Starting phenix.real_space_refine on Mon Apr 15 14:00:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opa_17046/04_2024/8opa_17046.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opa_17046/04_2024/8opa_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opa_17046/04_2024/8opa_17046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opa_17046/04_2024/8opa_17046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opa_17046/04_2024/8opa_17046.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opa_17046/04_2024/8opa_17046.pdb" } 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 Residue "Aa GLU 172": "OE1" <-> "OE2" Residue "Ab GLU 172": "OE1" <-> "OE2" Residue "Ac GLU 172": "OE1" <-> "OE2" Residue "Ad GLU 172": "OE1" <-> "OE2" Residue "Ae GLU 172": "OE1" <-> "OE2" Residue "Af GLU 172": "OE1" <-> "OE2" Residue "Ag GLU 172": "OE1" <-> "OE2" Residue "Ah GLU 172": "OE1" <-> "OE2" Residue "Ai GLU 172": "OE1" <-> "OE2" Residue "Aj GLU 172": "OE1" <-> "OE2" Residue "Ak GLU 172": "OE1" <-> "OE2" Residue "Al GLU 172": "OE1" <-> "OE2" Residue "Am GLU 172": "OE1" <-> "OE2" Residue "An GLU 172": "OE1" <-> "OE2" Residue "Ao GLU 172": "OE1" <-> "OE2" Residue "Ap GLU 172": "OE1" <-> "OE2" Residue "Aq GLU 172": "OE1" <-> "OE2" Residue "Ar GLU 172": "OE1" <-> "OE2" Residue "As GLU 172": "OE1" <-> "OE2" Residue "At GLU 172": "OE1" <-> "OE2" Residue "Au GLU 172": "OE1" <-> "OE2" Residue "Av GLU 172": "OE1" <-> "OE2" Residue "Aw GLU 172": "OE1" <-> "OE2" Residue "Ax GLU 172": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 34992 Number of models: 1 Model: "" Number of chains: 24 Chain: "Aa" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ab" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ac" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ad" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ae" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Af" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ag" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ah" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ai" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Aj" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ak" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Al" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Am" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "An" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ao" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ap" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Aq" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ar" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "As" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "At" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Au" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Av" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Aw" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Chain: "Ax" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 169} Time building chain proxies: 18.08, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.70 Conformation dependent library (CDL) restraints added in 6.5 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: 3.24 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: 10.38 Time building geometry restraints manager: 14.71 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: 99.43 - 106.36: 1482 106.36 - 113.29: 18928 113.29 - 120.22: 13212 120.22 - 127.15: 14378 127.15 - 134.08: 504 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 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' selection = chain 'At' selection = chain 'Au' selection = chain 'Av' selection = chain 'Aw' selection = chain 'Ax' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.280 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: 0.040 Extract box with map and model: 7.610 Check model and map are aligned: 0.420 Set scattering table: 0.340 Process input model: 87.480 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.300 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.610 ------------------------------------------------------------------------------- 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= 0.391 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 1275 time to evaluate : 3.924 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: 0.4941 time to fit residues: 1030.3454 Evaluate side-chains 1157 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1157 time to evaluate : 4.289 ------------------------------------------------------------------------------- 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: 0.0970 chunk 327 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 220 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 chunk 392 optimal weight: 0.5980 overall best weight: 2.2982 ------------------------------------------------------------------------------- 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** Ab 98 GLN Ac 89 GLN Ac 98 GLN ** 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 ** Ah 98 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 98 GLN ** 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35784 Z= 0.252 Angle : 0.580 7.111 48504 Z= 0.289 Chirality : 0.042 0.129 5280 Planarity : 0.005 0.038 6288 Dihedral : 4.370 15.890 4824 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.53 % Allowed : 24.66 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4296 helix: -0.24 (0.12), residues: 1752 sheet: -0.28 (0.34), residues: 288 loop : -1.30 (0.15), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPAe 132 HIS 0.009 0.001 HISAb 69 PHE 0.010 0.002 PHEAe 202 TYR 0.011 0.002 TYRAw 73 ARG 0.004 0.000 ARGAc 55 *********************** 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 1308 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1212 time to evaluate : 4.014 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 70 LEU cc_start: 0.8881 (tp) cc_final: 0.8642 (tp) REVERT: Ab 69 HIS cc_start: 0.8350 (t-170) cc_final: 0.8079 (t-170) REVERT: Ab 135 MET cc_start: 0.8733 (mmm) cc_final: 0.8502 (mmm) REVERT: Ab 136 ASP cc_start: 0.8215 (t0) cc_final: 0.7984 (t0) REVERT: Ab 190 LEU cc_start: 0.8990 (tp) cc_final: 0.8705 (tp) REVERT: Ac 48 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8442 (ttmm) REVERT: Ac 70 LEU cc_start: 0.8905 (tp) cc_final: 0.8665 (tp) REVERT: Ad 135 MET cc_start: 0.8738 (mmm) cc_final: 0.8513 (mmm) REVERT: Ad 136 ASP cc_start: 0.8240 (t0) cc_final: 0.8028 (t0) REVERT: Ad 190 LEU cc_start: 0.8992 (tp) cc_final: 0.8708 (tp) REVERT: Ae 70 LEU cc_start: 0.8893 (tp) cc_final: 0.8684 (tp) REVERT: Af 135 MET cc_start: 0.8743 (mmm) cc_final: 0.8518 (mmm) REVERT: Af 136 ASP cc_start: 0.8230 (t0) cc_final: 0.8007 (t0) REVERT: Af 190 LEU cc_start: 0.8976 (tp) cc_final: 0.8689 (tp) REVERT: Ag 70 LEU cc_start: 0.8877 (tp) cc_final: 0.8636 (tp) REVERT: Ah 135 MET cc_start: 0.8742 (mmm) cc_final: 0.8516 (mmm) REVERT: Ah 190 LEU cc_start: 0.8986 (tp) cc_final: 0.8700 (tp) REVERT: Ai 102 ASP cc_start: 0.8307 (t70) cc_final: 0.8084 (t0) REVERT: Ai 127 ASN cc_start: 0.7889 (p0) cc_final: 0.7527 (p0) REVERT: Ai 173 MET cc_start: 0.8904 (tmm) cc_final: 0.8513 (tmm) REVERT: Aj 70 LEU cc_start: 0.8856 (tp) cc_final: 0.8550 (tp) REVERT: Aj 89 GLN cc_start: 0.9130 (mt0) cc_final: 0.8875 (mt0) REVERT: Aj 102 ASP cc_start: 0.8256 (t70) cc_final: 0.7913 (t0) REVERT: Aj 127 ASN cc_start: 0.7834 (p0) cc_final: 0.7541 (p0) REVERT: Aj 136 ASP cc_start: 0.8178 (t0) cc_final: 0.7932 (t0) REVERT: Ak 102 ASP cc_start: 0.8293 (t70) cc_final: 0.8077 (t0) REVERT: Ak 173 MET cc_start: 0.8893 (tmm) cc_final: 0.8523 (tmm) REVERT: Al 89 GLN cc_start: 0.9131 (mt0) cc_final: 0.8868 (mt0) REVERT: Al 102 ASP cc_start: 0.8267 (t70) cc_final: 0.8056 (t0) REVERT: Al 127 ASN cc_start: 0.7851 (p0) cc_final: 0.7521 (p0) REVERT: Am 102 ASP cc_start: 0.8325 (t70) cc_final: 0.8088 (t0) REVERT: Am 127 ASN cc_start: 0.7898 (p0) cc_final: 0.7567 (p0) REVERT: Am 173 MET cc_start: 0.8871 (tmm) cc_final: 0.8494 (tmm) REVERT: An 127 ASN cc_start: 0.7842 (p0) cc_final: 0.7611 (p0) REVERT: Ao 102 ASP cc_start: 0.8301 (t70) cc_final: 0.8066 (t0) REVERT: Ao 127 ASN cc_start: 0.7895 (p0) cc_final: 0.7540 (p0) REVERT: Ao 173 MET cc_start: 0.8860 (tmm) cc_final: 0.8463 (tmm) REVERT: Ap 70 LEU cc_start: 0.8871 (tp) cc_final: 0.8537 (tp) REVERT: Ap 102 ASP cc_start: 0.8260 (t70) cc_final: 0.8044 (t0) REVERT: Ap 127 ASN cc_start: 0.7836 (p0) cc_final: 0.7511 (p0) REVERT: Aq 181 MET cc_start: 0.8543 (tpp) cc_final: 0.8320 (tpp) REVERT: Aq 190 LEU cc_start: 0.8947 (tp) cc_final: 0.8443 (tp) REVERT: Aq 198 TYR cc_start: 0.8904 (m-10) cc_final: 0.8699 (m-10) REVERT: Ar 89 GLN cc_start: 0.9103 (mt0) cc_final: 0.8783 (mt0) REVERT: Ar 127 ASN cc_start: 0.7872 (p0) cc_final: 0.7653 (p0) REVERT: Ar 136 ASP cc_start: 0.7941 (t0) cc_final: 0.7675 (t0) REVERT: Ar 179 PRO cc_start: 0.8601 (Cg_exo) cc_final: 0.8398 (Cg_endo) REVERT: As 69 HIS cc_start: 0.8242 (t-90) cc_final: 0.7967 (t-90) REVERT: As 181 MET cc_start: 0.8530 (tpp) cc_final: 0.8309 (tpp) REVERT: As 190 LEU cc_start: 0.8941 (tp) cc_final: 0.8445 (tp) REVERT: As 198 TYR cc_start: 0.8897 (m-10) cc_final: 0.8697 (m-10) REVERT: At 89 GLN cc_start: 0.9113 (mt0) cc_final: 0.8800 (mt0) REVERT: At 136 ASP cc_start: 0.7952 (t0) cc_final: 0.7684 (t0) REVERT: At 179 PRO cc_start: 0.8586 (Cg_exo) cc_final: 0.8375 (Cg_endo) REVERT: Au 69 HIS cc_start: 0.8269 (t-90) cc_final: 0.7958 (t-90) REVERT: Au 181 MET cc_start: 0.8543 (tpp) cc_final: 0.8319 (tpp) REVERT: Au 190 LEU cc_start: 0.8943 (tp) cc_final: 0.8447 (tp) REVERT: Au 198 TYR cc_start: 0.8914 (m-10) cc_final: 0.8708 (m-10) REVERT: Av 89 GLN cc_start: 0.9118 (mt0) cc_final: 0.8826 (mt0) REVERT: Av 127 ASN cc_start: 0.7899 (p0) cc_final: 0.7676 (p0) REVERT: Av 136 ASP cc_start: 0.7936 (t0) cc_final: 0.7674 (t0) REVERT: Aw 190 LEU cc_start: 0.8915 (tp) cc_final: 0.8525 (tp) REVERT: Aw 198 TYR cc_start: 0.8928 (m-10) cc_final: 0.8713 (m-10) REVERT: Ax 89 GLN cc_start: 0.9096 (mt0) cc_final: 0.8792 (mt0) REVERT: Ax 127 ASN cc_start: 0.7910 (p0) cc_final: 0.7690 (p0) REVERT: Ax 136 ASP cc_start: 0.7928 (t0) cc_final: 0.7658 (t0) outliers start: 96 outliers final: 92 residues processed: 1271 average time/residue: 0.4920 time to fit residues: 1049.9255 Evaluate side-chains 1238 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1146 time to evaluate : 4.534 ------------------------------------------------------------------------------- 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 80 ILE 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 80 ILE 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 80 ILE 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 80 ILE 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 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 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 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 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 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 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 141 VAL Chi-restraints excluded: chain Aq residue 43 THR Chi-restraints excluded: chain Aq residue 59 SER Chi-restraints excluded: chain Aq residue 80 ILE Chi-restraints excluded: chain Aq residue 88 SER Chi-restraints excluded: chain Ar residue 43 THR 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 As residue 43 THR Chi-restraints excluded: chain As residue 59 SER Chi-restraints excluded: chain As residue 80 ILE Chi-restraints excluded: chain As residue 88 SER Chi-restraints excluded: chain At residue 43 THR 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 43 THR Chi-restraints excluded: chain Au residue 59 SER Chi-restraints excluded: chain Au residue 80 ILE Chi-restraints excluded: chain Au residue 88 SER 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 150 GLU Chi-restraints excluded: chain Av residue 205 VAL 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 Ax residue 43 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 326 optimal weight: 6.9990 chunk 267 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 424 optimal weight: 0.9980 chunk 350 optimal weight: 10.0000 chunk 389 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- 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** Ac 89 GLN ** Ad 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 89 GLN ** Ae 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 89 GLN ** Ah 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 158 GLN ** Aj 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 175 ASN ** Ak 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 158 GLN ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 175 ASN ** Am 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 158 GLN ** An 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** An 175 ASN ** Ao 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 158 GLN ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 175 ASN ** Aq 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 35784 Z= 0.392 Angle : 0.644 8.420 48504 Z= 0.321 Chirality : 0.045 0.131 5280 Planarity : 0.005 0.034 6288 Dihedral : 4.432 15.488 4824 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.61 % Allowed : 26.08 % Favored : 69.30 % 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: -0.93 (0.14), residues: 4296 helix: 0.05 (0.12), residues: 1656 sheet: 0.15 (0.35), residues: 288 loop : -1.21 (0.15), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRPAl 93 HIS 0.007 0.001 HISAh 69 PHE 0.013 0.003 PHEAg 202 TYR 0.013 0.002 TYRAr 198 ARG 0.003 0.000 ARGAe 55 *********************** 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 1382 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1207 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Ab 136 ASP cc_start: 0.8287 (t0) cc_final: 0.7921 (t0) REVERT: Ab 188 ARG cc_start: 0.8381 (mtp-110) cc_final: 0.8049 (mtp-110) REVERT: Ab 190 LEU cc_start: 0.9039 (tp) cc_final: 0.8750 (tp) REVERT: Ad 136 ASP cc_start: 0.8244 (t0) cc_final: 0.7936 (t0) REVERT: Ad 188 ARG cc_start: 0.8358 (mtp-110) cc_final: 0.8123 (mtp-110) REVERT: Ad 190 LEU cc_start: 0.9034 (tp) cc_final: 0.8752 (tp) REVERT: Af 136 ASP cc_start: 0.8285 (t0) cc_final: 0.7914 (t0) REVERT: Af 188 ARG cc_start: 0.8352 (mtp-110) cc_final: 0.8026 (mtp-110) REVERT: Af 190 LEU cc_start: 0.9027 (tp) cc_final: 0.8726 (tp) REVERT: Ah 136 ASP cc_start: 0.8230 (t0) cc_final: 0.7973 (t0) REVERT: Ah 188 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.8049 (mtp-110) REVERT: Ah 190 LEU cc_start: 0.9038 (tp) cc_final: 0.8749 (tp) REVERT: Ai 48 LYS cc_start: 0.8569 (tppt) cc_final: 0.8367 (tptt) REVERT: Ai 102 ASP cc_start: 0.8399 (t70) cc_final: 0.8159 (t0) REVERT: Ai 127 ASN cc_start: 0.7897 (p0) cc_final: 0.7623 (p0) REVERT: Ai 136 ASP cc_start: 0.8215 (t0) cc_final: 0.7936 (t0) REVERT: Ai 201 ASP cc_start: 0.9018 (t0) cc_final: 0.8782 (t0) REVERT: Aj 70 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8626 (tp) REVERT: Aj 102 ASP cc_start: 0.8321 (t70) cc_final: 0.8062 (t0) REVERT: Aj 127 ASN cc_start: 0.7868 (p0) cc_final: 0.7581 (p0) REVERT: Aj 136 ASP cc_start: 0.8200 (t0) cc_final: 0.7878 (t0) REVERT: Aj 214 ARG cc_start: 0.8320 (mtp180) cc_final: 0.7966 (mtp180) REVERT: Ak 102 ASP cc_start: 0.8394 (t70) cc_final: 0.8147 (t0) REVERT: Ak 127 ASN cc_start: 0.7903 (p0) cc_final: 0.7580 (p0) REVERT: Ak 136 ASP cc_start: 0.8214 (t0) cc_final: 0.7942 (t0) REVERT: Ak 201 ASP cc_start: 0.9011 (t0) cc_final: 0.8778 (t0) REVERT: Al 70 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8640 (tp) REVERT: Al 102 ASP cc_start: 0.8310 (t70) cc_final: 0.8056 (t0) REVERT: Al 127 ASN cc_start: 0.7885 (p0) cc_final: 0.7580 (p0) REVERT: Al 136 ASP cc_start: 0.8275 (t0) cc_final: 0.8005 (t0) REVERT: Al 214 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7912 (mtp180) REVERT: Am 102 ASP cc_start: 0.8403 (t70) cc_final: 0.8157 (t0) REVERT: Am 127 ASN cc_start: 0.7930 (p0) cc_final: 0.7610 (p0) REVERT: Am 136 ASP cc_start: 0.8224 (t0) cc_final: 0.7950 (t0) REVERT: An 70 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8652 (tp) REVERT: An 127 ASN cc_start: 0.7951 (p0) cc_final: 0.7750 (p0) REVERT: An 136 ASP cc_start: 0.8280 (t0) cc_final: 0.8017 (t0) REVERT: An 190 LEU cc_start: 0.8862 (tp) cc_final: 0.8580 (tt) REVERT: An 214 ARG cc_start: 0.8300 (mtp180) cc_final: 0.7945 (mtp180) REVERT: Ao 48 LYS cc_start: 0.8639 (tppt) cc_final: 0.8437 (tptt) REVERT: Ao 102 ASP cc_start: 0.8400 (t70) cc_final: 0.8155 (t0) REVERT: Ao 127 ASN cc_start: 0.7921 (p0) cc_final: 0.7603 (p0) REVERT: Ao 136 ASP cc_start: 0.8228 (t0) cc_final: 0.7947 (t0) REVERT: Ap 102 ASP cc_start: 0.8310 (t70) cc_final: 0.8059 (t0) REVERT: Ap 127 ASN cc_start: 0.7902 (p0) cc_final: 0.7620 (p0) REVERT: Ap 136 ASP cc_start: 0.8281 (t0) cc_final: 0.8020 (t0) REVERT: Ap 214 ARG cc_start: 0.8299 (mtp180) cc_final: 0.7940 (mtp180) REVERT: Aq 107 GLU cc_start: 0.8413 (tp30) cc_final: 0.8068 (tm-30) REVERT: Aq 127 ASN cc_start: 0.7941 (p0) cc_final: 0.7536 (p0) REVERT: Aq 190 LEU cc_start: 0.8938 (tp) cc_final: 0.8494 (tp) REVERT: Ar 89 GLN cc_start: 0.9141 (mt0) cc_final: 0.8875 (mt0) REVERT: Ar 136 ASP cc_start: 0.8123 (t0) cc_final: 0.7732 (t0) REVERT: Ar 190 LEU cc_start: 0.9034 (tp) cc_final: 0.8820 (tp) REVERT: As 107 GLU cc_start: 0.8413 (tp30) cc_final: 0.8068 (tm-30) REVERT: As 190 LEU cc_start: 0.8944 (tp) cc_final: 0.8510 (tp) REVERT: At 89 GLN cc_start: 0.9146 (mt0) cc_final: 0.8877 (mt0) REVERT: At 127 ASN cc_start: 0.7999 (p0) cc_final: 0.7755 (p0) REVERT: At 136 ASP cc_start: 0.8128 (t0) cc_final: 0.7739 (t0) REVERT: At 190 LEU cc_start: 0.9026 (tp) cc_final: 0.8814 (tp) REVERT: Au 107 GLU cc_start: 0.8412 (tp30) cc_final: 0.8067 (tm-30) REVERT: Au 127 ASN cc_start: 0.7941 (p0) cc_final: 0.7542 (p0) REVERT: Au 190 LEU cc_start: 0.8954 (tp) cc_final: 0.8519 (tp) REVERT: Av 89 GLN cc_start: 0.9144 (mt0) cc_final: 0.8876 (mt0) REVERT: Av 136 ASP cc_start: 0.8136 (t0) cc_final: 0.7759 (t0) REVERT: Av 190 LEU cc_start: 0.9038 (tp) cc_final: 0.8832 (tp) REVERT: Aw 107 GLU cc_start: 0.8405 (tp30) cc_final: 0.8051 (tm-30) REVERT: Aw 127 ASN cc_start: 0.7971 (p0) cc_final: 0.7551 (p0) REVERT: Aw 190 LEU cc_start: 0.8948 (tp) cc_final: 0.8575 (tp) REVERT: Ax 89 GLN cc_start: 0.9140 (mt0) cc_final: 0.8870 (mt0) REVERT: Ax 107 GLU cc_start: 0.8485 (tp30) cc_final: 0.7976 (tm-30) REVERT: Ax 136 ASP cc_start: 0.8131 (t0) cc_final: 0.7747 (t0) REVERT: Ax 190 LEU cc_start: 0.9031 (tp) cc_final: 0.8809 (tp) outliers start: 175 outliers final: 141 residues processed: 1332 average time/residue: 0.4862 time to fit residues: 1028.6657 Evaluate side-chains 1243 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1099 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR Chi-restraints excluded: chain Aa residue 80 ILE Chi-restraints excluded: chain Aa residue 88 SER Chi-restraints excluded: chain Aa residue 116 MET Chi-restraints excluded: chain Aa residue 141 VAL Chi-restraints excluded: chain Ab residue 43 THR Chi-restraints excluded: chain Ab residue 80 ILE 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 88 SER Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 141 VAL Chi-restraints excluded: chain Ad residue 43 THR Chi-restraints excluded: chain Ad residue 80 ILE 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 80 ILE Chi-restraints excluded: chain Ae residue 88 SER Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 141 VAL Chi-restraints excluded: chain Af residue 43 THR Chi-restraints excluded: chain Af residue 80 ILE 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 80 ILE Chi-restraints excluded: chain Ag residue 88 SER Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 141 VAL Chi-restraints excluded: chain Ah residue 43 THR Chi-restraints excluded: chain Ah residue 80 ILE 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 133 VAL Chi-restraints excluded: chain Ai residue 134 MET 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 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 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 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 124 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain Am residue 141 VAL 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 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 124 THR Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 134 MET 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 124 THR Chi-restraints excluded: chain Ap residue 133 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 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 59 SER 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 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 59 SER 