac 56 MET cc_start: 0.8720 (mmm) cc_final: 0.8342 (mmt) REVERT: Ac 66 ASN cc_start: 0.8922 (t0) cc_final: 0.8484 (t0) REVERT: Ac 173 MET cc_start: 0.7255 (tmm) cc_final: 0.6824 (tmm) REVERT: Ac 181 MET cc_start: 0.7192 (tpp) cc_final: 0.6743 (tmm) REVERT: Ad 56 MET cc_start: 0.8623 (mmm) cc_final: 0.8328 (tpp) REVERT: Ad 181 MET cc_start: 0.7304 (tpp) cc_final: 0.6764 (tmm) REVERT: Ae 181 MET cc_start: 0.6744 (tmm) cc_final: 0.6439 (tmm) REVERT: Af 55 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.7123 (mtm180) REVERT: Af 116 MET cc_start: 0.8819 (ttp) cc_final: 0.8608 (ttp) REVERT: Af 181 MET cc_start: 0.7264 (tpp) cc_final: 0.6620 (tmm) REVERT: Ag 181 MET cc_start: 0.7249 (tpp) cc_final: 0.6669 (tmm) REVERT: Ah 173 MET cc_start: 0.7244 (tmm) cc_final: 0.6701 (tmm) REVERT: Ah 181 MET cc_start: 0.6652 (tmm) cc_final: 0.6321 (tmm) REVERT: Ai 56 MET cc_start: 0.8550 (mmm) cc_final: 0.8324 (mmm) REVERT: Ai 134 MET cc_start: 0.8796 (ttp) cc_final: 0.8394 (ttp) REVERT: Ai 181 MET cc_start: 0.7131 (tpp) cc_final: 0.6771 (tmm) REVERT: Aj 58 LYS cc_start: 0.9016 (mttp) cc_final: 0.8745 (mtpt) REVERT: Aj 77 GLN cc_start: 0.8673 (mt0) cc_final: 0.8009 (tm-30) REVERT: Aj 173 MET cc_start: 0.7185 (tmm) cc_final: 0.6607 (tmm) REVERT: Aj 181 MET cc_start: 0.7497 (tpp) cc_final: 0.6849 (tmm) REVERT: Ak 181 MET cc_start: 0.7153 (tpp) cc_final: 0.6519 (tmm) REVERT: Al 95 GLU cc_start: 0.8552 (mm-30) cc_final: 0.7964 (mp0) REVERT: Al 173 MET cc_start: 0.7290 (tmm) cc_final: 0.6813 (tmm) REVERT: Al 181 MET cc_start: 0.7181 (tpp) cc_final: 0.6880 (tmm) REVERT: Am 56 MET cc_start: 0.8833 (mmm) cc_final: 0.8625 (mmm) REVERT: Am 107 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: Am 181 MET cc_start: 0.6694 (tmm) cc_final: 0.6412 (tmm) REVERT: An 56 MET cc_start: 0.8665 (mmm) cc_final: 0.8197 (mmm) REVERT: An 77 GLN cc_start: 0.8657 (mt0) cc_final: 0.8118 (mp10) REVERT: An 107 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8107 (pt0) REVERT: An 173 MET cc_start: 0.7158 (tmm) cc_final: 0.6722 (tmm) REVERT: An 181 MET cc_start: 0.7206 (tpp) cc_final: 0.6731 (tmm) REVERT: Ao 136 ASP cc_start: 0.8560 (t0) cc_final: 0.8354 (t0) REVERT: Ao 151 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8135 (t0) REVERT: Ao 173 MET cc_start: 0.7246 (tmm) cc_final: 0.6901 (tmm) REVERT: Ao 181 MET cc_start: 0.7157 (tpp) cc_final: 0.6637 (tmm) REVERT: Ap 173 MET cc_start: 0.7451 (tmm) cc_final: 0.7033 (tmm) REVERT: Ap 181 MET cc_start: 0.7381 (tpp) cc_final: 0.6714 (tmm) REVERT: Aq 56 MET cc_start: 0.8602 (mmm) cc_final: 0.8183 (tpp) REVERT: Aq 160 MET cc_start: 0.9277 (mmp) cc_final: 0.9020 (mmm) REVERT: Aq 181 MET cc_start: 0.7246 (tpp) cc_final: 0.6698 (tmm) REVERT: Ar 107 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: Ar 181 MET cc_start: 0.7199 (tpp) cc_final: 0.6694 (tmm) REVERT: As 56 MET cc_start: 0.8623 (mmm) cc_final: 0.8331 (mmm) REVERT: As 173 MET cc_start: 0.7199 (tmm) cc_final: 0.6808 (tmm) REVERT: As 181 MET cc_start: 0.6717 (tmm) cc_final: 0.6404 (tmm) outliers start: 42 outliers final: 32 residues processed: 556 average time/residue: 0.1792 time to fit residues: 148.1521 Evaluate side-chains 558 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 520 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Ab residue 95 GLU Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Ad residue 119 CYS Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 77 GLN Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Ak residue 119 CYS Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 119 CYS Chi-restraints excluded: chain An residue 44 VAL Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ao residue 151 ASN Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Ap residue 119 CYS Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 77 GLN Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain Ar residue 107 GLU Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 251 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 129 optimal weight: 0.0570 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 overall best weight: 2.