Starting phenix.real_space_refine on Sun Jun 29 21:21:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opa_17046/06_2025/8opa_17046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opa_17046/06_2025/8opa_17046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8opa_17046/06_2025/8opa_17046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opa_17046/06_2025/8opa_17046.map" model { file = "/net/cci-nas-00/data/ceres_data/8opa_17046/06_2025/8opa_17046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opa_17046/06_2025/8opa_17046.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 0.176 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 288 5.16 5 C 22104 2.51 5 N 6096 2.21 5 O 6504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34992 Number of models: 1 Model: "" Number of chains: 1 Chain: "Aa" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Restraints were copied for chains: Ac, Ab, Ae, Ad, Ag, Af, Ai, Ah, Ak, Aj, Am, Al, Ao, An, Aq, Ap, As, Ar, Au, At, Aw, Av, Ax Time building chain proxies: 8.53, per 1000 atoms: 0.24 Number of scatterers: 34992 At special positions: 0 Unit cell: (139.65, 139.65, 162.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 288 16.00 O 6504 8.00 N 6096 7.00 C 22104 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: 8.47 Conformation dependent library (CDL) restraints added in 4.3 seconds 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 46.4% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 71 removed outlier: 3.629A pdb=" N LEUAa 70 " --> pdb=" O ASNAa 66 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAa 92 " --> pdb=" O SERAa 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAa 93 " --> pdb=" O GLNAa 89 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAa 114 " --> pdb=" O THRAa 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAa 116 " --> pdb=" O METAa 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAa 117 " --> pdb=" O ASNAa 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.899A pdb=" N GLUAa 168 " --> pdb=" O SERAa 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAa 169 " --> pdb=" O ASPAa 165 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 182 through 188 removed outlier: 3.911A pdb=" N ARGAa 188 " --> pdb=" O TYRAa 184 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAa 219 " --> pdb=" O GLUAa 215 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAb 70 " --> pdb=" O ASNAb 66 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAb 92 " --> pdb=" O SERAb 88 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRPAb 93 " --> pdb=" O GLNAb 89 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAb 111 " --> pdb=" O GLUAb 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAb 114 " --> pdb=" O THRAb 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAb 116 " --> pdb=" O METAb 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAb 117 " --> pdb=" O ASNAb 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.898A pdb=" N GLUAb 168 " --> pdb=" O SERAb 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAb 169 " --> pdb=" O ASPAb 165 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 182 through 188 removed outlier: 3.912A pdb=" N ARGAb 188 " --> pdb=" O TYRAb 184 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAb 219 " --> pdb=" O GLUAb 215 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 66 through 71 removed outlier: 3.629A pdb=" N LEUAc 70 " --> pdb=" O ASNAc 66 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAc 92 " --> pdb=" O SERAc 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAc 93 " --> pdb=" O GLNAc 89 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAc 114 " --> pdb=" O THRAc 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAc 116 " --> pdb=" O METAc 112 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VALAc 117 " --> pdb=" O ASNAc 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.898A pdb=" N GLUAc 168 " --> pdb=" O SERAc 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAc 169 " --> pdb=" O ASPAc 165 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 182 through 188 removed outlier: 3.911A pdb=" N ARGAc 188 " --> pdb=" O TYRAc 184 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 210 through 219 removed outlier: 3.522A pdb=" N GLNAc 219 " --> pdb=" O GLUAc 215 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAd 70 " --> pdb=" O ASNAd 66 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAd 92 " --> pdb=" O SERAd 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAd 93 " --> pdb=" O GLNAd 89 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAd 111 " --> pdb=" O GLUAd 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAd 114 " --> pdb=" O THRAd 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAd 116 " --> pdb=" O METAd 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAd 117 " --> pdb=" O ASNAd 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.898A pdb=" N GLUAd 168 " --> pdb=" O SERAd 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAd 169 " --> pdb=" O ASPAd 165 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 182 through 188 removed outlier: 3.910A pdb=" N ARGAd 188 " --> pdb=" O TYRAd 184 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAd 219 " --> pdb=" O GLUAd 215 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 66 through 71 removed outlier: 3.629A pdb=" N LEUAe 70 " --> pdb=" O ASNAe 66 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAe 92 " --> pdb=" O SERAe 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAe 93 " --> pdb=" O GLNAe 89 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 107 through 122 removed outlier: 3.914A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAe 114 " --> pdb=" O THRAe 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAe 116 " --> pdb=" O METAe 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAe 117 " --> pdb=" O ASNAe 113 " (cutoff:3.500A) removed outlier: 3.508A 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 176 removed outlier: 3.898A pdb=" N GLUAe 168 " --> pdb=" O SERAe 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAe 169 " --> pdb=" O ASPAe 165 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 182 through 188 removed outlier: 3.910A pdb=" N ARGAe 188 " --> pdb=" O TYRAe 184 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 210 through 219 removed outlier: 3.524A pdb=" N GLNAe 219 " --> pdb=" O GLUAe 215 " (cutoff:3.500A) Processing helix chain 'Af' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAf 70 " --> pdb=" O ASNAf 66 " (cutoff:3.500A) Processing helix chain 'Af' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAf 92 " --> pdb=" O SERAf 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAf 93 " --> pdb=" O GLNAf 89 " (cutoff:3.500A) Processing helix chain 'Af' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAf 111 " --> pdb=" O GLUAf 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAf 114 " --> pdb=" O THRAf 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAf 116 " --> pdb=" O METAf 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAf 117 " --> pdb=" O ASNAf 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.898A pdb=" N GLUAf 168 " --> pdb=" O SERAf 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAf 169 " --> pdb=" O ASPAf 165 " (cutoff:3.500A) Processing helix chain 'Af' and resid 182 through 188 removed outlier: 3.910A pdb=" N ARGAf 188 " --> pdb=" O TYRAf 184 " (cutoff:3.500A) Processing helix chain 'Af' and resid 210 through 219 removed outlier: 3.522A pdb=" N GLNAf 219 " --> pdb=" O GLUAf 215 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAg 70 " --> pdb=" O ASNAg 66 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAg 92 " --> pdb=" O SERAg 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRPAg 93 " --> pdb=" O GLNAg 89 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 107 through 122 removed outlier: 3.914A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAg 114 " --> pdb=" O THRAg 110 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METAg 116 " --> pdb=" O METAg 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAg 117 " --> pdb=" O ASNAg 113 " (cutoff:3.500A) removed outlier: 3.508A 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 176 removed outlier: 3.899A pdb=" N GLUAg 168 " --> pdb=" O SERAg 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAg 169 " --> pdb=" O ASPAg 165 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 182 through 188 removed outlier: 3.911A pdb=" N ARGAg 188 " --> pdb=" O TYRAg 184 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAg 219 " --> pdb=" O GLUAg 215 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAh 70 " --> pdb=" O ASNAh 66 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAh 92 " --> pdb=" O SERAh 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAh 93 " --> pdb=" O GLNAh 89 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 107 through 122 removed outlier: 3.914A pdb=" N VALAh 111 " --> pdb=" O GLUAh 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLYAh 114 " --> pdb=" O THRAh 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAh 116 " --> pdb=" O METAh 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAh 117 " --> pdb=" O ASNAh 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.898A pdb=" N GLUAh 168 " --> pdb=" O SERAh 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAh 169 " --> pdb=" O ASPAh 165 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 182 through 188 removed outlier: 3.911A pdb=" N ARGAh 188 " --> pdb=" O TYRAh 184 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAh 219 " --> pdb=" O GLUAh 215 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAi 70 " --> pdb=" O ASNAi 66 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAi 92 " --> pdb=" O SERAi 88 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRPAi 93 " --> pdb=" O GLNAi 89 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAi 114 " --> pdb=" O THRAi 110 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METAi 116 " --> pdb=" O METAi 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAi 117 " --> pdb=" O ASNAi 113 " (cutoff:3.500A) removed outlier: 3.508A 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 176 removed outlier: 3.899A pdb=" N GLUAi 168 " --> pdb=" O SERAi 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAi 169 " --> pdb=" O ASPAi 165 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 182 through 188 removed outlier: 3.910A pdb=" N ARGAi 188 " --> pdb=" O TYRAi 184 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 210 through 219 removed outlier: 3.524A pdb=" N GLNAi 219 " --> pdb=" O GLUAi 215 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAj 70 " --> pdb=" O ASNAj 66 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAj 92 " --> pdb=" O SERAj 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAj 93 " --> pdb=" O GLNAj 89 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAj 111 " --> pdb=" O GLUAj 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAj 114 " --> pdb=" O THRAj 110 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METAj 116 " --> pdb=" O METAj 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAj 117 " --> pdb=" O ASNAj 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.899A pdb=" N GLUAj 168 " --> pdb=" O SERAj 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAj 169 " --> pdb=" O ASPAj 165 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 182 through 188 removed outlier: 3.910A pdb=" N ARGAj 188 " --> pdb=" O TYRAj 184 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAj 219 " --> pdb=" O GLUAj 215 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 66 through 71 removed outlier: 3.629A pdb=" N LEUAk 70 " --> pdb=" O ASNAk 66 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAk 92 " --> pdb=" O SERAk 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAk 93 " --> pdb=" O GLNAk 89 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAk 114 " --> pdb=" O THRAk 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAk 116 " --> pdb=" O METAk 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAk 117 " --> pdb=" O ASNAk 113 " (cutoff:3.500A) removed outlier: 3.508A 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 176 removed outlier: 3.899A pdb=" N GLUAk 168 " --> pdb=" O SERAk 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAk 169 " --> pdb=" O ASPAk 165 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 182 through 188 removed outlier: 3.910A pdb=" N ARGAk 188 " --> pdb=" O TYRAk 184 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAk 219 " --> pdb=" O GLUAk 215 " (cutoff:3.500A) Processing helix chain 'Al' and resid 66 through 71 removed outlier: 3.631A pdb=" N LEUAl 70 " --> pdb=" O ASNAl 66 " (cutoff:3.500A) Processing helix chain 'Al' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAl 92 " --> pdb=" O SERAl 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRPAl 93 " --> pdb=" O GLNAl 89 " (cutoff:3.500A) Processing helix chain 'Al' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAl 111 " --> pdb=" O GLUAl 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAl 114 " --> pdb=" O THRAl 110 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METAl 116 " --> pdb=" O METAl 112 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VALAl 117 " --> pdb=" O ASNAl 113 " (cutoff:3.500A) removed outlier: 3.508A 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 176 removed outlier: 3.899A pdb=" N GLUAl 168 " --> pdb=" O SERAl 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAl 169 " --> pdb=" O ASPAl 165 " (cutoff:3.500A) Processing helix chain 'Al' and resid 182 through 188 removed outlier: 3.911A pdb=" N ARGAl 188 " --> pdb=" O TYRAl 184 " (cutoff:3.500A) Processing helix chain 'Al' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAl 219 " --> pdb=" O GLUAl 215 " (cutoff:3.500A) Processing helix chain 'Am' and resid 66 through 71 removed outlier: 3.629A pdb=" N LEUAm 70 " --> pdb=" O ASNAm 66 " (cutoff:3.500A) Processing helix chain 'Am' and resid 86 through 102 removed outlier: 3.557A pdb=" N THRAm 92 " --> pdb=" O SERAm 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRPAm 93 " --> pdb=" O GLNAm 89 " (cutoff:3.500A) Processing helix chain 'Am' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAm 114 " --> pdb=" O THRAm 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAm 116 " --> pdb=" O METAm 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAm 117 " --> pdb=" O ASNAm 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.899A pdb=" N GLUAm 168 " --> pdb=" O SERAm 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAm 169 " --> pdb=" O ASPAm 165 " (cutoff:3.500A) Processing helix chain 'Am' and resid 182 through 188 removed outlier: 3.910A pdb=" N ARGAm 188 " --> pdb=" O TYRAm 184 " (cutoff:3.500A) Processing helix chain 'Am' and resid 210 through 219 removed outlier: 3.524A pdb=" N GLNAm 219 " --> pdb=" O GLUAm 215 " (cutoff:3.500A) Processing helix chain 'An' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAn 70 " --> pdb=" O ASNAn 66 " (cutoff:3.500A) Processing helix chain 'An' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAn 92 " --> pdb=" O SERAn 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAn 93 " --> pdb=" O GLNAn 89 " (cutoff:3.500A) Processing helix chain 'An' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAn 111 " --> pdb=" O GLUAn 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLYAn 114 " --> pdb=" O THRAn 110 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METAn 116 " --> pdb=" O METAn 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAn 117 " --> pdb=" O ASNAn 113 " (cutoff:3.500A) removed outlier: 3.508A 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 176 removed outlier: 3.898A pdb=" N GLUAn 168 " --> pdb=" O SERAn 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAn 169 " --> pdb=" O ASPAn 165 " (cutoff:3.500A) Processing helix chain 'An' and resid 182 through 188 removed outlier: 3.911A pdb=" N ARGAn 188 " --> pdb=" O TYRAn 184 " (cutoff:3.500A) Processing helix chain 'An' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAn 219 " --> pdb=" O GLUAn 215 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 66 through 71 removed outlier: 3.629A pdb=" N LEUAo 70 " --> pdb=" O ASNAo 66 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAo 92 " --> pdb=" O SERAo 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRPAo 93 " --> pdb=" O GLNAo 89 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 107 through 122 removed outlier: 3.914A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLYAo 114 " --> pdb=" O THRAo 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAo 116 " --> pdb=" O METAo 112 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VALAo 117 " --> pdb=" O ASNAo 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.899A pdb=" N GLUAo 168 " --> pdb=" O SERAo 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAo 169 " --> pdb=" O ASPAo 165 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 182 through 188 removed outlier: 3.911A pdb=" N ARGAo 188 " --> pdb=" O TYRAo 184 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAo 219 " --> pdb=" O GLUAo 215 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 66 through 71 removed outlier: 3.629A pdb=" N LEUAp 70 " --> pdb=" O ASNAp 66 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 86 through 102 removed outlier: 3.555A pdb=" N THRAp 92 " --> pdb=" O SERAp 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAp 93 " --> pdb=" O GLNAp 89 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAp 111 " --> pdb=" O GLUAp 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAp 114 " --> pdb=" O THRAp 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAp 116 " --> pdb=" O METAp 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAp 117 " --> pdb=" O ASNAp 113 " (cutoff:3.500A) removed outlier: 3.508A 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 176 removed outlier: 3.899A pdb=" N GLUAp 168 " --> pdb=" O SERAp 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAp 169 " --> pdb=" O ASPAp 165 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 182 through 188 removed outlier: 3.911A pdb=" N ARGAp 188 " --> pdb=" O TYRAp 184 