Starting phenix.real_space_refine on Thu Apr 11 08:17:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opg_17052/04_2024/8opg_17052.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opg_17052/04_2024/8opg_17052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opg_17052/04_2024/8opg_17052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opg_17052/04_2024/8opg_17052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opg_17052/04_2024/8opg_17052.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opg_17052/04_2024/8opg_17052.pdb" } resolution = 3.2 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= 0.017 sd= 0.208 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 209 5.16 5 C 13984 2.51 5 N 3705 2.21 5 O 4161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Aa GLU 168": "OE1" <-> "OE2" Residue "Ab GLU 168": "OE1" <-> "OE2" Residue "Ac GLU 168": "OE1" <-> "OE2" Residue "Ad GLU 168": "OE1" <-> "OE2" Residue "Ae GLU 168": "OE1" <-> "OE2" Residue "Af GLU 168": "OE1" <-> "OE2" Residue "Ag GLU 168": "OE1" <-> "OE2" Residue "Ah GLU 168": "OE1" <-> "OE2" Residue "Ai GLU 168": "OE1" <-> "OE2" Residue "Aj GLU 168": "OE1" <-> "OE2" Residue "Ak GLU 168": "OE1" <-> "OE2" Residue "Al GLU 168": "OE1" <-> "OE2" Residue "Am GLU 168": "OE1" <-> "OE2" Residue "An GLU 168": "OE1" <-> "OE2" Residue "Ao GLU 168": "OE1" <-> "OE2" Residue "Ap GLU 168": "OE1" <-> "OE2" Residue "Aq GLU 168": "OE1" <-> "OE2" Residue "Ar GLU 168": "OE1" <-> "OE2" Residue "As GLU 168": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22059 Number of models: 1 Model: "" Number of chains: 19 Chain: "Aa" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Ab" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Ac" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Ad" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Ae" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Af" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Ag" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Ah" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Ai" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Aj" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Ak" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Al" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Am" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "An" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Ao" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Ap" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Aq" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "Ar" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Chain: "As" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1161 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 134} Time building chain proxies: 11.61, per 1000 atoms: 0.53 Number of scatterers: 22059 At special positions: 0 Unit cell: (135.85, 135.85, 158.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 209 16.00 O 4161 8.00 N 3705 7.00 C 13984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.98 Conformation dependent library (CDL) restraints added in 4.0 seconds 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5244 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 38 sheets defined 43.4% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'Aa' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAa 95 " --> pdb=" O ASPAa 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUAa 99 " --> pdb=" O GLUAa 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAa 100 " --> pdb=" O ALAAa 96 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAa 112 " --> pdb=" O METAa 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAa 114 " --> pdb=" O THRAa 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAa 121 " --> pdb=" O VALAa 117 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 151 Processing helix chain 'Aa' and resid 155 through 161 Processing helix chain 'Aa' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAa 169 " --> pdb=" O ASPAa 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAa 173 " --> pdb=" O ALAAa 169 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYSAa 177 " --> pdb=" O METAa 173 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAb 95 " --> pdb=" O ASPAb 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUAb 99 " --> pdb=" O GLUAb 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAb 100 " --> pdb=" O ALAAb 96 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAb 111 " --> pdb=" O GLUAb 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAb 112 " --> pdb=" O METAb 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAb 114 " --> pdb=" O THRAb 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAb 121 " --> pdb=" O VALAb 117 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 145 through 151 Processing helix chain 'Ab' and resid 155 through 161 Processing helix chain 'Ab' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAb 169 " --> pdb=" O ASPAb 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAb 173 " --> pdb=" O ALAAb 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAb 177 " --> pdb=" O METAb 173 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 86 through 102 removed outlier: 3.512A pdb=" N LEUAc 99 " --> pdb=" O GLUAc 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAc 100 " --> pdb=" O ALAAc 96 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAc 112 " --> pdb=" O METAc 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAc 114 " --> pdb=" O THRAc 110 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLUAc 121 " --> pdb=" O VALAc 117 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 151 Processing helix chain 'Ac' and resid 155 through 161 Processing helix chain 'Ac' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAc 169 " --> pdb=" O ASPAc 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAc 173 " --> pdb=" O ALAAc 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAc 177 " --> pdb=" O METAc 173 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAd 99 " --> pdb=" O GLUAd 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAd 100 " --> pdb=" O ALAAd 96 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAd 111 " --> pdb=" O GLUAd 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAd 112 " --> pdb=" O METAd 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAd 114 " --> pdb=" O THRAd 110 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLUAd 121 " --> pdb=" O VALAd 117 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 145 through 151 Processing helix chain 'Ad' and resid 155 through 161 Processing helix chain 'Ad' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAd 169 " --> pdb=" O ASPAd 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAd 173 " --> pdb=" O ALAAd 169 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYSAd 177 " --> pdb=" O METAd 173 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 86 through 102 removed outlier: 3.501A pdb=" N GLUAe 95 " --> pdb=" O ASPAe 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUAe 99 " --> pdb=" O GLUAe 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAe 100 " --> pdb=" O ALAAe 96 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N METAe 112 " --> pdb=" O METAe 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAe 114 " --> pdb=" O THRAe 110 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLUAe 121 " --> pdb=" O VALAe 117 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 151 Processing helix chain 'Ae' and resid 155 through 161 Processing helix chain 'Ae' and resid 163 through 178 removed outlier: 3.524A pdb=" N ALAAe 169 " --> pdb=" O ASPAe 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAe 173 " --> pdb=" O ALAAe 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAe 177 " --> pdb=" O METAe 173 " (cutoff:3.500A) Processing helix chain 'Af' and resid 86 through 102 removed outlier: 3.501A pdb=" N GLUAf 95 " --> pdb=" O ASPAf 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUAf 99 " --> pdb=" O GLUAf 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAf 100 " --> pdb=" O ALAAf 96 " (cutoff:3.500A) Processing helix chain 'Af' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAf 111 " --> pdb=" O GLUAf 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAf 112 " --> pdb=" O METAf 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAf 114 " --> pdb=" O THRAf 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAf 121 " --> pdb=" O VALAf 117 " (cutoff:3.500A) Processing helix chain 'Af' and resid 145 through 151 Processing helix chain 'Af' and resid 155 through 161 Processing helix chain 'Af' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAf 169 " --> pdb=" O ASPAf 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAf 173 " --> pdb=" O ALAAf 169 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYSAf 177 " --> pdb=" O METAf 173 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAg 99 " --> pdb=" O GLUAg 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAg 100 " --> pdb=" O ALAAg 96 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAg 112 " --> pdb=" O METAg 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAg 114 " --> pdb=" O THRAg 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAg 121 " --> pdb=" O VALAg 117 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 151 Processing helix chain 'Ag' and resid 155 through 161 Processing helix chain 'Ag' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAg 169 " --> pdb=" O ASPAg 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAg 173 " --> pdb=" O ALAAg 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAg 177 " --> pdb=" O METAg 173 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 86 through 102 removed outlier: 3.501A pdb=" N GLUAh 95 " --> pdb=" O ASPAh 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUAh 99 " --> pdb=" O GLUAh 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAh 100 " --> pdb=" O ALAAh 96 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAh 111 " --> pdb=" O GLUAh 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAh 112 " --> pdb=" O METAh 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLYAh 114 " --> pdb=" O THRAh 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAh 121 " --> pdb=" O VALAh 117 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 145 through 151 Processing helix chain 'Ah' and resid 155 through 161 Processing helix chain 'Ah' and resid 163 through 178 removed outlier: 3.524A pdb=" N ALAAh 169 " --> pdb=" O ASPAh 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAh 173 " --> pdb=" O ALAAh 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAh 177 " --> pdb=" O METAh 173 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAi 95 " --> pdb=" O ASPAi 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUAi 99 " --> pdb=" O GLUAi 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAi 100 " --> pdb=" O ALAAi 96 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAi 112 " --> pdb=" O METAi 108 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLYAi 114 " --> pdb=" O THRAi 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAi 121 " --> pdb=" O VALAi 117 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 