Starting phenix.real_space_refine on Sun Feb 8 05:51:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v27_64719/02_2026/9v27_64719.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v27_64719/02_2026/9v27_64719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v27_64719/02_2026/9v27_64719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v27_64719/02_2026/9v27_64719.map" model { file = "/net/cci-nas-00/data/ceres_data/9v27_64719/02_2026/9v27_64719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v27_64719/02_2026/9v27_64719.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 1129 5.49 5 S 90 5.16 5 C 21600 2.51 5 N 7604 2.21 5 O 10776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41199 Number of models: 1 Model: "" Number of chains: 22 Chain: "sB" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "sC" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 238 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 3, 'TRANS': 27} Chain: "sH" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Classifications: {'peptide': 2} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 1} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'UNK:plan-1': 2} Unresolved non-hydrogen planarities: 3 Chain: "sI" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 30, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 62} Chain breaks: 2 Chain: "sJ" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1530 Classifications: {'RNA': 72} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 1, 'rna3p_pur': 28, 'rna3p_pyr': 36} Link IDs: {'rna2p': 7, 'rna3p': 64} Chain breaks: 2 Chain: "sK" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 215 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "sa" Number of atoms: 20871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 975, 20871 Classifications: {'RNA': 975} Modifications used: {'rna2p_pur': 102, 'rna2p_pyr': 52, 'rna3p_pur': 466, 'rna3p_pyr': 355} Link IDs: {'rna2p': 153, 'rna3p': 821} Chain breaks: 13 Chain: "sb" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1626 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain: "sc" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1642 Classifications: {'peptide': 215} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 204} Chain: "se" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1042 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 12 Chain: "sf" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1949 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 15, 'TRANS': 230} Chain: "sh" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1132 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain breaks: 3 Chain: "si" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 568 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 68} Chain breaks: 2 Chain: "sj" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1012 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 2 Chain: "sk" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1288 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "sm" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1161 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 1 Chain: "so" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 644 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain breaks: 3 Chain: "sp" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 999 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "sr" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1022 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "sx" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 634 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "sy" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 836 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "sz" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 438 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Time building chain proxies: 8.89, per 1000 atoms: 0.22 Number of scatterers: 41199 At special positions: 0 Unit cell: (154.08, 206.51, 169.