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 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 88 SER Chi-restraints excluded: chain Ax residue 124 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 1.9990 chunk 295 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 394 optimal weight: 4.9990 chunk 417 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 373 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 98 GLN ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 98 GLN ** 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** ** Am 98 GLN ** 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 175 ASN ** As 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 175 ASN Au 76 GLN ** Au 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 175 ASN ** Aw 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 175 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2373 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= 0.246 Angle : 0.569 8.558 48504 Z= 0.283 Chirality : 0.041 0.134 5280 Planarity : 0.005 0.033 6288 Dihedral : 4.289 15.656 4824 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.14 % Allowed : 27.45 % Favored : 68.41 % 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: -0.80 (0.14), residues: 4296 helix: 0.20 (0.13), residues: 1656 sheet: 0.39 (0.36), residues: 288 loop : -1.19 (0.15), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPAa 132 HIS 0.007 0.001 HISAb 69 PHE 0.009 0.002 PHEAf 200 TYR 0.013 0.001 TYRAi 198 ARG 0.006 0.000 ARGAt 157 *********************** 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 1302 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1145 time to evaluate : 4.088 Fit side-chains revert: symmetry clash REVERT: Aa 71 LEU cc_start: 0.8373 (mt) cc_final: 0.8165 (pp) REVERT: Ab 71 LEU cc_start: 0.8471 (mt) cc_final: 0.8262 (pp) REVERT: Ab 136 ASP cc_start: 0.8267 (t0) cc_final: 0.7866 (t0) REVERT: Ab 190 LEU cc_start: 0.9037 (tp) cc_final: 0.8746 (tp) REVERT: Ac 71 LEU cc_start: 0.8369 (mt) cc_final: 0.8166 (pp) REVERT: Ad 136 ASP cc_start: 0.8238 (t0) cc_final: 0.7880 (t0) REVERT: Ad 190 LEU cc_start: 0.9055 (tp) cc_final: 0.8758 (tp) REVERT: Ae 71 LEU cc_start: 0.8359 (mt) cc_final: 0.8157 (pp) REVERT: Af 70 LEU cc_start: 0.8937 (tp) cc_final: 0.8518 (tp) REVERT: Af 136 ASP cc_start: 0.8267 (t0) cc_final: 0.7855 (t0) REVERT: Af 190 LEU cc_start: 0.9044 (tp) cc_final: 0.8748 (tp) REVERT: Ag 71 LEU cc_start: 0.8370 (mt) cc_final: 0.8156 (pp) REVERT: Ah 136 ASP cc_start: 0.8222 (t0) cc_final: 0.7917 (t0) REVERT: Ah 190 LEU cc_start: 0.9035 (tp) cc_final: 0.8738 (tp) REVERT: Ai 102 ASP cc_start: 0.8372 (t70) cc_final: 0.8169 (t0) REVERT: Ai 127 ASN cc_start: 0.7931 (p0) cc_final: 0.7599 (p0) REVERT: Ai 136 ASP cc_start: 0.8201 (t0) cc_final: 0.7893 (t0) REVERT: Ai 214 ARG cc_start: 0.8301 (mtp180) cc_final: 0.7956 (mtp180) REVERT: Aj 71 LEU cc_start: 0.8370 (mt) cc_final: 0.8152 (pp) REVERT: Aj 102 ASP cc_start: 0.8291 (t70) cc_final: 0.8060 (t0) REVERT: Aj 112 MET cc_start: 0.9036 (tpp) cc_final: 0.8269 (mmt) REVERT: Aj 127 ASN cc_start: 0.7829 (p0) cc_final: 0.7567 (p0) REVERT: Aj 136 ASP cc_start: 0.8235 (t0) cc_final: 0.7881 (t0) REVERT: Aj 214 ARG cc_start: 0.8302 (mtp180) cc_final: 0.7962 (mtp180) REVERT: Ak 102 ASP cc_start: 0.8371 (t70) cc_final: 0.8149 (t0) REVERT: Ak 127 ASN cc_start: 0.7925 (p0) cc_final: 0.7688 (p0) REVERT: Ak 136 ASP cc_start: 0.8191 (t0) cc_final: 0.7896 (t0) REVERT: Al 71 LEU cc_start: 0.8322 (mt) cc_final: 0.8091 (pp) REVERT: Al 102 ASP cc_start: 0.8297 (t70) cc_final: 0.8066 (t0) REVERT: Al 127 ASN cc_start: 0.7864 (p0) cc_final: 0.7557 (p0) REVERT: Al 136 ASP cc_start: 0.8246 (t0) cc_final: 0.7947 (t0) REVERT: Al 214 ARG cc_start: 0.8304 (mtp180) cc_final: 0.7960 (mtp180) REVERT: Am 102 ASP cc_start: 0.8375 (t70) cc_final: 0.8164 (t0) REVERT: Am 127 ASN cc_start: 0.7913 (p0) cc_final: 0.7644 (p0) REVERT: Am 136 ASP cc_start: 0.8229 (t0) cc_final: 0.7945 (t0) REVERT: Am 145 LEU cc_start: 0.9189 (tp) cc_final: 0.8962 (mp) REVERT: Am 214 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7977 (mtp180) REVERT: An 71 LEU cc_start: 0.8318 (mt) cc_final: 0.8085 (pp) REVERT: An 127 ASN cc_start: 0.7899 (p0) cc_final: 0.7616 (p0) REVERT: An 136 ASP cc_start: 0.8251 (t0) cc_final: 0.7946 (t0) REVERT: An 190 LEU cc_start: 0.8708 (tp) cc_final: 0.8448 (tt) REVERT: An 214 ARG cc_start: 0.8344 (mtp180) cc_final: 0.7993 (mtp180) REVERT: Ao 127 ASN cc_start: 0.7909 (p0) cc_final: 0.7667 (p0) REVERT: Ao 136 ASP cc_start: 0.8205 (t0) cc_final: 0.7921 (t0) REVERT: Ap 102 ASP cc_start: 0.8290 (t70) cc_final: 0.8059 (t0) REVERT: Ap 127 ASN cc_start: 0.7890 (p0) cc_final: 0.7635 (p0) REVERT: Ap 136 ASP cc_start: 0.8257 (t0) cc_final: 0.7954 (t0) REVERT: Ap 214 ARG cc_start: 0.8342 (mtp180) cc_final: 0.7989 (mtp180) REVERT: Aq 56 MET cc_start: 0.8914 (mmt) cc_final: 0.8661 (mmm) REVERT: Aq 107 GLU cc_start: 0.8331 (tp30) cc_final: 0.8052 (tm-30) REVERT: Aq 127 ASN cc_start: 0.7959 (p0) cc_final: 0.7552 (p0) REVERT: Aq 136 ASP cc_start: 0.8254 (t0) cc_final: 0.8032 (t0) REVERT: Aq 151 ASN cc_start: 0.8104 (t0) cc_final: 0.7776 (t0) REVERT: Aq 190 LEU cc_start: 0.8926 (tp) cc_final: 0.8568 (tp) REVERT: Ar 89 GLN cc_start: 0.9183 (mt0) cc_final: 0.8912 (mt0) REVERT: Ar 136 ASP cc_start: 0.8178 (t0) cc_final: 0.7756 (t0) REVERT: Ar 190 LEU cc_start: 0.9021 (tp) cc_final: 0.8811 (tp) REVERT: As 56 MET cc_start: 0.8908 (mmt) cc_final: 0.8651 (mmm) REVERT: As 70 LEU cc_start: 0.8953 (tp) cc_final: 0.8607 (tp) REVERT: As 107 GLU cc_start: 0.8334 (tp30) cc_final: 0.8031 (tm-30) REVERT: As 136 ASP cc_start: 0.8253 (t0) cc_final: 0.8036 (t0) REVERT: As 190 LEU cc_start: 0.8963 (tp) cc_final: 0.8605 (tp) REVERT: At 89 GLN cc_start: 0.9181 (mt0) cc_final: 0.8903 (mt0) REVERT: At 127 ASN cc_start: 0.7993 (p0) cc_final: 0.7737 (p0) REVERT: At 136 ASP cc_start: 0.8182 (t0) cc_final: 0.7759 (t0) REVERT: At 179 PRO cc_start: 0.8698 (Cg_exo) cc_final: 0.8464 (Cg_endo) REVERT: At 190 LEU cc_start: 0.9027 (tp) cc_final: 0.8814 (tp) REVERT: At 214 ARG cc_start: 0.8280 (mtp180) cc_final: 0.8010 (mtp180) REVERT: Au 56 MET cc_start: 0.8910 (mmt) cc_final: 0.8658 (mmm) REVERT: Au 107 GLU cc_start: 0.8341 (tp30) cc_final: 0.8034 (tm-30) REVERT: Au 127 ASN cc_start: 0.7961 (p0) cc_final: 0.7558 (p0) REVERT: Au 190 LEU cc_start: 0.8931 (tp) cc_final: 0.8572 (tp) REVERT: Av 89 GLN cc_start: 0.9176 (mt0) cc_final: 0.8929 (mt0) REVERT: Av 136 ASP cc_start: 0.8180 (t0) cc_final: 0.7762 (t0) REVERT: Aw 56 MET cc_start: 0.8898 (mmt) cc_final: 0.8654 (mmm) REVERT: Aw 107 GLU cc_start: 0.8343 (tp30) cc_final: 0.8033 (tm-30) REVERT: Aw 136 ASP cc_start: 0.8254 (t0) cc_final: 0.8022 (t0) REVERT: Aw 190 LEU cc_start: 0.8919 (tp) cc_final: 0.8564 (tp) REVERT: Ax 89 GLN cc_start: 0.9180 (mt0) cc_final: 0.8911 (mt0) REVERT: Ax 107 GLU cc_start: 0.8389 (tp30) cc_final: 0.7991 (tm-30) REVERT: Ax 136 ASP cc_start: 0.8182 (t0) cc_final: 0.7761 (t0) REVERT: Ax 190 LEU cc_start: 0.9027 (tp) cc_final: 0.8806 (tp) outliers start: 157 outliers final: 127 residues processed: 1248 average time/residue: 0.4321 time to fit residues: 869.1578 Evaluate side-chains 1230 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1103 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 141 VAL Chi-restraints excluded: chain Ab residue 88 SER Chi-restraints excluded: chain Ab residue 141 VAL 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 141 VAL Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 134 MET Chi-restraints excluded: chain Ad residue 141 VAL Chi-restraints excluded: chain Ae residue 78 ILE 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 88 SER Chi-restraints excluded: chain Af residue 141 VAL 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 141 VAL 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 80 ILE Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 133 VAL 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 124 THR Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 134 MET 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 80 ILE Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 133 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 133 VAL Chi-restraints excluded: chain Am residue 134 MET 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 80 ILE Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 133 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 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 133 VAL Chi-restraints excluded: chain Ap residue 141 VAL Chi-restraints excluded: chain Aq residue 59 SER 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 125 SER Chi-restraints excluded: chain Aq residue 133 VAL Chi-restraints excluded: chain Aq residue 150 GLU 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 141 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 As residue 150 GLU 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 Au residue 125 SER Chi-restraints excluded: chain Au residue 150 GLU 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 141 VAL Chi-restraints excluded: chain Av residue 150 GLU 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 124 THR Chi-restraints excluded: chain Aw residue 133 VAL Chi-restraints excluded: chain Aw residue 150 GLU 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 141 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 347 optimal weight: 6.9990 chunk 237 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 310 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 356 optimal weight: 6.9990 chunk 288 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 374 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Aa 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 151 ASN ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 151 ASN ** Ae 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** At 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Au 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aw 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ax 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 35784 Z= 0.382 Angle : 0.640 9.469 48504 Z= 0.316 Chirality : 0.044 0.149 5280 Planarity : 0.005 0.034 6288 Dihedral : 4.458 16.444 4824 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.17 % Allowed : 27.35 % Favored : 67.48 % 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: 0.19 (0.13), residues: 