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAp 219 " --> pdb=" O GLUAp 215 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 66 through 71 removed outlier: 3.629A pdb=" N LEUAq 70 " --> pdb=" O ASNAq 66 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 86 through 102 removed outlier: 3.555A pdb=" N THRAq 92 " --> pdb=" O SERAq 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAq 93 " --> pdb=" O GLNAq 89 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 107 through 122 removed outlier: 3.914A pdb=" N VALAq 111 " --> pdb=" O GLUAq 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLYAq 114 " --> pdb=" O THRAq 110 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METAq 116 " --> pdb=" O METAq 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAq 117 " --> pdb=" O ASNAq 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.900A pdb=" N GLUAq 168 " --> pdb=" O SERAq 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAq 169 " --> pdb=" O ASPAq 165 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 182 through 188 removed outlier: 3.910A pdb=" N ARGAq 188 " --> pdb=" O TYRAq 184 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAq 219 " --> pdb=" O GLUAq 215 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAr 70 " --> pdb=" O ASNAr 66 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAr 92 " --> pdb=" O SERAr 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRPAr 93 " --> pdb=" O GLNAr 89 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAr 111 " --> pdb=" O GLUAr 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAr 114 " --> pdb=" O THRAr 110 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METAr 116 " --> pdb=" O METAr 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAr 117 " --> pdb=" O ASNAr 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.898A pdb=" N GLUAr 168 " --> pdb=" O SERAr 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAr 169 " --> pdb=" O ASPAr 165 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 182 through 188 removed outlier: 3.912A pdb=" N ARGAr 188 " --> pdb=" O TYRAr 184 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 210 through 219 removed outlier: 3.522A pdb=" N GLNAr 219 " --> pdb=" O GLUAr 215 " (cutoff:3.500A) Processing helix chain 'As' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAs 70 " --> pdb=" O ASNAs 66 " (cutoff:3.500A) Processing helix chain 'As' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAs 92 " --> pdb=" O SERAs 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAs 93 " --> pdb=" O GLNAs 89 " (cutoff:3.500A) Processing helix chain 'As' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAs 114 " --> pdb=" O THRAs 110 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METAs 116 " --> pdb=" O METAs 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAs 117 " --> pdb=" O ASNAs 113 " (cutoff:3.500A) removed outlier: 3.509A 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 176 removed outlier: 3.898A pdb=" N GLUAs 168 " --> pdb=" O SERAs 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAs 169 " --> pdb=" O ASPAs 165 " (cutoff:3.500A) Processing helix chain 'As' and resid 182 through 188 removed outlier: 3.911A pdb=" N ARGAs 188 " --> pdb=" O TYRAs 184 " (cutoff:3.500A) Processing helix chain 'As' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAs 219 " --> pdb=" O GLUAs 215 " (cutoff:3.500A) Processing helix chain 'At' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAt 70 " --> pdb=" O ASNAt 66 " (cutoff:3.500A) Processing helix chain 'At' and resid 86 through 102 removed outlier: 3.557A pdb=" N THRAt 92 " --> pdb=" O SERAt 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAt 93 " --> pdb=" O GLNAt 89 " (cutoff:3.500A) Processing helix chain 'At' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAt 111 " --> pdb=" O GLUAt 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAt 114 " --> pdb=" O THRAt 110 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METAt 116 " --> pdb=" O METAt 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAt 117 " --> pdb=" O ASNAt 113 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLUAt 121 " --> pdb=" O VALAt 117 " (cutoff:3.500A) Processing helix chain 'At' and resid 145 through 151 Processing helix chain 'At' and resid 155 through 161 Processing helix chain 'At' and resid 163 through 176 removed outlier: 3.898A pdb=" N GLUAt 168 " --> pdb=" O SERAt 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAt 169 " --> pdb=" O ASPAt 165 " (cutoff:3.500A) Processing helix chain 'At' and resid 182 through 188 removed outlier: 3.912A pdb=" N ARGAt 188 " --> pdb=" O TYRAt 184 " (cutoff:3.500A) Processing helix chain 'At' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAt 219 " --> pdb=" O GLUAt 215 " (cutoff:3.500A) Processing helix chain 'Au' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAu 70 " --> pdb=" O ASNAu 66 " (cutoff:3.500A) Processing helix chain 'Au' and resid 86 through 102 removed outlier: 3.557A pdb=" N THRAu 92 " --> pdb=" O SERAu 88 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRPAu 93 " --> pdb=" O GLNAu 89 " (cutoff:3.500A) Processing helix chain 'Au' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAu 111 " --> pdb=" O GLUAu 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAu 114 " --> pdb=" O THRAu 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAu 116 " --> pdb=" O METAu 112 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VALAu 117 " --> pdb=" O ASNAu 113 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLUAu 121 " --> pdb=" O VALAu 117 " (cutoff:3.500A) Processing helix chain 'Au' and resid 145 through 151 Processing helix chain 'Au' and resid 155 through 161 Processing helix chain 'Au' and resid 163 through 176 removed outlier: 3.898A pdb=" N GLUAu 168 " --> pdb=" O SERAu 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAu 169 " --> pdb=" O ASPAu 165 " (cutoff:3.500A) Processing helix chain 'Au' and resid 182 through 188 removed outlier: 3.910A pdb=" N ARGAu 188 " --> pdb=" O TYRAu 184 " (cutoff:3.500A) Processing helix chain 'Au' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAu 219 " --> pdb=" O GLUAu 215 " (cutoff:3.500A) Processing helix chain 'Av' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAv 70 " --> pdb=" O ASNAv 66 " (cutoff:3.500A) Processing helix chain 'Av' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAv 92 " --> pdb=" O SERAv 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAv 93 " --> pdb=" O GLNAv 89 " (cutoff:3.500A) Processing helix chain 'Av' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAv 111 " --> pdb=" O GLUAv 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAv 114 " --> pdb=" O THRAv 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAv 116 " --> pdb=" O METAv 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAv 117 " --> pdb=" O ASNAv 113 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLUAv 121 " --> pdb=" O VALAv 117 " (cutoff:3.500A) Processing helix chain 'Av' and resid 145 through 151 Processing helix chain 'Av' and resid 155 through 161 Processing helix chain 'Av' and resid 163 through 176 removed outlier: 3.897A pdb=" N GLUAv 168 " --> pdb=" O SERAv 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALAAv 169 " --> pdb=" O ASPAv 165 " (cutoff:3.500A) Processing helix chain 'Av' and resid 182 through 188 removed outlier: 3.911A pdb=" N ARGAv 188 " --> pdb=" O TYRAv 184 " (cutoff:3.500A) Processing helix chain 'Av' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAv 219 " --> pdb=" O GLUAv 215 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 66 through 71 removed outlier: 3.629A pdb=" N LEUAw 70 " --> pdb=" O ASNAw 66 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 86 through 102 removed outlier: 3.555A pdb=" N THRAw 92 " --> pdb=" O SERAw 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAw 93 " --> pdb=" O GLNAw 89 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAw 111 " --> pdb=" O GLUAw 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAw 114 " --> pdb=" O THRAw 110 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N METAw 116 " --> pdb=" O METAw 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAw 117 " --> pdb=" O ASNAw 113 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLUAw 121 " --> pdb=" O VALAw 117 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 145 through 151 Processing helix chain 'Aw' and resid 155 through 161 Processing helix chain 'Aw' and resid 163 through 176 removed outlier: 3.899A pdb=" N GLUAw 168 " --> pdb=" O SERAw 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAw 169 " --> pdb=" O ASPAw 165 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 182 through 188 removed outlier: 3.910A pdb=" N ARGAw 188 " --> pdb=" O TYRAw 184 " (cutoff:3.500A) Processing helix chain 'Aw' and resid 210 through 219 removed outlier: 3.523A pdb=" N GLNAw 219 " --> pdb=" O GLUAw 215 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 66 through 71 removed outlier: 3.630A pdb=" N LEUAx 70 " --> pdb=" O ASNAx 66 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 86 through 102 removed outlier: 3.556A pdb=" N THRAx 92 " --> pdb=" O SERAx 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRPAx 93 " --> pdb=" O GLNAx 89 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 107 through 122 removed outlier: 3.913A pdb=" N VALAx 111 " --> pdb=" O GLUAx 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAx 114 " --> pdb=" O THRAx 110 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METAx 116 " --> pdb=" O METAx 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VALAx 117 " --> pdb=" O ASNAx 113 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLUAx 121 " --> pdb=" O VALAx 117 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 145 through 151 Processing helix chain 'Ax' and resid 155 through 161 Processing helix chain 'Ax' and resid 163 through 176 removed outlier: 3.898A pdb=" N GLUAx 168 " --> pdb=" O SERAx 164 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALAAx 169 " --> pdb=" O ASPAx 165 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 182 through 188 removed outlier: 3.911A pdb=" N ARGAx 188 " --> pdb=" O TYRAx 184 " (cutoff:3.500A) Processing helix chain 'Ax' and resid 210 through 219 removed outlier: 3.524A pdb=" N GLNAx 219 " --> pdb=" O GLUAx 215 " (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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 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 136 Processing sheet with id=AE3, first strand: chain 'At' and resid 58 through 59 Processing sheet with id=AE4, first strand: chain 'At' and resid 131 through 136 Processing sheet with id=AE5, first strand: chain 'Au' and resid 58 through 59 Processing sheet with id=AE6, first strand: chain 'Au' and resid 131 through 136 Processing sheet with id=AE7, first strand: chain 'Av' and resid 58 through 59 Processing sheet with id=AE8, first strand: chain 'Av' and resid 131 through 136 Processing sheet with id=AE9, first strand: chain 'Aw' and resid 58 through 59 Processing sheet with id=AF1, first strand: chain 'Aw' and resid 131 through 136 Processing sheet with id=AF2, first strand: chain 'Ax' and resid 58 through 59 Processing sheet with id=AF3, first strand: chain 'Ax' and resid 131 through 136 1152 hydrogen bonds defined for protein. 3312 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: 9.40 Time building geometry restraints manager: 10.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 10404 1.33 - 1.45: 5266 1.45 - 1.57: 19562 1.57 - 1.69: 0 1.69 - 1.81: 552 Bond restraints: 35784 Sorted by residual: bond pdb=" CA LYSAw 48 " pdb=" C LYSAw 48 " ideal model delta sigma weight residual 1.524 1.449 0.075 1.29e-02 6.01e+03 3.34e+01 bond pdb=" CA LYSAr 48 " pdb=" C LYSAr 48 " ideal model delta sigma weight residual 1.524 1.449 0.074 1.29e-02 6.01e+03 3.33e+01 bond pdb=" CA LYSAo 48 " pdb=" C LYSAo 48 " ideal model delta sigma weight residual 1.524 1.449 0.074 1.29e-02 6.01e+03 3.32e+01 bond pdb=" CA LYSAa 48 " pdb=" C LYSAa 48 " ideal model delta sigma weight residual 1.524 1.449 0.074 1.29e-02 6.01e+03 3.32e+01 bond pdb=" CA LYSAc 48 " pdb=" C LYSAc 48 " ideal model delta sigma weight residual 1.524 1.449 0.074 1.29e-02 6.01e+03 3.32e+01 ... (remaining 35779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 46975 2.12 - 4.25: 1193 4.25 - 6.37: 168 6.37 - 8.49: 120 8.49 - 10.61: 48 Bond angle restraints: 48504 Sorted by residual: angle pdb=" N ARGAb 46 " pdb=" CA ARGAb 46 " pdb=" C ARGAb 46 " ideal model delta sigma weight residual 110.24 119.12 -8.88 1.41e+00 5.03e-01 3.96e+01 angle pdb=" N ARGAh 46 " pdb=" CA ARGAh 46 " pdb=" C ARGAh 46 " ideal model delta sigma weight residual 110.24 119.12 -8.88 1.41e+00 5.03e-01 3.96e+01 angle pdb=" N ARGAv 46 " pdb=" CA ARGAv 46 " pdb=" C ARGAv 46 " ideal model delta sigma weight residual 110.24 119.11 -8.87 1.41e+00 5.03e-01 3.96e+01 angle pdb=" N ARGAx 46 " pdb=" CA ARGAx 46 " pdb=" C ARGAx 46 " ideal model delta sigma weight residual 110.24 119.10 -8.86 1.41e+00 5.03e-01 3.95e+01 angle pdb=" N ARGAt 46 " pdb=" CA ARGAt 46 " pdb=" C ARGAt 46 " ideal model delta sigma weight residual 110.24 119.10 -8.86 1.41e+00 5.03e-01 3.95e+01 ... (remaining 48499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 18239 16.23 - 32.46: 2641 32.46 - 48.69: 864 48.69 - 64.92: 192 64.92 - 81.14: 24 Dihedral angle restraints: 21960 sinusoidal: 9120 harmonic: 12840 Sorted by residual: dihedral pdb=" CA METAq 54 " pdb=" C METAq 54 " pdb=" N ARGAq 55 " pdb=" CA ARGAq 55 " ideal model delta harmonic sigma weight residual 180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA METAo 54 " pdb=" C METAo 54 " pdb=" N ARGAo 55 " pdb=" CA ARGAo 55 " ideal model delta harmonic sigma weight residual -180.00 -161.70 -18.30 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA METAj 54 " pdb=" C METAj 54 " pdb=" N ARGAj 55 " pdb=" CA ARGAj 55 " ideal model delta harmonic sigma weight residual 180.00 -161.71 -18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 21957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4355 0.061 - 0.123: 877 0.123 - 0.184: 0 0.184 - 0.245: 24 0.245 - 0.307: 24 Chirality restraints: 5280 Sorted by residual: chirality pdb=" CA ARGAv 46 " pdb=" N ARGAv 46 " pdb=" C ARGAv 46 " pdb=" CB ARGAv 46 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ARGAd 46 " pdb=" N ARGAd 46 " pdb=" C ARGAd 46 " pdb=" CB ARGAd 46 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ARGAw 46 " pdb=" N ARGAw 46 " pdb=" C ARGAw 46 " pdb=" CB ARGAw 46 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 5277 not shown) Planarity restraints: 6288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALAt 44 " -0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PROAt 45 " 0.061 5.00e-02 4.00e+02 pdb=" CA PROAt 45 " -0.018 5.00e-02 4.00e+02 pdb=" CD PROAt 45 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALAm 44 " -0.024 5.00e-02 4.00e+02 3.55e-02 2.01e+00 pdb=" N PROAm 45 " 0.061 5.00e-02 4.00e+02 pdb=" CA PROAm 45 " -0.018 5.00e-02 4.00e+02 pdb=" CD PROAm 45 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALAf 44 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PROAf 45 " -0.061 5.00e-02 4.00e+02 pdb=" CA PROAf 45 " 0.018 5.00e-02 4.00e+02 pdb=" CD PROAf 45 " 0.020 5.00e-02 4.00e+02 ... (remaining 6285 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 14575 2.89 - 3.39: 32777 3.39 - 3.90: 55064 3.90 - 4.40: 63413 4.40 - 4.90: 104526 Nonbonded interactions: 270355 Sorted by model distance: nonbonded pdb=" O ARGAk 191 " pdb=" OD1 ASPAk 192 " model vdw 2.391 3.040 nonbonded pdb=" O ARGAx 191 " pdb=" OD1 ASPAx 192 " model vdw 2.391 3.040 nonbonded pdb=" O ARGAe 191 " pdb=" OD1 ASPAe 192 " model vdw 2.392 3.040 nonbonded pdb=" O ARGAc 191 " pdb=" OD1 ASPAc 192 " model vdw 2.392 3.040 nonbonded pdb=" O ARGAh 191 " pdb=" OD1 ASPAh 192 " model vdw 2.392 3.040 ... (remaining 270350 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: 0.32 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ac' selection = chain 'Ab' selection = chain 'Ae' selection = chain 'Ad' selection = chain 'Ag' selection = chain 'Af' selection = chain 'Ai' selection = chain 'Ah' selection = chain 'Ak' selection = chain 'Aj' selection = chain 'Am' selection = chain 'Al' selection = chain 'Ao' selection = chain 'An' selection = chain 'Aq' selection = chain 'Ap' selection = chain 'As' selection = chain 'Ar' selection = chain 'Au' selection = chain 'At' selection = chain 'Aw' selection = chain 'Av' selection = chain 'Ax' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.400 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 59.360 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.150 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.006 0.075 35784 Z= 0.335 Angle : 0.864 10.613 48504 Z= 0.479 Chirality : 0.052 0.307 5280 Planarity : 0.005 0.036 6288 Dihedral : 16.746 81.144 13656 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 24.68 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.13), residues: 4296 helix: -1.12 (0.11), residues: 1800 sheet: 0.08 (0.35), residues: 240 loop : -1.70 (0.14), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRPAo 132 HIS 0.003 0.001 HISAk 217 PHE 0.012 0.002 PHEAb 202 TYR 0.011 0.002 TYRAu 73 ARG 0.006 0.001 ARGAo 55 Details of bonding type rmsd hydrogen bonds : bond 0.20195 ( 1152) hydrogen bonds : angle 7.58391 ( 3312) covalent geometry : bond 0.00596 (35784) covalent geometry : angle 0.86364 (48504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1275 time to evaluate : 4.