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 1129 15.00 O 10776 8.00 N 7604 7.00 C 21600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 925.6 milliseconds 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3978 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 25 sheets defined 27.8% alpha, 19.5% beta 330 base pairs and 554 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'sB' and resid 49 through 56 Processing helix chain 'sB' and resid 74 through 81 Processing helix chain 'sB' and resid 90 through 94 removed outlier: 3.572A pdb=" N ARGsB 93 " --> pdb=" O THRsB 90 " (cutoff:3.500A) Processing helix chain 'sC' and resid 12 through 19 removed outlier: 3.715A pdb=" N ALAsC 17 " --> pdb=" O ALAsC 13 " (cutoff:3.500A) Processing helix chain 'sC' and resid 20 through 24 removed outlier: 3.835A pdb=" N ARGsC 24 " --> pdb=" O LYSsC 21 " (cutoff:3.500A) Processing helix chain 'sb' and resid 10 through 14 removed outlier: 3.970A pdb=" N LYSsb 14 " --> pdb=" O ASPsb 11 " (cutoff:3.500A) Processing helix chain 'sb' and resid 16 through 26 Processing helix chain 'sb' and resid 36 through 40 Processing helix chain 'sb' and resid 55 through 75 Processing helix chain 'sb' and resid 76 through 79 removed outlier: 6.473A pdb=" N SERsb 79 " --> pdb=" O GLUsb 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'sb' and resid 76 through 79' Processing helix chain 'sb' and resid 87 through 89 No H-bonds generated for 'chain 'sb' and resid 87 through 89' Processing helix chain 'sb' and resid 90 through 102 Processing helix chain 'sb' and resid 137 through 145 removed outlier: 3.833A pdb=" N GLYsb 145 " --> pdb=" O LEUsb 141 " (cutoff:3.500A) Processing helix chain 'sb' and resid 174 through 193 Processing helix chain 'sb' and resid 205 through 210 removed outlier: 4.375A pdb=" N PHEsb 209 " --> pdb=" O METsb 205 " (cutoff:3.500A) Processing helix chain 'sc' and resid 41 through 49 removed outlier: 3.593A pdb=" N ASPsc 49 " --> pdb=" O ARGsc 45 " (cutoff:3.500A) Processing helix chain 'sc' and resid 55 through 61 removed outlier: 4.265A pdb=" N PHEsc 61 " --> pdb=" O GLNsc 57 " (cutoff:3.500A) Processing helix chain 'sc' and resid 67 through 75 removed outlier: 4.188A pdb=" N VALsc 71 " --> pdb=" O GLUsc 67 " (cutoff:3.500A) Processing helix chain 'sc' and resid 122 through 137 Processing helix chain 'sc' and resid 183 through 193 removed outlier: 3.763A pdb=" N PHEsc 189 " --> pdb=" O THRsc 185 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEUsc 192 " --> pdb=" O LYSsc 188 " (cutoff:3.500A) Processing helix chain 'sc' and resid 208 through 222 removed outlier: 3.513A pdb=" N PHEsc 212 " --> pdb=" O THRsc 208 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLNsc 222 " --> pdb=" O ASPsc 218 " (cutoff:3.500A) Processing helix chain 'sc' and resid 240 through 245 Processing helix chain 'sc' and resid 245 through 250 removed outlier: 3.568A pdb=" N ALAsc 250 " --> pdb=" O ALAsc 246 " (cutoff:3.500A) Processing helix chain 'se' and resid 72 through 77 Processing helix chain 'se' and resid 78 through 82 Processing helix chain 'se' and resid 108 through 115 Processing helix chain 'se' and resid 159 through 166 removed outlier: 3.680A pdb=" N LYSse 165 " --> pdb=" O ALAse 161 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILEse 166 " --> pdb=" O GLNse 162 " (cutoff:3.500A) Processing helix chain 'sf' and resid 13 through 17 Processing helix chain 'sf' and resid 42 through 48 removed outlier: 3.536A pdb=" N LEUsf 46 " --> pdb=" O LEUsf 42 " (cutoff:3.500A) Processing helix chain 'sf' and resid 56 through 64 removed outlier: 3.689A pdb=" N METsf 61 " --> pdb=" O ARGsf 57 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILEsf 62 " --> pdb=" O GLUsf 58 " (cutoff:3.500A) Processing helix chain 'sf' and resid 115 through 117 No H-bonds generated for 'chain 'sf' and resid 115 through 117' Processing helix chain 'sh' and resid 187 through 194 removed outlier: 3.533A pdb=" N HISsh 191 " --> pdb=" O ARGsh 187 " (cutoff:3.500A) Processing helix chain 'sh' and resid 195 through 216 removed outlier: 4.385A pdb=" N HISsh 202 " --> pdb=" O ALAsh 198 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYSsh 208 " --> pdb=" O ILEsh 204 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLUsh 209 " --> pdb=" O ALAsh 205 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALAsh 214 " --> pdb=" O ALAsh 210 " (cutoff:3.500A) Processing helix chain 'sh' and resid 220 through 225 removed outlier: 4.021A pdb=" N LYSsh 224 " --> pdb=" O TYRsh 220 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALAsh 225 " --> pdb=" O LYSsh 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'sh' and resid 220 