151 Processing helix chain 'Ai' and resid 155 through 161 Processing helix chain 'Ai' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAi 169 " --> pdb=" O ASPAi 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAi 173 " --> pdb=" O ALAAi 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAi 177 " --> pdb=" O METAi 173 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAj 99 " --> pdb=" O GLUAj 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAj 100 " --> pdb=" O ALAAj 96 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAj 111 " --> pdb=" O GLUAj 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N METAj 112 " --> pdb=" O METAj 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAj 114 " --> pdb=" O THRAj 110 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLUAj 121 " --> pdb=" O VALAj 117 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 145 through 151 Processing helix chain 'Aj' and resid 155 through 161 Processing helix chain 'Aj' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAj 169 " --> pdb=" O ASPAj 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAj 173 " --> pdb=" O ALAAj 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAj 177 " --> pdb=" O METAj 173 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAk 95 " --> pdb=" O ASPAk 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUAk 99 " --> pdb=" O GLUAk 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAk 100 " --> pdb=" O ALAAk 96 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAk 112 " --> pdb=" O METAk 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLYAk 114 " --> pdb=" O THRAk 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAk 121 " --> pdb=" O VALAk 117 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 151 Processing helix chain 'Ak' and resid 155 through 161 Processing helix chain 'Ak' and resid 163 through 178 removed outlier: 3.524A pdb=" N ALAAk 169 " --> pdb=" O ASPAk 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAk 173 " --> pdb=" O ALAAk 169 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYSAk 177 " --> pdb=" O METAk 173 " (cutoff:3.500A) Processing helix chain 'Al' and resid 86 through 102 removed outlier: 3.512A pdb=" N LEUAl 99 " --> pdb=" O GLUAl 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAl 100 " --> pdb=" O ALAAl 96 " (cutoff:3.500A) Processing helix chain 'Al' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAl 111 " --> pdb=" O GLUAl 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAl 112 " --> pdb=" O METAl 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLYAl 114 " --> pdb=" O THRAl 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAl 121 " --> pdb=" O VALAl 117 " (cutoff:3.500A) Processing helix chain 'Al' and resid 145 through 151 Processing helix chain 'Al' and resid 155 through 161 Processing helix chain 'Al' and resid 163 through 178 removed outlier: 3.524A pdb=" N ALAAl 169 " --> pdb=" O ASPAl 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAl 173 " --> pdb=" O ALAAl 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAl 177 " --> pdb=" O METAl 173 " (cutoff:3.500A) Processing helix chain 'Am' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAm 95 " --> pdb=" O ASPAm 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUAm 99 " --> pdb=" O GLUAm 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAm 100 " --> pdb=" O ALAAm 96 " (cutoff:3.500A) Processing helix chain 'Am' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAm 112 " --> pdb=" O METAm 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAm 114 " --> pdb=" O THRAm 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAm 121 " --> pdb=" O VALAm 117 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 151 Processing helix chain 'Am' and resid 155 through 161 Processing helix chain 'Am' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAm 169 " --> pdb=" O ASPAm 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAm 173 " --> pdb=" O ALAAm 169 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYSAm 177 " --> pdb=" O METAm 173 " (cutoff:3.500A) Processing helix chain 'An' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAn 99 " --> pdb=" O GLUAn 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAn 100 " --> pdb=" O ALAAn 96 " (cutoff:3.500A) Processing helix chain 'An' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAn 111 " --> pdb=" O GLUAn 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAn 112 " --> pdb=" O METAn 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAn 114 " --> pdb=" O THRAn 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAn 121 " --> pdb=" O VALAn 117 " (cutoff:3.500A) Processing helix chain 'An' and resid 145 through 151 Processing helix chain 'An' and resid 155 through 161 Processing helix chain 'An' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAn 169 " --> pdb=" O ASPAn 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAn 173 " --> pdb=" O ALAAn 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAn 177 " --> pdb=" O METAn 173 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAo 99 " --> pdb=" O GLUAo 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAo 100 " --> pdb=" O ALAAo 96 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N METAo 112 " --> pdb=" O METAo 108 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLYAo 114 " --> pdb=" O THRAo 110 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLUAo 121 " --> pdb=" O VALAo 117 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 151 Processing helix chain 'Ao' and resid 155 through 161 Processing helix chain 'Ao' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAo 169 " --> pdb=" O ASPAo 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAo 173 " --> pdb=" O ALAAo 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAo 177 " --> pdb=" O METAo 173 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 86 through 102 removed outlier: 3.513A pdb=" N LEUAp 99 " --> pdb=" O GLUAp 95 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALAAp 100 " --> pdb=" O ALAAp 96 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAp 111 " --> pdb=" O GLUAp 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N METAp 112 " --> pdb=" O METAp 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAp 114 " --> pdb=" O THRAp 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAp 121 " --> pdb=" O VALAp 117 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 145 through 151 Processing helix chain 'Ap' and resid 155 through 161 Processing helix chain 'Ap' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAp 169 " --> pdb=" O ASPAp 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAp 173 " --> pdb=" O ALAAp 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAp 177 " --> pdb=" O METAp 173 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 86 through 102 removed outlier: 3.512A pdb=" N LEUAq 99 " --> pdb=" O GLUAq 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAq 100 " --> pdb=" O ALAAq 96 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 107 through 122 removed outlier: 4.025A pdb=" N VALAq 111 " --> pdb=" O GLUAq 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAq 112 " --> pdb=" O METAq 108 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLYAq 114 " --> pdb=" O THRAq 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAq 121 " --> pdb=" O VALAq 117 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 145 through 151 Processing helix chain 'Aq' and resid 155 through 161 Processing helix chain 'Aq' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAq 169 " --> pdb=" O ASPAq 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAq 173 " --> pdb=" O ALAAq 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAq 177 " --> pdb=" O METAq 173 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 86 through 102 removed outlier: 3.500A pdb=" N GLUAr 95 " --> pdb=" O ASPAr 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUAr 99 " --> pdb=" O GLUAr 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAr 100 " --> pdb=" O ALAAr 96 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 107 through 122 removed outlier: 4.026A pdb=" N VALAr 111 " --> pdb=" O GLUAr 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N METAr 112 " --> pdb=" O METAr 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAr 114 " --> pdb=" O THRAr 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAr 121 " --> pdb=" O VALAr 117 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 145 through 151 Processing helix chain 'Ar' and resid 155 through 161 Processing helix chain 'Ar' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAr 169 " --> pdb=" O ASPAr 165 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N METAr 173 " --> pdb=" O ALAAr 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAr 177 " --> pdb=" O METAr 173 " (cutoff:3.500A) Processing helix chain 'As' and resid 86 through 102 removed outlier: 3.512A pdb=" N LEUAs 99 " --> pdb=" O GLUAs 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALAAs 100 " --> pdb=" O ALAAs 96 " (cutoff:3.500A) Processing helix chain 'As' and resid 107 through 122 removed outlier: 4.024A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N METAs 112 " --> pdb=" O METAs 108 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLYAs 114 " --> pdb=" O THRAs 110 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUAs 121 " --> pdb=" O VALAs 117 " (cutoff:3.500A) Processing helix chain 'As' and resid 145 through 151 Processing helix chain 'As' and resid 155 through 161 Processing helix chain 'As' and resid 163 through 178 removed outlier: 3.525A pdb=" N ALAAs 169 " --> pdb=" O ASPAs 165 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N METAs 173 " --> pdb=" O ALAAs 169 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYSAs 177 " --> pdb=" O METAs 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'Aa' and resid 131 through 133 Processing sheet with id=AA3, first strand: chain 'Ab' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'Ab' and resid 131 through 133 Processing sheet with id=AA5, first strand: chain 'Ac' and resid 58 through 59 Processing sheet with id=AA6, first strand: chain 'Ac' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'Ad' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'Ad' and resid 131 through 133 Processing sheet with id=AA9, first strand: chain 'Ae' and resid 58 through 59 Processing sheet with id=AB1, first strand: chain 'Ae' and resid 131 through 133 Processing sheet with id=AB2, first strand: chain 'Af' and resid 58 through 59 Processing sheet with id=AB3, first strand: chain 'Af' and resid 131 through 133 Processing sheet with id=AB4, first strand: chain 'Ag' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'Ag' and resid 131 through 133 Processing sheet with id=AB6, first strand: chain 'Ah' and resid 58 through 59 Processing sheet with id=AB7, first strand: chain 'Ah' and resid 131 through 133 Processing sheet with id=AB8, first strand: chain 'Ai' and resid 58 through 59 Processing sheet with id=AB9, first strand: chain 'Ai' and resid 131 through 133 Processing sheet with id=AC1, first strand: chain 'Aj' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'Aj' and resid 131 through 133 Processing sheet with id=AC3, first strand: chain 'Ak' and resid 58 through 59 Processing sheet with id=AC4, first strand: chain 'Ak' and resid 131 through 133 Processing sheet with id=AC5, first strand: chain 'Al' and resid 58 through 59 Processing sheet with id=AC6, first strand: chain 'Al' and resid 131 through 133 Processing sheet with id=AC7, first strand: chain 'Am' and resid 58 through 59 Processing sheet with id=AC8, first strand: chain 'Am' and resid 131 through 133 Processing sheet with id=AC9, first strand: chain 'An' and resid 58 through 59 Processing sheet with id=AD1, first strand: chain 'An' and resid 131 through 133 Processing sheet with id=AD2, first strand: chain 'Ao' and resid 58 through 59 Processing sheet with id=AD3, first strand: chain 'Ao' and resid 131 through 133 Processing sheet with id=AD4, first strand: chain 'Ap' and resid 58 through 59 Processing sheet with id=AD5, first strand: chain 'Ap' and resid 131 through 133 Processing sheet with id=AD6, first strand: chain 'Aq' and resid 58 through 59 Processing sheet with id=AD7, first strand: chain 'Aq' and resid 131 through 133 Processing sheet with id=AD8, first strand: chain 'Ar' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'Ar' and resid 131 through 133 Processing sheet with id=AE1, first strand: chain 'As' and resid 58 through 59 Processing sheet with id=AE2, first strand: chain 'As' and resid 131 through 133 713 hydrogen bonds defined for protein. 