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 56 MET cc_start: 0.8764 (mmt) cc_final: 0.8513 (mmp) REVERT: Ab 107 GLU cc_start: 0.8304 (tp30) cc_final: 0.7934 (tp30) REVERT: Ab 190 LEU cc_start: 0.8970 (tp) cc_final: 0.8707 (tp) REVERT: Ac 56 MET cc_start: 0.8757 (mmt) cc_final: 0.8513 (mmp) REVERT: Ad 107 GLU cc_start: 0.8283 (tp30) cc_final: 0.7930 (tp30) REVERT: Ad 190 LEU cc_start: 0.8989 (tp) cc_final: 0.8726 (tp) REVERT: Af 56 MET cc_start: 0.8763 (mmt) cc_final: 0.8461 (mmp) REVERT: Af 107 GLU cc_start: 0.8306 (tp30) cc_final: 0.7922 (tp30) REVERT: Af 190 LEU cc_start: 0.8973 (tp) cc_final: 0.8709 (tp) REVERT: Ag 56 MET cc_start: 0.8759 (mmt) cc_final: 0.8512 (mmp) REVERT: Ah 107 GLU cc_start: 0.8284 (tp30) cc_final: 0.7903 (tp30) REVERT: Ah 190 LEU cc_start: 0.8963 (tp) cc_final: 0.8696 (tp) REVERT: Ai 173 MET cc_start: 0.8929 (tmm) cc_final: 0.8565 (tmm) REVERT: Aj 60 LYS cc_start: 0.8932 (mttt) cc_final: 0.8732 (mttm) REVERT: Aj 89 GLN cc_start: 0.9034 (mt0) cc_final: 0.8832 (mt0) REVERT: Aj 127 ASN cc_start: 0.7804 (p0) cc_final: 0.7603 (p0) REVERT: Aj 220 MET cc_start: 0.7437 (mmt) cc_final: 0.6563 (ptm) REVERT: Ak 173 MET cc_start: 0.8947 (tmm) cc_final: 0.8579 (tmm) REVERT: Ak 220 MET cc_start: 0.7264 (mmt) cc_final: 0.6388 (ptm) REVERT: Al 89 GLN cc_start: 0.9044 (mt0) cc_final: 0.8827 (mt0) REVERT: Al 127 ASN cc_start: 0.7827 (p0) cc_final: 0.7617 (p0) REVERT: Al 179 PRO cc_start: 0.8619 (Cg_exo) cc_final: 0.8397 (Cg_endo) REVERT: Al 220 MET cc_start: 0.7321 (mmt) cc_final: 0.6455 (ptm) REVERT: Am 173 MET cc_start: 0.8953 (tmm) cc_final: 0.8581 (tmm) REVERT: An 60 LYS cc_start: 0.8964 (mttt) cc_final: 0.8762 (mttm) REVERT: An 89 GLN cc_start: 0.9042 (mt0) cc_final: 0.8826 (mt0) REVERT: An 179 PRO cc_start: 0.8606 (Cg_exo) cc_final: 0.8395 (Cg_endo) REVERT: An 220 MET cc_start: 0.7324 (mmt) cc_final: 0.6462 (ptm) REVERT: Ao 173 MET cc_start: 0.8943 (tmm) cc_final: 0.8560 (tmm) REVERT: Ap 89 GLN cc_start: 0.9032 (mt0) cc_final: 0.8818 (mt0) REVERT: Ap 127 ASN cc_start: 0.7825 (p0) cc_final: 0.7594 (p0) REVERT: Ap 179 PRO cc_start: 0.8551 (Cg_exo) cc_final: 0.8334 (Cg_endo) REVERT: Ap 220 MET cc_start: 0.7481 (mmt) cc_final: 0.6590 (ptm) REVERT: Aq 56 MET cc_start: 0.8844 (mmt) cc_final: 0.8606 (mmm) REVERT: Aq 179 PRO cc_start: 0.8633 (Cg_exo) cc_final: 0.8429 (Cg_endo) REVERT: Aq 190 LEU cc_start: 0.8924 (tp) cc_final: 0.8589 (tp) REVERT: Aq 220 MET cc_start: 0.7176 (mmt) cc_final: 0.6517 (ptm) REVERT: Ar 48 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8625 (ttmm) REVERT: Ar 56 MET cc_start: 0.8761 (mmt) cc_final: 0.8527 (mmp) REVERT: Ar 89 GLN cc_start: 0.9058 (mt0) cc_final: 0.8764 (mt0) REVERT: Ar 179 PRO cc_start: 0.8547 (Cg_exo) cc_final: 0.8321 (Cg_endo) REVERT: Ar 190 LEU cc_start: 0.8946 (tp) cc_final: 0.8706 (tp) REVERT: As 56 MET cc_start: 0.8851 (mmt) cc_final: 0.8604 (mmm) REVERT: As 190 LEU cc_start: 0.8934 (tp) cc_final: 0.8602 (tp) REVERT: As 220 MET cc_start: 0.7189 (mmt) cc_final: 0.6523 (ptm) REVERT: At 48 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8618 (ttmm) REVERT: At 56 MET cc_start: 0.8786 (mmt) cc_final: 0.8551 (mmp) REVERT: At 89 GLN cc_start: 0.9058 (mt0) cc_final: 0.8763 (mt0) REVERT: At 179 PRO cc_start: 0.8537 (Cg_exo) cc_final: 0.8302 (Cg_endo) REVERT: At 190 LEU cc_start: 0.8955 (tp) cc_final: 0.8718 (tp) REVERT: Au 179 PRO cc_start: 0.8646 (Cg_exo) cc_final: 0.8433 (Cg_endo) REVERT: Au 190 LEU cc_start: 0.8945 (tp) cc_final: 0.8597 (tp) REVERT: Au 220 MET cc_start: 0.7161 (mmt) cc_final: 0.6503 (ptm) REVERT: Av 48 LYS cc_start: 0.8851 (ttmm) cc_final: 0.8626 (ttmm) REVERT: Av 56 MET cc_start: 0.8749 (mmt) cc_final: 0.8514 (mmp) REVERT: Av 76 GLN cc_start: 0.8336 (mm110) cc_final: 0.8084 (mm-40) REVERT: Av 89 GLN cc_start: 0.9044 (mt0) cc_final: 0.8751 (mt0) REVERT: Av 179 PRO cc_start: 0.8570 (Cg_exo) cc_final: 0.8339 (Cg_endo) REVERT: Av 190 LEU cc_start: 0.8951 (tp) cc_final: 0.8713 (tp) REVERT: Aw 56 MET cc_start: 0.8840 (mmt) cc_final: 0.8638 (mmm) REVERT: Aw 179 PRO cc_start: 0.8620 (Cg_exo) cc_final: 0.8393 (Cg_endo) REVERT: Aw 190 LEU cc_start: 0.8932 (tp) cc_final: 0.8568 (tp) REVERT: Aw 220 MET cc_start: 0.7185 (mmt) cc_final: 0.6496 (ptm) REVERT: Ax 48 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8572 (ttmm) REVERT: Ax 56 MET cc_start: 0.8787 (mmt) cc_final: 0.8533 (mmp) REVERT: Ax 76 GLN cc_start: 0.8387 (mm110) cc_final: 0.8139 (mm-40) REVERT: Ax 89 GLN cc_start: 0.9039 (mt0) cc_final: 0.8741 (mt0) REVERT: Ax 179 PRO cc_start: 0.8537 (Cg_exo) cc_final: 0.8292 (Cg_endo) REVERT: Ax 190 LEU cc_start: 0.8943 (tp) cc_final: 0.8708 (tp) outliers start: 0 outliers final: 0 residues processed: 1275 average time/residue: 0.4622 time to fit residues: 961.0932 Evaluate side-chains 1157 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1157 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 8.9990 chunk 327 optimal weight: 0.0970 chunk 181 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 220 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 chunk 392 optimal weight: 5.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 89 GLN ** Aa 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 89 GLN ** Ac 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 89 GLN ** Ae 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 89 GLN ** Ag 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 151 ASN ** Aj 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 151 ASN ** Ak 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 151 ASN ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN ** Am 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 151 ASN ** An 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 151 ASN ** Ao 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 151 ASN ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 151 ASN ** Aq 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 151 ASN ** Ar 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 151 ASN ** As 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 151 ASN ** At 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 151 ASN ** Au 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 151 ASN ** Av 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 151 ASN ** Ax 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 151 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.093570 restraints weight = 52338.148| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.64 r_work: 0.2913 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 35784 Z= 0.255 Angle : 0.655 7.677 48504 Z= 0.329 Chirality : 0.045 0.135 5280 Planarity : 0.005 0.041 6288 Dihedral : 4.565 15.885 4824 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.74 % Allowed : 21.78 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 4296 helix: 0.06 (0.12), residues: 1584 sheet: -0.37 (0.34), residues: 288 loop : -1.18 (0.15), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRPAd 93 HIS 0.008 0.001 HISAb 69 PHE 0.013 0.003 PHEAc 202 TYR 0.012 0.002 TYRAb 94 ARG 0.003 0.001 ARGAa 55 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 1152) hydrogen bonds : angle 5.65278 ( 3312) covalent geometry : bond 0.00616 (35784) covalent geometry : angle 0.65494 (48504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1333 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1191 time to evaluate : 3.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 102 ASP cc_start: 0.8460 (t70) cc_final: 0.8260 (t0) REVERT: Ab 136 ASP cc_start: 0.8276 (t0) cc_final: 0.8065 (t0) REVERT: Ab 190 LEU cc_start: 0.8984 (tp) cc_final: 0.8721 (tp) REVERT: Ad 190 LEU cc_start: 0.8974 (tp) cc_final: 0.8712 (tp) REVERT: Af 102 ASP cc_start: 0.8446 (t70) cc_final: 0.8239 (t0) REVERT: Af 136 ASP cc_start: 0.8276 (t0) cc_final: 0.8064 (t0) REVERT: Af 190 LEU cc_start: 0.8984 (tp) cc_final: 0.8721 (tp) REVERT: Ag 48 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8471 (ttmm) REVERT: Ah 102 ASP cc_start: 0.8468 (t70) cc_final: 0.8261 (t0) REVERT: Ah 190 LEU cc_start: 0.8989 (tp) cc_final: 0.8725 (tp) REVERT: Ai 102 ASP cc_start: 0.8701 (t70) cc_final: 0.8422 (t0) REVERT: Ai 124 THR cc_start: 0.9292 (p) cc_final: 0.9043 (p) REVERT: Ai 127 ASN cc_start: 0.7995 (p0) cc_final: 0.7738 (p0) REVERT: Ai 173 MET cc_start: 0.8840 (tmm) cc_final: 0.8455 (tmm) REVERT: Ai 190 LEU cc_start: 0.8849 (tp) cc_final: 0.8523 (tp) REVERT: Aj 102 ASP cc_start: 0.8575 (t70) cc_final: 0.8322 (t0) REVERT: Aj 127 ASN cc_start: 0.7927 (p0) cc_final: 0.7593 (p0) REVERT: Aj 136 ASP cc_start: 0.8249 (t0) cc_final: 0.8029 (t0) REVERT: Ak 102 ASP cc_start: 0.8636 (t70) cc_final: 0.8365 (t0) REVERT: Ak 124 THR cc_start: 0.9310 (p) cc_final: 0.9056 (p) REVERT: Ak 173 MET cc_start: 0.8853 (tmm) cc_final: 0.8481 (tmm) REVERT: Ak 190 LEU cc_start: 0.8860 (tp) cc_final: 0.8540 (tp) REVERT: Al 102 ASP cc_start: 0.8577 (t70) cc_final: 0.8325 (t0) REVERT: Al 127 ASN cc_start: 0.7934 (p0) cc_final: 0.7607 (p0) REVERT: Al 136 ASP cc_start: 0.8246 (t0) cc_final: 0.8038 (t0) REVERT: Al 179 PRO cc_start: 0.8629 (Cg_exo) cc_final: 0.8423 (Cg_endo) REVERT: Am 102 ASP cc_start: 0.8692 (t70) cc_final: 0.8396 (t0) REVERT: Am 124 THR cc_start: 0.9298 (p) cc_final: 0.9050 (p) REVERT: Am 127 ASN cc_start: 0.8004 (p0) cc_final: 0.7761 (p0) REVERT: Am 173 MET cc_start: 0.8846 (tmm) cc_final: 0.8466 (tmm) REVERT: Am 190 LEU cc_start: 0.8837 (tp) cc_final: 0.8501 (tp) REVERT: An 102 ASP cc_start: 0.8569 (t70) cc_final: 0.8200 (t0) REVERT: An 127 ASN cc_start: 0.7934 (p0) cc_final: 0.7718 (p0) REVERT: An 136 ASP cc_start: 0.8250 (t0) cc_final: 0.8043 (t0) REVERT: Ao 102 ASP cc_start: 0.8687 (t70) cc_final: 0.8397 (t0) REVERT: Ao 124 THR cc_start: 0.9302 (p) cc_final: 0.9048 (p) REVERT: Ao 173 MET cc_start: 0.8836 (tmm) cc_final: 0.8443 (tmm) REVERT: Ao 190 LEU cc_start: 0.8838 (tp) cc_final: 0.8501 (tp) REVERT: Ap 102 ASP cc_start: 0.8558 (t70) cc_final: 0.8306 (t0) REVERT: Ap 127 ASN cc_start: 0.7937 (p0) cc_final: 0.7609 (p0) REVERT: Ap 136 ASP cc_start: 0.8224 (t0) cc_final: 0.8013 (t0) REVERT: Aq 127 ASN cc_start: 0.7928 (p0) cc_final: 0.7663 (p0) REVERT: Aq 190 LEU cc_start: 0.8925 (tp) cc_final: 0.8555 (tp) REVERT: Ar 89 GLN cc_start: 0.9115 (mt0) cc_final: 0.8824 (mt0) REVERT: Ar 136 ASP cc_start: 0.8037 (t0) cc_final: 0.7811 (t0) REVERT: Ar 179 PRO cc_start: 0.8655 (Cg_exo) cc_final: 0.8442 (Cg_endo) REVERT: As 69 HIS cc_start: 0.8231 (t-90) cc_final: 0.8014 (t-90) REVERT: As 70 LEU cc_start: 0.9100 (tp) cc_final: 0.8884 (tp) REVERT: As 190 LEU cc_start: 0.8932 (tp) cc_final: 0.8560 (tp) REVERT: At 89 GLN cc_start: 0.9119 (mt0) cc_final: 0.8833 (mt0) REVERT: At 127 ASN cc_start: 0.7928 (p0) cc_final: 0.7714 (p0) REVERT: At 136 ASP cc_start: 0.8033 (t0) cc_final: 0.7809 (t0) REVERT: At 179 PRO cc_start: 0.8634 (Cg_exo) cc_final: 0.8409 (Cg_endo) REVERT: Au 69 HIS cc_start: 0.8263 (t-90) cc_final: 0.8051 (t-90) REVERT: Au 70 LEU cc_start: 0.9095 (tp) cc_final: 0.8873 (tp) REVERT: Au 127 ASN cc_start: 0.7937 (p0) cc_final: 0.7677 (p0) REVERT: Au 190 LEU cc_start: 0.8942 (tp) cc_final: 0.8587 (tp) REVERT: Av 89 GLN cc_start: 0.9111 (mt0) cc_final: 0.8841 (mt0) REVERT: Av 136 ASP cc_start: 0.8086 (t0) cc_final: 0.7858 (t0) REVERT: Av 179 PRO cc_start: 0.8658 (Cg_exo) cc_final: 0.8437 (Cg_endo) REVERT: Aw 127 ASN cc_start: 0.7979 (p0) cc_final: 0.7711 (p0) REVERT: Aw 190 LEU cc_start: 0.8898 (tp) cc_final: 0.8513 (tp) REVERT: Ax 89 GLN cc_start: 0.9114 (mt0) cc_final: 0.8840 (mt0) REVERT: Ax 127 ASN cc_start: 0.7936 (p0) cc_final: 0.7721 (p0) REVERT: Ax 136 ASP cc_start: 0.8012 (t0) cc_final: 0.7782 (t0) REVERT: Ax 179 PRO cc_start: 0.8656 (Cg_exo) cc_final: 0.8441 (Cg_endo) outliers start: 142 outliers final: 115 residues processed: 1269 average time/residue: 0.4250 time to fit residues: 894.3246 Evaluate side-chains 1278 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1163 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 80 ILE Chi-restraints excluded: chain Aa residue 88 SER Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Ab residue 43 THR Chi-restraints excluded: chain Ab residue 88 SER Chi-restraints excluded: chain Ab residue 141 VAL Chi-restraints excluded: chain Ac residue 80 ILE Chi-restraints excluded: chain Ac residue 88 SER Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ad residue 43 THR Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 141 VAL Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Af residue 43 THR Chi-restraints excluded: chain Af residue 88 SER Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 88 SER Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ah residue 43 THR Chi-restraints excluded: chain Ah residue 88 SER Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ai residue 43 THR Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 70 LEU Chi-restraints excluded: chain Ai residue 80 ILE Chi-restraints excluded: chain Ai residue 88 SER Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Aj residue 43 THR Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 141 VAL Chi-restraints excluded: chain Ak residue 43 THR Chi-restraints excluded: chain Ak residue 44 VAL Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 88 SER Chi-restraints excluded: chain Ak residue 111 VAL Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Al residue 43 THR Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 111 VAL Chi-restraints excluded: chain Al residue 141 VAL Chi-restraints excluded: chain Am residue 43 THR Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 80 ILE Chi-restraints excluded: chain Am residue 88 SER Chi-restraints excluded: chain Am residue 111 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain An residue 43 THR Chi-restraints excluded: chain An residue 80 ILE Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 111 VAL Chi-restraints excluded: chain An residue 141 VAL Chi-restraints excluded: chain Ao residue 43 THR Chi-restraints excluded: chain Ao residue 44 VAL Chi-restraints excluded: chain Ao residue 80 ILE Chi-restraints excluded: chain Ao residue 88 SER Chi-restraints excluded: chain Ao residue 111 VAL Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ap residue 43 THR Chi-restraints excluded: chain Ap residue 80 ILE Chi-restraints excluded: chain Ap residue 88 SER Chi-restraints excluded: chain Ap residue 111 VAL Chi-restraints excluded: chain Ap residue 141 VAL Chi-restraints excluded: chain Aq residue 43 THR Chi-restraints excluded: chain Aq residue 80 ILE Chi-restraints excluded: chain Aq residue 88 SER Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 141 VAL Chi-restraints excluded: chain Ar residue 43 THR Chi-restraints excluded: chain Ar residue 78 ILE Chi-restraints excluded: chain Ar residue 80 ILE Chi-restraints excluded: chain Ar residue 88 SER Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 141 VAL Chi-restraints excluded: chain Ar residue 150 GLU Chi-restraints excluded: chain As residue 43 THR Chi-restraints excluded: chain As residue 80 ILE Chi-restraints excluded: chain As residue 88 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain At residue 43 THR Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 80 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 141 VAL Chi-restraints excluded: chain At residue 150 GLU Chi-restraints excluded: chain Au residue 43 THR Chi-restraints excluded: chain Au residue 80 ILE Chi-restraints excluded: chain Au residue 88 SER Chi-restraints excluded: chain Au residue 141 VAL Chi-restraints excluded: chain Av residue 43 THR Chi-restraints excluded: chain Av residue 78 ILE Chi-restraints excluded: chain Av residue 80 ILE Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 141 VAL Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Aw residue 43 THR Chi-restraints excluded: chain Aw residue 59 SER Chi-restraints excluded: chain Aw residue 80 ILE Chi-restraints excluded: chain Aw residue 88 SER Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 141 VAL Chi-restraints excluded: chain Ax residue 43 THR Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 80 ILE Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 141 VAL Chi-restraints excluded: chain Ax residue 150 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 148 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 245 optimal weight: 0.8980 chunk 361 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 390 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 383 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 89 GLN Aa 98 GLN ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 98 GLN Ac 89 GLN Ac 98 GLN ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 98 GLN Ad 189 ASN Ae 89 GLN Ae 98 GLN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 89 GLN Ag 98 GLN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 98 GLN Ah 189 ASN ** Ai 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 158 GLN ** Aj 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 158 GLN ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 158 GLN ** An 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 158 GLN ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 98 GLN ** As 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 76 GLN ** Au 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 98 GLN ** Ax 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.097082 restraints weight = 51467.369| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.67 r_work: 0.2992 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35784 Z= 0.109 Angle : 0.557 8.028 48504 Z= 0.278 Chirality : 0.040 0.129 5280 Planarity : 0.005 0.039 6288 Dihedral : 4.267 14.725 4824 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.93 % Allowed : 26.95 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4296 helix: 0.31 (0.12), residues: 1584 sheet: 0.08 (0.35), residues: 288 loop : -1.17 (0.14), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPAu 132 HIS 0.007 0.001 HISAd 69 PHE 0.009 0.002 PHEAh 200 TYR 0.020 0.001 TYRAs 198 ARG 0.003 0.000 ARGAl 55 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 1152) hydrogen bonds : angle 5.13663 ( 3312) covalent geometry : bond 0.00269 (35784) covalent geometry : angle 0.55680 (48504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1173 time to evaluate : 3.