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 151 ASN Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 77 GLN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 69 HIS ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 151 ASN Aj 69 HIS Ak 69 HIS ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 69 HIS ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108566 restraints weight = 28208.771| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.88 r_work: 0.3056 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 22572 Z= 0.195 Angle : 0.610 14.129 30647 Z= 0.294 Chirality : 0.042 0.129 3363 Planarity : 0.004 0.036 3952 Dihedral : 4.534 21.522 2983 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.89 % Allowed : 19.49 % Favored : 78.62 % 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 aren not related in a simple way. whole: -0.82 (0.16), residues: 2717 helix: 0.95 (0.16), residues: 1026 sheet: 0.81 (0.33), residues: 228 loop : -1.98 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAc 55 TYR 0.012 0.002 TYRAb 180 PHE 0.007 0.001 PHEAo 163 TRP 0.011 0.002 TRPAl 93 HIS 0.007 0.001 HISAb 69 Details of bonding type rmsd covalent geometry : bond 0.00480 (22572) covalent geometry : angle 0.61036 (30647) hydrogen bonds : bond 0.03940 ( 713) hydrogen bonds : angle 5.10453 ( 2082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 525 time to evaluate : 0.937 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8638 (mt0) cc_final: 0.8116 (mp10) REVERT: Aa 107 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8129 (pt0) REVERT: Aa 173 MET cc_start: 0.7524 (tmm) cc_final: 0.7105 (tmm) REVERT: Aa 181 MET cc_start: 0.7324 (tpp) cc_final: 0.6708 (tmm) REVERT: Ab 173 MET cc_start: 0.7389 (tmm) cc_final: 0.7000 (tmm) REVERT: Ab 181 MET cc_start: 0.6483 (tmm) cc_final: 0.6064 (tmm) REVERT: Ac 56 MET cc_start: 0.8844 (mmm) cc_final: 0.8524 (mmt) REVERT: Ac 66 ASN cc_start: 0.8989 (t0) cc_final: 0.8500 (t0) REVERT: Ac 77 GLN cc_start: 0.8731 (tt0) cc_final: 0.8143 (tm-30) REVERT: Ac 173 MET cc_start: 0.7320 (tmm) cc_final: 0.6848 (tmm) REVERT: Ac 181 MET cc_start: 0.7212 (tpp) cc_final: 0.6761 (tmm) REVERT: Ad 56 MET cc_start: 0.8631 (mmm) cc_final: 0.8335 (tpp) REVERT: Ad 181 MET cc_start: 0.7299 (tpp) cc_final: 0.6743 (tmm) REVERT: Ae 76 GLN cc_start: 0.8015 (mp10) cc_final: 0.7786 (mp10) REVERT: Ae 136 ASP cc_start: 0.8698 (t0) cc_final: 0.8424 (t0) REVERT: Ae 181 MET cc_start: 0.6776 (tmm) cc_final: 0.6548 (tmm) REVERT: Af 55 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.7144 (mtm180) REVERT: Af 181 MET cc_start: 0.7256 (tpp) cc_final: 0.6608 (tmm) REVERT: Ag 77 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: Ag 181 MET cc_start: 0.7234 (tpp) cc_final: 0.6789 (tmm) REVERT: Ah 77 GLN cc_start: 0.8649 (tt0) cc_final: 0.8032 (tm-30) REVERT: Ah 181 MET cc_start: 0.6662 (tmm) cc_final: 0.6337 (tmm) REVERT: Ai 56 MET cc_start: 0.8604 (mmm) cc_final: 0.8384 (mmm) REVERT: Ai 134 MET cc_start: 0.8798 (ttp) cc_final: 0.8363 (ttp) REVERT: Ai 181 MET cc_start: 0.7219 (tpp) cc_final: 0.6964 (tmm) REVERT: Aj 58 LYS cc_start: 0.9001 (mttp) cc_final: 0.8731 (mtpt) REVERT: Aj 77 GLN cc_start: 0.8714 (mt0) cc_final: 0.8131 (tm-30) REVERT: Aj 181 MET cc_start: 0.7485 (tpp) cc_final: 0.6839 (tmm) REVERT: Ak 173 MET cc_start: 0.7274 (tmm) cc_final: 0.6664 (tmm) REVERT: Ak 181 MET cc_start: 0.7116 (tpp) cc_final: 0.6517 (tmm) REVERT: Al 95 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7967 (mt-10) REVERT: Al 112 MET cc_start: 0.8992 (mmt) cc_final: 0.8763 (mmt) REVERT: Al 173 MET cc_start: 0.7351 (tmm) cc_final: 0.6914 (tmm) REVERT: Al 181 MET cc_start: 0.7203 (tpp) cc_final: 0.6721 (tmm) REVERT: Am 56 MET cc_start: 0.8889 (mmm) cc_final: 0.8685 (mmm) REVERT: Am 107 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8004 (pt0) REVERT: Am 181 MET cc_start: 0.6671 (tmm) cc_final: 0.6407 (tmm) REVERT: An 56 MET cc_start: 0.8704 (mmm) cc_final: 0.8236 (mmm) REVERT: An 77 GLN cc_start: 0.8675 (mt0) cc_final: 0.8181 (mp10) REVERT: An 107 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8110 (pt0) REVERT: An 181 MET cc_start: 0.7115 (tpp) cc_final: 0.6378 (tmm) REVERT: Ao 77 GLN cc_start: 0.8686 (mt0) cc_final: 0.8372 (mm-40) REVERT: Ao 173 MET cc_start: 0.7319 (tmm) cc_final: 0.6952 (tmm) REVERT: Ao 181 MET cc_start: 0.7149 (tpp) cc_final: 0.6632 (tmm) REVERT: Ap 173 MET cc_start: 0.7506 (tmm) cc_final: 0.7081 (tmm) REVERT: Ap 181 MET cc_start: 0.7327 (tpp) cc_final: 0.6588 (tmm) REVERT: Aq 56 MET cc_start: 0.8669 (mmm) cc_final: 0.8234 (tpp) REVERT: Aq 160 MET cc_start: 0.9286 (mmp) cc_final: 0.9015 (mmm) REVERT: Aq 181 MET cc_start: 0.7178 (tpp) cc_final: 0.6645 (tmm) REVERT: Ar 56 MET cc_start: 0.8750 (mmm) cc_final: 0.8462 (mmm) REVERT: Ar 181 MET cc_start: 0.7195 (tpp) cc_final: 0.6859 (tmm) REVERT: As 56 MET cc_start: 0.8661 (mmm) cc_final: 0.8381 (mmm) REVERT: As 77 GLN cc_start: 0.8681 (mt0) cc_final: 0.8305 (tm-30) REVERT: As 134 MET cc_start: 0.8883 (ttp) cc_final: 0.8188 (ttp) REVERT: As 173 MET cc_start: 0.7358 (tmm) cc_final: 0.6965 (tmm) outliers start: 46 outliers final: 35 residues processed: 543 average time/residue: 0.1855 time to fit residues: 148.8080 Evaluate side-chains 551 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 512 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Aa residue 119 CYS Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Ad residue 119 CYS Chi-restraints excluded: chain Ae residue 103 ILE Chi-restraints excluded: chain Ae residue 150 GLU Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Ag residue 77 GLN Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 77 GLN Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Ak residue 119 CYS Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain Am residue 119 CYS Chi-restraints excluded: chain An residue 44 VAL Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ap residue 119 CYS Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 23 optimal weight: 0.3980 chunk 1 optimal weight: 20.0000 chunk 161 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 248 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 237 optimal weight: 7.9990 chunk 230 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 77 GLN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 69 HIS ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS Ak 69 HIS ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 69 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.137317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108774 restraints weight = 28009.846| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.88 r_work: 0.3059 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 22572 Z= 0.169 Angle : 0.767 59.185 30647 Z= 0.408 Chirality : 0.041 0.395 3363 Planarity : 0.004 0.066 3952 Dihedral : 4.566 31.596 2983 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.52 % Allowed : 20.27 % Favored : 78.21 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.80 (0.16), residues: 2717 helix: 0.97 (0.16), residues: 1026 sheet: 0.80 (0.33), residues: 228 loop : -1.97 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAc 55 TYR 0.012 0.002 TYRAb 180 PHE 0.006 0.001 PHEAo 163 TRP 0.011 0.002 TRPAf 132 HIS 0.007 0.001 HISAb 69 Details of bonding type rmsd covalent geometry : bond 0.00401 (22572) covalent geometry : angle 0.76723 (30647) hydrogen bonds : bond 0.03807 ( 713) hydrogen bonds : angle 5.10792 ( 2082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4894.05 seconds wall clock time: 84 minutes 27.76 seconds (5067.76 seconds total)