2082 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.40 Time building geometry restraints manager: 8.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7144 1.34 - 1.46: 3921 1.46 - 1.58: 11108 1.58 - 1.69: 0 1.69 - 1.81: 399 Bond restraints: 22572 Sorted by residual: bond pdb=" C HISAh 69 " pdb=" N LEUAh 70 " ideal model delta sigma weight residual 1.335 1.275 0.060 1.36e-02 5.41e+03 1.91e+01 bond pdb=" C HISAp 69 " pdb=" N LEUAp 70 " ideal model delta sigma weight residual 1.335 1.276 0.059 1.36e-02 5.41e+03 1.90e+01 bond pdb=" C HISAq 69 " pdb=" N LEUAq 70 " ideal model delta sigma weight residual 1.335 1.276 0.059 1.36e-02 5.41e+03 1.90e+01 bond pdb=" C HISAg 69 " pdb=" N LEUAg 70 " ideal model delta sigma weight residual 1.335 1.276 0.059 1.36e-02 5.41e+03 1.90e+01 bond pdb=" C HISAe 69 " pdb=" N LEUAe 70 " ideal model delta sigma weight residual 1.335 1.276 0.059 1.36e-02 5.41e+03 1.89e+01 ... (remaining 22567 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.01: 1089 107.01 - 113.77: 12355 113.77 - 120.53: 8547 120.53 - 127.29: 8352 127.29 - 134.05: 304 Bond angle restraints: 30647 Sorted by residual: angle pdb=" CA PROAp 109 " pdb=" N PROAp 109 " pdb=" CD PROAp 109 " ideal model delta sigma weight residual 112.00 107.73 4.27 1.40e+00 5.10e-01 9.30e+00 angle pdb=" CA PROAg 109 " pdb=" N PROAg 109 " pdb=" CD PROAg 109 " ideal model delta sigma weight residual 112.00 107.74 4.26 1.40e+00 5.10e-01 9.25e+00 angle pdb=" CA PROAe 109 " pdb=" N PROAe 109 " pdb=" CD PROAe 109 " ideal model delta sigma weight residual 112.00 107.75 4.25 1.40e+00 5.10e-01 9.23e+00 angle pdb=" CA PROAr 109 " pdb=" N PROAr 109 " pdb=" CD PROAr 109 " ideal model delta sigma weight residual 112.00 107.75 4.25 1.40e+00 5.10e-01 9.21e+00 angle pdb=" CA PROAb 109 " pdb=" N PROAb 109 " pdb=" CD PROAb 109 " ideal model delta sigma weight residual 112.00 107.76 4.24 1.40e+00 5.10e-01 9.19e+00 ... (remaining 30642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 11942 16.83 - 33.66: 1358 33.66 - 50.48: 399 50.48 - 67.31: 114 67.31 - 84.14: 38 Dihedral angle restraints: 13851 sinusoidal: 5738 harmonic: 8113 Sorted by residual: dihedral pdb=" CA METAs 135 " pdb=" C METAs 135 " pdb=" N ASPAs 136 " pdb=" CA ASPAs 136 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA METAi 135 " pdb=" C METAi 135 " pdb=" N ASPAi 136 " pdb=" CA ASPAi 136 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA METAe 135 " pdb=" C METAe 135 " pdb=" N ASPAe 136 " pdb=" CA ASPAe 136 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 13848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1783 0.025 - 0.051: 932 0.051 - 0.076: 484 0.076 - 0.101: 123 0.101 - 0.126: 41 Chirality restraints: 3363 Sorted by residual: chirality pdb=" CA PROAe 109 " pdb=" N PROAe 109 " pdb=" C PROAe 109 " pdb=" CB PROAe 109 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA PROAr 109 " pdb=" N PROAr 109 " pdb=" C PROAr 109 " pdb=" CB PROAr 109 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA PROAd 109 " pdb=" N PROAd 109 " pdb=" C PROAd 109 " pdb=" CB PROAd 109 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 3360 not shown) Planarity restraints: 3952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C METAi 108 " -0.045 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PROAi 109 " 0.114 5.00e-02 4.00e+02 pdb=" CA PROAi 109 " -0.032 5.00e-02 4.00e+02 pdb=" CD PROAi 109 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C METAg 108 " -0.045 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PROAg 109 " 0.114 5.00e-02 4.00e+02 pdb=" CA PROAg 109 " -0.032 5.00e-02 4.00e+02 pdb=" CD PROAg 109 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C METAo 108 " -0.045 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PROAo 109 " 0.114 5.00e-02 4.00e+02 pdb=" CA PROAo 109 " -0.032 5.00e-02 4.00e+02 pdb=" CD PROAo 109 " -0.037 5.00e-02 4.00e+02 ... (remaining 3949 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 7415 2.84 - 3.36: 20233 3.36 - 3.87: 34832 3.87 - 4.39: 40205 4.39 - 4.90: 68634 Nonbonded interactions: 171319 Sorted by model distance: nonbonded pdb=" O PROAi 45 " pdb=" OH TYRAs 143 " model vdw 2.329 2.440 nonbonded pdb=" OH TYRAc 143 " pdb=" O PROAg 45 " model vdw 2.347 2.440 nonbonded pdb=" O PROAa 45 " pdb=" OH TYRAf 143 " model vdw 2.355 2.440 nonbonded pdb=" O PROAj 45 " pdb=" OH TYRAo 143 " model vdw 2.355 2.440 nonbonded pdb=" OH TYRAe 143 " pdb=" O PROAl 45 " model vdw 2.355 2.440 ... (remaining 171314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.020 Extract box with map and model: 6.620 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 53.140 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.190 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22572 Z= 0.250 Angle : 0.645 8.372 30647 Z= 0.340 Chirality : 0.039 0.126 3363 Planarity : 0.007 0.066 3952 Dihedral : 16.696 84.139 8607 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.78 % Allowed : 19.53 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.73 (0.14), residues: 2717 helix: -1.77 (0.15), residues: 969 sheet: 0.07 (0.30), residues: 228 loop : -2.18 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAi 93 HIS 0.002 0.001 HISAg 42 PHE 0.003 0.001 PHEAj 90 TYR 0.007 0.001 TYRAr 73 ARG 0.006 0.001 ARGAr 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 733 time to evaluate : 2.326 Fit side-chains REVERT: Aa 56 MET cc_start: 0.8579 (mmm) cc_final: 0.8370 (tpp) REVERT: Aa 77 GLN cc_start: 0.8383 (mt0) cc_final: 0.8100 (mp10) REVERT: Aa 107 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7894 (pt0) REVERT: Aa 108 MET cc_start: 0.8638 (tpt) cc_final: 0.8234 (tpt) REVERT: Ab 56 MET cc_start: 0.8533 (mmm) cc_final: 0.8149 (mmm) REVERT: Ac 150 GLU cc_start: 0.8341 (tt0) cc_final: 0.7898 (pt0) REVERT: Ad 46 ARG cc_start: 0.8983 (mtt90) cc_final: 0.8647 (mtt-85) REVERT: Ad 48 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8561 (mttp) REVERT: Ad 56 MET cc_start: 0.8588 (mmm) cc_final: 0.8161 (mmm) REVERT: Ad 77 GLN cc_start: 0.8404 (mt0) cc_final: 0.7987 (mp10) REVERT: Ae 76 GLN cc_start: 0.8076 (mp10) cc_final: 0.7718 (mp10) REVERT: Ae 107 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7978 (pt0) REVERT: Ae 160 MET cc_start: 0.9151 (mmt) cc_final: 0.8870 (mmm) REVERT: Af 55 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.6888 (mtm180) REVERT: Af 56 MET cc_start: 0.8603 (mmm) cc_final: 0.8283 (mmm) REVERT: Af 76 GLN cc_start: 0.8237 (mp10) cc_final: 0.8015 (mp10) REVERT: Af 150 GLU cc_start: 0.8282 (tt0) cc_final: 0.7942 (tt0) REVERT: Ag 76 GLN cc_start: 0.8129 (mp10) cc_final: 0.7802 (mp10) REVERT: Ag 150 GLU cc_start: 0.8230 (tt0) cc_final: 0.7911 (tt0) REVERT: Ag 160 MET cc_start: 0.9179 (mmt) cc_final: 0.8977 (mmm) REVERT: Ah 56 MET cc_start: 0.8515 (mmm) cc_final: 0.8271 (tpp) REVERT: Ah 150 GLU cc_start: 0.8348 (tt0) cc_final: 0.7978 (tt0) REVERT: Ai 56 MET cc_start: 0.8491 (mmm) cc_final: 0.8173 (mmm) REVERT: Ai 150 GLU cc_start: 0.8329 (tt0) cc_final: 0.7891 (pt0) REVERT: Aj 56 MET cc_start: 0.8570 (mmm) cc_final: 0.8360 (tpp) REVERT: Aj 58 LYS cc_start: 0.8576 (mttp) cc_final: 0.8276 (mtpt) REVERT: Aj 63 THR cc_start: 0.8439 (m) cc_final: 0.8225 (t) REVERT: Aj 108 MET cc_start: 0.8586 (tpt) cc_final: 0.8298 (tpt) REVERT: Aj 150 GLU cc_start: 0.8308 (tt0) cc_final: 0.7937 (tt0) REVERT: Ak 91 ASP cc_start: 0.8500 (m-30) cc_final: 0.8282 (m-30) REVERT: Ak 168 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8020 (mm-30) REVERT: Al 135 MET cc_start: 0.8515 (mmm) cc_final: 0.8193 (mmm) REVERT: Am 56 MET cc_start: 0.8705 (mmm) cc_final: 0.8263 (mmm) REVERT: Am 91 ASP cc_start: 0.8483 (m-30) cc_final: 0.8086 (m-30) REVERT: Am 107 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7949 (pt0) REVERT: An 56 MET cc_start: 0.8760 (mmm) cc_final: 0.8469 (tpp) REVERT: An 77 GLN cc_start: 0.8343 (mt0) cc_final: 0.8091 (mp10) REVERT: An 107 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7880 (pt0) REVERT: Ao 56 MET cc_start: 0.8575 (mmm) cc_final: 0.8217 (mmm) REVERT: Ao 77 GLN cc_start: 0.8444 (mt0) cc_final: 0.8134 (mp10) REVERT: Ao 91 ASP cc_start: 0.8500 (m-30) cc_final: 0.8297 (m-30) REVERT: Ap 58 LYS cc_start: 0.8608 (mttp) cc_final: 0.8396 (mttm) REVERT: Ap 66 ASN cc_start: 0.8585 (t0) cc_final: 0.7967 (t0) REVERT: Ap 135 MET cc_start: 0.8411 (mmm) cc_final: 0.8076 (mmm) REVERT: Ap 150 GLU cc_start: 0.8225 (tt0) cc_final: 0.7720 (pt0) REVERT: Aq 56 MET cc_start: 0.8589 (mmm) cc_final: 0.8330 (tpp) REVERT: Aq 150 GLU cc_start: 0.8318 (tt0) cc_final: 0.7892 (tt0) REVERT: Ar 56 MET cc_start: 0.8559 (mmm) cc_final: 0.8306 (mmm) REVERT: Ar 107 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7905 (pt0) REVERT: Ar 150 GLU cc_start: 0.8444 (tt0) cc_final: 0.8227 (tt0) REVERT: As 56 MET cc_start: 0.8565 (mmm) cc_final: 0.8271 (mmm) REVERT: As 77 GLN cc_start: 0.8369 (mt0) cc_final: 0.8110 (mp10) REVERT: As 91 ASP cc_start: 0.8516 (m-30) cc_final: 0.8278 (m-30) outliers start: 19 outliers final: 3 residues processed: 733 average time/residue: 0.4049 time to fit residues: 428.3715 Evaluate side-chains 615 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 611 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 48 LYS Chi-restraints excluded: chain Ad residue 48 LYS Chi-restraints excluded: chain Ae residue 48 LYS Chi-restraints excluded: chain Al residue 48 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 135 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 208 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 241 optimal weight: 0.0070 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 140 GLN Ad 69 HIS ** Ad 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 69 HIS ** Ae 