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 48 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8591 (ttmm) REVERT: Aa 70 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8704 (tp) REVERT: Aa 81 SER cc_start: 0.9499 (t) cc_final: 0.9291 (t) REVERT: Ab 70 LEU cc_start: 0.9112 (tp) cc_final: 0.8749 (tp) REVERT: Ab 136 ASP cc_start: 0.8321 (t0) cc_final: 0.8027 (t0) REVERT: Ab 190 LEU cc_start: 0.8968 (tp) cc_final: 0.8712 (tp) REVERT: Ac 70 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8684 (tp) REVERT: Ac 81 SER cc_start: 0.9499 (t) cc_final: 0.9293 (t) REVERT: Ad 70 LEU cc_start: 0.9106 (tp) cc_final: 0.8746 (tp) REVERT: Ad 135 MET cc_start: 0.8776 (mmm) cc_final: 0.8541 (mmm) REVERT: Ad 190 LEU cc_start: 0.8964 (tp) cc_final: 0.8715 (tp) REVERT: Ae 48 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8582 (ttmm) REVERT: Ae 70 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8692 (tp) REVERT: Ae 81 SER cc_start: 0.9495 (t) cc_final: 0.9287 (t) REVERT: Af 70 LEU cc_start: 0.9095 (tp) cc_final: 0.8719 (tp) REVERT: Af 136 ASP cc_start: 0.8319 (t0) cc_final: 0.8029 (t0) REVERT: Af 190 LEU cc_start: 0.8970 (tp) cc_final: 0.8705 (tp) REVERT: Ag 70 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8657 (tp) REVERT: Ag 81 SER cc_start: 0.9500 (t) cc_final: 0.9293 (t) REVERT: Ah 70 LEU cc_start: 0.9100 (tp) cc_final: 0.8737 (tp) REVERT: Ah 190 LEU cc_start: 0.8968 (tp) cc_final: 0.8720 (tp) REVERT: Ai 48 LYS cc_start: 0.8638 (tppt) cc_final: 0.8411 (tptt) REVERT: Ai 102 ASP cc_start: 0.8635 (t70) cc_final: 0.8412 (t0) REVERT: Ai 127 ASN cc_start: 0.7902 (p0) cc_final: 0.7666 (p0) REVERT: Ai 173 MET cc_start: 0.8828 (tmm) cc_final: 0.8466 (tmm) REVERT: Aj 70 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8624 (tp) REVERT: Aj 102 ASP cc_start: 0.8513 (t70) cc_final: 0.8258 (t0) REVERT: Aj 127 ASN cc_start: 0.7850 (p0) cc_final: 0.7540 (p0) REVERT: Aj 136 ASP cc_start: 0.8130 (t0) cc_final: 0.7909 (t0) REVERT: Ak 48 LYS cc_start: 0.8645 (tppt) cc_final: 0.8415 (tptt) REVERT: Ak 70 LEU cc_start: 0.9065 (tp) cc_final: 0.8751 (tp) REVERT: Ak 102 ASP cc_start: 0.8624 (t70) cc_final: 0.8402 (t0) REVERT: Ak 127 ASN cc_start: 0.7931 (p0) cc_final: 0.7584 (p0) REVERT: Ak 173 MET cc_start: 0.8840 (tmm) cc_final: 0.8498 (tmm) REVERT: Al 70 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8609 (tp) REVERT: Al 102 ASP cc_start: 0.8492 (t70) cc_final: 0.8166 (t0) REVERT: Al 127 ASN cc_start: 0.7856 (p0) cc_final: 0.7539 (p0) REVERT: Al 136 ASP cc_start: 0.8139 (t0) cc_final: 0.7923 (t0) REVERT: Am 48 LYS cc_start: 0.8639 (tppt) cc_final: 0.8409 (tptt) REVERT: Am 102 ASP cc_start: 0.8644 (t70) cc_final: 0.8396 (t0) REVERT: Am 127 ASN cc_start: 0.7912 (p0) cc_final: 0.7680 (p0) REVERT: Am 173 MET cc_start: 0.8825 (tmm) cc_final: 0.8474 (tmm) REVERT: An 70 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8604 (tp) REVERT: An 102 ASP cc_start: 0.8494 (t70) cc_final: 0.8241 (t0) REVERT: An 127 ASN cc_start: 0.7879 (p0) cc_final: 0.7660 (p0) REVERT: An 136 ASP cc_start: 0.8153 (t0) cc_final: 0.7938 (t0) REVERT: Ao 48 LYS cc_start: 0.8660 (tppt) cc_final: 0.8418 (tptt) REVERT: Ao 102 ASP cc_start: 0.8644 (t70) cc_final: 0.8409 (t0) REVERT: Ao 127 ASN cc_start: 0.7933 (p0) cc_final: 0.7633 (p0) REVERT: Ap 70 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8630 (tp) REVERT: Ap 102 ASP cc_start: 0.8480 (t70) cc_final: 0.8159 (t0) REVERT: Ap 127 ASN cc_start: 0.7869 (p0) cc_final: 0.7548 (p0) REVERT: Ap 136 ASP cc_start: 0.8143 (t0) cc_final: 0.7917 (t0) REVERT: Aq 127 ASN cc_start: 0.7863 (p0) cc_final: 0.7541 (p0) REVERT: Aq 181 MET cc_start: 0.8533 (tpp) cc_final: 0.8262 (tpp) REVERT: Aq 190 LEU cc_start: 0.8907 (tp) cc_final: 0.8389 (tp) REVERT: Ar 89 GLN cc_start: 0.9118 (mt0) cc_final: 0.8837 (mt0) REVERT: Ar 136 ASP cc_start: 0.8106 (t0) cc_final: 0.7741 (t0) REVERT: Ar 179 PRO cc_start: 0.8561 (Cg_exo) cc_final: 0.8315 (Cg_endo) REVERT: Ar 190 LEU cc_start: 0.8968 (tp) cc_final: 0.8704 (tp) REVERT: As 69 HIS cc_start: 0.8291 (t-90) cc_final: 0.8024 (t-90) REVERT: As 70 LEU cc_start: 0.9076 (tp) cc_final: 0.8723 (tp) REVERT: As 181 MET cc_start: 0.8519 (tpp) cc_final: 0.8254 (tpp) REVERT: As 190 LEU cc_start: 0.8912 (tp) cc_final: 0.8379 (tp) REVERT: At 89 GLN cc_start: 0.9106 (mt0) cc_final: 0.8834 (mt0) REVERT: At 136 ASP cc_start: 0.8099 (t0) cc_final: 0.7732 (t0) REVERT: At 190 LEU cc_start: 0.8969 (tp) cc_final: 0.8713 (tp) REVERT: Au 69 HIS cc_start: 0.8302 (t-90) cc_final: 0.8034 (t-90) REVERT: Au 70 LEU cc_start: 0.9109 (tp) cc_final: 0.8648 (tp) REVERT: Au 127 ASN cc_start: 0.7874 (p0) cc_final: 0.7495 (p0) REVERT: Au 181 MET cc_start: 0.8524 (tpp) cc_final: 0.8258 (tpp) REVERT: Au 190 LEU cc_start: 0.8940 (tp) cc_final: 0.8426 (tp) REVERT: Au 198 TYR cc_start: 0.9046 (m-10) cc_final: 0.8835 (m-10) REVERT: Av 89 GLN cc_start: 0.9098 (mt0) cc_final: 0.8817 (mt0) REVERT: Av 136 ASP cc_start: 0.8098 (t0) cc_final: 0.7729 (t0) REVERT: Av 179 PRO cc_start: 0.8596 (Cg_exo) cc_final: 0.8354 (Cg_endo) REVERT: Av 190 LEU cc_start: 0.9011 (tp) cc_final: 0.8743 (tp) REVERT: Aw 190 LEU cc_start: 0.8899 (tp) cc_final: 0.8538 (tp) REVERT: Aw 198 TYR cc_start: 0.9046 (m-10) cc_final: 0.8821 (m-10) REVERT: Ax 89 GLN cc_start: 0.9109 (mt0) cc_final: 0.8838 (mt0) REVERT: Ax 136 ASP cc_start: 0.8097 (t0) cc_final: 0.7738 (t0) REVERT: Ax 179 PRO cc_start: 0.8581 (Cg_exo) cc_final: 0.8338 (Cg_endo) REVERT: Ax 190 LEU cc_start: 0.8961 (tp) cc_final: 0.8687 (tp) outliers start: 111 outliers final: 57 residues processed: 1263 average time/residue: 0.4405 time to fit residues: 921.5832 Evaluate side-chains 1152 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1087 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 70 LEU Chi-restraints excluded: chain Aa residue 88 SER Chi-restraints excluded: chain Ab residue 88 SER Chi-restraints excluded: chain Ac residue 70 LEU Chi-restraints excluded: chain Ac residue 88 SER Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ae residue 43 THR Chi-restraints excluded: chain Ae residue 70 LEU Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Af residue 88 SER Chi-restraints excluded: chain Ag residue 70 LEU Chi-restraints excluded: chain Ag residue 88 SER Chi-restraints excluded: chain Ah residue 88 SER Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 70 LEU Chi-restraints excluded: chain Ai residue 88 SER Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 70 LEU Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Ak residue 44 VAL Chi-restraints excluded: chain Ak residue 88 SER Chi-restraints excluded: chain Ak residue 125 SER Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Al residue 70 LEU Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 88 SER Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 70 LEU Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain Ao residue 44 VAL Chi-restraints excluded: chain Ao residue 88 SER Chi-restraints excluded: chain Ao residue 125 SER Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ap residue 70 LEU Chi-restraints excluded: chain Ap residue 88 SER Chi-restraints excluded: chain Aq residue 59 SER Chi-restraints excluded: chain Aq residue 88 SER Chi-restraints excluded: chain Aq residue 125 SER Chi-restraints excluded: chain Ar residue 70 LEU Chi-restraints excluded: chain Ar residue 78 ILE Chi-restraints excluded: chain Ar residue 88 SER Chi-restraints excluded: chain Ar residue 150 GLU Chi-restraints excluded: chain Ar residue 205 VAL Chi-restraints excluded: chain As residue 59 SER Chi-restraints excluded: chain As residue 88 SER Chi-restraints excluded: chain At residue 70 LEU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 150 GLU Chi-restraints excluded: chain At residue 205 VAL Chi-restraints excluded: chain Au residue 59 SER Chi-restraints excluded: chain Au residue 88 SER Chi-restraints excluded: chain Au residue 125 SER Chi-restraints excluded: chain Av residue 70 LEU Chi-restraints excluded: chain Av residue 78 ILE Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Av residue 205 VAL Chi-restraints excluded: chain Aw residue 88 SER Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 150 GLU Chi-restraints excluded: chain Ax residue 205 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 190 optimal weight: 0.3980 chunk 312 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 206 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 289 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 89 GLN ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 151 ASN Ac 89 GLN ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 151 ASN Ae 89 GLN Af 98 GLN Af 151 ASN Ag 89 GLN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 151 ASN ** Ai 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 175 ASN ** Ak 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 175 ASN Am 98 GLN ** An 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 175 ASN ** Ao 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 175 ASN Aq 98 GLN Aq 175 ASN As 98 GLN As 175 ASN ** At 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 98 GLN Au 158 GLN Au 175 ASN ** Av 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aw 158 GLN Ax 98 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.097748 restraints weight = 52106.548| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.67 r_work: 0.2992 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35784 Z= 0.109 Angle : 0.554 8.498 48504 Z= 0.277 Chirality : 0.040 0.135 5280 Planarity : 0.005 0.047 6288 Dihedral : 4.187 16.677 4824 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.30 % Allowed : 28.48 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 4296 helix: 0.21 (0.12), residues: 1728 sheet: 0.39 (0.36), residues: 288 loop : -1.19 (0.15), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPAm 132 HIS 0.006 0.000 HISAb 69 PHE 0.009 0.002 PHEAd 200 TYR 0.013 0.001 TYRAq 198 ARG 0.006 0.000 ARGAe 55 Details of bonding type rmsd hydrogen bonds : bond 0.02664 ( 1152) hydrogen bonds : angle 5.00603 ( 3312) covalent geometry : bond 0.00269 (35784) covalent geometry : angle 0.55439 (48504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1262 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1137 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 54 MET cc_start: 0.7668 (ttp) cc_final: 0.7424 (ttp) REVERT: Aa 70 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8710 (tp) REVERT: Aa 81 SER cc_start: 0.9498 (t) cc_final: 0.9291 (t) REVERT: Ab 136 ASP cc_start: 0.8336 (t0) cc_final: 0.7980 (t0) REVERT: Ab 151 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.7980 (t0) REVERT: Ab 190 LEU cc_start: 0.8969 (tp) cc_final: 0.8691 (tp) REVERT: Ac 70 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8704 (tp) REVERT: Ac 81 SER cc_start: 0.9488 (t) cc_final: 0.9282 (t) REVERT: Ad 151 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.7998 (t0) REVERT: Ad 190 LEU cc_start: 0.8970 (tp) cc_final: 0.8710 (tp) REVERT: Ae 70 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8708 (tp) REVERT: Ae 81 SER cc_start: 0.9498 (t) cc_final: 0.9291 (t) REVERT: Af 70 LEU cc_start: 0.8692 (tp) cc_final: 0.8290 (tp) REVERT: Af 136 ASP cc_start: 0.8311 (t0) cc_final: 0.7978 (t0) REVERT: Af 151 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.7941 (t0) REVERT: Af 190 LEU cc_start: 0.8962 (tp) cc_final: 0.8684 (tp) REVERT: Ag 70 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8716 (tp) REVERT: Ag 81 SER cc_start: 0.9489 (t) cc_final: 0.9283 (t) REVERT: Ah 151 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.7976 (t0) REVERT: Ah 190 LEU cc_start: 0.8980 (tp) cc_final: 0.8715 (tp) REVERT: Ai 48 LYS cc_start: 0.8668 (tppt) cc_final: 0.8418 (tptt) REVERT: Ai 102 ASP cc_start: 0.8637 (t70) cc_final: 0.8428 (t0) REVERT: Ai 127 ASN cc_start: 0.7898 (p0) cc_final: 0.7659 (p0) REVERT: Ai 173 MET cc_start: 0.8827 (tmm) cc_final: 0.8475 (tmm) REVERT: Ai 198 TYR cc_start: 0.8965 (m-10) cc_final: 0.8615 (m-10) REVERT: Aj 70 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8563 (tp) REVERT: Aj 102 ASP cc_start: 0.8518 (t70) cc_final: 0.8316 (t0) REVERT: Aj 127 ASN cc_start: 0.7868 (p0) cc_final: 0.7591 (p0) REVERT: Aj 136 ASP cc_start: 0.8219 (t0) cc_final: 0.7986 (t0) REVERT: Ak 70 LEU cc_start: 0.9059 (tp) cc_final: 0.8737 (tp) REVERT: Ak 102 ASP cc_start: 0.8626 (t70) cc_final: 0.8405 (t0) REVERT: Ak 127 ASN cc_start: 0.7981 (p0) cc_final: 0.7671 (p0) REVERT: Ak 198 TYR cc_start: 0.8981 (m-10) cc_final: 0.8629 (m-10) REVERT: Al 70 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8601 (tp) REVERT: Al 127 ASN cc_start: 0.7880 (p0) cc_final: 0.7595 (p0) REVERT: Al 136 ASP cc_start: 0.8190 (t0) cc_final: 0.7946 (t0) REVERT: Al 142 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8626 (mt-10) REVERT: Am 48 LYS cc_start: 0.8658 (tppt) cc_final: 0.8417 (tptt) REVERT: Am 70 LEU cc_start: 0.9055 (tp) cc_final: 0.8660 (tp) REVERT: Am 102 ASP cc_start: 0.8655 (t70) cc_final: 0.8428 (t0) REVERT: Am 127 ASN cc_start: 0.7907 (p0) cc_final: 0.7663 (p0) REVERT: Am 198 TYR cc_start: 0.8969 (m-10) cc_final: 0.8628 (m-10) REVERT: An 70 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8614 (tp) REVERT: An 102 ASP cc_start: 0.8506 (t70) cc_final: 0.8295 (t0) REVERT: An 127 ASN cc_start: 0.7835 (p0) cc_final: 0.7607 (p0) REVERT: An 136 ASP cc_start: 0.8199 (t0) cc_final: 0.7962 (t0) REVERT: Ao 48 LYS cc_start: 0.8639 (tppt) cc_final: 0.8434 (tptt) REVERT: Ao 70 LEU cc_start: 0.9060 (tp) cc_final: 0.8662 (tp) REVERT: Ao 102 ASP cc_start: 0.8653 (t70) cc_final: 0.8435 (t0) REVERT: Ao 127 ASN cc_start: 0.7954 (p0) cc_final: 0.7652 (p0) REVERT: Ao 181 MET cc_start: 0.8649 (tpp) cc_final: 0.8332 (tpp) REVERT: Ap 70 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8615 (tp) REVERT: Ap 102 ASP cc_start: 0.8480 (t70) cc_final: 0.8277 (t0) REVERT: Ap 127 ASN cc_start: 0.7864 (p0) cc_final: 0.7589 (p0) REVERT: Ap 136 ASP cc_start: 0.8185 (t0) cc_final: 0.7946 (t0) REVERT: Ap 142 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8598 (mt-10) REVERT: Aq 127 ASN cc_start: 0.7920 (p0) cc_final: 0.7575 (p0) REVERT: Aq 181 MET cc_start: 0.8480 (tpp) cc_final: 0.8231 (tpp) REVERT: Aq 190 LEU cc_start: 0.8906 (tp) cc_final: 0.8394 (tp) REVERT: Ar 89 GLN cc_start: 0.9107 (mt0) cc_final: 0.8853 (mt0) REVERT: Ar 136 ASP cc_start: 0.8178 (t0) cc_final: 0.7781 (t0) REVERT: Ar 190 LEU cc_start: 0.8968 (tp) cc_final: 0.8735 (tp) REVERT: As 69 HIS cc_start: 0.8267 (t-90) cc_final: 0.7927 (t-90) REVERT: As 127 ASN cc_start: 0.7999 (p0) cc_final: 0.7628 (p0) REVERT: As 181 MET cc_start: 0.8517 (tpp) cc_final: 0.8269 (tpp) REVERT: As 190 LEU cc_start: 0.8876 (tp) cc_final: 0.8340 (tp) REVERT: At 89 GLN cc_start: 0.9123 (mt0) cc_final: 0.8875 (mt0) REVERT: At 127 ASN cc_start: 0.8038 (p0) cc_final: 0.7793 (p0) REVERT: At 136 ASP cc_start: 0.8221 (t0) cc_final: 0.7827 (t0) REVERT: At 190 LEU cc_start: 0.8949 (tp) cc_final: 0.8727 (tp) REVERT: Au 69 HIS cc_start: 0.8284 (t-90) cc_final: 0.7997 (t-90) REVERT: Au 127 ASN cc_start: 0.7977 (p0) cc_final: 0.7645 (p0) REVERT: Au 181 MET cc_start: 0.8489 (tpp) cc_final: 0.8244 (tpp) REVERT: Au 190 LEU cc_start: 0.8895 (tp) cc_final: 0.8378 (tp) REVERT: Au 198 TYR cc_start: 0.9016 (m-10) cc_final: 0.8782 (m-10) REVERT: Av 89 GLN cc_start: 0.9120 (mt0) cc_final: 0.8859 (mt0) REVERT: Av 136 ASP cc_start: 0.8150 (t0) cc_final: 0.7762 (t0) REVERT: Av 190 LEU cc_start: 0.8963 (tp) cc_final: 0.8732 (tp) REVERT: Aw 127 ASN cc_start: 0.7998 (p0) cc_final: 0.7634 (p0) REVERT: Aw 190 LEU cc_start: 0.8891 (tp) cc_final: 0.8543 (tp) REVERT: Aw 198 TYR cc_start: 0.9007 (m-10) cc_final: 0.8758 (m-10) REVERT: Ax 70 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8592 (tp) REVERT: Ax 89 GLN cc_start: 0.9105 (mt0) cc_final: 0.8847 (mt0) REVERT: Ax 127 ASN cc_start: 0.8042 (p0) cc_final: 0.7791 (p0) REVERT: Ax 136 ASP cc_start: 0.8175 (t0) cc_final: 0.7783 (t0) REVERT: Ax 181 MET cc_start: 0.8553 (tpp) cc_final: 0.8291 (tpp) REVERT: Ax 190 LEU cc_start: 0.8936 (tp) cc_final: 0.8705 (tp) outliers start: 125 outliers final: 68 residues processed: 1222 average time/residue: 0.4034 time to fit residues: 834.3417 Evaluate side-chains 1190 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1109 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR Chi-restraints excluded: chain Aa residue 70 LEU Chi-restraints excluded: chain Aa residue 88 SER Chi-restraints excluded: chain Ab residue 88 SER Chi-restraints excluded: chain Ab residue 150 GLU Chi-restraints excluded: chain Ab residue 151 ASN Chi-restraints excluded: chain Ac residue 43 THR Chi-restraints excluded: chain Ac residue 70 LEU Chi-restraints excluded: chain Ac residue 88 SER Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 150 GLU Chi-restraints excluded: chain Ad residue 151 ASN Chi-restraints excluded: chain Ae residue 43 THR Chi-restraints excluded: chain Ae residue 70 LEU Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Af residue 88 SER Chi-restraints excluded: chain Af residue 150 GLU Chi-restraints excluded: chain Af residue 151 ASN Chi-restraints excluded: chain Ag residue 43 THR Chi-restraints excluded: chain Ag residue 70 LEU Chi-restraints excluded: chain Ag residue 88 SER Chi-restraints excluded: chain Ah residue 88 SER Chi-restraints excluded: chain Ah residue 150 GLU Chi-restraints excluded: chain Ah residue 151 ASN Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 70 LEU Chi-restraints excluded: chain Ai residue 88 SER Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 150 GLU Chi-restraints excluded: chain Aj residue 70 LEU Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 124 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 44 VAL Chi-restraints excluded: chain Ak residue 88 SER Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 150 GLU Chi-restraints excluded: chain Al residue 70 LEU Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 124 THR Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 88 SER Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 150 GLU Chi-restraints excluded: chain An residue 70 LEU Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain Ao residue 44 VAL Chi-restraints excluded: chain Ao residue 88 SER Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 150 GLU Chi-restraints excluded: chain Ap residue 70 LEU Chi-restraints excluded: chain Ap residue 88 SER Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Aq residue 88 SER Chi-restraints excluded: chain Ar residue 70 LEU Chi-restraints excluded: chain Ar residue 78 ILE Chi-restraints excluded: chain Ar residue 88 SER Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 150 GLU Chi-restraints excluded: chain As residue 88 SER Chi-restraints excluded: chain At residue 70 LEU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 150 GLU Chi-restraints excluded: chain Au residue 88 SER Chi-restraints excluded: chain Av residue 70 LEU Chi-restraints excluded: chain Av residue 78 ILE Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Aw residue 88 SER Chi-restraints excluded: chain Aw residue 150 GLU Chi-restraints excluded: chain Ax residue 70 LEU Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 150 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 352 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 347 optimal weight: 3.9990 chunk 325 optimal weight: 0.9980 chunk 314 optimal weight: 0.5980 chunk 345 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 370 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 430 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 89 GLN ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 151 ASN Ac 89 GLN ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 151 ASN Ae 89 GLN Af 151 ASN Ag 89 GLN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 151 ASN ** Ai 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 175 ASN ** Ak 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 175 ASN ** An 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 175 ASN ** Ao 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 175 ASN Ar 151 ASN ** At 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 175 ASN ** Av 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 151 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.129035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097099 restraints weight = 52658.063| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.68 r_work: 0.2968 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35784 Z= 0.142 Angle : 0.574 8.818 48504 Z= 0.285 Chirality : 0.041 0.139 5280 Planarity : 0.005 0.052 6288 Dihedral : 4.196 15.480 4824 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.85 % Allowed : 27.56 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 4296 helix: 0.09 (0.12), residues: 1800 sheet: 0.53 (0.36), residues: 288 loop : -1.30 (0.15), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPAm 132 HIS 0.002 0.000 HISAw 69 PHE 0.009 0.002 PHEAi 200 TYR 0.015 0.001 TYRAq 198 ARG 0.004 0.000 ARGAf 46 Details of bonding type rmsd hydrogen bonds : bond 0.02725 ( 1152) hydrogen bonds : angle 5.07092 ( 3312) covalent geometry : bond 0.00352 (35784) covalent geometry : angle 0.57450 (48504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1118 time to evaluate : 4.