through 225' Processing helix chain 'si' and resid 119 through 122 Processing helix chain 'si' and resid 123 through 136 Processing helix chain 'sj' and resid 49 through 51 No H-bonds generated for 'chain 'sj' and resid 49 through 51' Processing helix chain 'sj' and resid 88 through 94 removed outlier: 3.605A pdb=" N ARGsj 92 " --> pdb=" O ASNsj 88 " (cutoff:3.500A) Processing helix chain 'sk' and resid 20 through 35 removed outlier: 3.953A pdb=" N ALAsk 26 " --> pdb=" O GLUsk 22 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEUsk 30 " --> pdb=" O ALAsk 26 " (cutoff:3.500A) Processing helix chain 'sk' and resid 39 through 60 removed outlier: 3.721A pdb=" N METsk 52 " --> pdb=" O METsk 48 " (cutoff:3.500A) Processing helix chain 'sk' and resid 66 through 84 Processing helix chain 'sk' and resid 93 through 98 removed outlier: 3.835A pdb=" N LEUsk 97 " --> pdb=" O LEUsk 93 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALAsk 98 " --> pdb=" O GLUsk 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'sk' and resid 93 through 98' Processing helix chain 'sk' and resid 100 through 106 removed outlier: 4.247A pdb=" N LEUsk 104 " --> pdb=" O LYSsk 100 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEUsk 105 " --> pdb=" O GLUsk 101 " (cutoff:3.500A) Processing helix chain 'sk' and resid 108 through 116 removed outlier: 3.618A pdb=" N TYRsk 114 " --> pdb=" O GLNsk 110 " (cutoff:3.500A) Processing helix chain 'sk' and resid 121 through 131 removed outlier: 4.004A pdb=" N ARGsk 126 " --> pdb=" O ILEsk 122 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VALsk 127 " --> pdb=" O HISsk 123 " (cutoff:3.500A) Processing helix chain 'sm' and resid 44 through 48 Processing helix chain 'so' and resid 87 through 91 Processing helix chain 'so' and resid 95 through 99 Processing helix chain 'so' and resid 101 through 104 Processing helix chain 'so' and resid 110 through 132 removed outlier: 4.189A pdb=" N ILEso 116 " --> pdb=" O LYSso 112 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SERso 131 " --> pdb=" O ARGso 127 " (cutoff:3.500A) Processing helix chain 'sp' and resid 54 through 57 removed outlier: 3.520A pdb=" N VALsp 57 " --> pdb=" O GLYsp 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'sp' and resid 54 through 57' Processing helix chain 'sp' and resid 59 through 63 removed outlier: 3.659A pdb=" N GLUsp 63 " --> pdb=" O ASPsp 60 " (cutoff:3.500A) Processing helix chain 'sp' and resid 65 through 83 removed outlier: 3.636A pdb=" N ASPsp 75 " --> pdb=" O THRsp 71 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VALsp 76 " --> pdb=" O ALAsp 72 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALAsp 77 " --> pdb=" O ALAsp 73 " (cutoff:3.500A) Processing helix chain 'sp' and resid 105 through 116 removed outlier: 4.201A pdb=" N ALAsp 109 " --> pdb=" O PROsp 105 " (cutoff:3.500A) Processing helix chain 'sr' and resid 5 through 20 Processing helix chain 'sr' and resid 31 through 44 removed outlier: 3.590A pdb=" N VALsr 40 " --> pdb=" O GLUsr 36 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HISsr 44 " --> pdb=" O VALsr 40 " (cutoff:3.500A) Processing helix chain 'sr' and resid 82 through 84 No H-bonds generated for 'chain 'sr' and resid 82 through 84' Processing helix chain 'sr' and resid 85 through 94 removed outlier: 3.617A pdb=" N ASNsr 92 " --> pdb=" O LYSsr 88 " (cutoff:3.500A) Processing helix chain 'sr' and resid 113 through 120 removed outlier: 3.554A pdb=" N ALAsr 118 " --> pdb=" O THRsr 114 " (cutoff:3.500A) Processing helix chain 'sx' and resid 53 through 58 removed outlier: 3.598A pdb=" N ARGsx 57 " --> pdb=" O LYSsx 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYSsx 58 " --> pdb=" O GLYsx 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'sx' and resid 53 through 58' Processing helix chain 'sx' and resid 61 through 74 Processing helix chain 'sx' and resid 81 through 85 Processing helix chain 'sy' and resid 7 through 19 removed outlier: 3.816A pdb=" N METsy 11 " --> pdb=" O ALAsy 7 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARGsy 15 " --> pdb=" O METsy 11 " (cutoff:3.500A) Processing helix chain 'sy' and resid 20 through 22 No H-bonds generated for 'chain 'sy' and resid 20 through 22' Processing helix chain 'sz' and resid 82 through 89 removed outlier: 3.609A pdb=" N LEUsz 86 " --> pdb=" O THRsz 