1656 sheet: 0.44 (0.37), residues: 288 loop : -1.16 (0.14), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRPAd 93 HIS 0.007 0.001 HISAb 69 PHE 0.012 0.003 PHEAc 202 TYR 0.025 0.002 TYRAq 198 ARG 0.006 0.000 ARGAt 212 *********************** 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 1403 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1207 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 136 ASP cc_start: 0.8281 (t0) cc_final: 0.7871 (t0) REVERT: Ab 151 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.7989 (t0) REVERT: Ab 190 LEU cc_start: 0.9068 (tp) cc_final: 0.8696 (tp) REVERT: Ad 136 ASP cc_start: 0.8257 (t0) cc_final: 0.7864 (t0) REVERT: Ad 151 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.7997 (t0) REVERT: Ad 190 LEU cc_start: 0.9062 (tp) cc_final: 0.8713 (tp) REVERT: Af 70 LEU cc_start: 0.8993 (tp) cc_final: 0.8566 (tp) REVERT: Af 136 ASP cc_start: 0.8229 (t0) cc_final: 0.7816 (t0) REVERT: Af 151 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.7982 (t0) REVERT: Af 190 LEU cc_start: 0.9063 (tp) cc_final: 0.8691 (tp) REVERT: Ah 136 ASP cc_start: 0.8257 (t0) cc_final: 0.7868 (t0) REVERT: Ah 151 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8004 (t0) REVERT: Ah 190 LEU cc_start: 0.9068 (tp) cc_final: 0.8695 (tp) REVERT: Ai 102 ASP cc_start: 0.8437 (t70) cc_final: 0.8206 (t0) REVERT: Ai 127 ASN cc_start: 0.7921 (p0) cc_final: 0.7603 (p0) REVERT: Ai 136 ASP cc_start: 0.8216 (t0) cc_final: 0.7805 (t0) REVERT: Ai 201 ASP cc_start: 0.8977 (t0) cc_final: 0.8754 (t0) REVERT: Aj 71 LEU cc_start: 0.8422 (mt) cc_final: 0.8222 (pp) REVERT: Aj 127 ASN cc_start: 0.7865 (p0) cc_final: 0.7581 (p0) REVERT: Aj 136 ASP cc_start: 0.8314 (t0) cc_final: 0.7920 (t0) REVERT: Aj 151 ASN cc_start: 0.8339 (t0) cc_final: 0.8103 (t0) REVERT: Aj 214 ARG cc_start: 0.8272 (mtp180) cc_final: 0.7777 (mtp180) REVERT: Ak 48 LYS cc_start: 0.8616 (tppt) cc_final: 0.8409 (tptt) REVERT: Ak 102 ASP cc_start: 0.8441 (t70) cc_final: 0.8188 (t0) REVERT: Ak 127 ASN cc_start: 0.7961 (p0) cc_final: 0.7654 (p0) REVERT: Ak 136 ASP cc_start: 0.8214 (t0) cc_final: 0.7792 (t0) REVERT: Ak 201 ASP cc_start: 0.8974 (t0) cc_final: 0.8750 (t0) REVERT: Ak 214 ARG cc_start: 0.8398 (mtp180) cc_final: 0.8153 (mtp180) REVERT: Al 71 LEU cc_start: 0.8428 (mt) cc_final: 0.8161 (pp) REVERT: Al 102 ASP cc_start: 0.8355 (t70) cc_final: 0.8106 (t0) REVERT: Al 127 ASN cc_start: 0.7875 (p0) cc_final: 0.7591 (p0) REVERT: Al 136 ASP cc_start: 0.8291 (t0) cc_final: 0.7990 (t0) REVERT: Al 214 ARG cc_start: 0.8313 (mtp180) cc_final: 0.7822 (mtp180) REVERT: Am 102 ASP cc_start: 0.8441 (t70) cc_final: 0.8201 (t0) REVERT: Am 127 ASN cc_start: 0.7922 (p0) cc_final: 0.7643 (p0) REVERT: Am 136 ASP cc_start: 0.8218 (t0) cc_final: 0.7802 (t0) REVERT: Am 201 ASP cc_start: 0.8979 (t0) cc_final: 0.8757 (t0) REVERT: An 71 LEU cc_start: 0.8429 (mt) cc_final: 0.8161 (pp) REVERT: An 127 ASN cc_start: 0.7927 (p0) cc_final: 0.7634 (p0) REVERT: An 136 ASP cc_start: 0.8320 (t0) cc_final: 0.7939 (t0) REVERT: An 190 LEU cc_start: 0.8738 (tp) cc_final: 0.8387 (tt) REVERT: An 214 ARG cc_start: 0.8324 (mtp180) cc_final: 0.7827 (mtp180) REVERT: Ao 127 ASN cc_start: 0.7949 (p0) cc_final: 0.7642 (p0) REVERT: Ao 136 ASP cc_start: 0.8216 (t0) cc_final: 0.7791 (t0) REVERT: Ao 201 ASP cc_start: 0.8981 (t0) cc_final: 0.8762 (t0) REVERT: Ao 214 ARG cc_start: 0.8404 (mtp180) cc_final: 0.8174 (mtp180) REVERT: Ap 102 ASP cc_start: 0.8353 (t70) cc_final: 0.8103 (t0) REVERT: Ap 127 ASN cc_start: 0.7900 (p0) cc_final: 0.7600 (p0) REVERT: Ap 136 ASP cc_start: 0.8296 (t0) cc_final: 0.7993 (t0) REVERT: Ap 214 ARG cc_start: 0.8320 (mtp180) cc_final: 0.7821 (mtp180) REVERT: Aq 56 MET cc_start: 0.8896 (mmt) cc_final: 0.8688 (mmm) REVERT: Aq 69 HIS cc_start: 0.8318 (t-90) cc_final: 0.7984 (t-90) REVERT: Aq 107 GLU cc_start: 0.8392 (tp30) cc_final: 0.8045 (tm-30) REVERT: Aq 127 ASN cc_start: 0.7974 (p0) cc_final: 0.7615 (p0) REVERT: Aq 136 ASP cc_start: 0.8264 (t0) cc_final: 0.8054 (t0) REVERT: Aq 190 LEU cc_start: 0.8976 (tp) cc_final: 0.8636 (tp) REVERT: Ar 71 LEU cc_start: 0.8409 (mt) cc_final: 0.8163 (pp) REVERT: Ar 89 GLN cc_start: 0.9194 (mt0) cc_final: 0.8945 (mt0) REVERT: Ar 136 ASP cc_start: 0.8171 (t0) cc_final: 0.7745 (t0) REVERT: Ar 212 ARG cc_start: 0.9036 (ptm-80) cc_final: 0.8821 (ttp-110) REVERT: Ar 214 ARG cc_start: 0.8296 (mtp180) cc_final: 0.8037 (mtp180) REVERT: As 107 GLU cc_start: 0.8392 (tp30) cc_final: 0.8037 (tm-30) REVERT: As 136 ASP cc_start: 0.8271 (t0) cc_final: 0.8059 (t0) REVERT: As 190 LEU cc_start: 0.8969 (tp) cc_final: 0.8616 (tp) REVERT: At 71 LEU cc_start: 0.8401 (mt) cc_final: 0.8162 (pp) REVERT: At 89 GLN cc_start: 0.9183 (mt0) cc_final: 0.8936 (mt0) REVERT: At 127 ASN cc_start: 0.7996 (p0) cc_final: 0.7759 (p0) REVERT: At 136 ASP cc_start: 0.8176 (t0) cc_final: 0.7751 (t0) REVERT: At 214 ARG cc_start: 0.8265 (mtp180) cc_final: 0.7959 (mtp180) REVERT: Au 107 GLU cc_start: 0.8392 (tp30) cc_final: 0.8046 (tm-30) REVERT: Au 127 ASN cc_start: 0.7970 (p0) cc_final: 0.7579 (p0) REVERT: Au 190 LEU cc_start: 0.8975 (tp) cc_final: 0.8612 (tp) REVERT: Av 71 LEU cc_start: 0.8401 (mt) cc_final: 0.8161 (pp) REVERT: Av 89 GLN cc_start: 0.9193 (mt0) cc_final: 0.8945 (mt0) REVERT: Av 136 ASP cc_start: 0.8172 (t0) cc_final: 0.7736 (t0) REVERT: Av 214 ARG cc_start: 0.8273 (mtp180) cc_final: 0.8026 (mtp180) REVERT: Aw 56 MET cc_start: 0.8896 (mmt) cc_final: 0.8684 (mmm) REVERT: Aw 107 GLU cc_start: 0.8397 (tp30) cc_final: 0.8044 (tm-30) REVERT: Aw 127 ASN cc_start: 0.7948 (p0) cc_final: 0.7621 (p0) REVERT: Aw 136 ASP cc_start: 0.8253 (t0) cc_final: 0.8021 (t0) REVERT: Aw 190 LEU cc_start: 0.8987 (tp) cc_final: 0.8647 (tp) REVERT: Ax 71 LEU cc_start: 0.8403 (mt) cc_final: 0.8189 (pp) REVERT: Ax 89 GLN cc_start: 0.9190 (mt0) cc_final: 0.8947 (mt0) REVERT: Ax 107 GLU cc_start: 0.8478 (tp30) cc_final: 0.7920 (tm-30) REVERT: Ax 127 ASN cc_start: 0.8067 (p0) cc_final: 0.7836 (p0) REVERT: Ax 136 ASP cc_start: 0.8176 (t0) cc_final: 0.7744 (t0) REVERT: Ax 214 ARG cc_start: 0.8293 (mtp180) cc_final: 0.8034 (mtp180) outliers start: 196 outliers final: 162 residues processed: 1340 average time/residue: 0.4743 time to fit residues: 1001.7504 Evaluate side-chains 1338 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1172 time to evaluate : 4.404 ------------------------------------------------------------------------------- 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 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 134 MET Chi-restraints excluded: chain Ab residue 141 VAL Chi-restraints excluded: chain Ab residue 151 ASN 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 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 Ac residue 171 ILE Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 134 MET Chi-restraints excluded: chain Ad residue 141 VAL Chi-restraints excluded: chain Ad residue 151 ASN Chi-restraints excluded: chain Ae residue 43 THR Chi-restraints excluded: chain Ae residue 78 ILE 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 134 MET Chi-restraints excluded: chain Af residue 141 VAL Chi-restraints excluded: chain Af residue 151 ASN Chi-restraints excluded: chain Ag residue 43 THR Chi-restraints excluded: chain Ag residue 78 ILE 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 Ag residue 171 ILE Chi-restraints excluded: chain Ah residue 88 SER Chi-restraints excluded: chain Ah residue 134 MET Chi-restraints excluded: chain Ah residue 141 VAL Chi-restraints excluded: chain Ah residue 151 ASN 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 78 ILE 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 134 MET 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 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 190 LEU 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 111 VAL Chi-restraints excluded: chain Ak residue 124 THR Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 134 MET 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 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 190 LEU Chi-restraints excluded: chain Am residue 43 THR Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 78 ILE 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 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 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 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 111 VAL Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 134 MET 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 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 190 LEU Chi-restraints excluded: chain Aq residue 43 THR 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 141 VAL Chi-restraints excluded: chain Aq residue 150 GLU 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 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 124 THR Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 141 VAL Chi-restraints excluded: chain As residue 150 GLU 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 141 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 Au residue 141 VAL Chi-restraints excluded: chain Au residue 150 GLU 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 141 VAL Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Aw residue 43 THR 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 141 VAL Chi-restraints excluded: chain Aw residue 150 GLU 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 141 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 140 optimal weight: 8.9990 chunk 376 optimal weight: 9.9990 chunk 82 optimal weight: 0.4980 chunk 245 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 417 optimal weight: 0.9990 chunk 346 optimal weight: 0.4980 chunk 193 optimal weight: 7.9990 chunk 34 optimal weight: 0.0970 chunk 138 optimal weight: 0.9980 chunk 219 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 98 GLN ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 151 ASN ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 98 GLN Ad 151 ASN Ae 98 GLN ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 151 ASN ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 98 GLN Aj 98 GLN Ak 98 GLN ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 98 GLN An 98 GLN Ao 98 GLN ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 151 ASN Aq 98 GLN Ar 98 GLN Ar 151 ASN Ar 175 ASN As 98 GLN At 98 GLN At 151 ASN