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 54 MET cc_start: 0.7705 (ttp) cc_final: 0.7414 (ttp) REVERT: Aa 70 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8761 (tp) REVERT: Aa 81 SER cc_start: 0.9496 (t) cc_final: 0.9277 (t) REVERT: Aa 151 ASN cc_start: 0.8041 (t0) cc_final: 0.7762 (t0) REVERT: Ab 70 LEU cc_start: 0.8956 (tp) cc_final: 0.8569 (tp) REVERT: Ab 136 ASP cc_start: 0.8341 (t0) cc_final: 0.7972 (t0) REVERT: Ab 190 LEU cc_start: 0.8969 (tp) cc_final: 0.8691 (tp) REVERT: Ac 70 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8740 (tp) REVERT: Ac 81 SER cc_start: 0.9487 (t) cc_final: 0.9265 (t) REVERT: Ac 151 ASN cc_start: 0.8051 (t0) cc_final: 0.7771 (t0) REVERT: Ad 70 LEU cc_start: 0.8966 (tp) cc_final: 0.8578 (tp) REVERT: Ad 190 LEU cc_start: 0.8980 (tp) cc_final: 0.8717 (tp) REVERT: Ae 70 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8760 (tp) REVERT: Ae 81 SER cc_start: 0.9494 (t) cc_final: 0.9277 (t) REVERT: Ae 151 ASN cc_start: 0.7959 (t0) cc_final: 0.7661 (t0) REVERT: Af 70 LEU cc_start: 0.8948 (tp) cc_final: 0.8569 (tp) REVERT: Af 136 ASP cc_start: 0.8338 (t0) cc_final: 0.7986 (t0) REVERT: Af 190 LEU cc_start: 0.8973 (tp) cc_final: 0.8690 (tp) REVERT: Ag 70 LEU cc_start: 0.9064 (tp) cc_final: 0.8754 (tp) REVERT: Ag 81 SER cc_start: 0.9486 (t) cc_final: 0.9264 (t) REVERT: Ag 151 ASN cc_start: 0.7985 (t0) cc_final: 0.7694 (t0) REVERT: Ah 190 LEU cc_start: 0.8976 (tp) cc_final: 0.8709 (tp) REVERT: Ai 102 ASP cc_start: 0.8671 (t70) cc_final: 0.8453 (t0) REVERT: Ai 127 ASN cc_start: 0.7902 (p0) cc_final: 0.7658 (p0) REVERT: Ai 150 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7798 (pt0) REVERT: Ai 181 MET cc_start: 0.8698 (tpp) cc_final: 0.8403 (tpp) REVERT: Aj 70 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8478 (tp) REVERT: Aj 102 ASP cc_start: 0.8537 (t70) cc_final: 0.8313 (t0) REVERT: Aj 127 ASN cc_start: 0.7896 (p0) cc_final: 0.7587 (p0) REVERT: Aj 136 ASP cc_start: 0.8231 (t0) cc_final: 0.8028 (t0) REVERT: Ak 70 LEU cc_start: 0.9122 (tp) cc_final: 0.8680 (tp) REVERT: Ak 102 ASP cc_start: 0.8672 (t70) cc_final: 0.8443 (t0) REVERT: Ak 127 ASN cc_start: 0.7981 (p0) cc_final: 0.7723 (p0) REVERT: Ak 151 ASN cc_start: 0.8410 (t0) cc_final: 0.8159 (t0) REVERT: Al 70 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8518 (tp) REVERT: Al 127 ASN cc_start: 0.7902 (p0) cc_final: 0.7626 (p0) REVERT: Al 136 ASP cc_start: 0.8180 (t0) cc_final: 0.7966 (t0) REVERT: Am 70 LEU cc_start: 0.9079 (tp) cc_final: 0.8693 (tp) REVERT: Am 102 ASP cc_start: 0.8665 (t70) cc_final: 0.8451 (t0) REVERT: Am 127 ASN cc_start: 0.7920 (p0) cc_final: 0.7679 (p0) REVERT: An 70 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8526 (tp) REVERT: An 102 ASP cc_start: 0.8525 (t70) cc_final: 0.8296 (t0) REVERT: An 127 ASN cc_start: 0.7868 (p0) cc_final: 0.7636 (p0) REVERT: An 136 ASP cc_start: 0.8258 (t0) cc_final: 0.8039 (t0) REVERT: Ao 70 LEU cc_start: 0.9094 (tp) cc_final: 0.8697 (tp) REVERT: Ao 102 ASP cc_start: 0.8676 (t70) cc_final: 0.8454 (t0) REVERT: Ao 127 ASN cc_start: 0.7977 (p0) cc_final: 0.7669 (p0) REVERT: Ap 70 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8485 (tp) REVERT: Ap 102 ASP cc_start: 0.8529 (t70) cc_final: 0.8294 (t0) REVERT: Ap 127 ASN cc_start: 0.7890 (p0) cc_final: 0.7575 (p0) REVERT: Ap 136 ASP cc_start: 0.8161 (t0) cc_final: 0.7949 (t0) REVERT: Aq 127 ASN cc_start: 0.7983 (p0) cc_final: 0.7645 (p0) REVERT: Aq 151 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.8008 (t0) REVERT: Aq 181 MET cc_start: 0.8543 (tpp) cc_final: 0.8269 (tpp) REVERT: Aq 190 LEU cc_start: 0.8875 (tp) cc_final: 0.8318 (tp) REVERT: Ar 89 GLN cc_start: 0.9180 (mt0) cc_final: 0.8939 (mt0) REVERT: Ar 136 ASP cc_start: 0.8173 (t0) cc_final: 0.7767 (t0) REVERT: As 69 HIS cc_start: 0.8260 (t-90) cc_final: 0.7916 (t-90) REVERT: As 127 ASN cc_start: 0.8033 (p0) cc_final: 0.7688 (p0) REVERT: As 181 MET cc_start: 0.8584 (tpp) cc_final: 0.8321 (tpp) REVERT: As 190 LEU cc_start: 0.8882 (tp) cc_final: 0.8314 (tp) REVERT: At 89 GLN cc_start: 0.9179 (mt0) cc_final: 0.8922 (mt0) REVERT: At 127 ASN cc_start: 0.8016 (p0) cc_final: 0.7755 (p0) REVERT: At 136 ASP cc_start: 0.8165 (t0) cc_final: 0.7754 (t0) REVERT: At 190 LEU cc_start: 0.8918 (tp) cc_final: 0.8675 (tp) REVERT: Au 127 ASN cc_start: 0.7996 (p0) cc_final: 0.7666 (p0) REVERT: Au 181 MET cc_start: 0.8512 (tpp) cc_final: 0.8245 (tpp) REVERT: Au 190 LEU cc_start: 0.8873 (tp) cc_final: 0.8314 (tp) REVERT: Av 89 GLN cc_start: 0.9179 (mt0) cc_final: 0.8925 (mt0) REVERT: Av 136 ASP cc_start: 0.8252 (t0) cc_final: 0.7850 (t0) REVERT: Aw 127 ASN cc_start: 0.8008 (p0) cc_final: 0.7673 (p0) REVERT: Aw 150 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: Aw 190 LEU cc_start: 0.8849 (tp) cc_final: 0.8492 (tp) REVERT: Ax 70 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8581 (tp) REVERT: Ax 89 GLN cc_start: 0.9166 (mt0) cc_final: 0.8912 (mt0) REVERT: Ax 127 ASN cc_start: 0.8032 (p0) cc_final: 0.7787 (p0) REVERT: Ax 136 ASP cc_start: 0.8272 (t0) cc_final: 0.7878 (t0) outliers start: 146 outliers final: 106 residues processed: 1210 average time/residue: 0.4067 time to fit residues: 836.7829 Evaluate side-chains 1221 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1104 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR Chi-restraints excluded: chain Aa residue 70 LEU Chi-restraints excluded: chain Aa residue 80 ILE Chi-restraints excluded: chain Aa residue 88 SER Chi-restraints excluded: chain Aa residue 150 GLU Chi-restraints excluded: chain Ab residue 88 SER Chi-restraints excluded: chain Ab residue 150 GLU Chi-restraints excluded: chain Ac residue 43 THR Chi-restraints excluded: chain Ac residue 70 LEU Chi-restraints excluded: chain Ac residue 80 ILE Chi-restraints excluded: chain Ac residue 88 SER Chi-restraints excluded: chain Ac residue 150 GLU Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 150 GLU Chi-restraints excluded: chain Ae residue 43 THR Chi-restraints excluded: chain Ae residue 70 LEU Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Ae residue 150 GLU Chi-restraints excluded: chain Af residue 88 SER Chi-restraints excluded: chain Af residue 150 GLU Chi-restraints excluded: chain Ag residue 43 THR Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 88 SER Chi-restraints excluded: chain Ag residue 150 GLU Chi-restraints excluded: chain Ah residue 88 SER Chi-restraints excluded: chain Ah residue 150 GLU Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 70 LEU Chi-restraints excluded: chain Ai residue 80 ILE Chi-restraints excluded: chain Ai residue 88 SER Chi-restraints excluded: chain Ai residue 124 THR Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 150 GLU Chi-restraints excluded: chain Aj residue 43 THR Chi-restraints excluded: chain Aj residue 70 LEU Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 124 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Aj residue 141 VAL Chi-restraints excluded: chain Ak residue 44 VAL Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 88 SER Chi-restraints excluded: chain Ak residue 124 THR Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 150 GLU Chi-restraints excluded: chain Al residue 43 THR Chi-restraints excluded: chain Al residue 70 LEU Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 124 THR Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 141 VAL Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 80 ILE Chi-restraints excluded: chain Am residue 88 SER Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 150 GLU Chi-restraints excluded: chain An residue 43 THR Chi-restraints excluded: chain An residue 70 LEU Chi-restraints excluded: chain An residue 80 ILE Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 141 VAL Chi-restraints excluded: chain Ao residue 44 VAL Chi-restraints excluded: chain Ao residue 80 ILE Chi-restraints excluded: chain Ao residue 88 SER Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 150 GLU Chi-restraints excluded: chain Ap residue 43 THR Chi-restraints excluded: chain Ap residue 70 LEU Chi-restraints excluded: chain Ap residue 80 ILE Chi-restraints excluded: chain Ap residue 88 SER Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 141 VAL Chi-restraints excluded: chain Aq residue 80 ILE Chi-restraints excluded: chain Aq residue 88 SER Chi-restraints excluded: chain Aq residue 124 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 151 ASN Chi-restraints excluded: chain Ar residue 78 ILE Chi-restraints excluded: chain Ar residue 88 SER Chi-restraints excluded: chain Ar residue 124 THR Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 150 GLU Chi-restraints excluded: chain As residue 80 ILE Chi-restraints excluded: chain As residue 88 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 124 THR Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 150 GLU Chi-restraints excluded: chain Au residue 72 GLU Chi-restraints excluded: chain Au residue 80 ILE Chi-restraints excluded: chain Au residue 88 SER Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Av residue 78 ILE Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Aw residue 80 ILE Chi-restraints excluded: chain Aw residue 88 SER Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 150 GLU Chi-restraints excluded: chain Ax residue 70 LEU Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 150 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 135 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 286 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 331 optimal weight: 6.9990 chunk 430 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 335 optimal weight: 0.5980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ai 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 175 ASN ** An 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 151 ASN Ar 175 ASN ** At 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 175 ASN Ax 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.097060 restraints weight = 52135.193| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.70 r_work: 0.2968 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35784 Z= 0.141 Angle : 0.578 8.989 48504 Z= 0.285 Chirality : 0.041 0.149 5280 Planarity : 0.005 0.055 6288 Dihedral : 4.221 16.869 4824 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.25 % Allowed : 27.85 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.14), residues: 4296 helix: 0.27 (0.13), residues: 1728 sheet: 0.57 (0.36), residues: 288 loop : -1.20 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPAi 132 HIS 0.001 0.000 HISAq 69 PHE 0.009 0.002 PHEAg 200 TYR 0.028 0.002 TYRAw 198 ARG 0.005 0.000 ARGAe 55 Details of bonding type rmsd hydrogen bonds : bond 0.02643 ( 1152) hydrogen bonds : angle 5.14895 ( 3312) covalent geometry : bond 0.00350 (35784) covalent geometry : angle 0.57766 (48504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1199 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 71 LEU cc_start: 0.8553 (mt) cc_final: 0.8345 (pp) REVERT: Aa 81 SER cc_start: 0.9482 (t) cc_final: 0.9251 (t) REVERT: Ab 70 LEU cc_start: 0.8881 (tp) cc_final: 0.8381 (tp) REVERT: Ab 136 ASP cc_start: 0.8327 (t0) cc_final: 0.7967 (t0) REVERT: Ab 190 LEU cc_start: 0.8986 (tp) cc_final: 0.8696 (tp) REVERT: Ac 71 LEU cc_start: 0.8544 (mt) cc_final: 0.8328 (pp) REVERT: Ac 81 SER cc_start: 0.9469 (t) cc_final: 0.9246 (t) REVERT: Ad 70 LEU cc_start: 0.8893 (tp) cc_final: 0.8390 (tp) REVERT: Ad 190 LEU cc_start: 0.8996 (tp) cc_final: 0.8723 (tp) REVERT: Ae 48 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8563 (ttmm) REVERT: Ae 70 LEU cc_start: 0.9093 (tp) cc_final: 0.8740 (tp) REVERT: Ae 81 SER cc_start: 0.9489 (t) cc_final: 0.9262 (t) REVERT: Af 69 HIS cc_start: 0.8103 (t-90) cc_final: 0.7773 (t-170) REVERT: Af 70 LEU cc_start: 0.8907 (tp) cc_final: 0.8392 (tp) REVERT: Af 72 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8734 (pt0) REVERT: Af 136 ASP cc_start: 0.8302 (t0) cc_final: 0.7938 (t0) REVERT: Af 190 LEU cc_start: 0.8973 (tp) cc_final: 0.8680 (tp) REVERT: Ag 70 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8734 (tp) REVERT: Ag 71 LEU cc_start: 0.8535 (mt) cc_final: 0.8311 (pp) REVERT: Ag 81 SER cc_start: 0.9469 (t) cc_final: 0.9244 (t) REVERT: Ah 70 LEU cc_start: 0.8871 (tp) cc_final: 0.8376 (tp) REVERT: Ah 190 LEU cc_start: 0.8990 (tp) cc_final: 0.8718 (tp) REVERT: Ai 48 LYS cc_start: 0.8759 (tppt) cc_final: 0.8552 (tptt) REVERT: Ai 151 ASN cc_start: 0.8230 (t0) cc_final: 0.7963 (t0) REVERT: Aj 70 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8528 (tp) REVERT: Aj 102 ASP cc_start: 0.8546 (t70) cc_final: 0.8328 (t0) REVERT: Aj 112 MET cc_start: 0.8762 (tpp) cc_final: 0.7888 (mmt) REVERT: Aj 127 ASN cc_start: 0.7761 (p0) cc_final: 0.7513 (p0) REVERT: Aj 150 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: Aj 151 ASN cc_start: 0.8353 (t0) cc_final: 0.8041 (t0) REVERT: Aj 214 ARG cc_start: 0.8302 (mtp180) cc_final: 0.8011 (mtp180) REVERT: Ak 48 LYS cc_start: 0.8779 (tppt) cc_final: 0.8554 (tptt) REVERT: Ak 70 LEU cc_start: 0.9164 (tp) cc_final: 0.8669 (tp) REVERT: Ak 102 ASP cc_start: 0.8642 (t70) cc_final: 0.8441 (t0) REVERT: Ak 127 ASN cc_start: 0.7981 (p0) cc_final: 0.7736 (p0) REVERT: Ak 214 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7892 (mtp180) REVERT: Al 70 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8513 (tp) REVERT: Al 71 LEU cc_start: 0.8376 (mt) cc_final: 0.8102 (pp) REVERT: Al 112 MET cc_start: 0.8762 (tpp) cc_final: 0.7872 (mmt) REVERT: Al 127 ASN cc_start: 0.7900 (p0) cc_final: 0.7631 (p0) REVERT: Al 214 ARG cc_start: 0.8314 (mtp180) cc_final: 0.8021 (mtp180) REVERT: Am 48 LYS cc_start: 0.8766 (tppt) cc_final: 0.8535 (tptt) REVERT: Am 102 ASP cc_start: 0.8642 (t70) cc_final: 0.8437 (t0) REVERT: An 70 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8530 (tp) REVERT: An 71 LEU cc_start: 0.8341 (mt) cc_final: 0.8078 (pp) REVERT: An 102 ASP cc_start: 0.8531 (t70) cc_final: 0.8306 (t0) REVERT: An 112 MET cc_start: 0.8774 (tpp) cc_final: 0.7890 (mmt) REVERT: An 127 ASN cc_start: 0.7879 (p0) cc_final: 0.7654 (p0) REVERT: An 214 ARG cc_start: 0.8322 (mtp180) cc_final: 0.8014 (mtp180) REVERT: Ao 48 LYS cc_start: 0.8766 (tppt) cc_final: 0.8533 (tptt) REVERT: Ao 102 ASP cc_start: 0.8639 (t70) cc_final: 0.8422 (t0) REVERT: Ao 127 ASN cc_start: 0.7973 (p0) cc_final: 0.7719 (p0) REVERT: Ap 70 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8509 (tp) REVERT: Ap 102 ASP cc_start: 0.8531 (t70) cc_final: 0.8309 (t0) REVERT: Ap 127 ASN cc_start: 0.7765 (p0) cc_final: 0.7520 (p0) REVERT: Ap 150 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7803 (pt0) REVERT: Ap 151 ASN cc_start: 0.8410 (t0) cc_final: 0.8017 (t0) REVERT: Ap 214 ARG cc_start: 0.8320 (mtp180) cc_final: 0.8008 (mtp180) REVERT: Aq 127 ASN cc_start: 0.8035 (p0) cc_final: 0.7784 (p0) REVERT: Aq 181 MET cc_start: 0.8543 (tpp) cc_final: 0.8266 (tpp) REVERT: Aq 190 LEU cc_start: 0.8869 (tp) cc_final: 0.8291 (tp) REVERT: Ar 70 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8598 (tp) REVERT: Ar 89 GLN cc_start: 0.9175 (mt0) cc_final: 0.8946 (mt0) REVERT: Ar 136 ASP cc_start: 0.8259 (t0) cc_final: 0.7872 (t0) REVERT: Ar 151 ASN cc_start: 0.8040 (t0) cc_final: 0.7839 (t0) REVERT: As 127 ASN cc_start: 0.8056 (p0) cc_final: 0.7795 (p0) REVERT: As 190 LEU cc_start: 0.8882 (tp) cc_final: 0.8390 (tp) REVERT: At 70 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8596 (tp) REVERT: At 89 GLN cc_start: 0.9170 (mt0) cc_final: 0.8945 (mt0) REVERT: At 127 ASN cc_start: 0.8017 (p0) cc_final: 0.7766 (p0) REVERT: At 136 ASP cc_start: 0.8243 (t0) cc_final: 0.7847 (t0) REVERT: At 190 LEU cc_start: 0.8912 (tp) cc_final: 0.8643 (tp) REVERT: Au 127 ASN cc_start: 0.8030 (p0) cc_final: 0.7714 (p0) REVERT: Au 181 MET cc_start: 0.8541 (tpp) cc_final: 0.8271 (tpp) REVERT: Au 190 LEU cc_start: 0.8865 (tp) cc_final: 0.8266 (tp) REVERT: Au 198 TYR cc_start: 0.9028 (m-10) cc_final: 0.8779 (m-10) REVERT: Av 89 GLN cc_start: 0.9167 (mt0) cc_final: 