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'sB' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'sB' and resid 36 through 43 Processing sheet with id=AA3, first strand: chain 'sb' and resid 43 through 46 removed outlier: 7.048A pdb=" N ILEsb 53 " --> pdb=" O TYRsb 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'sb' and resid 81 through 84 removed outlier: 6.330A pdb=" N VALsb 82 " --> pdb=" O ILEsb 130 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILEsb 166 " --> pdb=" O THRsb 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'sc' and resid 80 through 91 removed outlier: 5.208A pdb=" N VALsc 82 " --> pdb=" O ALAsc 105 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALAsc 105 " --> pdb=" O VALsc 82 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THRsc 84 " --> pdb=" O TYRsc 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'sc' and resid 160 through 163 Processing sheet with id=AA7, first strand: chain 'se' and resid 29 through 31 Processing sheet with id=AA8, first strand: chain 'se' and resid 67 through 71 removed outlier: 5.758A pdb=" N ILEse 214 " --> pdb=" O ILEse 142 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILEse 142 " --> pdb=" O ILEse 214 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYSse 216 " --> pdb=" O PHEse 140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYSse 141 " --> pdb=" O THRse 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'sf' and resid 40 through 41 Processing sheet with id=AB1, first strand: chain 'sf' and resid 69 through 70 removed outlier: 3.592A pdb=" N LEUsf 88 " --> pdb=" O PHEsf 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'sf' and resid 144 through 145 removed outlier: 3.873A pdb=" N ILEsf 137 " --> pdb=" O ILEsf 145 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILEsf 134 " --> pdb=" O LEUsf 129 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEUsf 129 " --> pdb=" O ILEsf 134 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYRsf 136 " --> pdb=" O ARGsf 127 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARGsf 127 " --> pdb=" O TYRsf 136 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VALsf 138 " --> pdb=" O GLUsf 125 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASPsf 169 " --> pdb=" O LYSsf 159 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASNsf 161 " --> pdb=" O ILEsf 167 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILEsf 167 " --> pdb=" O ASNsf 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'sf' and resid 215 through 219 removed outlier: 6.239A pdb=" N LYSsf 209 " --> pdb=" O ILEsf 193 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILEsf 193 " --> pdb=" O LYSsf 209 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'sh' and resid 75 through 77 Processing sheet with id=AB5, first strand: chain 'si' and resid 154 through 156 removed outlier: 3.504A pdb=" N THRsi 149 " --> pdb=" O ALAsi 156 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYSsi 159 " --> pdb=" O LYSsi 194 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'si' and resid 154 through 156 removed outlier: 3.504A pdb=" N THRsi 149 " --> pdb=" O ALAsi 156 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYRsr 50 " --> pdb=" O ALAsi 148 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEUsi 150 " --> pdb=" O THRsr 48 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N THRsr 48 " --> pdb=" O LEUsi 150 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASPsr 49 " --> pdb=" O ASNsr 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'sj' and resid 37 through 38 removed outlier: 6.310A pdb=" N ARGsj 37 " --> pdb=" O LEUsj 60 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARGsj 42 " --> pdb=" O LEUsj 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'sj' and resid 62 through 67 removed outlier: 5.691A pdb=" N VALsj 81 " --> pdb=" O GLUsj 103 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLUsj 103 " --> pdb=" O VALsj 81 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASNsj 62 " --> pdb=" O VALsj 215 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLYsj 217 " --> pdb=" O ASNsj 62 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASNsj 64 " --> pdb=" O GLYsj 217 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILEsj 219 " --> pdb=" O ASNsj 64 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N SERsj 66 " --> pdb=" O ILEsj 