Au 98 GLN Av 98 GLN Av 151 ASN Av 175 ASN Aw 98 GLN Ax 98 GLN Ax 151 ASN Ax 175 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35784 Z= 0.158 Angle : 0.563 9.093 48504 Z= 0.275 Chirality : 0.040 0.145 5280 Planarity : 0.004 0.032 6288 Dihedral : 4.157 15.280 4824 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.48 % Allowed : 31.01 % Favored : 66.51 % 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: -0.70 (0.14), residues: 4296 helix: 0.20 (0.13), residues: 1728 sheet: 0.61 (0.36), residues: 288 loop : -1.13 (0.15), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPAu 132 HIS 0.009 0.001 HISAd 69 PHE 0.009 0.002 PHEAw 200 TYR 0.029 0.002 TYRAw 198 ARG 0.007 0.000 ARGAt 212 *********************** 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 1281 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1187 time to evaluate : 4.321 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: Ab 136 ASP cc_start: 0.8257 (t0) cc_final: 0.7836 (t0) REVERT: Ab 190 LEU cc_start: 0.8962 (tp) cc_final: 0.8722 (tp) REVERT: Ac 102 ASP cc_start: 0.8550 (t0) cc_final: 0.8324 (t0) REVERT: Ad 136 ASP cc_start: 0.8243 (t0) cc_final: 0.7843 (t0) REVERT: Ad 190 LEU cc_start: 0.9027 (tp) cc_final: 0.8740 (tp) REVERT: Ae 70 LEU cc_start: 0.8892 (tp) cc_final: 0.8518 (tp) REVERT: Af 54 MET cc_start: 0.8049 (ttp) cc_final: 0.7831 (ttp) REVERT: Af 136 ASP cc_start: 0.8260 (t0) cc_final: 0.7842 (t0) REVERT: Af 190 LEU cc_start: 0.8962 (tp) cc_final: 0.8719 (tp) REVERT: Ag 48 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8521 (ttmm) REVERT: Ag 70 LEU cc_start: 0.8899 (tp) cc_final: 0.8513 (tp) REVERT: Ag 102 ASP cc_start: 0.8549 (t0) cc_final: 0.8327 (t0) REVERT: Ah 136 ASP cc_start: 0.8254 (t0) cc_final: 0.7859 (t0) REVERT: Ah 190 LEU cc_start: 0.8960 (tp) cc_final: 0.8721 (tp) REVERT: Ai 48 LYS cc_start: 0.8752 (tppt) cc_final: 0.8551 (tptt) REVERT: Ai 127 ASN cc_start: 0.7860 (p0) cc_final: 0.7503 (p0) REVERT: Ai 136 ASP cc_start: 0.8291 (t0) cc_final: 0.7913 (t0) REVERT: Aj 112 MET cc_start: 0.8978 (tpp) cc_final: 0.8249 (mmt) REVERT: Aj 127 ASN cc_start: 0.7784 (p0) cc_final: 0.7524 (p0) REVERT: Aj 136 ASP cc_start: 0.8276 (t0) cc_final: 0.8022 (t0) REVERT: Aj 151 ASN cc_start: 0.8280 (t0) cc_final: 0.7956 (t0) REVERT: Aj 214 ARG cc_start: 0.8315 (mtp180) cc_final: 0.8053 (mtp180) REVERT: Ak 136 ASP cc_start: 0.8239 (t0) cc_final: 0.7854 (t0) REVERT: Al 71 LEU cc_start: 0.8324 (mt) cc_final: 0.8092 (pp) REVERT: Al 127 ASN cc_start: 0.7782 (p0) cc_final: 0.7523 (p0) REVERT: Al 136 ASP cc_start: 0.8269 (t0) cc_final: 0.8020 (t0) REVERT: Al 190 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8489 (tt) REVERT: Al 214 ARG cc_start: 0.8318 (mtp180) cc_final: 0.8052 (mtp180) REVERT: Am 127 ASN cc_start: 0.7855 (p0) cc_final: 0.7506 (p0) REVERT: Am 136 ASP cc_start: 0.8296 (t0) cc_final: 0.7922 (t0) REVERT: An 71 LEU cc_start: 0.8321 (mt) cc_final: 0.8090 (pp) REVERT: An 112 MET cc_start: 0.9005 (tpp) cc_final: 0.8265 (mmt) REVERT: An 127 ASN cc_start: 0.7905 (p0) cc_final: 0.7585 (p0) REVERT: An 136 ASP cc_start: 0.8334 (t0) cc_final: 0.8081 (t0) REVERT: An 214 ARG cc_start: 0.8329 (mtp180) cc_final: 0.8061 (mtp180) REVERT: Ao 136 ASP cc_start: 0.8303 (t0) cc_final: 0.7895 (t0) REVERT: Ap 70 LEU cc_start: 0.8640 (tp) cc_final: 0.8154 (tp) REVERT: Ap 127 ASN cc_start: 0.7818 (p0) cc_final: 0.7556 (p0) REVERT: Ap 136 ASP cc_start: 0.8277 (t0) cc_final: 0.8031 (t0) REVERT: Ap 190 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8451 (tt) REVERT: Ap 214 ARG cc_start: 0.8325 (mtp180) cc_final: 0.8055 (mtp180) REVERT: Aq 48 LYS cc_start: 0.8883 (tptt) cc_final: 0.8675 (ttmm) REVERT: Aq 69 HIS cc_start: 0.8273 (t-90) cc_final: 0.7974 (t-90) REVERT: Aq 107 GLU cc_start: 0.8189 (tp30) cc_final: 0.7973 (tm-30) REVERT: Aq 127 ASN cc_start: 0.8014 (p0) cc_final: 0.7592 (p0) REVERT: Aq 151 ASN cc_start: 0.8192 (t0) cc_final: 0.7990 (t0) REVERT: Aq 190 LEU cc_start: 0.8966 (tp) cc_final: 0.8551 (tt) REVERT: Aq 198 TYR cc_start: 0.8876 (m-10) cc_final: 0.8653 (m-10) REVERT: Ar 136 ASP cc_start: 0.8105 (t0) cc_final: 0.7696 (t0) REVERT: Ar 214 ARG cc_start: 0.8281 (mtp180) cc_final: 0.7995 (mtp180) REVERT: As 48 LYS cc_start: 0.8883 (tptt) cc_final: 0.8678 (ttmm) REVERT: As 107 GLU cc_start: 0.8190 (tp30) cc_final: 0.7972 (tm-30) REVERT: As 136 ASP cc_start: 0.8311 (t0) cc_final: 0.8103 (t0) REVERT: As 190 LEU cc_start: 0.8981 (tp) cc_final: 0.8574 (tt) REVERT: At 127 ASN cc_start: 0.7957 (p0) cc_final: 0.7635 (p0) REVERT: At 136 ASP cc_start: 0.8104 (t0) cc_final: 0.7691 (t0) REVERT: At 214 ARG cc_start: 0.8298 (mtp180) cc_final: 0.8001 (mtp180) REVERT: Au 48 LYS cc_start: 0.8891 (tptt) cc_final: 0.8681 (ttmm) REVERT: Au 107 GLU cc_start: 0.8198 (tp30) cc_final: 0.7976 (tm-30) REVERT: Au 127 ASN cc_start: 0.7959 (p0) cc_final: 0.7533 (p0) REVERT: Au 150 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7784 (pt0) REVERT: Au 151 ASN cc_start: 0.7987 (t0) cc_final: 0.7749 (t0) REVERT: Au 190 LEU cc_start: 0.8970 (tp) cc_final: 0.8583 (tt) REVERT: Au 198 TYR cc_start: 0.8864 (m-10) cc_final: 0.8655 (m-10) REVERT: Av 136 ASP cc_start: 0.8081 (t0) cc_final: 0.7650 (t0) REVERT: Av 214 ARG cc_start: 0.8253 (mtp180) cc_final: 0.7971 (mtp180) REVERT: Aw 48 LYS cc_start: 0.8883 (tptt) cc_final: 0.8680 (ttmm) REVERT: Aw 56 MET cc_start: 0.8846 (mmt) cc_final: 0.8366 (mmp) REVERT: Aw 107 GLU cc_start: 0.8198 (tp30) cc_final: 0.7976 (tm-30) REVERT: Aw 127 ASN cc_start: 0.7913 (p0) cc_final: 0.7469 (p0) REVERT: Aw 136 ASP cc_start: 0.8313 (t0) cc_final: 0.8091 (t0) REVERT: Aw 150 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7771 (pt0) REVERT: Aw 190 LEU cc_start: 0.8991 (tp) cc_final: 0.8599 (tt) REVERT: Aw 198 TYR cc_start: 0.8881 (m-10) cc_final: 0.8676 (m-10) REVERT: Ax 107 GLU cc_start: 0.8320 (tp30) cc_final: 0.7862 (tm-30) REVERT: Ax 127 ASN cc_start: 0.8050 (p0) cc_final: 0.7769 (p0) REVERT: Ax 136 ASP cc_start: 0.8089 (t0) cc_final: 0.7663 (t0) REVERT: Ax 214 ARG cc_start: 0.8285 (mtp180) cc_final: 0.7988 (mtp180) outliers start: 94 outliers final: 66 residues processed: 1243 average time/residue: 0.4680 time to fit residues: 937.1481 Evaluate side-chains 1209 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1139 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Ag residue 88 SER Chi-restraints excluded: chain Ag 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 88 SER Chi-restraints excluded: chain Ai residue 150 GLU Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Ak residue 44 VAL Chi-restraints excluded: chain Ak residue 78 ILE Chi-restraints excluded: chain Ak residue 133 VAL Chi-restraints excluded: chain Ak residue 150 GLU Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 190 LEU 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 88 SER Chi-restraints excluded: chain Ao residue 44 VAL Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 150 GLU Chi-restraints excluded: chain Ap residue 88 SER Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 190 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 Aq residue 150 GLU 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 88 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 150 GLU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 103 ILE 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 43 THR Chi-restraints excluded: chain Au residue 59 SER Chi-restraints excluded: chain Au residue 78 ILE Chi-restraints excluded: chain Au residue 88 SER Chi-restraints excluded: chain Au residue 150 GLU Chi-restraints excluded: chain Av residue 78 ILE Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 103 ILE 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 133 VAL Chi-restraints excluded: chain Aw residue 150 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 238 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 chunk 351 optimal weight: 8.9990 chunk 233 optimal weight: 0.7980 chunk 416 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 175 ASN ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 175 ASN ** Ap 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 175 ASN ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 175 ASN At 151 ASN ** Av 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 175 ASN ** Ax 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2926 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= 0.234 Angle : 0.597 9.423 48504 Z= 0.291 Chirality : 0.041 0.140 5280 Planarity : 0.005 0.065 6288 Dihedral : 4.227 15.935 4824 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.61 % Allowed : 30.20 % 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: -0.90 (0.14), residues: 4296 helix: 0.07 (0.12), residues: 1800 sheet: 0.66 (0.37), residues: 288 loop : -1.33 (0.15), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPAu 132 HIS 0.008 0.001 HISAf 69 PHE 0.009 0.002 PHEAa 200 TYR 0.028 0.002 TYRAs 198 ARG 0.008 0.000 ARGAt 212 *********************** 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 1335 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1198 time to evaluate : 4.291 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: Aa 70 LEU cc_start: 0.8943 (tp) cc_final: 0.8536 (tp) REVERT: Ab 136 ASP cc_start: 0.8293 (t0) cc_final: 0.7889 (t0) REVERT: Ab 190 LEU cc_start: 0.9024 (tp) cc_final: 0.8744 (tp) REVERT: Ac 70 LEU cc_start: 0.8959 (tp) cc_final: 0.8546 (tp) REVERT: Ac 175 ASN cc_start: 0.9009 (t0) cc_final: 0.8807 (t0) REVERT: Ad 136 ASP cc_start: 0.8286 (t0) cc_final: 0.7875 (t0) REVERT: Ad 190 LEU cc_start: 0.9032 (tp) cc_final: 0.8745 (tp) REVERT: Ae 70 LEU cc_start: 0.8936 (tp) cc_final: 0.8539 (tp) REVERT: Af 54 MET cc_start: 0.8069 (ttp) cc_final: 0.7856 (ttp) REVERT: Af 136 ASP cc_start: 0.8296 (t0) cc_final: 0.7895 (t0) REVERT: Af 190 LEU cc_start: 0.9037 (tp) cc_final: 0.8747 (tp) REVERT: Ag 48 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8534 (ttmm) REVERT: Ag 70 LEU cc_start: 0.8952 (tp) cc_final: 0.8536 (tp) REVERT: Ah 136 ASP cc_start: 0.8297 (t0) cc_final: 0.7922 (t0) REVERT: Ah 190 LEU cc_start: 0.9023 (tp) cc_final: 0.8742 (tp) REVERT: Ai 127 ASN cc_start: 0.7908 (p0) cc_final: 0.7615 (p0) REVERT: Aj 127 ASN cc_start: 0.7811 (p0) cc_final: 0.7575 (p0) REVERT: Aj 136 ASP cc_start: 0.8287 (t0) cc_final: 0.8031 (t0) REVERT: Aj 151 ASN cc_start: 0.8339 (t0) cc_final: 0.8136 (t0) REVERT: Ak 127 ASN cc_start: 0.7936 (p0) cc_final: 0.7643 (p0) REVERT: Ak 136 ASP cc_start: 0.8314 (t0) cc_final: 0.7929 (t0) REVERT: Al 127 ASN cc_start: 0.7855 (p0) cc_final: 0.7612 (p0) REVERT: Al 136 ASP cc_start: 0.8301 (t0) cc_final: 0.8052 (t0) REVERT: Al 190 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8441 (tt) REVERT: Am 127 ASN cc_start: 0.7875 (p0) cc_final: 0.7590 (p0) REVERT: Am 136 ASP cc_start: 0.8278 (t0) cc_final: 0.7883 (t0) REVERT: An 127 ASN cc_start: 0.7914 (p0) cc_final: 0.7638 (p0) REVERT: An 136 ASP cc_start: 0.8303 (t0) cc_final: 0.8050 (t0) REVERT: Ao 127 ASN cc_start: 0.7909 (p0) cc_final: 0.7610 (p0) REVERT: Ao 136 ASP cc_start: 0.8312 (t0) cc_final: 0.7908 (t0) REVERT: Ap 127 ASN cc_start: 0.7887 (p0) cc_final: 0.7637 (p0) REVERT: Ap 136 ASP cc_start: 0.8311 (t0) cc_final: 0.8061 (t0) REVERT: Ap 190 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8464 (tt) REVERT: Aq 69 HIS cc_start: 0.8327 (t-90) cc_final: 0.8067 (t-90) REVERT: Aq 107 GLU cc_start: 0.8232 (tp30) cc_final: 0.7932 (tm-30) REVERT: Aq 127 ASN cc_start: 0.8065 (p0) cc_final: 0.7741 (p0) REVERT: Aq 198 TYR cc_start: 0.8860 (m-10) cc_final: 0.8646 (m-10) REVERT: Ar 71 LEU cc_start: 0.8432 (mt) cc_final: 0.8231 (pp) REVERT: Ar 136 ASP cc_start: 0.8114 (t0) cc_final: 0.7735 (t0) REVERT: Ar 214 ARG cc_start: 0.8283 (mtp180) cc_final: 0.7968 (mtp180) REVERT: As 107 GLU cc_start: 0.8237 (tp30) cc_final: 0.7931 (tm-30) REVERT: As 127 ASN cc_start: 0.8034 (p0) cc_final: 0.7719 (p0) REVERT: As 136 ASP cc_start: 0.8325 (t0) cc_final: 0.8111 (t0) REVERT: As 150 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: At 71 LEU cc_start: 0.8432 (mt) cc_final: 0.8229 (pp) REVERT: At 127 ASN cc_start: 0.8050 (p0) cc_final: 0.7803 (p0) REVERT: At 136 ASP cc_start: 0.8133 (t0) cc_final: 0.7756 (t0) REVERT: At 214 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7963 (mtp180) REVERT: Au 107 GLU cc_start: 0.8238 (tp30) cc_final: 0.7936 (tm-30) REVERT: Au 127 ASN cc_start: 0.7970 (p0) cc_final: 0.7618 (p0) REVERT: Au 150 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7801 (pt0) REVERT: Au 151 ASN cc_start: 0.8030 (t0) cc_final: 0.7807 (t0) REVERT: Au 198 TYR cc_start: 0.8857 (m-10) cc_final: 0.8624 (m-10) REVERT: Av 71 LEU cc_start: 0.8428 (mt) cc_final: 0.8227 (pp) REVERT: Av 136 ASP cc_start: 0.8186 (t0) cc_final: 0.7761 (t0) REVERT: Av 214 ARG cc_start: 0.8257 (mtp180) cc_final: 0.7958 (mtp180) REVERT: Aw 56 MET cc_start: 0.8870 (mmt) cc_final: 0.8379 (mmp) REVERT: Aw 107 GLU cc_start: 0.8238 (tp30) cc_final: 0.7932 (tm-30) REVERT: Aw 127 ASN cc_start: 0.8028 (p0) cc_final: 0.7711 (p0) REVERT: Aw 136 ASP cc_start: 0.8333 (t0) cc_final: 0.8106 (t0) REVERT: Aw 150 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: Ax 71 LEU cc_start: 0.8440 (mt) cc_final: 0.8237 (pp) REVERT: Ax 107 GLU cc_start: 0.8347 (tp30) cc_final: 0.7886 (tm-30) REVERT: Ax 127 ASN cc_start: 0.8091 (p0) cc_final: 0.7825 (p0) REVERT: Ax 136 ASP cc_start: 0.8188 (t0) cc_final: 0.7769 (t0) REVERT: Ax 214 ARG cc_start: 0.8268 (mtp180) cc_final: 0.7950 (mtp180) outliers start: 137 outliers final: 109 residues processed: 1271 average time/residue: 0.4783 time to fit residues: 973.3196 Evaluate side-chains 1292 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1178 time to evaluate : 3.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Ac residue 43 THR 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 Ac residue 159 ILE Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 134 MET 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 Ae residue 159 ILE Chi-restraints excluded: chain Af residue 43 THR Chi-restraints excluded: chain Af residue 88 SER 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 Ag residue 159 ILE 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 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 80 ILE Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Aj residue 150 GLU Chi-restraints excluded: chain Aj residue 165 ASP 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 80 ILE Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 190 LEU Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 78 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 80 ILE Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 150 GLU 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 124 THR Chi-restraints excluded: chain Ao residue 133 VAL Chi-restraints excluded: chain Ao residue 150 GLU Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 80 ILE Chi-restraints excluded: chain Ap residue 88 SER Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 150 GLU Chi-restraints excluded: chain Ap residue 190 LEU Chi-restraints excluded: chain Aq residue 43 THR 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 Aq residue 150 GLU 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 59 SER Chi-restraints excluded: chain As residue 67 LEU 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 As residue 150 GLU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 103 ILE 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 43 THR Chi-restraints excluded: chain Au residue 67 LEU 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 150 GLU Chi-restraints excluded: chain Av residue 78 ILE Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 103 ILE 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 43 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 283 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 327 optimal weight: 1.9990 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** ** Ab 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 69 HIS ** 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 151 ASN Ak 151 ASN ** Al 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 151 ASN ** Ap 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 151 ASN Ar 175 ASN At 175 ASN Av 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3067 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= 0.204 Angle : 0.605 9.427 48504 Z= 0.293 Chirality : 0.040 0.149 5280 Planarity : 0.005 0.043 6288 Dihedral : 4.188 15.535 4824 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.11 % Allowed : 31.78 % Favored : 65.11 % 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: -0.89 (0.14), residues: 4296 helix: 0.10 (0.12), residues: 1800 sheet: 0.68 (0.36), residues: 288 loop : -1.35 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAg 132 HIS 0.009 0.001 HISAd 69 PHE 0.009 0.002 PHEAa 200 TYR 0.030 0.002 TYRAs 198 ARG 0.008 0.000 ARGAt 212 *********************** 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 1345 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1227 time to evaluate : 4.453 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: Aa 70 LEU cc_start: 0.8940 (tp) cc_final: 0.8540 (tp) REVERT: Aa 184 TYR cc_start: 0.8986 (t80) cc_final: 0.8768 (t80) REVERT: Ab 70 LEU cc_start: 0.8718 (tp) cc_final: 0.8243 (tp) REVERT: Ab 136 ASP cc_start: 0.8306 (t0) cc_final: 0.7893 (t0) REVERT: Ab 190 LEU cc_start: 0.9018 (tp) cc_final: 0.8738 (tp) REVERT: Ac 175 ASN cc_start: 0.9024 (t0) cc_final: 0.8801 (t0) REVERT: Ac 184 TYR cc_start: 0.8994 (t80) cc_final: 0.8781 (t80) REVERT: Ad 136 ASP cc_start: 0.8317 (t0) cc_final: 0.7911 (t0) REVERT: Ad 190 LEU cc_start: 0.9020 (tp) cc_final: 0.8727 (tp) REVERT: Ae 70 LEU cc_start: 0.8920 (tp) cc_final: 0.8506 (tp) REVERT: Af 136 ASP cc_start: 0.8303 (t0) cc_final: 0.7900 (t0) REVERT: Af 190 LEU cc_start: 0.9027 (tp) cc_final: 0.8745 (tp) REVERT: Ag 48 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8509 (ttmm) REVERT: Ag 184 TYR cc_start: 0.8986 (t80) cc_final: 0.8769 (t80) REVERT: Ah 136 ASP cc_start: 0.8292 (t0) cc_final: 0.7890 (t0) REVERT: Ah 190 LEU cc_start: 0.9018 (tp) cc_final: 0.8740 (tp) REVERT: Ai 127 ASN cc_start: 0.7884 (p0) cc_final: 0.7634 (p0) REVERT: Aj 127 ASN cc_start: 0.7859 (p0) cc_final: 0.7616 (p0) REVERT: Aj 136 ASP cc_start: 0.8387 (t0) cc_final: 0.8157 (t0) REVERT: Ak 127 ASN cc_start: 0.7895 (p0) cc_final: 0.7644 (p0) REVERT: Ak 136 ASP cc_start: 0.8319 (t0) cc_final: 0.8067 (t0) REVERT: Al 70 LEU cc_start: 0.8728 (tp) cc_final: 0.8230 (tp) REVERT: Al 127 ASN cc_start: 0.7880 (p0) cc_final: 0.7636 (p0) REVERT: Al 188 ARG cc_start: 0.8332 (mtp-110) cc_final: 0.8062 (mtp-110) REVERT: Al 190 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8423 (tt) REVERT: Am 70 LEU cc_start: 0.9042 (tp) cc_final: 0.8760 (tp) REVERT: Am 127 ASN cc_start: 0.7859 (p0) cc_final: 0.7608 (p0) REVERT: Am 136 ASP cc_start: 0.8317 (t0) cc_final: 0.7941 (t0) REVERT: An 70 LEU cc_start: 0.8744 (tp) cc_final: 0.8253 (tp) REVERT: An 127 ASN cc_start: 0.7902 (p0) cc_final: 0.7630 (p0) REVERT: An 136 ASP cc_start: 0.8364 (t0) cc_final: 0.8145 (t0) REVERT: Ao 48 LYS cc_start: 0.8683 (tppt) cc_final: 0.8477 (tptt) REVERT: Ao 70 LEU cc_start: 0.9035 (tp) cc_final: 0.8745 (tp) REVERT: Ao 127 ASN cc_start: 0.7892 (p0) cc_final: 0.7643 (p0) REVERT: Ao 136 ASP cc_start: 0.8314 (t0) cc_final: 0.7944 (t0) REVERT: Ap 127 ASN cc_start: 0.7908 (p0) cc_final: 0.7619 (p0) REVERT: Ap 190 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8438 (tt) REVERT: Aq 69 HIS cc_start: 0.8289 (t-90) cc_final: 0.8002 (t-90) REVERT: Aq 107 GLU cc_start: 0.8212 (tp30) cc_final: 0.7927 (tm-30) REVERT: Aq 127 ASN cc_start: 0.7973 (p0) cc_final: 0.7629 (p0) REVERT: Aq 198 TYR cc_start: 0.8804 (m-10) cc_final: 0.8590 (m-10) REVERT: Ar 71 LEU cc_start: 0.8489 (mt) cc_final: 0.8273 (pp) REVERT: Ar 136 ASP cc_start: 0.7959 (t0) cc_final: 0.7586 (t0) REVERT: Ar 214 ARG cc_start: 0.8286 (mtp180) cc_final: 0.7935 (mtp180) REVERT: As 107 GLU cc_start: 0.8218 (tp30) cc_final: 0.7930 (tm-30) REVERT: As 127 ASN cc_start: 0.7950 (p0) cc_final: 0.7592 (p0) REVERT: As 150 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: As 151 ASN cc_start: 0.8051 (t0) cc_final: 0.7762 (t0) REVERT: At 71 LEU cc_start: 0.8490 (mt) cc_final: 0.8271 (pp) REVERT: At 127 ASN cc_start: 0.8027 (p0) cc_final: 0.7770 (p0) REVERT: At 136 ASP cc_start: 0.7964 (t0) cc_final: 0.7582 (t0) REVERT: At 214 ARG cc_start: 0.8256 (mtp180) cc_final: 0.7902 (mtp180) REVERT: Au 127 ASN cc_start: 0.7915 (p0) cc_final: 0.7562 (p0) REVERT: Au 150 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: Av 136 ASP cc_start: 0.7957 (t0) cc_final: 0.7569 (t0) REVERT: Av 214 ARG cc_start: 0.8263 (mtp180) cc_final: 0.7924 (mtp180) REVERT: Aw 56 MET cc_start: 0.8858 (mmt) cc_final: 0.8646 (mmp) REVERT: Aw 107 GLU cc_start: 0.8216 (tp30) cc_final: 0.7926 (tm-30) REVERT: Aw 127 ASN cc_start: 0.7953 (p0) cc_final: 0.7595 (p0) REVERT: Aw 136 ASP cc_start: 0.8257 (t0) cc_final: 0.8023 (t0) REVERT: Aw 150 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: Aw 151 ASN cc_start: 0.8095 (t0) cc_final: 0.7649 (t0) REVERT: Ax 71 LEU cc_start: 0.8436 (mt) cc_final: 0.8218 (pp) REVERT: Ax 107 GLU cc_start: 0.8256 (tp30) cc_final: 0.7981 (tm-30) REVERT: Ax 127 ASN cc_start: 0.8044 (p0) cc_final: 0.7776 (p0) REVERT: Ax 136 ASP cc_start: 0.7961 (t0) cc_final: 0.7572 (t0) REVERT: Ax 214 ARG cc_start: 0.8286 (mtp180) cc_final: 0.7937 (mtp180) outliers start: 118 outliers final: 101 residues processed: 1292 average time/residue: 0.4751 time to fit residues: 979.5744 Evaluate side-chains 1282 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1176 time to evaluate : 4.