0.8944 (mt0) REVERT: Av 136 ASP cc_start: 0.8261 (t0) cc_final: 0.7866 (t0) REVERT: Aw 127 ASN cc_start: 0.8030 (p0) cc_final: 0.7751 (p0) REVERT: Aw 150 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7881 (pt0) REVERT: Aw 190 LEU cc_start: 0.8829 (tp) cc_final: 0.8473 (tp) REVERT: Aw 198 TYR cc_start: 0.9010 (m-10) cc_final: 0.8757 (m-10) REVERT: Ax 70 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8574 (tp) REVERT: Ax 89 GLN cc_start: 0.9160 (mt0) cc_final: 0.8930 (mt0) REVERT: Ax 127 ASN cc_start: 0.8024 (p0) cc_final: 0.7768 (p0) REVERT: Ax 136 ASP cc_start: 0.8283 (t0) cc_final: 0.7891 (t0) outliers start: 161 outliers final: 121 residues processed: 1299 average time/residue: 0.4476 time to fit residues: 943.0460 Evaluate side-chains 1284 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 1151 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR Chi-restraints excluded: chain Aa residue 78 ILE Chi-restraints excluded: chain Aa residue 80 ILE Chi-restraints excluded: chain Aa residue 88 SER Chi-restraints excluded: chain Aa residue 150 GLU Chi-restraints excluded: chain Ab residue 88 SER Chi-restraints excluded: chain Ac residue 43 THR Chi-restraints excluded: chain Ac residue 78 ILE Chi-restraints excluded: chain Ac residue 80 ILE Chi-restraints excluded: chain Ac residue 88 SER Chi-restraints excluded: chain Ac residue 150 GLU Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ae residue 43 THR Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Ae residue 150 GLU Chi-restraints excluded: chain Af residue 72 GLU Chi-restraints excluded: chain Af residue 88 SER Chi-restraints excluded: chain Ag residue 43 THR Chi-restraints excluded: chain Ag residue 70 LEU Chi-restraints excluded: chain Ag residue 78 ILE Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 88 SER Chi-restraints excluded: chain Ag residue 150 GLU Chi-restraints excluded: chain Ah residue 88 SER Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ai residue 43 THR Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 70 LEU Chi-restraints excluded: chain Ai residue 80 ILE Chi-restraints excluded: chain Ai residue 88 SER Chi-restraints excluded: chain Ai residue 124 THR Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 150 GLU Chi-restraints excluded: chain Aj residue 43 THR Chi-restraints excluded: chain Aj residue 70 LEU Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 124 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Aj residue 141 VAL Chi-restraints excluded: chain Aj residue 150 GLU Chi-restraints excluded: chain Ak residue 43 THR Chi-restraints excluded: chain Ak residue 44 VAL Chi-restraints excluded: chain Ak residue 78 ILE Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 88 SER Chi-restraints excluded: chain Ak residue 124 THR Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 150 GLU Chi-restraints excluded: chain Al residue 43 THR Chi-restraints excluded: chain Al residue 70 LEU Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 124 THR Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 141 VAL Chi-restraints excluded: chain Al residue 150 GLU Chi-restraints excluded: chain Am residue 43 THR Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 80 ILE Chi-restraints excluded: chain Am residue 88 SER Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 150 GLU Chi-restraints excluded: chain An residue 43 THR Chi-restraints excluded: chain An residue 70 LEU Chi-restraints excluded: chain An residue 80 ILE Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 141 VAL Chi-restraints excluded: chain An residue 150 GLU Chi-restraints excluded: chain Ao residue 43 THR Chi-restraints excluded: chain Ao residue 44 VAL Chi-restraints excluded: chain Ao residue 80 ILE Chi-restraints excluded: chain Ao residue 88 SER Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 141 VAL Chi-restraints excluded: chain Ao residue 150 GLU Chi-restraints excluded: chain Ap residue 43 THR Chi-restraints excluded: chain Ap residue 70 LEU Chi-restraints excluded: chain Ap residue 80 ILE Chi-restraints excluded: chain Ap residue 88 SER Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 141 VAL Chi-restraints excluded: chain Ap residue 150 GLU Chi-restraints excluded: chain Aq residue 80 ILE Chi-restraints excluded: chain Aq residue 88 SER Chi-restraints excluded: chain Aq residue 124 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Ar residue 43 THR Chi-restraints excluded: chain Ar residue 70 LEU Chi-restraints excluded: chain Ar residue 78 ILE Chi-restraints excluded: chain Ar residue 88 SER Chi-restraints excluded: chain Ar residue 103 ILE Chi-restraints excluded: chain Ar residue 124 THR Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 150 GLU Chi-restraints excluded: chain As residue 80 ILE Chi-restraints excluded: chain As residue 88 SER Chi-restraints excluded: chain As residue 124 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain At residue 70 LEU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 124 THR Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 150 GLU Chi-restraints excluded: chain Au residue 80 ILE Chi-restraints excluded: chain Au residue 88 SER Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Av residue 78 ILE Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Aw residue 80 ILE Chi-restraints excluded: chain Aw residue 88 SER Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 150 GLU Chi-restraints excluded: chain Ax residue 70 LEU Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 103 ILE Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 150 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 344 optimal weight: 0.2980 chunk 139 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 338 optimal weight: 0.0270 chunk 285 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 166 optimal weight: 0.0050 overall best weight: 1.8656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 98 GLN ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 151 ASN ** Ao 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 151 ASN ** At 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 175 ASN Au 151 ASN ** Av 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 151 ASN Aw 151 ASN ** Ax 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 = 0.3598 r_free = 0.3598 target = 0.129045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.096949 restraints weight = 52113.033| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.72 r_work: 0.2974 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35784 Z= 0.136 Angle : 0.585 9.204 48504 Z= 0.290 Chirality : 0.041 0.149 5280 Planarity : 0.005 0.054 6288 Dihedral : 4.230 16.889 4824 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.40 % Allowed : 28.72 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 4296 helix: 0.34 (0.13), residues: 1728 sheet: 0.59 (0.36), residues: 288 loop : -1.21 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPAf 93 HIS 0.002 0.000 HISAo 69 PHE 0.009 0.002 PHEAa 200 TYR 0.018 0.001 TYRAq 198 ARG 0.007 0.000 ARGAp 157 Details of bonding type rmsd hydrogen bonds : bond 0.02557 ( 1152) hydrogen bonds : angle 5.16333 ( 3312) covalent geometry : bond 0.00335 (35784) covalent geometry : angle 0.58491 (48504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1180 time to evaluate : 3.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 70 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8747 (tp) REVERT: Aa 71 LEU cc_start: 0.8576 (mt) cc_final: 0.8361 (pp) REVERT: Aa 81 SER cc_start: 0.9468 (t) cc_final: 0.9238 (t) REVERT: Ab 71 LEU cc_start: 0.8618 (mt) cc_final: 0.8300 (pp) REVERT: Ab 136 ASP cc_start: 0.8338 (t0) cc_final: 0.7978 (t0) REVERT: Ab 190 LEU cc_start: 0.8969 (tp) cc_final: 0.8650 (tp) REVERT: Ac 71 LEU cc_start: 0.8571 (mt) cc_final: 0.8351 (pp) REVERT: Ac 81 SER cc_start: 0.9466 (t) cc_final: 0.9240 (t) REVERT: Ad 54 MET cc_start: 0.8036 (ttp) cc_final: 0.7761 (ttp) REVERT: Ad 71 LEU cc_start: 0.8649 (mt) cc_final: 0.8342 (pp) REVERT: Ad 190 LEU cc_start: 0.8990 (tp) cc_final: 0.8715 (tp) REVERT: Ae 48 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8544 (ttmm) REVERT: Ae 70 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8736 (tp) REVERT: Ae 71 LEU cc_start: 0.8556 (mt) cc_final: 0.8351 (pp) REVERT: Ae 81 SER cc_start: 0.9471 (t) cc_final: 0.9242 (t) REVERT: Af 69 HIS cc_start: 0.8128 (t-90) cc_final: 0.7866 (t-170) REVERT: Af 71 LEU cc_start: 0.8607 (mt) cc_final: 0.8335 (pp) REVERT: Af 136 ASP cc_start: 0.8311 (t0) cc_final: 0.7943 (t0) REVERT: Af 190 LEU cc_start: 0.8968 (tp) cc_final: 0.8633 (tp) REVERT: Ag 70 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8743 (tp) REVERT: Ag 71 LEU cc_start: 0.8551 (mt) cc_final: 0.8338 (pp) REVERT: Ag 81 SER cc_start: 0.9464 (t) cc_final: 0.9235 (t) REVERT: Ah 71 LEU cc_start: 0.8641 (mt) cc_final: 0.8337 (pp) REVERT: Ah 190 LEU cc_start: 0.8973 (tp) cc_final: 0.8656 (tp) REVERT: Ai 151 ASN cc_start: 0.8213 (t0) cc_final: 0.7994 (t0) REVERT: Ai 214 ARG cc_start: 0.8173 (mtp180) cc_final: 0.7873 (mtp180) REVERT: Aj 70 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8465 (tp) REVERT: Aj 102 ASP cc_start: 0.8504 (t70) cc_final: 0.8283 (t0) REVERT: Aj 127 ASN cc_start: 0.7755 (p0) cc_final: 0.7515 (p0) REVERT: Aj 151 ASN cc_start: 0.8380 (t0) cc_final: 0.8100 (t0) REVERT: Aj 214 ARG cc_start: 0.8314 (mtp180) cc_final: 0.8011 (mtp180) REVERT: Ak 48 LYS cc_start: 0.8659 (tppt) cc_final: 0.8418 (tptt) REVERT: Ak 70 LEU cc_start: 0.9159 (tp) cc_final: 0.8626 (tp) REVERT: Ak 127 ASN cc_start: 0.7993 (p0) cc_final: 0.7763 (p0) REVERT: Al 70 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8476 (tp) REVERT: Al 71 LEU cc_start: 0.8352 (mt) cc_final: 0.8081 (pp) REVERT: Al 127 ASN cc_start: 0.7906 (p0) cc_final: 0.7641 (p0) REVERT: Al 214 ARG cc_start: 0.8278 (mtp180) cc_final: 0.7978 (mtp180) REVERT: Am 48 LYS cc_start: 0.8696 (tppt) cc_final: 0.8473 (tptt) REVERT: Am 214 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7900 (mtp180) REVERT: An 70 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8495 (tp) REVERT: An 71 LEU cc_start: 0.8338 (mt) cc_final: 0.8070 (pp) REVERT: An 102 ASP cc_start: 0.8530 (t70) cc_final: 0.8296 (t0) REVERT: An 127 ASN cc_start: 0.7865 (p0) cc_final: 0.7630 (p0) REVERT: An 214 ARG cc_start: 0.8327 (mtp180) cc_final: 0.8006 (mtp180) REVERT: Ao 48 LYS cc_start: 0.8687 (tppt) cc_final: 0.8465 (tptt) REVERT: Ao 127 ASN cc_start: 0.7973 (p0) cc_final: 0.7727 (p0) REVERT: Ap 70 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8461 (tp) REVERT: Ap 71 LEU cc_start: 0.8421 (mt) cc_final: 0.8211 (pt) REVERT: Ap 127 ASN cc_start: 0.7775 (p0) cc_final: 0.7525 (p0) REVERT: Ap 214 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7963 (mtp180) REVERT: Aq 127 ASN cc_start: 0.8026 (p0) cc_final: 0.7759 (p0) REVERT: Aq 181 MET cc_start: 0.8528 (tpp) cc_final: 0.8223 (tpp) REVERT: Aq 190 LEU cc_start: 0.8941 (tp) cc_final: 0.8371 (tp) REVERT: Ar 70 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8597 (tp) REVERT: Ar 89 GLN cc_start: 0.9168 (mt0) cc_final: 0.8951 (mt0) REVERT: Ar 136 ASP cc_start: 0.8252 (t0) cc_final: 0.7906 (t0) REVERT: As 127 ASN cc_start: 0.8053 (p0) cc_final: 0.7798 (p0) REVERT: As 190 LEU cc_start: 0.8904 (tp) cc_final: 0.8537 (tp) REVERT: At 70 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8604 (tp) REVERT: At 89 GLN cc_start: 0.9132 (mt0) cc_final: 0.8915 (mt0) REVERT: At 127 ASN cc_start: 0.8010 (p0) cc_final: 0.7745 (p0) REVERT: At 136 ASP cc_start: 0.8224 (t0) cc_final: 0.7879 (t0) REVERT: At 190 LEU cc_start: 0.8893 (tp) cc_final: 0.8651 (tp) REVERT: Au 127 ASN cc_start: 0.8025 (p0) cc_final: 0.7766 (p0) REVERT: Au 181 MET cc_start: 0.8533 (tpp) cc_final: 0.8229 (tpp) REVERT: Au 190 LEU cc_start: 0.8920 (tp) cc_final: 0.8352 (tp) REVERT: Au 198 TYR cc_start: 0.8983 (m-10) cc_final: 0.8738 (m-10) REVERT: Av 89 GLN cc_start: 0.9154 (mt0) cc_final: 0.8948 (mt0) REVERT: Av 136 ASP cc_start: 0.8251 (t0) cc_final: 0.7912 (t0) REVERT: Aw 127 ASN cc_start: 0.8011 (p0) cc_final: 0.7747 (p0) REVERT: Aw 151 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8238 (t0) REVERT: Aw 190 LEU cc_start: 0.8873 (tp) cc_final: 0.8532 (tp) REVERT: Aw 198 TYR cc_start: 0.8977 (m-10) cc_final: 0.8728 (m-10) REVERT: Ax 70 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8552 (tp) REVERT: Ax 89 GLN cc_start: 0.9127 (mt0) cc_final: 0.8907 (mt0) REVERT: Ax 127 ASN cc_start: 0.8016 (p0) cc_final: 0.7769 (p0) REVERT: Ax 136 ASP cc_start: 0.8263 (t0) cc_final: 0.7930 (t0) outliers start: 167 outliers final: 136 residues processed: 1288 average time/residue: 0.4561 time to fit residues: 960.2403 Evaluate side-chains 1304 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1157 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR Chi-restraints excluded: chain Aa residue 70 LEU Chi-restraints excluded: chain Aa residue 80 ILE Chi-restraints excluded: chain Aa residue 86 THR Chi-restraints excluded: chain Aa residue 88 SER Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Aa residue 150 GLU Chi-restraints excluded: chain Ab residue 88 SER Chi-restraints excluded: chain Ab residue 141 VAL Chi-restraints excluded: chain Ac residue 43 THR Chi-restraints excluded: chain Ac residue 80 ILE Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 88 SER Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ac residue 150 GLU Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 141 VAL Chi-restraints excluded: chain Ae residue 43 THR Chi-restraints excluded: chain Ae residue 70 LEU Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 86 THR Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Ae residue 150 GLU Chi-restraints excluded: chain Af residue 88 SER Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Ag residue 43 THR Chi-restraints excluded: chain Ag residue 70 LEU Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 86 THR Chi-restraints excluded: chain Ag residue 88 SER Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ag residue 150 GLU Chi-restraints excluded: chain Ah residue 88 SER Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ai residue 43 THR Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 70 LEU Chi-restraints excluded: chain Ai residue 80 ILE Chi-restraints excluded: chain Ai residue 88 SER Chi-restraints excluded: chain Ai residue 124 THR Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 141 VAL Chi-restraints excluded: chain Ai residue 145 LEU Chi-restraints excluded: chain Aj residue 43 THR Chi-restraints excluded: chain Aj residue 70 LEU Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 124 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Aj residue 150 GLU Chi-restraints excluded: chain Ak residue 43 THR Chi-restraints excluded: chain Ak residue 44 VAL Chi-restraints excluded: chain Ak residue 78 ILE Chi-restraints excluded: chain Ak residue 88 SER Chi-restraints excluded: chain Ak residue 124 THR Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 141 VAL Chi-restraints excluded: chain Ak residue 150 GLU Chi-restraints excluded: chain Al residue 43 THR Chi-restraints excluded: chain Al residue 70 LEU Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 124 THR Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 141 VAL Chi-restraints excluded: chain Al residue 150 GLU Chi-restraints excluded: chain Am residue 43 THR Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 80 ILE Chi-restraints excluded: chain Am residue 88 SER Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL Chi-restraints excluded: chain Am residue 145 LEU Chi-restraints excluded: chain An residue 43 THR Chi-restraints excluded: chain An residue 70 LEU Chi-restraints excluded: chain An residue 80 ILE Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 150 GLU Chi-restraints excluded: chain Ao residue 43 THR Chi-restraints excluded: chain Ao residue 44 VAL Chi-restraints excluded: chain Ao residue 78 ILE Chi-restraints excluded: chain Ao residue 80 ILE Chi-restraints excluded: chain Ao residue 88 SER Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 150 GLU Chi-restraints excluded: chain Ap residue 43 THR Chi-restraints excluded: chain Ap residue 70 LEU Chi-restraints excluded: chain Ap residue 80 ILE Chi-restraints excluded: chain Ap residue 88 SER Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 141 VAL Chi-restraints excluded: chain Ap residue 150 GLU Chi-restraints excluded: chain Aq residue 70 LEU Chi-restraints excluded: chain Aq residue 78 ILE Chi-restraints excluded: chain Aq residue 80 ILE Chi-restraints excluded: chain Aq residue 88 SER Chi-restraints excluded: chain Aq residue 124 THR Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 151 ASN Chi-restraints excluded: chain Ar residue 43 THR Chi-restraints excluded: chain Ar residue 70 LEU Chi-restraints excluded: chain Ar residue 78 ILE Chi-restraints excluded: chain Ar residue 88 SER Chi-restraints excluded: chain Ar residue 103 ILE Chi-restraints excluded: chain Ar residue 124 THR Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 150 GLU Chi-restraints excluded: chain As residue 43 THR Chi-restraints excluded: chain As residue 80 ILE Chi-restraints excluded: chain As residue 88 SER Chi-restraints excluded: chain As residue 124 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain At residue 70 LEU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 124 THR Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 150 GLU Chi-restraints excluded: chain Au residue 78 ILE Chi-restraints excluded: chain Au residue 80 ILE Chi-restraints excluded: chain Au residue 88 SER Chi-restraints excluded: chain Au residue 124 THR Chi-restraints excluded: chain Av residue 43 THR Chi-restraints excluded: chain Av residue 78 ILE Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 124 THR Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Aw residue 80 ILE Chi-restraints excluded: chain Aw residue 88 SER Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 150 GLU Chi-restraints excluded: chain Aw residue 151 ASN Chi-restraints excluded: chain Ax residue 70 LEU Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 103 ILE Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 150 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 286 optimal weight: 