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'sk' and resid 139 through 140 Processing sheet with id=AC1, first strand: chain 'sm' and resid 66 through 79 removed outlier: 26.722A pdb=" N GLYsm 67 " --> pdb=" O TYRsm 92 " (cutoff:3.500A) removed outlier: 23.077A pdb=" N TYRsm 92 " --> pdb=" O GLYsm 67 " (cutoff:3.500A) removed outlier: 17.372A pdb=" N THRsm 69 " --> pdb=" O PHEsm 90 " (cutoff:3.500A) removed outlier: 14.758A pdb=" N PHEsm 90 " --> pdb=" O THRsm 69 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N SERsm 71 " --> pdb=" O ASPsm 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASPsm 88 " --> pdb=" O SERsm 71 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILEsm 84 " --> pdb=" O LYSsm 75 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N CYSsm 77 " --> pdb=" O THRsm 82 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THRsm 82 " --> pdb=" O CYSsm 77 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARGsm 98 " --> pdb=" O VALsm 93 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N PHEsm 137 " --> pdb=" O ASNsm 105 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALAsm 107 " --> pdb=" O PHEsm 137 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VALsm 139 " --> pdb=" O ALAsm 107 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N HISsm 109 " --> pdb=" O VALsm 139 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LYSsm 141 " --> pdb=" O HISsm 109 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VALsm 124 " --> pdb=" O LEUsm 140 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHEsm 142 " --> pdb=" O HISsm 122 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N HISsm 122 " --> pdb=" O PHEsm 142 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARGsm 68 " --> pdb=" O GLNsm 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'sp' and resid 47 through 52 removed outlier: 3.760A pdb=" N ILEsp 49 " --> pdb=" O VALsp 39 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALAsp 22 " --> pdb=" O SERsp 87 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N HISsp 89 " --> pdb=" O ALAsp 22 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLYsp 24 " --> pdb=" O HISsp 89 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LYSsp 91 " --> pdb=" O GLYsp 24 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALAsp 26 " --> pdb=" O LYSsp 91 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARGsp 93 " --> pdb=" O ALAsp 26 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILEsp 28 " --> pdb=" O ARGsp 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'sr' and resid 72 through 74 Processing sheet with id=AC4, first strand: chain 'sr' and resid 72 through 74 removed outlier: 6.977A pdb=" N VALsr 103 " --> pdb=" O LEUsr 126 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHEsr 128 " --> pdb=" O ALAsr 101 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALAsr 101 " --> pdb=" O PHEsr 128 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'sx' and resid 30 through 37 removed outlier: 3.747A pdb=" N VALsx 52 " --> pdb=" O VALsx 30 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLUsx 46 " --> pdb=" O HISsx 36 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'sy' and resid 78 through 82 removed outlier: 3.697A pdb=" N GLUsy 51 " --> pdb=" O ARGsy 69 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARGsy 71 " --> pdb=" O VALsy 49 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VALsy 49 " --> pdb=" O ARGsy 71 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'sz' and resid 15 through 18 removed outlier: 3.605A pdb=" N ILEsz 79 " --> pdb=" O LYSsz 24 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SERsz 74 " --> pdb=" O PHEsz 64 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHEsz 64 " --> pdb=" O SERsz 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHEsz 76 " --> pdb=" O ASNsz 62 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASNsz 62 " --> pdb=" O PHEsz 76 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 791 hydrogen bonds 1272 hydrogen bond angles 0 basepair planarities 330 basepair parallelities 554 stacking parallelities Total time for adding SS restraints: 13.48 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 3703 1.26 - 1.40: 13296 1.40 - 1.54: 24910 1.54 - 1.68: 2310 1.68 - 1.83: 142 Bond restraints: 44361 Sorted by residual: bond pdb=" CA ILEsh 106 " pdb=" C ILEsh 106 " ideal