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR 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 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 Ac residue 159 ILE Chi-restraints excluded: chain Ad residue 88 SER Chi-restraints excluded: chain Ad residue 134 MET 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 Ae residue 159 ILE Chi-restraints excluded: chain Af residue 88 SER 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 Ag residue 159 ILE Chi-restraints excluded: chain Ah residue 88 SER Chi-restraints excluded: chain Ah residue 134 MET 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 150 GLU Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Aj residue 150 GLU 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 150 GLU Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 190 LEU Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 78 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 88 SER Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 150 GLU Chi-restraints excluded: chain An residue 190 LEU 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 80 ILE Chi-restraints excluded: chain Ap residue 88 SER Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 150 GLU Chi-restraints excluded: chain Ap residue 190 LEU Chi-restraints excluded: chain Aq residue 43 THR Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 78 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 150 GLU 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 43 THR Chi-restraints excluded: chain As residue 59 SER Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 88 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 150 GLU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 103 ILE 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 43 THR Chi-restraints excluded: chain Au residue 67 LEU Chi-restraints excluded: chain Au residue 78 ILE Chi-restraints excluded: chain Au residue 88 SER Chi-restraints excluded: chain Au residue 150 GLU Chi-restraints excluded: chain Av residue 78 ILE Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 103 ILE Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Aw residue 43 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 9.9990 chunk 398 optimal weight: 0.9990 chunk 363 optimal weight: 7.9990 chunk 388 optimal weight: 0.9980 chunk 233 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 304 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 350 optimal weight: 0.5980 chunk 366 optimal weight: 0.8980 chunk 386 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 69 HIS ** 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 89 GLN ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 98 GLN Am 89 GLN An 151 ASN ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 98 GLN Ar 175 ASN At 151 ASN Au 151 ASN ** Av 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 151 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3210 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= 0.171 Angle : 0.600 11.263 48504 Z= 0.292 Chirality : 0.040 0.176 5280 Planarity : 0.005 0.044 6288 Dihedral : 4.134 15.979 4824 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.56 % Allowed : 33.02 % Favored : 64.43 % 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: -0.66 (0.14), residues: 4296 helix: 0.34 (0.13), residues: 1728 sheet: 0.73 (0.36), residues: 288 loop : -1.21 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAa 132 HIS 0.010 0.001 HISAb 69 PHE 0.009 0.002 PHEAr 200 TYR 0.033 0.002 TYRAs 198 ARG 0.009 0.000 ARGAr 212 *********************** 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 1344 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1247 time to evaluate : 3.897 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 70 LEU cc_start: 0.8845 (tp) cc_final: 0.8593 (tp) REVERT: Ab 70 LEU cc_start: 0.8237 (tp) cc_final: 0.7812 (tp) REVERT: Ab 136 ASP cc_start: 0.8300 (t0) cc_final: 0.7900 (t0) REVERT: Ab 190 LEU cc_start: 0.9002 (tp) cc_final: 0.8721 (tp) REVERT: Ac 70 LEU cc_start: 0.8842 (tp) cc_final: 0.8559 (tp) REVERT: Ac 175 ASN cc_start: 0.9033 (t0) cc_final: 0.8793 (t0) REVERT: Ad 70 LEU cc_start: 0.8221 (tp) cc_final: 0.7828 (tp) REVERT: Ad 136 ASP cc_start: 0.8304 (t0) cc_final: 0.7908 (t0) REVERT: Ad 190 LEU cc_start: 0.9018 (tp) cc_final: 0.8740 (tp) REVERT: Ae 70 LEU cc_start: 0.8833 (tp) cc_final: 0.8558 (tp) REVERT: Ae 184 TYR cc_start: 0.8986 (t80) cc_final: 0.8771 (t80) REVERT: Af 136 ASP cc_start: 0.8301 (t0) cc_final: 0.7906 (t0) REVERT: Af 190 LEU cc_start: 0.9001 (tp) cc_final: 0.8729 (tp) REVERT: Ag 70 LEU cc_start: 0.8842 (tp) cc_final: 0.8558 (tp) REVERT: Ah 70 LEU cc_start: 0.8233 (tp) cc_final: 0.7821 (tp) REVERT: Ah 136 ASP cc_start: 0.8338 (t0) cc_final: 0.7951 (t0) REVERT: Ah 190 LEU cc_start: 0.9002 (tp) cc_final: 0.8720 (tp) REVERT: Ai 127 ASN cc_start: 0.7902 (p0) cc_final: 0.7647 (p0) REVERT: Ai 151 ASN cc_start: 0.8194 (t160) cc_final: 0.7930 (t0) REVERT: Aj 70 LEU cc_start: 0.8343 (tp) cc_final: 0.7965 (tp) REVERT: Aj 127 ASN cc_start: 0.7901 (p0) cc_final: 0.7683 (p0) REVERT: Aj 173 MET cc_start: 0.8939 (tmm) cc_final: 0.8530 (tmm) REVERT: Aj 188 ARG cc_start: 0.8327 (mtp-110) cc_final: 0.8097 (mtp-110) REVERT: Ak 127 ASN cc_start: 0.7896 (p0) cc_final: 0.7629 (p0) REVERT: Ak 136 ASP cc_start: 0.8279 (t0) cc_final: 0.8003 (t0) REVERT: Ak 151 ASN cc_start: 0.8239 (t160) cc_final: 0.7971 (t0) REVERT: Al 70 LEU cc_start: 0.8672 (tp) cc_final: 0.8312 (tp) REVERT: Al 127 ASN cc_start: 0.7915 (p0) cc_final: 0.7692 (p0) REVERT: Al 188 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7999 (mtp-110) REVERT: Al 190 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8470 (tt) REVERT: Am 127 ASN cc_start: 0.7847 (p0) cc_final: 0.7597 (p0) REVERT: Am 136 ASP cc_start: 0.8268 (t0) cc_final: 0.8001 (t0) REVERT: An 70 LEU cc_start: 0.8669 (tp) cc_final: 0.8319 (tp) REVERT: An 127 ASN cc_start: 0.7861 (p0) cc_final: 0.7609 (p0) REVERT: An 188 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.8033 (mtp-110) REVERT: Ao 48 LYS cc_start: 0.8659 (tppt) cc_final: 0.8419 (tptt) REVERT: Ao 127 ASN cc_start: 0.7896 (p0) cc_final: 0.7632 (p0) REVERT: Ao 136 ASP cc_start: 0.8306 (t0) cc_final: 0.8051 (t0) REVERT: Ao 151 ASN cc_start: 0.8172 (t160) cc_final: 0.7947 (t0) REVERT: Ap 127 ASN cc_start: 0.7742 (p0) cc_final: 0.7524 (p0) REVERT: Ap 190 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8439 (tt) REVERT: Aq 69 HIS cc_start: 0.8266 (t-90) cc_final: 0.7990 (t-90) REVERT: Aq 127 ASN cc_start: 0.8017 (p0) cc_final: 0.7748 (p0) REVERT: Ar 71 LEU cc_start: 0.8556 (mt) cc_final: 0.8337 (pp) REVERT: Ar 89 GLN cc_start: 0.8973 (mt0) cc_final: 0.8751 (mt0) REVERT: Ar 136 ASP cc_start: 0.7960 (t0) cc_final: 0.7590 (t0) REVERT: Ar 214 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7848 (mtp180) REVERT: As 127 ASN cc_start: 0.7975 (p0) cc_final: 0.7707 (p0) REVERT: As 150 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: As 151 ASN cc_start: 0.7996 (t0) cc_final: 0.7657 (t0) REVERT: At 71 LEU cc_start: 0.8558 (mt) cc_final: 0.8338 (pp) REVERT: At 79 ASP cc_start: 0.8359 (m-30) cc_final: 0.8130 (m-30) REVERT: At 89 GLN cc_start: 0.8974 (mt0) cc_final: 0.8751 (mt0) REVERT: At 127 ASN cc_start: 0.8001 (p0) cc_final: 0.7759 (p0) REVERT: At 136 ASP cc_start: 0.7960 (t0) cc_final: 0.7579 (t0) REVERT: At 214 ARG cc_start: 0.8204 (mtp180) cc_final: 0.7839 (mtp180) REVERT: Au 127 ASN cc_start: 0.7948 (p0) cc_final: 0.7685 (p0) REVERT: Au 150 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7816 (pt0) REVERT: Av 70 LEU cc_start: 0.8842 (tp) cc_final: 0.8449 (tp) REVERT: Av 79 ASP cc_start: 0.8332 (m-30) cc_final: 0.8118 (m-30) REVERT: Av 136 ASP cc_start: 0.7974 (t0) cc_final: 0.7597 (t0) REVERT: Av 214 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7822 (mtp180) REVERT: Aw 127 ASN cc_start: 0.7974 (p0) cc_final: 0.7708 (p0) REVERT: Aw 150 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7786 (pt0) REVERT: Aw 151 ASN cc_start: 0.8018 (t0) cc_final: 0.7717 (t0) REVERT: Aw 220 MET cc_start: 0.7262 (mmm) cc_final: 0.6224 (ptm) REVERT: Ax 71 LEU cc_start: 0.8554 (mt) cc_final: 0.8333 (pp) REVERT: Ax 79 ASP cc_start: 0.8357 (m-30) cc_final: 0.8140 (m-30) REVERT: Ax 89 GLN cc_start: 0.8959 (mt0) cc_final: 0.8736 (mt0) REVERT: Ax 127 ASN cc_start: 0.8018 (p0) cc_final: 0.7758 (p0) REVERT: Ax 136 ASP cc_start: 0.7976 (t0) cc_final: 0.7598 (t0) REVERT: Ax 214 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7851 (mtp180) outliers start: 97 outliers final: 82 residues processed: 1296 average time/residue: 0.4010 time to fit residues: 834.8561 Evaluate side-chains 1281 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1194 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR 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 Ab residue 150 GLU 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 Ad residue 150 GLU 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 43 THR Chi-restraints excluded: chain Ag residue 86 THR Chi-restraints excluded: chain Ag residue 150 GLU Chi-restraints excluded: chain Ag residue 159 ILE 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 Ai residue 150 GLU Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 133 VAL 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 133 VAL Chi-restraints excluded: chain Ak residue 150 GLU Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 190 LEU Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 78 ILE 