9.9990 chunk 421 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 356 optimal weight: 2.9990 chunk 405 optimal weight: 7.9990 chunk 348 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 309 optimal weight: 0.0980 chunk 132 optimal weight: 3.9990 chunk 411 optimal weight: 9.9990 chunk 403 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 98 GLN ** Aj 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 151 ASN ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 98 GLN At 151 ASN ** Av 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 151 ASN Av 175 ASN ** Ax 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 175 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098191 restraints weight = 51955.522| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.67 r_work: 0.2989 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35784 Z= 0.125 Angle : 0.583 9.144 48504 Z= 0.290 Chirality : 0.040 0.152 5280 Planarity : 0.005 0.058 6288 Dihedral : 4.226 16.431 4824 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.11 % Allowed : 29.69 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 4296 helix: 0.39 (0.13), residues: 1728 sheet: 0.63 (0.36), residues: 288 loop : -1.20 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPAb 93 HIS 0.002 0.000 HISAo 69 PHE 0.009 0.002 PHEAa 200 TYR 0.020 0.001 TYRAo 198 ARG 0.006 0.000 ARGAj 157 Details of bonding type rmsd hydrogen bonds : bond 0.02502 ( 1152) hydrogen bonds : angle 5.14088 ( 3312) covalent geometry : bond 0.00310 (35784) covalent geometry : angle 0.58313 (48504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1339 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1183 time to evaluate : 4.285 Fit side-chains revert: symmetry clash REVERT: Aa 48 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8522 (ttmm) REVERT: Aa 70 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8728 (tp) REVERT: Aa 71 LEU cc_start: 0.8556 (mt) cc_final: 0.8326 (pp) REVERT: Aa 81 SER cc_start: 0.9457 (t) cc_final: 0.9214 (t) REVERT: Ab 69 HIS cc_start: 0.8201 (t-90) cc_final: 0.7673 (t-170) REVERT: Ab 71 LEU cc_start: 0.8625 (mt) cc_final: 0.8330 (pp) REVERT: Ab 136 ASP cc_start: 0.8336 (t0) cc_final: 0.7972 (t0) REVERT: Ab 151 ASN cc_start: 0.8355 (t0) cc_final: 0.8122 (t0) REVERT: Ab 190 LEU cc_start: 0.8972 (tp) cc_final: 0.8662 (tp) REVERT: Ac 70 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8697 (tp) REVERT: Ac 71 LEU cc_start: 0.8562 (mt) cc_final: 0.8336 (pp) REVERT: Ac 81 SER cc_start: 0.9457 (t) cc_final: 0.9221 (t) REVERT: Ad 69 HIS cc_start: 0.8196 (t-90) cc_final: 0.7670 (t-170) REVERT: Ad 71 LEU cc_start: 0.8605 (mt) cc_final: 0.8361 (pp) REVERT: Ad 190 LEU cc_start: 0.9005 (tp) cc_final: 0.8726 (tp) REVERT: Ae 70 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8739 (tp) REVERT: Ae 71 LEU cc_start: 0.8537 (mt) cc_final: 0.8333 (pp) REVERT: Ae 81 SER cc_start: 0.9461 (t) cc_final: 0.9226 (t) REVERT: Af 136 ASP cc_start: 0.8326 (t0) cc_final: 0.7964 (t0) REVERT: Af 151 ASN cc_start: 0.8353 (t0) cc_final: 0.8151 (t0) REVERT: Af 190 LEU cc_start: 0.8973 (tp) cc_final: 0.8654 (tp) REVERT: Ag 70 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8727 (tp) REVERT: Ag 71 LEU cc_start: 0.8543 (mt) cc_final: 0.8327 (pp) REVERT: Ag 81 SER cc_start: 0.9460 (t) cc_final: 0.9226 (t) REVERT: Ag 89 GLN cc_start: 0.9161 (mt0) cc_final: 0.8955 (mt0) REVERT: Ah 69 HIS cc_start: 0.8197 (t-90) cc_final: 0.7673 (t-170) REVERT: Ah 71 LEU cc_start: 0.8596 (mt) cc_final: 0.8343 (pp) REVERT: Ah 190 LEU cc_start: 0.8965 (tp) cc_final: 0.8666 (tp) REVERT: Ai 150 GLU cc_start: 0.8508 (pt0) cc_final: 0.7979 (pt0) REVERT: Ai 151 ASN cc_start: 0.8154 (t0) cc_final: 0.7831 (t0) REVERT: Ai 181 MET cc_start: 0.8576 (tpp) cc_final: 0.8251 (tpp) REVERT: Ai 214 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7883 (mtp180) REVERT: Aj 70 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8428 (tp) REVERT: Aj 71 LEU cc_start: 0.8380 (mt) cc_final: 0.8171 (pt) REVERT: Aj 127 ASN cc_start: 0.7813 (p0) cc_final: 0.7587 (p0) REVERT: Aj 151 ASN cc_start: 0.8355 (t0) cc_final: 0.8115 (t0) REVERT: Aj 214 ARG cc_start: 0.8332 (mtp180) cc_final: 0.8028 (mtp180) REVERT: Ak 48 LYS cc_start: 0.8653 (tppt) cc_final: 0.8427 (tptt) REVERT: Ak 70 LEU cc_start: 0.9126 (tp) cc_final: 0.8744 (tp) REVERT: Ak 127 ASN cc_start: 0.7971 (p0) cc_final: 0.7729 (p0) REVERT: Al 70 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8441 (tp) REVERT: Al 71 LEU cc_start: 0.8325 (mt) cc_final: 0.8071 (pp) REVERT: Al 127 ASN cc_start: 0.7930 (p0) cc_final: 0.7671 (p0) REVERT: Al 214 ARG cc_start: 0.8284 (mtp180) cc_final: 0.7864 (mtp180) REVERT: Am 48 LYS cc_start: 0.8692 (tppt) cc_final: 0.8481 (tptt) REVERT: Am 70 LEU cc_start: 0.9167 (tp) cc_final: 0.8801 (tp) REVERT: Am 150 GLU cc_start: 0.8474 (pt0) cc_final: 0.7909 (pt0) REVERT: Am 214 ARG cc_start: 0.8217 (mtp180) cc_final: 0.7882 (mtp180) REVERT: An 70 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8451 (tp) REVERT: An 71 LEU cc_start: 0.8327 (mt) cc_final: 0.8078 (pp) REVERT: An 112 MET cc_start: 0.8668 (tpp) cc_final: 0.7837 (mmt) REVERT: An 127 ASN cc_start: 0.7875 (p0) cc_final: 0.7620 (p0) REVERT: An 214 ARG cc_start: 0.8335 (mtp180) cc_final: 0.8002 (mtp180) REVERT: Ao 48 LYS cc_start: 0.8681 (tppt) cc_final: 0.8470 (tptt) REVERT: Ao 70 LEU cc_start: 0.9135 (tp) cc_final: 0.8758 (tp) REVERT: Ao 127 ASN cc_start: 0.7960 (p0) cc_final: 0.7734 (p0) REVERT: Ao 181 MET cc_start: 0.8598 (tpp) cc_final: 0.8300 (tpp) REVERT: Ap 70 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8458 (tp) REVERT: Ap 71 LEU cc_start: 0.8442 (mt) cc_final: 0.8194 (pt) REVERT: Ap 127 ASN cc_start: 0.7838 (p0) cc_final: 0.7608 (p0) REVERT: Ap 214 ARG cc_start: 0.8280 (mtp180) cc_final: 0.7847 (mtp180) REVERT: Aq 127 ASN cc_start: 0.8020 (p0) cc_final: 0.7784 (p0) REVERT: Aq 150 GLU cc_start: 0.8505 (pt0) cc_final: 0.8176 (pt0) REVERT: Aq 181 MET cc_start: 0.8517 (tpp) cc_final: 0.8230 (tpp) REVERT: Aq 190 LEU cc_start: 0.8944 (tp) cc_final: 0.8428 (tp) REVERT: Aq 220 MET cc_start: 0.7383 (mmm) cc_final: 0.6267 (ptm) REVERT: Ar 70 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8558 (tp) REVERT: Ar 107 GLU cc_start: 0.8243 (tp30) cc_final: 0.7776 (tm-30) REVERT: Ar 112 MET cc_start: 0.8876 (tpp) cc_final: 0.8615 (mmm) REVERT: Ar 136 ASP cc_start: 0.8029 (t0) cc_final: 0.7673 (t0) REVERT: As 71 LEU cc_start: 0.8547 (mt) cc_final: 0.8331 (pt) REVERT: As 127 ASN cc_start: 0.8037 (p0) cc_final: 0.7772 (p0) REVERT: As 150 GLU cc_start: 0.8520 (pt0) cc_final: 0.8033 (pt0) REVERT: As 190 LEU cc_start: 0.8889 (tp) cc_final: 0.8575 (tp) REVERT: As 220 MET cc_start: 0.7385 (mmm) cc_final: 0.6271 (ptm) REVERT: At 70 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8554 (tp) REVERT: At 107 GLU cc_start: 0.8329 (tp30) cc_final: 0.7805 (tm-30) REVERT: At 112 MET cc_start: 0.8876 (tpp) cc_final: 0.8645 (mmm) REVERT: At 127 ASN cc_start: 0.7991 (p0) cc_final: 0.7737 (p0) REVERT: At 136 ASP cc_start: 0.7980 (t0) cc_final: 0.7619 (t0) REVERT: At 190 LEU cc_start: 0.8939 (tp) cc_final: 0.8717 (tp) REVERT: Au 71 LEU cc_start: 0.8656 (mt) cc_final: 0.8422 (pt) REVERT: Au 127 ASN cc_start: 0.8007 (p0) cc_final: 0.7734 (p0) REVERT: Au 150 GLU cc_start: 0.8538 (pt0) cc_final: 0.8050 (pt0) REVERT: Au 181 MET cc_start: 0.8530 (tpp) cc_final: 0.8251 (tpp) REVERT: Au 190 LEU cc_start: 0.8940 (tp) cc_final: 0.8432 (tp) REVERT: Au 198 TYR cc_start: 0.8962 (m-10) cc_final: 0.8750 (m-10) REVERT: Av 136 ASP cc_start: 0.7990 (t0) cc_final: 0.7625 (t0) REVERT: Aw 127 ASN cc_start: 0.7990 (p0) cc_final: 0.7728 (p0) REVERT: Aw 190 LEU cc_start: 0.8900 (tp) cc_final: 0.8583 (tp) REVERT: Aw 198 TYR cc_start: 0.8953 (m-10) cc_final: 0.8740 (m-10) REVERT: Aw 220 MET cc_start: 0.7391 (mmm) cc_final: 0.6275 (ptm) REVERT: Ax 70 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8518 (tp) REVERT: Ax 89 GLN cc_start: 0.9061 (mt0) cc_final: 0.8858 (mt0) REVERT: Ax 127 ASN cc_start: 0.8032 (p0) cc_final: 0.7796 (p0) REVERT: Ax 136 ASP cc_start: 0.8125 (t0) cc_final: 0.7774 (t0) outliers start: 156 outliers final: 126 residues processed: 1280 average time/residue: 0.4548 time to fit residues: 948.5006 Evaluate side-chains 1294 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 1157 time to evaluate : 3.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR Chi-restraints excluded: chain Aa residue 70 LEU Chi-restraints excluded: chain Aa residue 80 ILE Chi-restraints excluded: chain Aa residue 86 THR Chi-restraints excluded: chain Aa residue 88 SER Chi-restraints excluded: chain Aa residue 150 GLU Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Ab residue 88 SER Chi-restraints excluded: chain Ab residue 141 VAL Chi-restraints excluded: chain Ab residue 150 GLU Chi-restraints excluded: chain Ac residue 43 THR Chi-restraints excluded: chain Ac residue 70 LEU Chi-restraints excluded: chain Ac residue 80 ILE Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 88 SER Chi-restraints excluded: chain Ac residue 150 GLU Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 141 VAL Chi-restraints excluded: chain Ad residue 150 GLU Chi-restraints excluded: chain Ae residue 43 THR Chi-restraints excluded: chain Ae residue 70 LEU Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 86 THR Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Ae residue 150 GLU Chi-restraints excluded: chain Af residue 43 THR Chi-restraints excluded: chain Af residue 88 SER Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Af residue 150 GLU Chi-restraints excluded: chain Ag residue 43 THR Chi-restraints excluded: chain Ag residue 70 LEU Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 86 THR Chi-restraints excluded: chain Ag residue 88 SER Chi-restraints excluded: chain Ag residue 150 GLU Chi-restraints excluded: chain Ah residue 88 SER Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ah residue 150 GLU Chi-restraints excluded: chain Ai residue 43 THR Chi-restraints excluded: chain Ai residue 44 VAL Chi-restraints excluded: chain Ai residue 70 LEU Chi-restraints excluded: chain Ai residue 88 SER Chi-restraints excluded: chain Ai residue 124 THR Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 145 LEU Chi-restraints excluded: chain Aj residue 43 THR Chi-restraints excluded: chain Aj residue 70 LEU Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 124 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Aj residue 150 GLU Chi-restraints excluded: chain Ak residue 43 THR Chi-restraints excluded: chain Ak residue 44 VAL Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 88 SER Chi-restraints excluded: chain Ak residue 124 THR Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 150 GLU Chi-restraints excluded: chain Al residue 43 THR Chi-restraints excluded: chain Al residue 70 LEU Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 124 THR Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 141 VAL Chi-restraints excluded: chain Al residue 150 GLU Chi-restraints excluded: chain Am residue 43 THR Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 88 SER Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 145 LEU Chi-restraints excluded: chain An residue 43 THR Chi-restraints excluded: chain An residue 70 LEU Chi-restraints excluded: chain An residue 80 ILE Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 124 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 141 VAL Chi-restraints excluded: chain An residue 150 GLU Chi-restraints excluded: chain Ao residue 43 THR Chi-restraints excluded: chain Ao residue 44 VAL Chi-restraints excluded: chain Ao residue 78 ILE Chi-restraints excluded: chain Ao residue 80 ILE Chi-restraints excluded: chain Ao residue 88 SER Chi-restraints excluded: chain Ao residue 124 THR Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 150 GLU Chi-restraints excluded: chain Ap residue 43 THR Chi-restraints excluded: chain Ap residue 70 LEU Chi-restraints excluded: chain Ap residue 80 ILE Chi-restraints excluded: chain Ap residue 88 SER Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 141 VAL Chi-restraints excluded: chain Ap residue 150 GLU Chi-restraints excluded: chain Aq residue 70 LEU Chi-restraints excluded: chain Aq residue 78 ILE Chi-restraints excluded: chain Aq residue 80 ILE Chi-restraints excluded: chain Aq residue 88 SER Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 151 ASN Chi-restraints excluded: chain Ar residue 43 THR Chi-restraints excluded: chain Ar residue 70 LEU Chi-restraints excluded: chain Ar residue 78 ILE Chi-restraints excluded: chain Ar residue 88 SER Chi-restraints excluded: chain Ar residue 103 ILE Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 150 GLU Chi-restraints excluded: chain As residue 80 ILE Chi-restraints excluded: chain As residue 88 SER Chi-restraints excluded: chain As residue 124 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain At residue 70 LEU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 124 THR Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 150 GLU Chi-restraints excluded: chain Au residue 78 ILE Chi-restraints excluded: chain Au residue 80 ILE Chi-restraints excluded: chain Au residue 88 SER Chi-restraints excluded: chain Av residue 78 ILE Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Aw residue 88 SER Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 150 GLU Chi-restraints excluded: chain Ax residue 70 LEU Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 103 ILE Chi-restraints excluded: chain Ax residue 124 THR Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 150 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 412 optimal weight: 7.9990 chunk 224 optimal weight: 0.0370 chunk 322 optimal weight: 0.0870 chunk 47 optimal weight: 0.6980 chunk 339 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 349 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 406 optimal weight: 0.0050 chunk 270 optimal weight: 10.0000 overall best weight: 0.5652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 151 ASN ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 151 ASN ** Aj 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 151 ASN ** An 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 98 GLN ** Ao 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 151 ASN Aq 151 ASN Ar 151 ASN At 175 ASN Au 151 ASN Av 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.134399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101917 restraints weight = 51837.361| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.80 r_work: 0.3030 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35784 Z= 0.102 Angle : 0.572 9.092 48504 Z= 0.286 Chirality : 0.039 0.151 5280 Planarity : 0.005 0.061 6288 Dihedral : 4.120 18.009 4824 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.03 % Allowed : 32.17 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 4296 helix: 0.42 (0.13), residues: 1872 sheet: 0.66 (0.35), residues: 288 loop : -1.19 (0.15), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPAd 93 HIS 0.002 0.000 HISAw 69 PHE 0.009 0.002 PHEAf 200 TYR 0.022 0.001 TYRAo 198 ARG 0.015 0.000 ARGAk 191 Details of bonding type rmsd hydrogen bonds : bond 0.02297 ( 1152) hydrogen bonds : angle 5.03878 ( 3312) covalent geometry : bond 0.00251 (35784) covalent geometry : angle 0.57236 (48504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1235 time to evaluate : 5.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 70 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8621 (tp) REVERT: Aa 71 LEU cc_start: 0.8530 (mt) cc_final: 0.8280 (pp) REVERT: Aa 81 SER cc_start: 0.9385 (t) cc_final: 0.9148 (t) REVERT: Aa 89 GLN cc_start: 0.9100 (mt0) cc_final: 0.8787 (tt0) REVERT: Aa 184 TYR cc_start: 0.8897 (t80) cc_final: 0.8685 (t80) REVERT: Ab 71 LEU cc_start: 0.8634 (mt) cc_final: 0.8424 (mp) REVERT: Ab 136 ASP cc_start: 0.8347 (t0) cc_final: 0.7993 (t0) REVERT: Ab 190 LEU cc_start: 0.8875 (tp) cc_final: 0.8658 (tp) REVERT: Ab 220 MET cc_start: 0.7332 (mmm) cc_final: 0.6311 (ptp) REVERT: Ac 71 LEU cc_start: 0.8524 (mt) cc_final: 0.8296 (pp) REVERT: Ac 81 SER cc_start: 0.9398 (t) cc_final: 0.9169 (t) REVERT: Ad 71 LEU cc_start: 0.8649 (mt) cc_final: 0.8429 (mp) REVERT: Ad 190 LEU cc_start: 0.8962 (tp) cc_final: 0.8656 (tp) REVERT: Ad 220 MET cc_start: 0.7344 (mmm) cc_final: 0.6275 (ptp) REVERT: Ae 70 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8629 (tp) REVERT: Ae 71 LEU cc_start: 0.8526 (mt) cc_final: 0.8275 (pp) REVERT: Ae 81 SER cc_start: 0.9393 (t) cc_final: 0.9155 (t) REVERT: Af 71 LEU cc_start: 0.8630 (mt) cc_final: 0.8428 (mp) REVERT: Af 136 ASP cc_start: 0.8330 (t0) cc_final: 0.7970 (t0) REVERT: Af 190 LEU cc_start: 0.8878 (tp) cc_final: 0.8650 (tp) REVERT: Af 220 MET cc_start: 0.7311 (mmm) cc_final: 0.6258 (ptp) REVERT: Ag 70 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8637 (tp) REVERT: Ag 71 LEU cc_start: 0.8513 (mt) cc_final: 0.8275 (pp) REVERT: Ag 81 SER cc_start: 0.9388 (t) cc_final: 0.9160 (t) REVERT: Ah 71 LEU cc_start: 0.8654 (mt) cc_final: 0.8433 (mp) REVERT: Ah 190 LEU cc_start: 0.8880 (tp) cc_final: 0.8667 (tp) REVERT: Ah 220 MET cc_start: 0.7355 (mmm) cc_final: 0.6271 (ptp) REVERT: Ai 150 GLU cc_start: 0.8383 (pt0) cc_final: 0.7901 (pt0) REVERT: Ai 151 ASN cc_start: 0.8119 (t0) cc_final: 0.7875 (t0) REVERT: Ai 181 MET cc_start: 0.8488 (tpp) cc_final: 0.8174 (tpp) REVERT: Aj 127 ASN cc_start: 0.7773 (p0) cc_final: 0.7562 (p0) REVERT: Aj 142 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8636 (mt-10) REVERT: Aj 214 ARG cc_start: 0.8330 (mtp180) cc_final: 0.8021 (mtp180) REVERT: Ak 48 LYS cc_start: 0.8623 (tppt) cc_final: 0.8398 (tptt) REVERT: Ak 70 LEU cc_start: 0.9041 (tp) cc_final: 0.8732 (tp) REVERT: Ak 127 ASN cc_start: 0.7883 (p0) cc_final: 0.7647 (p0) REVERT: Ak 181 MET cc_start: 0.8474 (tpp) cc_final: 0.8157 (tpp) REVERT: Al 127 ASN cc_start: 0.7843 (p0) cc_final: 0.7576 (p0) REVERT: Al 142 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8660 (mt-10) REVERT: Al 214 ARG cc_start: 0.8259 (mtp180) cc_final: 0.8040 (mtp180) REVERT: Am 48 LYS cc_start: 0.8699 (tppt) cc_final: 0.8488 (tptt) REVERT: Am 135 MET cc_start: 0.8602 (mmm) cc_final: 0.8294 (mmm) REVERT: Am 150 GLU cc_start: 0.8425 (pt0) cc_final: 0.7946 (pt0) REVERT: Am 181 MET cc_start: 