model delta sigma weight residual 1.523 1.314 0.209 1.30e-02 5.92e+03 2.58e+02 bond pdb=" CA ILEsh 121 " pdb=" C ILEsh 121 " ideal model delta sigma weight residual 1.523 1.380 0.143 1.27e-02 6.20e+03 1.27e+02 bond pdb=" C ILEsh 106 " pdb=" O ILEsh 106 " ideal model delta sigma weight residual 1.238 1.114 0.124 1.10e-02 8.26e+03 1.26e+02 bond pdb=" CA ILEsh 106 " pdb=" CB ILEsh 106 " ideal model delta sigma weight residual 1.535 1.394 0.141 1.29e-02 6.01e+03 1.19e+02 bond pdb=" N ARGsh 142 " pdb=" CA ARGsh 142 " ideal model delta sigma weight residual 1.459 1.338 0.121 1.18e-02 7.18e+03 1.05e+02 ... (remaining 44356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.01: 65117 4.01 - 8.01: 173 8.01 - 12.02: 25 12.02 - 16.02: 5 16.02 - 20.03: 6 Bond angle restraints: 65326 Sorted by residual: angle pdb=" O VALsh 102 " pdb=" C VALsh 102 " pdb=" N ALAsh 103 " ideal model delta sigma weight residual 122.57 103.30 19.27 1.07e+00 8.73e-01 3.24e+02 angle pdb=" N SERsh 139 " pdb=" CA SERsh 139 " pdb=" C SERsh 139 " ideal model delta sigma weight residual 113.17 94.34 18.83 1.26e+00 6.30e-01 2.23e+02 angle pdb=" CA VALsh 102 " pdb=" C VALsh 102 " pdb=" N ALAsh 103 " ideal model delta sigma weight residual 115.77 131.21 -15.44 1.25e+00 6.40e-01 1.53e+02 angle pdb=" C VALsh 113 " pdb=" CA VALsh 113 " pdb=" CB VALsh 113 " ideal model delta sigma weight residual 111.29 131.32 -20.03 1.64e+00 3.72e-01 1.49e+02 angle pdb=" C THRsh 111 " pdb=" CA THRsh 111 " pdb=" CB THRsh 111 " ideal model delta sigma weight residual 110.42 90.78 19.64 1.99e+00 2.53e-01 9.74e+01 ... (remaining 65321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 24803 35.73 - 71.45: 2623 71.45 - 107.18: 267 107.18 - 142.90: 10 142.90 - 178.63: 22 Dihedral angle restraints: 27725 sinusoidal: 21573 harmonic: 6152 Sorted by residual: dihedral pdb=" C5' GsI 15 " pdb=" C4' GsI 15 " pdb=" C3' GsI 15 " pdb=" O3' GsI 15 " ideal model delta sinusoidal sigma weight residual 147.00 77.06 69.94 1 8.00e+00 1.56e-02 9.85e+01 dihedral pdb=" O4' Usa 59 " pdb=" C1' Usa 59 " pdb=" N1 Usa 59 " pdb=" C2 Usa 59 " ideal model delta sinusoidal sigma weight residual 200.00 27.70 172.30 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' GsI 15 " pdb=" C4' GsI 15 " pdb=" C3' GsI 15 " pdb=" C2' GsI 15 " ideal model delta sinusoidal sigma weight residual 24.00 -39.96 63.96 1 8.00e+00 1.56e-02 8.41e+01 ... (remaining 27722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 7979 0.097 - 0.194: 243 0.194 - 0.291: 25 0.291 - 0.388: 4 0.388 - 0.485: 3 Chirality restraints: 8254 Sorted by residual: chirality pdb=" CA GLUsh 118 " pdb=" N GLUsh 118 " pdb=" C GLUsh 118 " pdb=" CB GLUsh 118 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA VALsh 108 " pdb=" N VALsh 108 " pdb=" C VALsh 108 " pdb=" CB VALsh 108 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CA ALAsh 138 " pdb=" N ALAsh 138 " pdb=" C ALAsh 138 " pdb=" CB ALAsh 138 " both_signs ideal model delta sigma weight residual False 2.48 2.05 0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 8251 not shown) Planarity restraints: 4046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VALsh 102 " -0.044 2.00e-02 2.50e+03 7.42e-02 5.51e+01 pdb=" C VALsh 102 " 0.129 2.00e-02 2.50e+03 pdb=" O VALsh 102 " -0.041 2.00e-02 2.50e+03 pdb=" N ALAsh 103 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' Asa 295 " -0.069 2.00e-02 2.50e+03 3.10e-02 2.65e+01 pdb=" N9 Asa 295 " 0.071 2.00e-02 2.50e+03 pdb=" C8 Asa 295 " 0.004 2.00e-02 2.50e+03 pdb=" N7 Asa 295 " 0.005 2.00e-02 2.50e+03 pdb=" C5 Asa 295 " -0.001 2.00e-02 2.50e+03 pdb=" C6 Asa 295 " -0.009 2.00e-02 2.50e+03 pdb=" N6 Asa 295 " -0.023 2.00e-02 2.50e+03 pdb=" N1 Asa 295 " 0.001 2.00e-02 2.50e+03 pdb=" C2 Asa 295 " 0.005 2.00e-02 2.50e+03 pdb=" N3 Asa 295 " 0.010 2.00e-02 2.50e+03 pdb=" C4 Asa 295 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SERsr 76 " -0.066 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PROsr 77 " 0.173 5.00e-02 4.00e+02 pdb=" CA PROsr 77 " -0.053 5.00e-02 4.00e+02 pdb=" CD PROsr 77 " -0.054 5.00e-02 4.00e+02 ... (remaining 4043 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1680 2.65 - 3.21: 34827 3.21 - 3.77: 76150 3.77 - 4.34: 104412 4.34 - 4.90: 146147 Nonbonded interactions: 363216 Sorted by model distance: nonbonded pdb=" OP2 Usa 103 " pdb=" N6 Asa 305 " model vdw 2.087 3.120 nonbonded