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 140 GLN Ag 69 HIS Ag 77 GLN ** Ag 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 69 HIS Ah 113 ASN Ai 69 HIS ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS ** Aj 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 69 HIS ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 113 ASN Al 140 GLN Am 69 HIS ** Am 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 69 HIS ** An 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 69 HIS ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 69 HIS Ap 77 GLN ** Ap 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 140 GLN Aq 69 HIS Aq 77 GLN ** Aq 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 66 ASN ** As 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22572 Z= 0.163 Angle : 0.511 5.447 30647 Z= 0.259 Chirality : 0.039 0.122 3363 Planarity : 0.004 0.035 3952 Dihedral : 4.855 36.217 2999 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.69 % Allowed : 17.85 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.71 (0.15), residues: 2717 helix: -0.15 (0.15), residues: 1064 sheet: 0.11 (0.30), residues: 228 loop : -2.20 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAf 93 HIS 0.007 0.001 HISAk 69 PHE 0.002 0.001 PHEAh 163 TYR 0.012 0.001 TYRAh 94 ARG 0.006 0.001 ARGAj 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 661 time to evaluate : 2.568 Fit side-chains REVERT: Aa 56 MET cc_start: 0.8576 (mmm) cc_final: 0.8244 (tpp) REVERT: Aa 77 GLN cc_start: 0.8378 (mt0) cc_final: 0.8098 (mp10) REVERT: Aa 107 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8043 (pt0) REVERT: Aa 173 MET cc_start: 0.6998 (tmm) cc_final: 0.6656 (tmm) REVERT: Ab 56 MET cc_start: 0.8429 (mmm) cc_final: 0.8126 (mmm) REVERT: Ab 95 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: Ab 150 GLU cc_start: 0.8226 (tt0) cc_final: 0.7871 (pt0) REVERT: Ab 181 MET cc_start: 0.6735 (tmm) cc_final: 0.6332 (tmm) REVERT: Ac 56 MET cc_start: 0.8673 (mmm) cc_final: 0.8350 (tpp) REVERT: Ac 95 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8163 (mm-30) REVERT: Ac 150 GLU cc_start: 0.8395 (tt0) cc_final: 0.7968 (pt0) REVERT: Ac 173 MET cc_start: 0.6837 (tmm) cc_final: 0.6635 (tmm) REVERT: Ad 56 MET cc_start: 0.8592 (mmm) cc_final: 0.8267 (tpp) REVERT: Ad 77 GLN cc_start: 0.8407 (mt0) cc_final: 0.8020 (mp10) REVERT: Ad 95 GLU cc_start: 0.8584 (tp30) cc_final: 0.8230 (mm-30) REVERT: Ad 136 ASP cc_start: 0.8599 (t0) cc_final: 0.8301 (t0) REVERT: Ad 150 GLU cc_start: 0.8293 (tt0) cc_final: 0.8018 (pt0) REVERT: Ae 60 LYS cc_start: 0.8709 (mttm) cc_final: 0.8452 (mtpt) REVERT: Ae 76 GLN cc_start: 0.8163 (mp10) cc_final: 0.7794 (mp10) REVERT: Ae 107 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8238 (pt0) REVERT: Ae 160 MET cc_start: 0.9088 (mmt) cc_final: 0.8869 (mmm) REVERT: Af 48 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8570 (mtmm) REVERT: Af 55 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.7065 (mtm180) REVERT: Af 56 MET cc_start: 0.8654 (mmm) cc_final: 0.8393 (tpp) REVERT: Af 95 GLU cc_start: 0.8553 (tp30) cc_final: 0.8312 (mm-30) REVERT: Af 150 GLU cc_start: 0.8335 (tt0) cc_final: 0.7987 (pt0) REVERT: Ag 76 GLN cc_start: 0.8074 (mp10) cc_final: 0.7834 (mp10) REVERT: Ah 56 MET cc_start: 0.8471 (mmm) cc_final: 0.8165 (tpp) REVERT: Ah 91 ASP cc_start: 0.8553 (m-30) cc_final: 0.8334 (m-30) REVERT: Ah 150 GLU cc_start: 0.8310 (tt0) cc_final: 0.7923 (pt0) REVERT: Ah 181 MET cc_start: 0.6878 (tmm) cc_final: 0.6547 (tmm) REVERT: Ai 56 MET cc_start: 0.8465 (mmm) cc_final: 0.8242 (mmm) REVERT: Ai 136 ASP cc_start: 0.8530 (t0) cc_final: 0.8315 (t0) REVERT: Aj 58 LYS cc_start: 0.8660 (mttp) cc_final: 0.8349 (mtpt) REVERT: Aj 95 GLU cc_start: 0.8576 (tp30) cc_final: 0.8076 (mm-30) REVERT: Aj 150 GLU cc_start: 0.8331 (tt0) cc_final: 0.7977 (pt0) REVERT: Ak 56 MET cc_start: 0.8512 (mmm) cc_final: 0.8232 (tpp) REVERT: Ak 58 LYS cc_start: 0.8709 (mttp) cc_final: 0.8447 (mttm) REVERT: Ak 95 GLU cc_start: 0.8589 (tp30) cc_final: 0.8323 (mm-30) REVERT: Ak 150 GLU cc_start: 0.8238 (tt0) cc_final: 0.7900 (pt0) REVERT: Al 135 MET cc_start: 0.8757 (mmm) cc_final: 0.8493 (mmm) REVERT: Al 150 GLU cc_start: 0.8170 (tt0) cc_final: 0.7863 (pt0) REVERT: Al 181 MET cc_start: 0.7426 (tpp) cc_final: 0.6862 (tmm) REVERT: Am 56 MET cc_start: 0.8695 (mmm) cc_final: 0.8403 (mmm) REVERT: Am 91 ASP cc_start: 0.8529 (m-30) cc_final: 0.8084 (m-30) REVERT: Am 95 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: Am 173 MET cc_start: 0.6994 (tmm) cc_final: 0.6790 (tmm) REVERT: An 56 MET cc_start: 0.8713 (mmm) cc_final: 0.8370 (tpp) REVERT: An 77 GLN cc_start: 0.8340 (mt0) cc_final: 0.8040 (mp10) REVERT: An 95 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8265 (mm-30) REVERT: An 107 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8055 (pt0) REVERT: An 150 GLU cc_start: 0.8475 (tt0) cc_final: 0.8128 (pt0) REVERT: An 181 MET cc_start: 0.7396 (tpp) cc_final: 0.6802 (tmm) REVERT: Ao 56 MET cc_start: 0.8588 (mmm) cc_final: 0.8336 (mmm) REVERT: Ao 77 GLN cc_start: 0.8432 (mt0) cc_final: 0.8126 (mp10) REVERT: Ap 66 ASN cc_start: 0.8712 (t0) cc_final: 0.8360 (t0) REVERT: Ap 135 MET cc_start: 0.8788 (mmm) cc_final: 0.8577 (mmm) REVERT: Aq 56 MET cc_start: 0.8504 (mmm) cc_final: 0.8238 (tpp) REVERT: Aq 107 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: Aq 136 ASP cc_start: 0.8498 (t0) cc_final: 0.8178 (t0) REVERT: Aq 173 MET cc_start: 0.6801 (tmm) cc_final: 0.6570 (tmm) REVERT: Ar 66 ASN cc_start: 0.8679 (t0) cc_final: 0.8412 (t0) REVERT: Ar 95 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: As 56 MET cc_start: 0.8543 (mmm) cc_final: 0.8237 (tpp) REVERT: As 77 GLN cc_start: 0.8419 (mt0) cc_final: 0.8098 (mp10) REVERT: As 150 GLU cc_start: 0.8392 (tt0) cc_final: 0.7970 (pt0) REVERT: As 181 MET cc_start: 0.6627 (tmm) cc_final: 0.6240 (tmm) outliers start: 41 outliers final: 21 residues processed: 679 average time/residue: 0.3973 time to fit residues: 391.8580 Evaluate side-chains 588 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 560 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 48 LYS Chi-restraints excluded: chain Ab residue 95 GLU Chi-restraints excluded: chain Ab residue 107 GLU Chi-restraints excluded: chain Ac residue 48 LYS Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 106 THR Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 110 THR Chi-restraints excluded: chain Af residue 48 LYS Chi-restraints excluded: chain Af residue 110 THR Chi-restraints excluded: chain Ag residue 77 GLN Chi-restraints excluded: chain Ag residue 110 THR Chi-restraints excluded: chain Ai residue 110 THR Chi-restraints excluded: chain Aj residue 48 LYS Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Aj residue 110 THR Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 107 GLU Chi-restraints excluded: chain Am residue 95 GLU Chi-restraints excluded: chain Am residue 110 THR Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain Ao residue 103 ILE Chi-restraints excluded: chain Ap residue 77 GLN Chi-restraints excluded: chain Aq residue 77 GLN Chi-restraints excluded: chain Aq residue 107 GLU Chi-restraints excluded: chain Ar residue 48 LYS Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain As residue 48 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 241 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 239 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Aa 113 ASN Ab 69 HIS Ab 113 ASN ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 113 ASN Ad 69 HIS Ad 113 ASN Ad 140 GLN Ae 69 HIS Ae 113 ASN Af 69 HIS Af 113 ASN ** Af 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 69 HIS Ag 113 ASN ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 69 HIS Ah 151 ASN Ai 69 HIS Ai 113 ASN ** Ai 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 69 HIS Aj 113 ASN Ak 69 HIS Ak 113 ASN Am 69 HIS Am 113 ASN Am 140 GLN An 69 HIS An 113 ASN ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 69 HIS ** Ap 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 66 ASN Aq 69 HIS Aq 113 ASN ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 69 HIS Ar 113 ASN ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 66 ASN As 113 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22572 Z= 0.295 Angle : 0.540 5.483 30647 Z= 0.270 Chirality : 0.042 0.125 3363 Planarity : 0.004 0.026 3952 Dihedral : 4.489 16.110 2983 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.59 % Allowed : 18.09 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.33 (0.16), residues: 2717 helix: 0.37 (0.16), residues: 1083 sheet: 0.39 (0.30), residues: 228 loop : -2.22 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAn 93 HIS 0.006 0.001 HISAd 69 PHE 0.004 0.001 PHEAo 163 TYR 0.012 0.002 TYRAb 180 ARG 0.006 0.001 ARGAg 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 566 time to evaluate : 2.401 Fit side-chains REVERT: Aa 60 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8536 (mttm) REVERT: Aa 77 GLN cc_start: 0.8374 (mt0) cc_final: 0.8039 (mp10) REVERT: Aa 173 MET cc_start: 0.7257 (tmm) cc_final: 0.6907 (tmm) REVERT: Aa 181 MET cc_start: 0.7328 (tpp) cc_final: 0.6575 (tmm) REVERT: Ab 56 MET cc_start: 0.8468 (mmm) cc_final: 0.8095 (mmm) REVERT: Ab 66 ASN cc_start: 0.8822 (t0) cc_final: 0.8492 (t0) REVERT: Ab 173 MET cc_start: 0.7085 (tmm) cc_final: 0.6740 (tmm) REVERT: Ab 181 MET cc_start: 0.6764 (tmm) cc_final: 0.6359 (tmm) REVERT: Ac 66 ASN cc_start: 0.8965 (t0) cc_final: 0.8735 (t0) REVERT: Ac 95 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8207 (mm-30) REVERT: Ac 134 MET cc_start: 0.8818 (ttp) cc_final: 0.8531 (ttp) REVERT: Ac 173 MET cc_start: 0.6919 (tmm) cc_final: 0.6602 (tmm) REVERT: Ac 181 MET cc_start: 0.7398 (tpp) cc_final: 0.6772 (tmm) REVERT: Ad 136 ASP cc_start: 0.8632 (t0) cc_final: 0.8284 (t0) REVERT: Ad 181 MET cc_start: 0.7315 (tpp) cc_final: 0.6580 (tmm) REVERT: Ae 76 GLN cc_start: 0.8034 (mp10) cc_final: 0.7681 (mp10) REVERT: Ae 181 MET cc_start: 0.7326 (tpp) cc_final: 0.6714 (tmm) REVERT: Af 55 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.6972 (mtm180) REVERT: Af 56 MET cc_start: 0.8732 (mmm) cc_final: 0.8400 (mmm) REVERT: Af 67 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8719 (tt) REVERT: Af 181 MET cc_start: 0.7292 (tpp) cc_final: 0.6649 (tmm) REVERT: Ag 76 GLN cc_start: 0.8074 (mp10) cc_final: 0.7788 (mp10) REVERT: Ag 181 MET cc_start: 0.7403 (tpp) cc_final: 0.6736 (tmm) REVERT: Ah 56 MET cc_start: 0.8626 (mmm) cc_final: 0.8225 (tpp) REVERT: Ah 91 ASP cc_start: 0.8593 (m-30) cc_final: 0.8381 (m-30) REVERT: Ah 112 MET cc_start: 0.9039 (mmp) cc_final: 0.8673 (mmt) REVERT: Ah 181 MET cc_start: 0.6785 (tmm) cc_final: 0.6408 (tmm) REVERT: Ai 56 MET cc_start: 0.8482 (mmm) cc_final: 0.8041 (mmm) REVERT: Ai 181 MET cc_start: 0.7271 (tpp) cc_final: 0.6639 (tmm) REVERT: Aj 58 LYS cc_start: 0.8747 (mttp) cc_final: 0.8405 (mtpt) REVERT: Aj 181 MET cc_start: 0.7318 (tpp) cc_final: 0.6751 (tmm) REVERT: Ak 150 GLU cc_start: 0.8292 (tt0) cc_final: 0.7886 (pt0) REVERT: Ak 181 MET cc_start: 0.7233 (tpp) cc_final: 0.6646 (tmm) REVERT: Al 136 ASP cc_start: 0.8463 (t0) cc_final: 0.8078 (t0) REVERT: Al 173 MET cc_start: 0.7175 (tmm) cc_final: 0.6662 (tmm) REVERT: Al 181 MET cc_start: 0.7362 (tpp) cc_final: 0.6790 (tmm) REVERT: Am 91 ASP cc_start: 0.8616 (m-30) cc_final: 0.8398 (m-30) REVERT: Am 181 MET cc_start: 0.6659 (tmm) cc_final: 0.6331 (tmm) REVERT: An 56 MET cc_start: 0.8699 (mmm) cc_final: 0.8268 (tpp) REVERT: An 77 GLN cc_start: 0.8372 (mt0) cc_final: 0.8058 (mp10) REVERT: An 95 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8263 (mm-30) REVERT: An 181 MET cc_start: 0.7317 (tpp) cc_final: 0.6700 (tmm) REVERT: Ao 77 GLN cc_start: 0.8432 (mt0) cc_final: 0.8084 (mp10) REVERT: Ao 136 ASP cc_start: 0.8489 (t0) cc_final: 0.8274 (t0) REVERT: Ao 181 MET cc_start: 0.7076 (tpp) cc_final: 0.6501 (tmm) REVERT: Ap 66 ASN cc_start: 0.8810 (t0) cc_final: 0.8341 (t0) REVERT: Ap 136 ASP cc_start: 0.8599 (t0) cc_final: 0.8369 (t0) REVERT: Ap 181 MET cc_start: 0.7310 (tpp) cc_final: 0.6566 (tmm) REVERT: Aq 56 MET cc_start: 0.8580 (mmm) cc_final: 0.8135 (tpp) REVERT: Aq 136 ASP cc_start: 0.8616 (t0) cc_final: 0.8207 (t0) REVERT: Aq 160 MET cc_start: 0.9233 (mmp) cc_final: 0.8980 (mmm) REVERT: Aq 181 MET cc_start: 0.7400 (tpp) cc_final: 0.6665 (tmm) REVERT: Ar 56 MET cc_start: 0.8602 (mmm) cc_final: 0.8277 (mmm) REVERT: Ar 66 ASN cc_start: 0.8678 (t0) cc_final: 0.8416 (t0) REVERT: Ar 95 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: Ar 181 MET cc_start: 0.7162 (tpp) cc_final: 0.6654 (tmm) REVERT: As 56 MET cc_start: 0.8568 (mmm) cc_final: 0.8116 (tpp) REVERT: As 77 GLN cc_start: 0.8470 (mt0) cc_final: 0.8134 (mp10) REVERT: As 181 MET cc_start: 0.6722 (tmm) cc_final: 0.6305 (tmm) outliers start: 63 outliers final: 33 residues processed: 605 average time/residue: 0.3900 time to fit residues: 346.9948 Evaluate side-chains 590 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 553 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 110 THR Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 110 THR Chi-restraints excluded: chain Af residue 67 LEU Chi-restraints excluded: chain Af residue 77 GLN Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 110 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 110 THR Chi-restraints excluded: chain Ah residue 110 THR Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 110 THR Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Aj residue 110 THR Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 107 GLU Chi-restraints excluded: chain Am residue 110 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 110 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 103 ILE Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Ap residue 107 GLU Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain As residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 125 optimal weight: 0.0050 chunk 26 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 162 optimal weight: 0.4980 chunk 242 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 overall best weight: 3.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 69 HIS Af 69 HIS ** Ag 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 69 HIS ** Ai 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 69 HIS Am 69 HIS An 151 ASN ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 69 HIS ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22572 Z= 0.355 Angle : 0.581 7.133 30647 Z= 0.284 Chirality : 0.043 0.128 3363 Planarity : 0.003 0.029 3952 Dihedral : 4.601 19.547 2983 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.43 % Allowed : 16.98 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.47 (0.16), residues: 2717 helix: -0.09 (0.15), residues: 1197 sheet: 0.62 (0.31), residues: 228 loop : -2.19 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAh 132 HIS 0.005 0.001 HISAf 69 PHE 0.007 0.001 PHEAo 163 TYR 0.011 0.002 TYRAh 94 ARG 0.006 0.001 ARGAh 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 535 time to evaluate : 2.472 Fit side-chains REVERT: Aa 181 MET cc_start: 0.7325 (tpp) cc_final: 0.6569 (tmm) REVERT: Ab 56 MET cc_start: 0.8521 (mmm) cc_final: 0.8148 (mmm) REVERT: Ab 66 ASN cc_start: 0.8735 (t0) cc_final: 0.8290 (t0) REVERT: Ab 112 MET cc_start: 0.9038 (mmt) cc_final: 0.8792 (mmt) REVERT: Ab 173 MET cc_start: 0.7157 (tmm) cc_final: 0.6793 (tmm) REVERT: Ab 181 MET cc_start: 0.6727 (tmm) cc_final: 0.6265 (tmm) REVERT: Ac 66 ASN cc_start: 0.8990 (t0) cc_final: 0.8689 (t0) REVERT: Ac 134 MET cc_start: 0.8911 (ttp) cc_final: 0.8697 (ttp) REVERT: Ac 173 MET cc_start: 0.7151 (tmm) cc_final: 0.6594 (tmm) REVERT: Ac 181 MET cc_start: 0.7363 (tpp) cc_final: 0.6685 (tmm) REVERT: Ad 136 ASP cc_start: 0.8715 (t0) cc_final: 0.8461 (t0) REVERT: Ad 181 MET cc_start: 0.7351 (tpp) cc_final: 0.6623 (tmm) REVERT: Ae 76 GLN cc_start: 0.8025 (mp10) cc_final: 0.7642 (mp10) REVERT: Ae 181 MET cc_start: 0.7235 (tpp) cc_final: 0.6588 (tmm) REVERT: Af 55 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.6940 (mtm180) REVERT: Af 56 MET cc_start: 0.8759 (mmm) cc_final: 0.8394 (mmm) REVERT: Af 67 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8730 (tt) REVERT: Af 173 MET cc_start: 0.7219 (tmm) cc_final: 0.6892 (tmm) REVERT: Af 181 MET cc_start: 0.7252 (tpp) cc_final: 0.6603 (tmm) REVERT: Ag 76 GLN cc_start: 0.8012 (mp10) cc_final: 0.7784 (mp10) REVERT: Ag 181 MET cc_start: 0.7341 (tpp) cc_final: 0.6596 (tmm) REVERT: Ah 76 GLN cc_start: 0.8028 (mp10) cc_final: 0.7687 (mp10) REVERT: Ah 91 ASP cc_start: 0.8561 (m-30) cc_final: 0.8167 (m-30) REVERT: Ah 95 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8206 (mp0) REVERT: Ah 136 ASP cc_start: 0.8664 (t0) cc_final: 0.8448 (t0) REVERT: Ah 181 MET cc_start: 0.6776 (tmm) cc_final: 0.6338 (tmm) REVERT: Ai 56 MET cc_start: 0.8547 (mmm) cc_final: 0.8338 (mmm) REVERT: Ai 135 MET cc_start: 0.9168 (mmm) cc_final: 0.8775 (mmm) REVERT: Ai 181 MET cc_start: 0.7317 (tpp) cc_final: 0.6704 (tmm) REVERT: Aj 58 LYS cc_start: 0.8782 (mttp) cc_final: 0.8437 (mtpt) REVERT: Aj 66 ASN cc_start: 0.8827 (t0) cc_final: 0.8444 (t0) REVERT: Aj 181 MET cc_start: 0.7362 (tpp) cc_final: 0.6666 (tmm) REVERT: Ak 181 MET cc_start: 0.7313 (tpp) cc_final: 0.6660 (tmm) REVERT: Al 136 ASP cc_start: 0.8576 (t0) cc_final: 0.8337 (t0) REVERT: Al 173 MET cc_start: 0.7251 (tmm) cc_final: 0.6846 (tmm) REVERT: Al 181 MET cc_start: 0.7340 (tpp) cc_final: 0.6796 (tmm) REVERT: Am 181 MET cc_start: 0.6619 (tmm) cc_final: 0.6274 (tmm) REVERT: An 56 MET cc_start: 0.8695 (mmm) cc_final: 0.8231 (mmm) REVERT: An 77 GLN cc_start: 0.8437 (mt0) cc_final: 0.8103 (mp10) REVERT: An 181 MET cc_start: 0.7282 (tpp) cc_final: 0.6691 (tmm) REVERT: Ao 77 GLN cc_start: 0.8416 (mt0) cc_final: 0.8049 (mp10) REVERT: Ao 136 ASP cc_start: 0.8640 (t0) cc_final: 0.8431 (t0) REVERT: Ao 181 MET cc_start: 0.7146 (tpp) cc_final: 0.6578 (tmm) REVERT: Ap 66 ASN cc_start: 0.8726 (t0) cc_final: 0.8361 (t0) REVERT: Ap 181 MET cc_start: 0.7309 (tpp) cc_final: 0.6526 (tmm) REVERT: Aq 56 MET cc_start: 0.8575 (mmm) cc_final: 0.8134 (tpp) REVERT: Aq 181 MET cc_start: 0.7390 (tpp) cc_final: 0.6711 (tmm) REVERT: Ar 95 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: Ar 136 ASP cc_start: 0.8617 (t0) cc_final: 0.8329 (t0) REVERT: Ar 181 MET cc_start: 0.7178 (tpp) cc_final: 0.6639 (tmm) REVERT: As 77 GLN cc_start: 0.8484 (mt0) cc_final: 0.8100 (mp10) REVERT: As 181 MET cc_start: 0.6586 (tmm) cc_final: 0.6184 (tmm) outliers start: 59 outliers final: 48 residues processed: 554 average time/residue: 0.3830 time to fit residues: 312.0864 Evaluate side-chains 582 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 531 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 133 VAL Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ac residue 103 ILE Chi-restraints excluded: chain Ac residue 110 THR Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 103 ILE Chi-restraints excluded: chain Ae residue 110 THR Chi-restraints excluded: chain Af residue 67 LEU Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ah residue 106 THR Chi-restraints excluded: chain Ah residue 110 THR Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 103 ILE Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Aj residue 110 THR Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 99 LEU Chi-restraints excluded: chain Am residue 110 THR Chi-restraints excluded: chain Am residue 133 VAL Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 110 THR Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 103 ILE Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ap residue 103 ILE Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Ap residue 107 GLU Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain Ar residue 133 VAL Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 106 THR Chi-restraints excluded: chain As residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 191 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 219 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 230 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ab 69 HIS Ab 151 ASN Af 151 ASN Ag 151 ASN Ah 69 HIS Ai 69 HIS Aj 66 ASN Aj 69 HIS ** Aj 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 69 HIS Am 66 ASN ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 69 HIS Ap 113 ASN Aq 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 69 HIS Ar 151 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22572 Z= 0.150 Angle : 0.481 6.198 30647 Z= 0.234 Chirality : 0.039 0.117 3363 Planarity : 0.003 0.025 3952 Dihedral : 4.283 18.747 2983 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.36 % Allowed : 18.79 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.75 (0.17), residues: 2717 helix: 1.04 (0.16), residues: 1083 sheet: 0.92 (0.33), residues: 228 loop : -2.11 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAf 132 HIS 0.005 0.001 HISAr 69 PHE 0.002 0.000 PHEAg 163 TYR 0.011 0.001 TYRAc 180 ARG 0.007 0.001 ARGAd 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 550 time to evaluate : 2.584 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8316 (mt0) cc_final: 0.7969 (mp10) REVERT: Aa 107 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: Aa 173 MET cc_start: 0.7292 (tmm) cc_final: 0.6888 (tmm) REVERT: Aa 181 MET cc_start: 0.7311 (tpp) cc_final: 0.6573 (tmm) REVERT: Ab 56 MET cc_start: 0.8428 (mmm) cc_final: 0.8014 (mmm) REVERT: Ab 66 ASN cc_start: 0.8712 (t0) cc_final: 0.8280 (t0) REVERT: Ab 112 MET cc_start: 0.8906 (mmt) cc_final: 0.8693 (mmt) REVERT: Ab 173 MET cc_start: 0.7085 (tmm) cc_final: 0.6714 (tmm) REVERT: Ab 181 MET cc_start: 0.6743 (tmm) cc_final: 0.6292 (tmm) REVERT: Ac 56 MET cc_start: 0.8680 (mmm) cc_final: 0.8436 (mmm) REVERT: Ac 66 ASN cc_start: 0.9004 (t0) cc_final: 0.8728 (t0) REVERT: Ac 95 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: Ac 173 MET cc_start: 0.6960 (tmm) cc_final: 0.6548 (tmm) REVERT: Ac 181 MET cc_start: 0.7306 (tpp) cc_final: 0.6763 (tmm) REVERT: Ad 181 MET cc_start: 0.7343 (tpp) cc_final: 0.6643 (tmm) REVERT: Ae 76 GLN cc_start: 0.7929 (mp10) cc_final: 0.7650 (mp10) REVERT: Ae 181 MET cc_start: 0.7243 (tpp) cc_final: 0.6623 (tmm) REVERT: Af 55 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.7029 (mtm180) REVERT: Af 56 MET cc_start: 0.8712 (mmm) cc_final: 0.8323 (mmm) REVERT: Af 67 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8731 (tt) REVERT: Af 181 MET cc_start: 0.7236 (tpp) cc_final: 0.6607 (tmm) REVERT: Ag 181 MET cc_start: 0.7262 (tpp) cc_final: 0.6579 (tmm) REVERT: Ah 56 MET cc_start: 0.8639 (mmm) cc_final: 0.8267 (tpp) REVERT: Ah 91 ASP cc_start: 0.8504 (m-30) cc_final: 0.8238 (m-30) REVERT: Ah 112 MET cc_start: 0.9004 (mmp) cc_final: 0.8756 (mmp) REVERT: Ah 136 ASP cc_start: 0.8533 (t0) cc_final: 0.8306 (t0) REVERT: Ah 181 MET cc_start: 0.6750 (tmm) cc_final: 0.6296 (tmm) REVERT: Ai 56 MET cc_start: 0.8464 (mmm) cc_final: 0.8015 (mmm) REVERT: Ai 142 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8237 (mt-10) REVERT: Ai 150 GLU cc_start: 0.8245 (tt0) cc_final: 0.7902 (tt0) REVERT: Ai 181 MET cc_start: 0.7297 (tpp) cc_final: 0.6704 (tmm) REVERT: Aj 58 LYS cc_start: 0.8749 (mttp) cc_final: 0.8487 (mtpt) REVERT: Aj 173 MET cc_start: 0.7077 (tmm) cc_final: 0.6519 (tmm) REVERT: Aj 181 MET cc_start: 0.7379 (tpp) cc_final: 0.6776 (tmm) REVERT: Ak 66 ASN cc_start: 0.8743 (t0) cc_final: 0.8473 (t0) REVERT: Ak 181 MET cc_start: 0.7330 (tpp) cc_final: 0.6651 (tmm) REVERT: Al 173 MET cc_start: 0.7129 (tmm) cc_final: 0.6672 (tmm) REVERT: Al 181 MET cc_start: 0.7320 (tpp) cc_final: 0.6801 (tmm) REVERT: Am 56 MET cc_start: 0.8557 (mmm) cc_final: 0.8109 (mmm) REVERT: Am 91 ASP cc_start: 0.8473 (m-30) cc_final: 0.8160 (m-30) REVERT: Am 181 MET cc_start: 0.6597 (tmm) cc_final: 0.6264 (tmm) REVERT: An 56 MET cc_start: 0.8643 (mmm) cc_final: 0.8182 (tpp) REVERT: An 77 GLN cc_start: 0.8384 (mt0) cc_final: 0.8032 (mp10) REVERT: An 107 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: An 181 MET cc_start: 0.7274 (tpp) cc_final: 0.6646 (tmm) REVERT: Ao 58 LYS cc_start: 0.8818 (mttm) cc_final: 0.8570 (mttm) REVERT: Ao 77 GLN cc_start: 0.8336 (mt0) cc_final: 0.7968 (mp10) REVERT: Ao 181 MET cc_start: 0.7173 (tpp) cc_final: 0.6597 (tmm) REVERT: Ap 136 ASP cc_start: 0.8621 (t0) cc_final: 0.8395 (t0) REVERT: Ap 181 MET cc_start: 0.7286 (tpp) cc_final: 0.6566 (tmm) REVERT: Aq 56 MET cc_start: 0.8505 (mmm) cc_final: 0.8112 (tpp) REVERT: Aq 136 ASP cc_start: 0.8665 (t0) cc_final: 0.8358 (t0) REVERT: Aq 160 MET cc_start: 0.9232 (mmp) cc_final: 0.8980 (mmm) REVERT: Aq 181 MET cc_start: 0.7345 (tpp) cc_final: 0.6664 (tmm) REVERT: Ar 56 MET cc_start: 0.8627 (mmm) cc_final: 0.8341 (tpp) REVERT: Ar 136 ASP cc_start: 0.8607 (t0) cc_final: 0.8353 (t0) REVERT: Ar 181 MET cc_start: 0.7184 (tpp) cc_final: 0.6685 (tmm) REVERT: As 56 MET cc_start: 0.8482 (mmm) cc_final: 0.8177 (mmm) REVERT: As 77 GLN cc_start: 0.8375 (mt0) cc_final: 0.7966 (mp10) REVERT: As 181 MET cc_start: 0.6564 (tmm) cc_final: 0.6162 (tmm) outliers start: 33 outliers final: 20 residues processed: 564 average time/residue: 0.3898 time to fit residues: 322.8453 Evaluate side-chains 555 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 531 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Ab residue 60 LYS Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ac residue 48 LYS Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Af residue 67 LEU Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Ah residue 106 THR Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Ap residue 107 GLU Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 48 LYS Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain As residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 86 optimal weight: 8.9990 chunk 231 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 150 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Ab 69 HIS Ad 151 ASN Ae 151 ASN Af 151 ASN Ag 151 ASN Ah 151 ASN Ai 69 HIS Aj 151 ASN Ak 69 HIS Am 66 ASN Am 77 GLN An 151 ASN ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22572 Z= 0.156 Angle : 0.482 5.975 30647 Z= 0.233 Chirality : 0.039 0.116 3363 Planarity : 0.003 0.030 3952 Dihedral : 4.197 18.917 2983 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.69 % Allowed : 19.04 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2717 helix: 1.53 (0.17), residues: 969 sheet: 1.01 (0.33), residues: 228 loop : -2.07 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAi 132 HIS 0.005 0.001 HISAb 69 PHE 0.003 0.000 PHEAo 163 TYR 0.009 0.001 TYRAm 180 ARG 0.007 0.001 ARGAs 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 523 time to evaluate : 2.460 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8251 (mt0) cc_final: 0.7920 (mp10) REVERT: Aa 107 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8023 (pt0) REVERT: Aa 173 MET cc_start: 0.7299 (tmm) cc_final: 0.6914 (tmm) REVERT: Aa 181 MET cc_start: 0.7317 (tpp) cc_final: 0.6572 (tmm) REVERT: Ab 66 ASN cc_start: 0.8722 (t0) cc_final: 0.8013 (t0) REVERT: Ab 112 MET cc_start: 0.8917 (mmt) cc_final: 0.8715 (mmt) REVERT: Ab 173 MET cc_start: 0.7088 (tmm) cc_final: 0.6714 (tmm) REVERT: Ab 181 MET cc_start: 0.6717 (tmm) cc_final: 0.6266 (tmm) REVERT: Ac 56 MET cc_start: 0.8660 (mmm) cc_final: 0.8381 (mmm) REVERT: Ac 66 ASN cc_start: 0.8969 (t0) cc_final: 0.8765 (t0) REVERT: Ac 173 MET cc_start: 0.6927 (tmm) cc_final: 0.6533 (tmm) REVERT: Ac 181 MET cc_start: 0.7366 (tpp) cc_final: 0.6853 (tmm) REVERT: Ad 181 MET cc_start: 0.7350 (tpp) cc_final: 0.6650 (tmm) REVERT: Ae 76 GLN cc_start: 0.7999 (mp10) cc_final: 0.7744 (mp10) REVERT: Ae 151 ASN cc_start: 0.8251 (m-40) cc_final: 0.8047 (m-40) REVERT: Ae 181 MET cc_start: 0.7227 (tpp) cc_final: 0.6609 (tmm) REVERT: Af 55 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.7032 (mtm180) REVERT: Af 56 MET cc_start: 0.8677 (mmm) cc_final: 0.8248 (mmm) REVERT: Af 116 MET cc_start: 0.8849 (ttp) cc_final: 0.8583 (ttp) REVERT: Af 181 MET cc_start: 0.7271 (tpp) cc_final: 0.6617 (tmm) REVERT: Ag 181 MET cc_start: 0.7287 (tpp) cc_final: 0.6635 (tmm) REVERT: Ah 91 ASP cc_start: 0.8492 (m-30) cc_final: 0.8287 (m-30) REVERT: Ah 112 MET cc_start: 0.8977 (mmp) cc_final: 0.8774 (mmp) REVERT: Ah 173 MET cc_start: 0.7087 (tmm) cc_final: 0.6603 (tmm) REVERT: Ah 181 MET cc_start: 0.6760 (tmm) cc_final: 0.6309 (tmm) REVERT: Ai 56 MET cc_start: 0.8439 (mmm) cc_final: 0.8181 (mmm) REVERT: Ai 134 MET cc_start: 0.8596 (ttp) cc_final: 0.8367 (ttp) REVERT: Ai 181 MET cc_start: 0.7396 (tpp) cc_final: 0.6790 (tmm) REVERT: Aj 58 LYS cc_start: 0.8793 (mttp) cc_final: 0.8432 (mtpt) REVERT: Aj 173 MET cc_start: 0.7009 (tmm) cc_final: 0.6427 (tmm) REVERT: Aj 181 MET cc_start: 0.7418 (tpp) cc_final: 0.6809 (tmm) REVERT: Ak 181 MET cc_start: 0.7364 (tpp) cc_final: 0.6659 (tmm) REVERT: Al 173 MET cc_start: 0.7152 (tmm) cc_final: 0.6672 (tmm) REVERT: Al 181 MET cc_start: 0.7387 (tpp) cc_final: 0.6868 (tmm) REVERT: Am 56 MET cc_start: 0.8584 (mmm) cc_final: 0.8118 (mmm) REVERT: Am 181 MET cc_start: 0.6606 (tmm) cc_final: 0.6274 (tmm) REVERT: An 56 MET cc_start: 0.8622 (mmm) cc_final: 0.8139 (tpp) REVERT: An 77 GLN cc_start: 0.8368 (mt0) cc_final: 0.8036 (mp10) REVERT: An 107 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: An 181 MET cc_start: 0.7307 (tpp) cc_final: 0.6719 (tmm) REVERT: Ao 58 LYS cc_start: 0.8806 (mttm) cc_final: 0.8599 (mttm) REVERT: Ao 77 GLN cc_start: 0.8348 (mt0) cc_final: 0.7985 (mp10) REVERT: Ao 181 MET cc_start: 0.7291 (tpp) cc_final: 0.6698 (tmm) REVERT: Ap 66 ASN cc_start: 0.8689 (t0) cc_final: 0.8259 (t0) REVERT: Ap 136 ASP cc_start: 0.8686 (t0) cc_final: 0.8479 (t0) REVERT: Ap 181 MET cc_start: 0.7272 (tpp) cc_final: 0.6552 (tmm) REVERT: Aq 56 MET cc_start: 0.8477 (mmm) cc_final: 0.8047 (tpp) REVERT: Aq 136 ASP cc_start: 0.8656 (t0) cc_final: 0.8405 (t0) REVERT: Aq 160 MET cc_start: 0.9231 (mmp) cc_final: 0.8975 (mmm) REVERT: Aq 181 MET cc_start: 0.7354 (tpp) cc_final: 0.6679 (tmm) REVERT: Ar 56 MET cc_start: 0.8603 (mmm) cc_final: 0.8293 (tpp) REVERT: Ar 136 ASP cc_start: 0.8584 (t0) cc_final: 0.8349 (t0) REVERT: Ar 181 MET cc_start: 0.7217 (tpp) cc_final: 0.6747 (tmm) REVERT: As 56 MET cc_start: 0.8465 (mmm) cc_final: 0.8142 (mmm) REVERT: As 77 GLN cc_start: 0.8294 (mt0) cc_final: 0.7924 (mp10) REVERT: As 181 MET cc_start: 0.6637 (tmm) cc_final: 0.6258 (tmm) outliers start: 41 outliers final: 27 residues processed: 542 average time/residue: 0.3850 time to fit residues: 306.5525 Evaluate side-chains 554 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 525 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 102 ASP Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Ab residue 60 LYS Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Ag residue 77 GLN Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Ap residue 107 GLU Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 48 LYS Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain As residue 48 LYS Chi-restraints excluded: chain As residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 216 optimal weight: 0.0270 chunk 143 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 overall best weight: 1.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 151 ASN Ag 77 GLN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 66 ASN Aj 69 HIS Aj 151 ASN Ak 69 HIS ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 66 ASN An 151 ASN ** Ao 113 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** ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22572 Z= 0.203 Angle : 0.507 8.736 30647 Z= 0.244 Chirality : 0.040 0.119 3363 Planarity : 0.003 0.030 3952 Dihedral : 4.206 18.929 2983 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.73 % Allowed : 19.00 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.35 (0.17), residues: 2717 helix: 1.54 (0.16), residues: 1083 sheet: 0.91 (0.33), residues: 228 loop : -1.99 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPAg 132 HIS 0.006 0.001 HISAb 69 PHE 0.005 0.001 PHEAo 163 TYR 0.009 0.001 TYRAh 94 ARG 0.007 0.001 ARGAi 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 523 time to evaluate : 2.487 Fit side-chains REVERT: Aa 107 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: Aa 173 MET cc_start: 0.7347 (tmm) cc_final: 0.6947 (tmm) REVERT: Aa 181 MET cc_start: 0.7309 (tpp) cc_final: 0.6573 (tmm) REVERT: Ab 66 ASN cc_start: 0.8745 (t0) cc_final: 0.8041 (t0) REVERT: Ab 173 MET cc_start: 0.7121 (tmm) cc_final: 0.6747 (tmm) REVERT: Ab 181 MET cc_start: 0.6674 (tmm) cc_final: 0.6228 (tmm) REVERT: Ac 56 MET cc_start: 0.8656 (mmm) cc_final: 0.8360 (mmm) REVERT: Ac 66 ASN cc_start: 0.8953 (t0) cc_final: 0.8732 (t0) REVERT: Ac 95 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8064 (mm-30) REVERT: Ac 173 MET cc_start: 0.7057 (tmm) cc_final: 0.6613 (tmm) REVERT: Ac 181 MET cc_start: 0.7349 (tpp) cc_final: 0.6728 (tmm) REVERT: Ad 181 MET cc_start: 0.7411 (tpp) cc_final: 0.6726 (tmm) REVERT: Ae 76 GLN cc_start: 0.8011 (mp10) cc_final: 0.7748 (mp10) REVERT: Ae 181 MET cc_start: 0.7218 (tpp) cc_final: 0.6651 (tmm) REVERT: Af 55 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.7080 (mtm180) REVERT: Af 116 MET cc_start: 0.8872 (ttp) cc_final: 0.8618 (ttp) REVERT: Af 181 MET cc_start: 0.7184 (tpp) cc_final: 0.6544 (tmm) REVERT: Ag 181 MET cc_start: 0.7263 (tpp) cc_final: 0.6606 (tmm) REVERT: Ah 91 ASP cc_start: 0.8469 (m-30) cc_final: 0.8198 (m-30) REVERT: Ah 112 MET cc_start: 0.9055 (mmp) cc_final: 0.8777 (mmp) REVERT: Ah 173 MET cc_start: 0.7116 (tmm) cc_final: 0.6596 (tmm) REVERT: Ah 181 MET cc_start: 0.6738 (tmm) cc_final: 0.6317 (tmm) REVERT: Ai 56 MET