0.8486 (tpp) cc_final: 0.8178 (tpp) REVERT: An 127 ASN cc_start: 0.7866 (p0) cc_final: 0.7627 (p0) REVERT: An 142 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8625 (mt-10) REVERT: An 214 ARG cc_start: 0.8327 (mtp180) cc_final: 0.7999 (mtp180) REVERT: Ao 48 LYS cc_start: 0.8687 (tppt) cc_final: 0.8476 (tptt) REVERT: Ao 127 ASN cc_start: 0.7888 (p0) cc_final: 0.7643 (p0) REVERT: Ao 181 MET cc_start: 0.8522 (tpp) cc_final: 0.8229 (tpp) REVERT: Ap 127 ASN cc_start: 0.7761 (p0) cc_final: 0.7545 (p0) REVERT: Ap 142 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8617 (mt-10) REVERT: Ap 214 ARG cc_start: 0.8262 (mtp180) cc_final: 0.8055 (mtp180) REVERT: Aq 127 ASN cc_start: 0.7992 (p0) cc_final: 0.7758 (p0) REVERT: Aq 150 GLU cc_start: 0.8487 (pt0) cc_final: 0.8105 (pt0) REVERT: Aq 181 MET cc_start: 0.8519 (tpp) cc_final: 0.8262 (tpp) REVERT: Aq 190 LEU cc_start: 0.8952 (tp) cc_final: 0.8450 (tp) REVERT: Aq 220 MET cc_start: 0.7341 (mmm) cc_final: 0.6241 (ptm) REVERT: Ar 70 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8559 (tp) REVERT: Ar 136 ASP cc_start: 0.8031 (t0) cc_final: 0.7659 (t0) REVERT: As 127 ASN cc_start: 0.7999 (p0) cc_final: 0.7768 (p0) REVERT: As 150 GLU cc_start: 0.8546 (pt0) cc_final: 0.8119 (pt0) REVERT: As 190 LEU cc_start: 0.8915 (tp) cc_final: 0.8568 (tp) REVERT: As 220 MET cc_start: 0.7333 (mmm) cc_final: 0.6239 (ptm) REVERT: At 70 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8542 (tp) REVERT: At 127 ASN cc_start: 0.7992 (p0) cc_final: 0.7672 (p0) REVERT: At 136 ASP cc_start: 0.8032 (t0) cc_final: 0.7663 (t0) REVERT: Au 127 ASN cc_start: 0.7988 (p0) cc_final: 0.7763 (p0) REVERT: Au 150 GLU cc_start: 0.8505 (pt0) cc_final: 0.8031 (pt0) REVERT: Au 181 MET cc_start: 0.8554 (tpp) cc_final: 0.8284 (tpp) REVERT: Au 190 LEU cc_start: 0.8953 (tp) cc_final: 0.8454 (tp) REVERT: Au 198 TYR cc_start: 0.8883 (m-10) cc_final: 0.8653 (m-10) REVERT: Au 220 MET cc_start: 0.7201 (mmm) cc_final: 0.6183 (ptm) REVERT: Av 79 ASP cc_start: 0.8061 (m-30) cc_final: 0.7859 (m-30) REVERT: Av 136 ASP cc_start: 0.8030 (t0) cc_final: 0.7663 (t0) REVERT: Aw 127 ASN cc_start: 0.7984 (p0) cc_final: 0.7746 (p0) REVERT: Aw 190 LEU cc_start: 0.8873 (tp) cc_final: 0.8549 (tp) REVERT: Aw 198 TYR cc_start: 0.8858 (m-10) cc_final: 0.8645 (m-10) REVERT: Aw 220 MET cc_start: 0.7341 (mmm) cc_final: 0.6253 (ptm) REVERT: Ax 70 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8501 (tp) REVERT: Ax 127 ASN cc_start: 0.7983 (p0) cc_final: 0.7658 (p0) REVERT: Ax 136 ASP cc_start: 0.8063 (t0) cc_final: 0.7699 (t0) outliers start: 77 outliers final: 54 residues processed: 1274 average time/residue: 0.4521 time to fit residues: 944.2738 Evaluate side-chains 1257 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 1197 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 70 LEU Chi-restraints excluded: chain Aa residue 86 THR Chi-restraints excluded: chain Aa residue 150 GLU Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 150 GLU Chi-restraints excluded: chain Ae residue 70 LEU Chi-restraints excluded: chain Ae residue 86 THR Chi-restraints excluded: chain Ae residue 150 GLU Chi-restraints excluded: chain Ae residue 159 ILE Chi-restraints excluded: chain Af residue 43 THR Chi-restraints excluded: chain Ag residue 70 LEU Chi-restraints excluded: chain Ag residue 86 THR Chi-restraints excluded: chain Ag residue 88 SER Chi-restraints excluded: chain Ag residue 150 GLU Chi-restraints excluded: chain Ah residue 88 SER Chi-restraints excluded: chain Ai residue 43 THR Chi-restraints excluded: chain Ai residue 70 LEU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Ai residue 148 ILE Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Aj residue 150 GLU Chi-restraints excluded: chain Ak residue 78 ILE Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 150 GLU Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 150 GLU Chi-restraints excluded: chain Am residue 88 SER Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 150 GLU Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 150 GLU Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 150 GLU Chi-restraints excluded: chain Ap residue 151 ASN Chi-restraints excluded: chain Aq residue 70 LEU Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Ar residue 70 LEU Chi-restraints excluded: chain Ar residue 78 ILE Chi-restraints excluded: chain Ar residue 103 ILE Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 150 GLU Chi-restraints excluded: chain As residue 43 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain At residue 70 LEU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 150 GLU Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 150 GLU Chi-restraints excluded: chain Ax residue 70 LEU Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 103 ILE Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 372 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 304 optimal weight: 8.9990 chunk 221 optimal weight: 3.9990 chunk 343 optimal weight: 0.0570 chunk 381 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 151 ASN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 ASN ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 151 ASN Ai 98 GLN ** Aj 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 98 GLN Ak 151 ASN ** Ak 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 98 GLN ** An 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 98 GLN Ao 151 ASN ** Ao 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 151 ASN Aq 98 GLN ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 98 GLN As 98 GLN At 98 GLN Au 98 GLN Av 98 GLN Aw 98 GLN Aw 151 ASN Ax 98 GLN Ax 151 ASN Ax 175 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097389 restraints weight = 52060.841| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.74 r_work: 0.2970 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35784 Z= 0.166 Angle : 0.622 9.212 48504 Z= 0.311 Chirality : 0.042 0.165 5280 Planarity : 0.005 0.056 6288 Dihedral : 4.310 18.892 4824 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.24 % Allowed : 32.44 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 4296 helix: 0.32 (0.13), residues: 1800 sheet: 0.65 (0.35), residues: 288 loop : -1.21 (0.15), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPAb 93 HIS 0.004 0.001 HISAj 69 PHE 0.009 0.002 PHEAe 202 TYR 0.022 0.002 TYRAo 198 ARG 0.007 0.000 ARGAk 191 Details of bonding type rmsd hydrogen bonds : bond 0.02685 ( 1152) hydrogen bonds : angle 5.20582 ( 3312) covalent geometry : bond 0.00407 (35784) covalent geometry : angle 0.62235 (48504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8592 Ramachandran restraints generated. 4296 Oldfield, 0 Emsley, 4296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1182 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 70 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8713 (tp) REVERT: Aa 81 SER cc_start: 0.9408 (t) cc_final: 0.9140 (t) REVERT: Ab 69 HIS cc_start: 0.8238 (t-90) cc_final: 0.7939 (t-170) REVERT: Ab 71 LEU cc_start: 0.8660 (mt) cc_final: 0.8327 (mp) REVERT: Ab 136 ASP cc_start: 0.8373 (t0) cc_final: 0.7996 (t0) REVERT: Ab 190 LEU cc_start: 0.8958 (tp) cc_final: 0.8667 (tp) REVERT: Ab 220 MET cc_start: 0.7209 (mmm) cc_final: 0.6271 (ptp) REVERT: Ac 48 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8616 (ttmm) REVERT: Ac 70 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8705 (tp) REVERT: Ac 81 SER cc_start: 0.9405 (t) cc_final: 0.9137 (t) REVERT: Ac 89 GLN cc_start: 0.9167 (mt0) cc_final: 0.8906 (tt0) REVERT: Ad 69 HIS cc_start: 0.8203 (t-90) cc_final: 0.7913 (t-170) REVERT: Ad 71 LEU cc_start: 0.8694 (mt) cc_final: 0.8376 (mp) REVERT: Ad 190 LEU cc_start: 0.8988 (tp) cc_final: 0.8685 (tp) REVERT: Ad 220 MET cc_start: 0.7217 (mmm) cc_final: 0.6267 (ptp) REVERT: Ae 70 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8702 (tp) REVERT: Ae 81 SER cc_start: 0.9421 (t) cc_final: 0.9159 (t) REVERT: Ae 135 MET cc_start: 0.8933 (mmm) cc_final: 0.8730 (mmt) REVERT: Af 69 HIS cc_start: 0.8277 (t-90) cc_final: 0.7972 (t-170) REVERT: Af 136 ASP cc_start: 0.8387 (t0) cc_final: 0.8003 (t0) REVERT: Af 190 LEU cc_start: 0.8969 (tp) cc_final: 0.8668 (tp) REVERT: Af 220 MET cc_start: 0.7197 (mmm) cc_final: 0.6268 (ptp) REVERT: Ag 70 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8726 (tp) REVERT: Ag 81 SER cc_start: 0.9408 (t) cc_final: 0.9148 (t) REVERT: Ag 89 GLN cc_start: 0.9084 (mt0) cc_final: 0.8774 (mt0) REVERT: Ah 69 HIS cc_start: 0.8256 (t-90) cc_final: 0.7914 (t-170) REVERT: Ah 71 LEU cc_start: 0.8721 (mt) cc_final: 0.8396 (mp) REVERT: Ah 135 MET cc_start: 0.8781 (mmm) cc_final: 0.8523 (mmm) REVERT: Ah 190 LEU cc_start: 0.8955 (tp) cc_final: 0.8683 (tp) REVERT: Ah 220 MET cc_start: 0.7241 (mmm) cc_final: 0.6239 (ptp) REVERT: Ai 48 LYS cc_start: 0.8796 (tptt) cc_final: 0.8577 (tppt) REVERT: Ai 150 GLU cc_start: 0.8536 (pt0) cc_final: 0.8123 (pt0) REVERT: Ai 151 ASN cc_start: 0.8211 (t0) cc_final: 0.8002 (t0) REVERT: Ai 181 MET cc_start: 0.8629 (tpp) cc_final: 0.8297 (tpp) REVERT: Ai 214 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7833 (mtp180) REVERT: Aj 112 MET cc_start: 0.8763 (tpp) cc_final: 0.7920 (mmt) REVERT: Aj 127 ASN cc_start: 0.7803 (p0) cc_final: 0.7582 (p0) REVERT: Aj 214 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7972 (mtp180) REVERT: Ak 48 LYS cc_start: 0.8655 (tppt) cc_final: 0.8436 (tptt) REVERT: Ak 70 LEU cc_start: 0.9188 (tp) cc_final: 0.8768 (tp) REVERT: Ak 98 GLN cc_start: 0.8254 (tt0) cc_final: 0.8043 (tt0) REVERT: Ak 127 ASN cc_start: 0.7959 (p0) cc_final: 0.7716 (p0) REVERT: Al 127 ASN cc_start: 0.7868 (p0) cc_final: 0.7611 (p0) REVERT: Al 214 ARG cc_start: 0.8274 (mtp180) cc_final: 0.7989 (mtp180) REVERT: Am 48 LYS cc_start: 0.8656 (tppt) cc_final: 0.8435 (tptt) REVERT: Am 150 GLU cc_start: 0.8499 (pt0) cc_final: 0.8034 (pt0) REVERT: An 127 ASN cc_start: 0.7862 (p0) cc_final: 0.7623 (p0) REVERT: An 214 ARG cc_start: 0.8305 (mtp180) cc_final: 0.7888 (mtp180) REVERT: Ao 127 ASN cc_start: 0.7933 (p0) cc_final: 0.7713 (p0) REVERT: Ap 127 ASN cc_start: 0.7817 (p0) cc_final: 0.7598 (p0) REVERT: Ap 214 ARG cc_start: 0.8279 (mtp180) cc_final: 0.7985 (mtp180) REVERT: Aq 127 ASN cc_start: 0.8008 (p0) cc_final: 0.7763 (p0) REVERT: Aq 150 GLU cc_start: 0.8524 (pt0) cc_final: 0.8128 (pt0) REVERT: Aq 181 MET cc_start: 0.8552 (tpp) cc_final: 0.8250 (tpp) REVERT: Aq 190 LEU cc_start: 0.8951 (tp) cc_final: 0.8438 (tp) REVERT: Aq 220 MET cc_start: 0.7348 (mmm) cc_final: 0.6271 (ptm) REVERT: Ar 70 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8578 (tp) REVERT: Ar 71 LEU cc_start: 0.8655 (mt) cc_final: 0.8334 (pp) REVERT: Ar 107 GLU cc_start: 0.8263 (tp30) cc_final: 0.7753 (tm-30) REVERT: Ar 136 ASP cc_start: 0.8049 (t0) cc_final: 0.7698 (t0) REVERT: Ar 220 MET cc_start: 0.7468 (mmt) cc_final: 0.6502 (ptm) REVERT: As 127 ASN cc_start: 0.8019 (p0) cc_final: 0.7779 (p0) REVERT: As 150 GLU cc_start: 0.8566 (pt0) cc_final: 0.8131 (pt0) REVERT: As 190 LEU cc_start: 0.8877 (tp) cc_final: 0.8540 (tp) REVERT: As 220 MET cc_start: 0.7361 (mmm) cc_final: 0.6277 (ptm) REVERT: At 70 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8578 (tp) REVERT: At 71 LEU cc_start: 0.8650 (mt) cc_final: 0.8325 (pp) REVERT: At 107 GLU cc_start: 0.8333 (tp30) cc_final: 0.7697 (tm-30) REVERT: At 127 ASN cc_start: 0.7985 (p0) cc_final: 0.7770 (p0) REVERT: At 136 ASP cc_start: 0.8047 (t0) cc_final: 0.7703 (t0) REVERT: Au 127 ASN cc_start: 0.7999 (p0) cc_final: 0.7771 (p0) REVERT: Au 150 GLU cc_start: 0.8607 (pt0) cc_final: 0.8170 (pt0) REVERT: Au 181 MET cc_start: 0.8520 (tpp) cc_final: 0.8210 (tpp) REVERT: Au 190 LEU cc_start: 0.8943 (tp) cc_final: 0.8427 (tp) REVERT: Au 198 TYR cc_start: 0.8915 (m-10) cc_final: 0.8674 (m-10) REVERT: Au 220 MET cc_start: 0.7261 (mmm) cc_final: 0.6259 (ptm) REVERT: Av 71 LEU cc_start: 0.8679 (mt) cc_final: 0.8368 (pp) REVERT: Av 107 GLU cc_start: 0.8401 (tp30) cc_final: 0.7691 (tm-30) REVERT: Av 136 ASP cc_start: 0.8093 (t0) cc_final: 0.7756 (t0) REVERT: Av 220 MET cc_start: 0.7478 (mmt) cc_final: 0.6505 (ptm) REVERT: Aw 107 GLU cc_start: 0.8378 (tp30) cc_final: 0.8098 (tm-30) REVERT: Aw 127 ASN cc_start: 0.7946 (p0) cc_final: 0.7709 (p0) REVERT: Aw 190 LEU cc_start: 0.8886 (tp) cc_final: 0.8553 (tp) REVERT: Aw 220 MET cc_start: 0.7348 (mmm) cc_final: 0.6252 (ptm) REVERT: Ax 70 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8570 (tp) REVERT: Ax 71 LEU cc_start: 0.8672 (mt) cc_final: 0.8371 (pp) REVERT: Ax 98 GLN cc_start: 0.8368 (tt0) cc_final: 0.8136 (tt0) REVERT: Ax 127 ASN cc_start: 0.7964 (p0) cc_final: 0.7750 (p0) REVERT: Ax 136 ASP cc_start: 0.8068 (t0) cc_final: 0.7719 (t0) REVERT: Ax 181 MET cc_start: 0.8594 (tpp) cc_final: 0.8218 (tpp) REVERT: Ax 220 MET cc_start: 0.7456 (mmt) cc_final: 0.6466 (ptm) outliers start: 85 outliers final: 74 residues processed: 1234 average time/residue: 0.5064 time to fit residues: 1014.3195 Evaluate side-chains 1230 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1149 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR Chi-restraints excluded: chain Aa residue 70 LEU Chi-restraints excluded: chain Aa residue 86 THR Chi-restraints excluded: chain Aa residue 150 GLU Chi-restraints excluded: chain Aa residue 159 ILE Chi-restraints excluded: chain Ab residue 88 SER Chi-restraints excluded: chain Ac residue 43 THR Chi-restraints excluded: chain Ac residue 70 LEU Chi-restraints excluded: chain Ac residue 86 THR Chi-restraints excluded: chain Ac residue 150 GLU Chi-restraints excluded: chain Ac residue 159 ILE Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ae residue 70 LEU Chi-restraints excluded: chain Ae residue 86 THR Chi-restraints excluded: chain Ae residue 150 GLU Chi-restraints excluded: chain Ae residue 159 ILE Chi-restraints excluded: chain Af residue 88 SER Chi-restraints excluded: chain Ag residue 43 THR Chi-restraints excluded: chain Ag residue 70 LEU Chi-restraints excluded: chain Ag residue 86 THR Chi-restraints excluded: chain Ag residue 88 SER Chi-restraints excluded: chain Ag residue 150 GLU Chi-restraints excluded: chain Ah residue 88 SER Chi-restraints excluded: chain Ai residue 43 THR Chi-restraints excluded: chain Ai residue 70 LEU Chi-restraints excluded: chain Ai residue 133 VAL Chi-restraints excluded: chain Aj residue 124 THR Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Aj residue 150 GLU Chi-restraints excluded: chain Ak residue 78 ILE Chi-restraints excluded: chain Ak residue 80 ILE Chi-restraints excluded: chain Ak residue 88 SER Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 150 GLU Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 150 GLU Chi-restraints excluded: chain Am residue 43 THR Chi-restraints excluded: chain Am residue 80 ILE Chi-restraints excluded: chain Am residue 88 SER Chi-restraints excluded: chain Am residue 124 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 150 GLU Chi-restraints excluded: chain Ao residue 43 THR Chi-restraints excluded: chain Ao residue 78 ILE Chi-restraints excluded: chain Ao residue 88 SER Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 150 GLU Chi-restraints excluded: chain Ao residue 151 ASN Chi-restraints excluded: chain Ap residue 124 THR Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 150 GLU Chi-restraints excluded: chain Ap residue 151 ASN Chi-restraints excluded: chain Aq residue 70 LEU Chi-restraints excluded: chain Aq residue 78 ILE Chi-restraints excluded: chain Aq residue 88 SER Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Ar residue 43 THR Chi-restraints excluded: chain Ar residue 70 LEU Chi-restraints excluded: chain Ar residue 78 ILE Chi-restraints excluded: chain Ar residue 103 ILE Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain Ar residue 150 GLU Chi-restraints excluded: chain As residue 124 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain At residue 70 LEU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 133 VAL Chi-restraints excluded: chain At residue 150 GLU Chi-restraints excluded: chain Av residue 43 THR Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Aw residue 124 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 150 GLU Chi-restraints excluded: chain Ax residue 70 LEU Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 88 SER Chi-restraints excluded: chain Ax residue 103 ILE Chi-restraints excluded: chain Ax residue 133 VAL Chi-restraints excluded: chain Ax residue 150 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 414 optimal weight: 0.0870 chunk 230 optimal weight: 3.9990 chunk 375 optimal weight: 9.9990 chunk 403 optimal weight: 0.9980 chunk 276 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 348 optimal weight: 0.9980 chunk 306 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 151 ASN ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 140 GLN ** Aj 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 151 ASN ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 151 ASN ** An 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 151 ASN ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 151 ASN Aq 151 ASN Ar 98 GLN Ar 175 ASN As 98 GLN ** Au 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Au 98 GLN Aw 69 HIS Aw 175 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101568 restraints weight = 51866.362| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.78 r_work: 0.3031 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35784 Z= 0.111 Angle : 0.604 9.340 48504 Z= 0.300 Chirality : 0.040 0.143 5280 Planarity : 0.005 0.059 6288 Dihedral : 4.228 19.910 4824 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.82 % Allowed : 33.65 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 4296 helix: 0.40 (0.13), residues: 1872 sheet: 0.61 (0.34), residues: 288 loop : -1.12 (0.15), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPAb 93 HIS 0.011 0.001 HISAu 69 PHE 0.009 0.002 PHEAh 200 TYR 0.022 0.002 TYRAo 198 ARG 0.008 0.000 ARGAk 191 Details of bonding type rmsd hydrogen bonds : bond 0.02423 ( 1152) hydrogen bonds : angle 5.14959 ( 3312) covalent geometry : bond 0.00273 (35784) covalent geometry : angle 0.60365 (48504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19792.09 seconds wall clock time: 340 minutes 30.04 seconds (20430.04 seconds total)