pdb=" O2' Usa 125 " pdb=" O2 Csa 203 " model vdw 2.101 3.040 nonbonded pdb=" O2' Usa 115 " pdb=" O2 Csa 328 " model vdw 2.113 3.040 nonbonded pdb=" OP1 Usa 243 " pdb=" OH TYRsm 33 " model vdw 2.115 3.040 nonbonded pdb=" O2' AsI 58 " pdb=" OP2 UsI 60 " model vdw 2.127 3.040 ... (remaining 363211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 44.590 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.209 44361 Z= 0.343 Angle : 0.681 20.030 65326 Z= 0.381 Chirality : 0.040 0.485 8254 Planarity : 0.004 0.100 4046 Dihedral : 22.831 178.625 23747 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 1.11 % Allowed : 7.15 % Favored : 91.74 % Rotamer: Outliers : 7.24 % Allowed : 27.83 % Favored : 64.92 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.18), residues: 2069 helix: -0.74 (0.23), residues: 491 sheet: -0.32 (0.28), residues: 383 loop : -1.51 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsy 69 TYR 0.021 0.001 TYRsc 217 PHE 0.012 0.001 PHEsf 224 TRP 0.009 0.001 TRPsy 25 HIS 0.011 0.001 HISsh 191 Details of bonding type rmsd covalent geometry : bond 0.00551 (44361) covalent geometry : angle 0.68097 (65326) hydrogen bonds : bond 0.17689 ( 1294) hydrogen bonds : angle 6.67699 ( 2667) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 225 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: sb 21 LYS cc_start: 0.7747 (tmtt) cc_final: 0.7466 (tmtt) REVERT: sc 247 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8184 (tptt) REVERT: sf 149 HIS cc_start: 0.7519 (t-90) cc_final: 0.7254 (t-90) REVERT: sf 151 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7449 (mm-30) REVERT: sh 64 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6828 (tpt) REVERT: sh 87 LEU cc_start: -0.0541 (OUTLIER) cc_final: -0.1304 (tp) REVERT: sh 209 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7012 (pm20) REVERT: sh 212 ARG cc_start: 0.8839 (ttp-110) cc_final: 0.8555 (ptt-90) REVERT: sj 103 GLU cc_start: 0.6247 (pt0) cc_final: 0.4978 (tp30) REVERT: sk 3 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6077 (mtm-85) REVERT: sk 120 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6678 (ptpt) REVERT: sm 79 MET cc_start: 0.8550 (mtm) cc_final: 0.8012 (mtm) REVERT: sr 119 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8549 (mttt) outliers start: 133 outliers final: 53 residues processed: 331 average time/residue: 0.2356 time to fit residues: 127.9853 Evaluate side-chains 237 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 60 THR Chi-restraints excluded: chain sB residue 67 THR Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 31 SER Chi-restraints excluded: chain sb residue 199 ASP Chi-restraints excluded: chain sb residue 204 VAL Chi-restraints excluded: chain sc residue 87 SER Chi-restraints excluded: chain sc residue 203 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain sc residue 247 LYS Chi-restraints excluded: chain se residue 45 VAL Chi-restraints excluded: chain se residue 70 VAL Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 82 VAL Chi-restraints excluded: chain sf residue 198 VAL Chi-restraints excluded: chain sf residue 232 THR Chi-restraints excluded: chain sh residue 58 LYS Chi-restraints excluded: chain sh residue 64 MET Chi-restraints excluded: chain sh residue 73 VAL Chi-restraints excluded: chain sh residue 85 LYS Chi-restraints excluded: chain sh residue 87 LEU Chi-restraints excluded: chain sh residue 97 VAL Chi-restraints excluded: chain sh residue 109 LEU Chi-restraints excluded: chain sh residue 116 LYS Chi-restraints excluded: chain sh residue 118 GLU Chi-restraints excluded: chain sh residue 121 ILE Chi-restraints excluded: chain sh residue 141 ILE Chi-restraints excluded: chain sh residue 184 VAL Chi-restraints excluded: chain sh residue 185 THR Chi-restraints excluded: chain sh residue 209 GLU Chi-restraints excluded: chain sh residue 216 ILE Chi-restraints excluded: chain sj residue 43 VAL Chi-restraints excluded: chain sj residue 82 VAL Chi-restraints excluded: chain sj residue 93 THR Chi-restraints excluded: chain sk residue 3 ARG Chi-restraints excluded: chain sk residue 5 LEU Chi-restraints excluded: chain sk residue 66 ASP Chi-restraints excluded: chain sk residue 82 ASN Chi-restraints excluded: chain sk residue 89 ASP Chi-restraints excluded: chain sk residue 120 LYS Chi-restraints excluded: chain sk residue 158 