cc_start: 0.8467 (mmm) cc_final: 0.8225 (mmm) REVERT: Ai 67 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8675 (tt) REVERT: Ai 134 MET cc_start: 0.8652 (ttp) cc_final: 0.8403 (ttp) REVERT: Ai 181 MET cc_start: 0.7385 (tpp) cc_final: 0.6781 (tmm) REVERT: Aj 58 LYS cc_start: 0.8804 (mttp) cc_final: 0.8525 (mtpt) REVERT: Aj 66 ASN cc_start: 0.8711 (t0) cc_final: 0.8385 (t0) REVERT: Aj 173 MET cc_start: 0.7055 (tmm) cc_final: 0.6485 (tmm) REVERT: Aj 181 MET cc_start: 0.7445 (tpp) cc_final: 0.6806 (tmm) REVERT: Ak 173 MET cc_start: 0.7059 (tmm) cc_final: 0.6438 (tmm) REVERT: Ak 181 MET cc_start: 0.7339 (tpp) cc_final: 0.6642 (tmm) REVERT: Al 173 MET cc_start: 0.7207 (tmm) cc_final: 0.6712 (tmm) REVERT: Al 181 MET cc_start: 0.7273 (tpp) cc_final: 0.6780 (tmm) REVERT: Am 56 MET cc_start: 0.8651 (mmm) cc_final: 0.8408 (mmm) REVERT: Am 181 MET cc_start: 0.6626 (tmm) cc_final: 0.6286 (tmm) REVERT: An 56 MET cc_start: 0.8626 (mmm) cc_final: 0.8117 (tpp) REVERT: An 77 GLN cc_start: 0.8375 (mt0) cc_final: 0.8041 (mp10) REVERT: An 107 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: An 181 MET cc_start: 0.7330 (tpp) cc_final: 0.6754 (tmm) REVERT: Ao 58 LYS cc_start: 0.8820 (mttm) cc_final: 0.8609 (mttm) REVERT: Ao 77 GLN cc_start: 0.8354 (mt0) cc_final: 0.8009 (mp10) REVERT: Ao 181 MET cc_start: 0.7217 (tpp) cc_final: 0.6665 (tmm) REVERT: Ap 66 ASN cc_start: 0.8704 (t0) cc_final: 0.8335 (t0) REVERT: Ap 136 ASP cc_start: 0.8685 (t0) cc_final: 0.8481 (t0) REVERT: Ap 181 MET cc_start: 0.7186 (tpp) cc_final: 0.6445 (tmm) REVERT: Aq 56 MET cc_start: 0.8474 (mmm) cc_final: 0.8026 (tpp) REVERT: Aq 136 ASP cc_start: 0.8614 (t0) cc_final: 0.8364 (t0) REVERT: Aq 160 MET cc_start: 0.9244 (mmp) cc_final: 0.8998 (mmm) REVERT: Aq 181 MET cc_start: 0.7358 (tpp) cc_final: 0.6669 (tmm) REVERT: Ar 56 MET cc_start: 0.8614 (mmm) cc_final: 0.8401 (mmm) REVERT: Ar 136 ASP cc_start: 0.8611 (t0) cc_final: 0.8353 (t0) REVERT: Ar 181 MET cc_start: 0.7211 (tpp) cc_final: 0.6747 (tmm) REVERT: As 56 MET cc_start: 0.8478 (mmm) cc_final: 0.8151 (mmm) REVERT: As 77 GLN cc_start: 0.8364 (mt0) cc_final: 0.7970 (mp10) REVERT: As 181 MET cc_start: 0.6589 (tmm) cc_final: 0.6198 (tmm) outliers start: 42 outliers final: 32 residues processed: 541 average time/residue: 0.4091 time to fit residues: 326.9615 Evaluate side-chains 551 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 515 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 60 LYS Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Ab residue 60 LYS Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ab residue 107 GLU Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Af residue 106 THR Chi-restraints excluded: chain Ag residue 77 GLN Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ai residue 67 LEU Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 103 ILE Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 106 THR Chi-restraints excluded: chain Ap residue 107 GLU Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain As residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 23 optimal weight: 0.0470 chunk 201 optimal weight: 8.9990 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 77 GLN Ai 69 HIS ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 151 ASN Ak 69 HIS ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 66 ASN ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 151 ASN Ap 69 HIS Aq 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 22572 Z= 0.294 Angle : 0.556 10.913 30647 Z= 0.268 Chirality : 0.042 0.122 3363 Planarity : 0.003 0.034 3952 Dihedral : 4.363 19.986 2983 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.26 % Allowed : 18.87 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2717 helix: 1.33 (0.16), residues: 1083 sheet: 0.82 (0.33), residues: 228 loop : -2.01 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPAh 132 HIS 0.008 0.001 HISAc 69 PHE 0.007 0.001 PHEAo 163 TYR 0.010 0.002 TYRAh 94 ARG 0.007 0.001 ARGAc 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 522 time to evaluate : 2.454 Fit side-chains REVERT: Aa 107 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8064 (pt0) REVERT: Aa 173 MET cc_start: 0.7355 (tmm) cc_final: 0.6922 (tmm) REVERT: Aa 181 MET cc_start: 0.7317 (tpp) cc_final: 0.6573 (tmm) REVERT: Ab 66 ASN cc_start: 0.8787 (t0) cc_final: 0.8253 (t0) REVERT: Ab 173 MET cc_start: 0.7139 (tmm) cc_final: 0.6738 (tmm) REVERT: Ab 181 MET cc_start: 0.6620 (tmm) cc_final: 0.6177 (tmm) REVERT: Ac 56 MET cc_start: 0.8708 (mmm) cc_final: 0.8399 (mmm) REVERT: Ac 66 ASN cc_start: 0.8952 (t0) cc_final: 0.8745 (t0) REVERT: Ac 77 GLN cc_start: 0.8409 (mt0) cc_final: 0.7896 (tm-30) REVERT: Ac 173 MET cc_start: 0.7118 (tmm) cc_final: 0.6630 (tmm) REVERT: Ac 181 MET cc_start: 0.7337 (tpp) cc_final: 0.6639 (tmm) REVERT: Ad 76 GLN cc_start: 0.8068 (mp10) cc_final: 0.7842 (mp10) REVERT: Ad 181 MET cc_start: 0.7386 (tpp) cc_final: 0.6694 (tmm) REVERT: Ae 76 GLN cc_start: 0.7994 (mp10) cc_final: 0.7680 (mp10) REVERT: Ae 181 MET cc_start: 0.7184 (tpp) cc_final: 0.6626 (tmm) REVERT: Af 55 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.7021 (mtm180) REVERT: Af 181 MET cc_start: 0.7320 (tpp) cc_final: 0.6582 (tmm) REVERT: Ag 181 MET cc_start: 0.7296 (tpp) cc_final: 0.6836 (tmm) REVERT: Ah 76 GLN cc_start: 0.8052 (mp10) cc_final: 0.7783 (mp10) REVERT: Ah 77 GLN cc_start: 0.8333 (tt0) cc_final: 0.8052 (tm-30) REVERT: Ah 91 ASP cc_start: 0.8493 (m-30) cc_final: 0.8280 (m-30) REVERT: Ah 181 MET cc_start: 0.6640 (tmm) cc_final: 0.6235 (tmm) REVERT: Ai 56 MET cc_start: 0.8484 (mmm) cc_final: 0.8253 (mmm) REVERT: Ai 67 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8700 (tt) REVERT: Ai 181 MET cc_start: 0.7329 (tpp) cc_final: 0.6677 (tmm) REVERT: Aj 58 LYS cc_start: 0.8827 (mttp) cc_final: 0.8541 (mtpt) REVERT: Aj 66 ASN cc_start: 0.8681 (t0) cc_final: 0.8479 (t0) REVERT: Aj 173 MET cc_start: 0.7046 (tmm) cc_final: 0.6546 (tmm) REVERT: Aj 181 MET cc_start: 0.7499 (tpp) cc_final: 0.6803 (tmm) REVERT: Ak 173 MET cc_start: 0.7109 (tmm) cc_final: 0.6480 (tmm) REVERT: Ak 181 MET cc_start: 0.7291 (tpp) cc_final: 0.6584 (tmm) REVERT: Al 173 MET cc_start: 0.7242 (tmm) cc_final: 0.6783 (tmm) REVERT: Al 181 MET cc_start: 0.7300 (tpp) cc_final: 0.6712 (tmm) REVERT: Am 56 MET cc_start: 0.8762 (mmm) cc_final: 0.8537 (mmm) REVERT: Am 107 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7919 (pt0) REVERT: Am 181 MET cc_start: 0.6606 (tmm) cc_final: 0.6298 (tmm) REVERT: An 56 MET cc_start: 0.8664 (mmm) cc_final: 0.8142 (mmm) REVERT: An 77 GLN cc_start: 0.8399 (mt0) cc_final: 0.8054 (mp10) REVERT: An 107 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8035 (pt0) REVERT: An 181 MET cc_start: 0.7312 (tpp) cc_final: 0.6704 (tmm) REVERT: Ao 58 LYS cc_start: 0.8831 (mttm) cc_final: 0.8554 (mttm) REVERT: Ao 77 GLN cc_start: 0.8402 (mt0) cc_final: 0.8037 (mp10) REVERT: Ao 181 MET cc_start: 0.7206 (tpp) cc_final: 0.6663 (tmm) REVERT: Ap 181 MET cc_start: 0.7240 (tpp) cc_final: 0.6462 (tmm) REVERT: Aq 56 MET cc_start: 0.8512 (mmm) cc_final: 0.8042 (tpp) REVERT: Aq 136 ASP cc_start: 0.8650 (t0) cc_final: 0.8373 (t0) REVERT: Aq 160 MET cc_start: 0.9236 (mmp) cc_final: 0.8995 (mmm) REVERT: Aq 181 MET cc_start: 0.7332 (tpp) cc_final: 0.6623 (tmm) REVERT: Ar 56 MET cc_start: 0.8642 (mmm) cc_final: 0.8424 (mmm) REVERT: Ar 136 ASP cc_start: 0.8615 (t0) cc_final: 0.8318 (t0) REVERT: Ar 181 MET cc_start: 0.7263 (tpp) cc_final: 0.6658 (tmm) REVERT: As 56 MET cc_start: 0.8501 (mmm) cc_final: 0.8172 (mmm) REVERT: As 181 MET cc_start: 0.6649 (tmm) cc_final: 0.6324 (tmm) outliers start: 55 outliers final: 43 residues processed: 544 average time/residue: 0.3812 time to fit residues: 305.0361 Evaluate side-chains 560 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 513 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 60 LYS Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Ab residue 60 LYS Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ac residue 44 VAL Chi-restraints excluded: chain Ac residue 103 ILE Chi-restraints excluded: chain Ac residue 110 THR Chi-restraints excluded: chain Ac residue 133 VAL Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Ae residue 77 GLN Chi-restraints excluded: chain Ag residue 77 GLN Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 103 ILE Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ah residue 110 THR Chi-restraints excluded: chain Ai residue 67 LEU Chi-restraints excluded: chain Ai residue 71 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 103 ILE Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Ak residue 119 CYS Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 44 VAL Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain An residue 44 VAL Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain An residue 133 VAL Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ao residue 119 CYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 107 GLU Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain As residue 99 LEU Chi-restraints excluded: chain As residue 106 THR Chi-restraints excluded: chain As residue 133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 224 optimal weight: 0.4980 chunk 238 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 215 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 77 GLN Ah 151 ASN Ai 69 HIS Aj 69 HIS Aj 151 ASN Ak 69 HIS ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 66 ASN ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 151 ASN Ap 69 HIS Aq 69 HIS ** Aq 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 151 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22572 Z= 0.179 Angle : 0.520 10.405 30647 Z= 0.249 Chirality : 0.039 0.121 3363 Planarity : 0.003 0.032 3952 Dihedral : 4.254 20.013 2983 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.56 % Allowed : 20.07 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.24 (0.17), residues: 2717 helix: 1.63 (0.16), residues: 1083 sheet: 0.87 (0.33), residues: 228 loop : -1.91 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAf 132 HIS 0.009 0.001 HISAc 69 PHE 0.003 0.000 PHEAo 163 TYR 0.010 0.001 TYRAe 180 ARG 0.007 0.001 ARGAh 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 514 time to evaluate : 2.307 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8287 (mt0) cc_final: 0.7870 (mp10) REVERT: Aa 107 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: Aa 173 MET cc_start: 0.7329 (tmm) cc_final: 0.6893 (tmm) REVERT: Aa 181 MET cc_start: 0.7335 (tpp) cc_final: 0.6604 (tmm) REVERT: Ab 173 MET cc_start: 0.7100 (tmm) cc_final: 0.6698 (tmm) REVERT: Ab 181 MET cc_start: 0.6594 (tmm) cc_final: 0.6164 (tmm) REVERT: Ac 173 MET cc_start: 0.7081 (tmm) cc_final: 0.6596 (tmm) REVERT: Ac 181 MET cc_start: 0.7240 (tpp) cc_final: 0.6692 (tmm) REVERT: Ad 76 GLN cc_start: 0.8048 (mp10) cc_final: 0.7816 (mp10) REVERT: Ad 181 MET cc_start: 0.7348 (tpp) cc_final: 0.6736 (tmm) REVERT: Ae 181 MET cc_start: 0.7286 (tpp) cc_final: 0.6800 (tmm) REVERT: Af 55 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.7024 (mtm180) REVERT: Af 56 MET cc_start: 0.8682 (mmm) cc_final: 0.8273 (mmm) REVERT: Af 60 LYS cc_start: 0.8854 (mttm) cc_final: 0.8566 (mttp) REVERT: Af 181 MET cc_start: 0.7336 (tpp) cc_final: 0.6570 (tmm) REVERT: Ag 181 MET cc_start: 0.7295 (tpp) cc_final: 0.6680 (tmm) REVERT: Ah 91 ASP cc_start: 0.8429 (m-30) cc_final: 0.8181 (m-30) REVERT: Ah 112 MET cc_start: 0.9051 (mmp) cc_final: 0.8771 (mmp) REVERT: Ah 181 MET cc_start: 0.6632 (tmm) cc_final: 0.6245 (tmm) REVERT: Ai 56 MET cc_start: 0.8481 (mmm) cc_final: 0.8250 (mmm) REVERT: Ai 134 MET cc_start: 0.8697 (ttp) cc_final: 0.8444 (ttp) REVERT: Ai 181 MET cc_start: 0.7307 (tpp) cc_final: 0.6688 (tmm) REVERT: Aj 58 LYS cc_start: 0.8803 (mttp) cc_final: 0.8526 (mtpt) REVERT: Aj 66 ASN cc_start: 0.8657 (t0) cc_final: 0.8361 (t0) REVERT: Aj 173 MET cc_start: 0.7004 (tmm) cc_final: 0.6475 (tmm) REVERT: Aj 181 MET cc_start: 0.7497 (tpp) cc_final: 0.6850 (tmm) REVERT: Ak 173 MET cc_start: 0.7095 (tmm) cc_final: 0.6459 (tmm) REVERT: Ak 181 MET cc_start: 0.7290 (tpp) cc_final: 0.6622 (tmm) REVERT: Al 173 MET cc_start: 0.7203 (tmm) cc_final: 0.6730 (tmm) REVERT: Al 181 MET cc_start: 0.7303 (tpp) cc_final: 0.6786 (tmm) REVERT: Am 56 MET cc_start: 0.8720 (mmm) cc_final: 0.8462 (mmm) REVERT: Am 107 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: Am 181 MET cc_start: 0.6696 (tmm) cc_final: 0.6378 (tmm) REVERT: An 56 MET cc_start: 0.8627 (mmm) cc_final: 0.8126 (tpp) REVERT: An 77 GLN cc_start: 0.8359 (mt0) cc_final: 0.8020 (mp10) REVERT: An 107 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8009 (pt0) REVERT: An 181 MET cc_start: 0.7290 (tpp) cc_final: 0.6702 (tmm) REVERT: Ao 58 LYS cc_start: 0.8808 (mttm) cc_final: 0.8553 (mttm) REVERT: Ao 77 GLN cc_start: 0.8345 (mt0) cc_final: 0.8013 (mp10) REVERT: Ao 181 MET cc_start: 0.7247 (tpp) cc_final: 0.6740 (tmm) REVERT: Ap 181 MET cc_start: 0.7243 (tpp) cc_final: 0.6488 (tmm) REVERT: Aq 56 MET cc_start: 0.8486 (mmm) cc_final: 0.8036 (tpp) REVERT: Aq 136 ASP cc_start: 0.8620 (t0) cc_final: 0.8377 (t0) REVERT: Aq 160 MET cc_start: 0.9232 (mmp) cc_final: 0.8988 (mmm) REVERT: Aq 181 MET cc_start: 0.7357 (tpp) cc_final: 0.6695 (tmm) REVERT: Ar 56 MET cc_start: 0.8632 (mmm) cc_final: 0.8293 (tpp) REVERT: Ar 136 ASP cc_start: 0.8567 (t0) cc_final: 0.8361 (t0) REVERT: Ar 181 MET cc_start: 0.7222 (tpp) cc_final: 0.6774 (tmm) REVERT: As 56 MET cc_start: 0.8465 (mmm) cc_final: 0.8133 (mmm) REVERT: As 77 GLN cc_start: 0.8357 (mt0) cc_final: 0.7961 (mp10) REVERT: As 181 MET cc_start: 0.6644 (tmm) cc_final: 0.6270 (tmm) outliers start: 38 outliers final: 30 residues processed: 532 average time/residue: 0.3971 time to fit residues: 310.5717 Evaluate side-chains 539 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 506 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Ab residue 60 LYS Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ac residue 44 VAL Chi-restraints excluded: chain Ac residue 103 ILE Chi-restraints excluded: chain Ac residue 106 THR Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Ag residue 77 GLN Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ah residue 107 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Ak residue 119 CYS Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain An residue 44 VAL Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ao residue 119 CYS Chi-restraints excluded: chain Ap residue 107 GLU Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain As residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.0070 chunk 154 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 265 optimal weight: 0.0670 chunk 243 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 77 GLN Ag 77 GLN Ag 151 ASN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 69 HIS Aj 69 HIS Aj 151 ASN Ak 69 HIS ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 66 ASN ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 69 HIS Aq 151 ASN ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22572 Z= 0.179 Angle : 0.525 10.070 30647 Z= 0.251 Chirality : 0.039 0.122 3363 Planarity : 0.003 0.034 3952 Dihedral : 4.233 20.442 2983 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.52 % Allowed : 20.11 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.26 (0.17), residues: 2717 helix: 1.60 (0.16), residues: 1026 sheet: 0.88 (0.33), residues: 228 loop : -1.77 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAf 132 HIS 0.009 0.001 HISAc 69 PHE 0.003 0.001 PHEAo 163 TYR 0.010 0.001 TYRAe 180 ARG 0.007 0.001 ARGAh 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 506 time to evaluate : 2.806 Fit side-chains REVERT: Aa 77 GLN cc_start: 0.8303 (mt0) cc_final: 0.7893 (mp10) REVERT: Aa 107 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: Aa 173 MET cc_start: 0.7322 (tmm) cc_final: 0.6887 (tmm) REVERT: Aa 181 MET cc_start: 0.7307 (tpp) cc_final: 0.6567 (tmm) REVERT: Ab 173 MET cc_start: 0.7101 (tmm) cc_final: 0.6697 (tmm) REVERT: Ab 181 MET cc_start: 0.6587 (tmm) cc_final: 0.6162 (tmm) REVERT: Ac 56 MET cc_start: 0.8617 (mmm) cc_final: 0.8249 (mmm) REVERT: Ac 173 MET cc_start: 0.7078 (tmm) cc_final: 0.6594 (tmm) REVERT: Ac 181 MET cc_start: 0.7316 (tpp) cc_final: 0.6749 (tmm) REVERT: Ad 76 GLN cc_start: 0.8049 (mp10) cc_final: 0.7816 (mp10) REVERT: Ad 181 MET cc_start: 0.7452 (tpp) cc_final: 0.6762 (tmm) REVERT: Ae 181 MET cc_start: 0.7300 (tpp) cc_final: 0.6796 (tmm) REVERT: Af 55 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.7032 (mtm180) REVERT: Af 60 LYS cc_start: 0.8855 (mttm) cc_final: 0.8551 (mttp) REVERT: Af 181 MET cc_start: 0.7332 (tpp) cc_final: 0.6572 (tmm) REVERT: Ag 181 MET cc_start: 0.7299 (tpp) cc_final: 0.6677 (tmm) REVERT: Ah 91 ASP cc_start: 0.8450 (m-30) cc_final: 0.8194 (m-30) REVERT: Ah 112 MET cc_start: 0.9047 (mmp) cc_final: 0.8789 (mmp) REVERT: Ah 181 MET cc_start: 0.6599 (tmm) cc_final: 0.6213 (tmm) REVERT: Ai 56 MET cc_start: 0.8520 (mmm) cc_final: 0.8262 (mmm) REVERT: Ai 134 MET cc_start: 0.8674 (ttp) cc_final: 0.8432 (ttp) REVERT: Ai 181 MET cc_start: 0.7259 (tpp) cc_final: 0.6644 (tmm) REVERT: Aj 58 LYS cc_start: 0.8771 (mttp) cc_final: 0.8492 (mtpt) REVERT: Aj 66 ASN cc_start: 0.8635 (t0) cc_final: 0.8340 (t0) REVERT: Aj 173 MET cc_start: 0.7044 (tmm) cc_final: 0.6515 (tmm) REVERT: Aj 181 MET cc_start: 0.7471 (tpp) cc_final: 0.6810 (tmm) REVERT: Ak 173 MET cc_start: 0.7087 (tmm) cc_final: 0.6446 (tmm) REVERT: Ak 181 MET cc_start: 0.7205 (tpp) cc_final: 0.6511 (tmm) REVERT: Al 173 MET cc_start: 0.7204 (tmm) cc_final: 0.6723 (tmm) REVERT: Al 181 MET cc_start: 0.7275 (tpp) cc_final: 0.6771 (tmm) REVERT: Am 56 MET cc_start: 0.8710 (mmm) cc_final: 0.8449 (mmm) REVERT: Am 107 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: Am 181 MET cc_start: 0.6673 (tmm) cc_final: 0.6371 (tmm) REVERT: An 56 MET cc_start: 0.8619 (mmm) cc_final: 0.8121 (tpp) REVERT: An 77 GLN cc_start: 0.8338 (mt0) cc_final: 0.8016 (mp10) REVERT: An 107 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8047 (pt0) REVERT: An 181 MET cc_start: 0.7278 (tpp) cc_final: 0.6702 (tmm) REVERT: Ao 58 LYS cc_start: 0.8808 (mttm) cc_final: 0.8575 (mttm) REVERT: Ao 77 GLN cc_start: 0.8357 (mt0) cc_final: 0.8016 (mp10) REVERT: Ao 181 MET cc_start: 0.7229 (tpp) cc_final: 0.6723 (tmm) REVERT: Ap 181 MET cc_start: 0.7241 (tpp) cc_final: 0.6491 (tmm) REVERT: Aq 56 MET cc_start: 0.8481 (mmm) cc_final: 0.8029 (tpp) REVERT: Aq 136 ASP cc_start: 0.8606 (t0) cc_final: 0.8371 (t0) REVERT: Aq 160 MET cc_start: 0.9235 (mmp) cc_final: 0.8995 (mmm) REVERT: Aq 181 MET cc_start: 0.7378 (tpp) cc_final: 0.6719 (tmm) REVERT: Ar 56 MET cc_start: 0.8629 (mmm) cc_final: 0.8286 (tpp) REVERT: Ar 136 ASP cc_start: 0.8542 (t0) cc_final: 0.8327 (t0) REVERT: Ar 181 MET cc_start: 0.7219 (tpp) cc_final: 0.6785 (tmm) REVERT: As 56 MET cc_start: 0.8453 (mmm) cc_final: 0.8117 (mmm) REVERT: As 77 GLN cc_start: 0.8360 (mt0) cc_final: 0.7964 (mp10) REVERT: As 181 MET cc_start: 0.6644 (tmm) cc_final: 0.6266 (tmm) outliers start: 37 outliers final: 31 residues processed: 526 average time/residue: 0.3964 time to fit residues: 305.3180 Evaluate side-chains 531 residues out of total 2432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 497 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 106 THR Chi-restraints excluded: chain Aa residue 107 GLU Chi-restraints excluded: chain Ab residue 60 LYS Chi-restraints excluded: chain Ab residue 106 THR Chi-restraints excluded: chain Ac residue 44 VAL Chi-restraints excluded: chain Ac residue 48 LYS Chi-restraints excluded: chain Ac residue 106 THR Chi-restraints excluded: chain Ad residue 106 THR Chi-restraints excluded: chain Ag residue 77 GLN Chi-restraints excluded: chain Ag residue 99 LEU Chi-restraints excluded: chain Ag residue 106 THR Chi-restraints excluded: chain Ah residue 107 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 106 THR Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 106 THR Chi-restraints excluded: chain Ak residue 106 THR Chi-restraints excluded: chain Ak residue 119 CYS Chi-restraints excluded: chain Al residue 71 LEU Chi-restraints excluded: chain Al residue 77 GLN Chi-restraints excluded: chain Al residue 106 THR Chi-restraints excluded: chain Am residue 107 GLU Chi-restraints excluded: chain An residue 44 VAL Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 106 THR Chi-restraints excluded: chain An residue 107 GLU Chi-restraints excluded: chain Ao residue 106 THR Chi-restraints excluded: chain Ao residue 119 CYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Aq residue 106 THR Chi-restraints excluded: chain Ar residue 106 THR Chi-restraints excluded: chain As residue 44 VAL Chi-restraints excluded: chain As residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 194 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 211 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 185 optimal weight: 0.0370 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 69 HIS ** Aa 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 69 HIS ** Ab 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 151 ASN Ag 77 GLN Ag 151 ASN ** Ah 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 69 HIS ** Ai 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 69 HIS ** Ak 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 66 ASN ** Am 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ao 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aq 69 HIS ** Ar 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.140344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112013 restraints weight = 28067.255| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.89 r_work: 0.3103 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22572 Z= 0.198 Angle : 0.529 9.431 30647 Z= 0.252 Chirality : 0.040 0.124 3363 Planarity : 0.003 0.034 3952 Dihedral : 4.239 19.696 2983 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.52 % Allowed : 20.39 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.27 (0.17), residues: 2717 helix: 1.55 (0.16), residues: 1026 sheet: 0.85 (0.33), residues: 228 loop : -1.73 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPAf 132 HIS 0.009 0.001 HISAb 69 PHE 0.004 0.001 PHEAo 163 TYR 0.010 0.001 TYRAe 180 ARG 0.007 0.001 ARGAh 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6083.87 seconds wall clock time: 110 minutes 19.16 seconds (6619.16 seconds total)