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 88 SER Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 150 GLU Chi-restraints excluded: chain An residue 190 LEU Chi-restraints excluded: chain Ao residue 44 VAL 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 Ap residue 88 SER Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 150 GLU Chi-restraints excluded: chain Ap residue 165 ASP Chi-restraints excluded: chain Ap residue 190 LEU Chi-restraints excluded: chain Aq residue 43 THR 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 Aq residue 150 GLU 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 59 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 150 GLU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 103 ILE 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 88 SER Chi-restraints excluded: chain Au residue 150 GLU Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 103 ILE Chi-restraints excluded: chain Av residue 133 VAL Chi-restraints excluded: chain Av residue 150 GLU Chi-restraints excluded: chain Aw residue 43 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 3.9990 chunk 410 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 430 optimal weight: 3.9990 chunk 396 optimal weight: 1.9990 chunk 342 optimal weight: 0.3980 chunk 35 optimal weight: 8.9990 chunk 264 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 158 GLN ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 151 ASN Am 151 ASN Ao 98 GLN ** Ao 151 ASN ** 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 175 ASN ** Au 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ax 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 35784 Z= 0.315 Angle : 0.674 11.970 48504 Z= 0.326 Chirality : 0.043 0.176 5280 Planarity : 0.005 0.051 6288 Dihedral : 4.324 16.624 4824 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.95 % Allowed : 32.94 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 4296 helix: 0.08 (0.13), residues: 1800 sheet: 0.72 (0.37), residues: 288 loop : -1.28 (0.14), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPAe 132 HIS 0.010 0.001 HISAd 69 PHE 0.010 0.002 PHEAu 202 TYR 0.041 0.002 TYRAq 198 ARG 0.009 0.000 ARGAr 212 ********************** 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 1316 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1204 time to evaluate : 4.349 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: Aa 70 LEU cc_start: 0.8998 (tp) cc_final: 0.8551 (tp) REVERT: Ab 136 ASP cc_start: 0.8288 (t0) cc_final: 0.7899 (t0) REVERT: Ab 190 LEU cc_start: 0.9039 (tp) cc_final: 0.8748 (tp) REVERT: Ac 70 LEU cc_start: 0.8977 (tp) cc_final: 0.8533 (tp) REVERT: Ac 175 ASN cc_start: 0.8983 (t0) cc_final: 0.8719 (t0) REVERT: Ad 136 ASP cc_start: 0.8291 (t0) cc_final: 0.7921 (t0) REVERT: Ad 190 LEU cc_start: 0.9048 (tp) cc_final: 0.8734 (tp) REVERT: Ae 184 TYR cc_start: 0.9016 (t80) cc_final: 0.8809 (t80) REVERT: Af 136 ASP cc_start: 0.8287 (t0) cc_final: 0.7900 (t0) REVERT: Af 190 LEU cc_start: 0.9040 (tp) cc_final: 0.8744 (tp) REVERT: Ag 70 LEU cc_start: 0.8990 (tp) cc_final: 0.8541 (tp) REVERT: Ah 136 ASP cc_start: 0.8294 (t0) cc_final: 0.7916 (t0) REVERT: Ah 190 LEU cc_start: 0.9036 (tp) cc_final: 0.8747 (tp) REVERT: Ai 71 LEU cc_start: 0.8862 (mt) cc_final: 0.8638 (pp) REVERT: Ai 127 ASN cc_start: 0.7910 (p0) cc_final: 0.7671 (p0) REVERT: Aj 127 ASN cc_start: 0.7916 (p0) cc_final: 0.7687 (p0) REVERT: Aj 173 MET cc_start: 0.8886 (tmm) cc_final: 0.8618 (tmm) REVERT: Aj 188 ARG cc_start: 0.8409 (mtp-110) cc_final: 0.8178 (mtp-110) REVERT: Ak 127 ASN cc_start: 0.7894 (p0) cc_final: 0.7651 (p0) REVERT: Ak 136 ASP cc_start: 0.8380 (t0) cc_final: 0.8038 (t0) REVERT: Al 127 ASN cc_start: 0.7926 (p0) cc_final: 0.7689 (p0) REVERT: Al 190 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8415 (tt) REVERT: Am 70 LEU cc_start: 0.9002 (tp) cc_final: 0.8754 (tp) REVERT: Am 127 ASN cc_start: 0.7882 (p0) cc_final: 0.7636 (p0) REVERT: Am 136 ASP cc_start: 0.8370 (t0) cc_final: 0.7978 (t0) REVERT: An 127 ASN cc_start: 0.7890 (p0) cc_final: 0.7595 (p0) REVERT: An 188 ARG cc_start: 0.8366 (mtp-110) cc_final: 0.8123 (mtp-110) REVERT: Ao 48 LYS cc_start: 0.8643 (tppt) cc_final: 0.8431 (tptt) REVERT: Ao 70 LEU cc_start: 0.9009 (tp) cc_final: 0.8770 (tp) REVERT: Ao 127 ASN cc_start: 0.7901 (p0) cc_final: 0.7650 (p0) REVERT: Ao 136 ASP cc_start: 0.8372 (t0) cc_final: 0.8016 (t0) REVERT: Ap 89 GLN cc_start: 0.9068 (mt0) cc_final: 0.8827 (tt0) REVERT: Ap 127 ASN cc_start: 0.7806 (p0) cc_final: 0.7583 (p0) REVERT: Ap 190 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8415 (tt) REVERT: Aq 69 HIS cc_start: 0.8345 (t-90) cc_final: 0.8095 (t-90) REVERT: Aq 127 ASN cc_start: 0.7973 (p0) cc_final: 0.7626 (p0) REVERT: Ar 89 GLN cc_start: 0.9065 (mt0) cc_final: 0.8848 (mt0) REVERT: Ar 136 ASP cc_start: 0.8050 (t0) cc_final: 0.7677 (t0) REVERT: Ar 214 ARG cc_start: 0.8263 (mtp180) cc_final: 0.7835 (mtp-110) REVERT: As 127 ASN cc_start: 0.7955 (p0) cc_final: 0.7602 (p0) REVERT: As 150 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7877 (pt0) REVERT: As 151 ASN cc_start: 0.8188 (t0) cc_final: 0.7903 (t0) REVERT: At 89 GLN cc_start: 0.9073 (mt0) cc_final: 0.8841 (mt0) REVERT: At 127 ASN cc_start: 0.7999 (p0) cc_final: 0.7751 (p0) REVERT: At 136 ASP cc_start: 0.8057 (t0) cc_final: 0.7660 (t0) REVERT: At 214 ARG cc_start: 0.8271 (mtp180) cc_final: 0.7875 (mtp180) REVERT: Au 127 ASN cc_start: 0.7925 (p0) cc_final: 0.7580 (p0) REVERT: Au 150 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: Av 89 GLN cc_start: 0.9072 (mt0) cc_final: 0.8853 (mt0) REVERT: Av 107 GLU cc_start: 0.8263 (tp30) cc_final: 0.7857 (tm-30) REVERT: Av 136 ASP cc_start: 0.8045 (t0) cc_final: 0.7651 (t0) REVERT: Av 214 ARG cc_start: 0.8231 (mtp180) cc_final: 0.7809 (mtp-110) REVERT: Aw 127 ASN cc_start: 0.7948 (p0) cc_final: 0.7597 (p0) REVERT: Aw 150 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: Aw 151 ASN cc_start: 0.8216 (t0) cc_final: 0.7764 (t0) REVERT: Ax 89 GLN cc_start: 0.9062 (mt0) cc_final: 0.8843 (mt0) REVERT: Ax 107 GLU cc_start: 0.8238 (tp30) cc_final: 0.7839 (tm-30) REVERT: Ax 127 ASN cc_start: 0.8016 (p0) cc_final: 0.7744 (p0) REVERT: Ax 136 ASP cc_start: 0.8048 (t0) cc_final: 0.7653 (t0) REVERT: Ax 214 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7811 (mtp-110) outliers start: 112 outliers final: 93 residues processed: 1260 average time/residue: 0.4989 time to fit residues: 989.6430 Evaluate side-chains 1268 residues out of total 3792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1170 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 43 THR 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 Ab residue 150 GLU Chi-restraints excluded: chain Ac residue 43 THR 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 86 THR 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 86 THR Chi-restraints excluded: chain Ae residue 88 SER 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 86 THR Chi-restraints excluded: chain Ag residue 150 GLU Chi-restraints excluded: chain Ag residue 159 ILE 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 Ai residue 150 GLU Chi-restraints excluded: chain Aj residue 80 ILE Chi-restraints excluded: chain Aj residue 88 SER Chi-restraints excluded: chain Aj residue 133 VAL Chi-restraints excluded: chain Aj residue 150 GLU 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 133 VAL Chi-restraints excluded: chain Ak residue 150 GLU Chi-restraints excluded: chain Al residue 88 SER Chi-restraints excluded: chain Al residue 133 VAL Chi-restraints excluded: chain Al residue 190 LEU Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 78 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 80 ILE Chi-restraints excluded: chain An residue 88 SER Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain An residue 150 GLU Chi-restraints excluded: chain Ao residue 44 VAL Chi-restraints excluded: chain Ao residue 78 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 88 SER Chi-restraints excluded: chain Ap residue 133 VAL Chi-restraints excluded: chain Ap residue 150 GLU Chi-restraints excluded: chain Ap residue 165 ASP Chi-restraints excluded: chain Ap residue 190 LEU Chi-restraints excluded: chain Aq residue 78 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 150 GLU 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 59 SER Chi-restraints excluded: chain As residue 88 SER Chi-restraints excluded: chain As residue 133 VAL Chi-restraints excluded: chain As residue 150 GLU Chi-restraints excluded: chain At residue 78 ILE Chi-restraints excluded: chain At residue 88 SER Chi-restraints excluded: chain At residue 103 ILE 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 150 GLU Chi-restraints excluded: chain Av residue 78 ILE Chi-restraints excluded: chain Av residue 88 SER Chi-restraints excluded: chain Av residue 103 ILE 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 133 VAL Chi-restraints excluded: chain Aw residue 150 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 1.9990 chunk 365 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 316 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 343 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 352 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 151 ASN ** 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 189 ASN ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 151 ASN Ar 151 ASN ** Au 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099195 restraints weight = 51709.001| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.64 r_work: 0.3015 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3402 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= 0.180 Angle : 0.624 11.628 48504 Z= 0.300 Chirality : 0.040 0.156 5280 Planarity : 0.005 0.075 6288 Dihedral : 4.215 16.596 4824 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.40 % Allowed : 33.47 % Favored : 64.14 % 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: -0.63 (0.14), residues: 4296 helix: 0.28 (0.13), residues: 1728 sheet: 0.70 (0.36), residues: 288 loop : -1.12 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPAb 93 HIS 0.011 0.001 HISAe 69 PHE 0.008 0.002 PHEAt 200 TYR 0.035 0.002 TYRAs 198 ARG 0.009 0.000 ARGAr 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13270.06 seconds wall clock time: 244 minutes 39.85 seconds (14679.85 seconds total)