LEU Chi-restraints excluded: chain sm residue 5 THR Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 40 THR Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 52 THR Chi-restraints excluded: chain sp residue 62 ASP Chi-restraints excluded: chain sr residue 53 VAL Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sx residue 37 VAL Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sy residue 86 ASP Chi-restraints excluded: chain sy residue 92 VAL Chi-restraints excluded: chain sy residue 95 ASN Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sz residue 65 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 30.0000 overall best weight: 7.6130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sf 96 ASN sh 110 ASN sk 82 ASN sr 66 ASN ** sz 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.065411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.053690 restraints weight = 212065.761| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.44 r_work: 0.3287 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 44361 Z= 0.231 Angle : 0.656 10.202 65326 Z= 0.338 Chirality : 0.039 0.372 8254 Planarity : 0.005 0.104 4046 Dihedral : 22.678 179.832 19544 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.75 % Favored : 93.91 % Rotamer: Outliers : 6.54 % Allowed : 24.84 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.18), residues: 2069 helix: -0.33 (0.22), residues: 513 sheet: -0.45 (0.27), residues: 386 loop : -1.57 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGsh 88 TYR 0.016 0.002 TYRsh 213 PHE 0.018 0.002 PHEsz 89 TRP 0.012 0.002 TRPsy 20 HIS 0.004 0.001 HISsh 140 Details of bonding type rmsd covalent geometry : bond 0.00455 (44361) covalent geometry : angle 0.65577 (65326) hydrogen bonds : bond 0.06388 ( 1294) hydrogen bonds : angle 4.30528 ( 2667) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 212 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sb 21 LYS cc_start: 0.7977 (tmtt) cc_final: 0.7675 (tttm) REVERT: sc 247 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8255 (tptt) REVERT: sf 36 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7963 (tpp) REVERT: sf 127 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7357 (ttt180) REVERT: sf 187 MET cc_start: 0.7459 (ttt) cc_final: 0.7256 (ttt) REVERT: sh 64 MET cc_start: 0.7872 (tmm) cc_final: 0.6899 (tpt) REVERT: sh 159 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6627 (mtp85) REVERT: sh 212 ARG cc_start: 0.8874 (ttp-110) cc_final: 0.8446 (ptt-90) REVERT: si 100 LYS cc_start: 0.7545 (tptp) cc_final: 0.6752 (tppt) REVERT: sj 103 GLU cc_start: 0.7017 (pt0) cc_final: 0.6761 (pt0) REVERT: sk 3 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.5893 (mtm-85) REVERT: sp 81 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8304 (mtmm) REVERT: sr 112 ASP cc_start: 0.8726 (p0) cc_final: 0.7475 (p0) REVERT: sr 119 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8887 (mttt) REVERT: sx 50 TYR cc_start: 0.8830 (m-80) cc_final: 0.8626 (m-10) REVERT: sy 19 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8971 (mtmt) REVERT: sz 67 LYS cc_start: 0.6658 (mtpt) cc_final: 0.6445 (mtmt) REVERT: sz 68 TYR cc_start: 0.5983 (t80) cc_final: 0.5674 (t80) outliers start: 120 outliers final: 60 residues processed: 315 average time/residue: 0.2303 time to fit residues: 121.7547 Evaluate side-chains 255 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 187 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 3 SER Chi-restraints excluded: chain sB residue 30 VAL Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 59 LEU Chi-restraints excluded: chain sB residue 76 SER Chi-restraints excluded: chain sC residue 10 ASN Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 31 SER Chi-restraints excluded: chain sb residue 199 ASP Chi-restraints excluded: chain sb residue 204 VAL Chi-restraints excluded: chain sb residue 206 VAL Chi-restraints excluded: chain sc residue 87 SER Chi-restraints excluded: chain sc residue 203 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain sc residue 247 LYS Chi-restraints excluded: chain se residue 45 VAL Chi-restraints excluded: chain se residue 48 ILE Chi-restraints excluded: chain se residue 70 VAL Chi-restraints excluded: chain se residue 121 THR Chi-restraints excluded: chain se residue 200 VAL Chi-restraints excluded: chain sf residue 24 THR Chi-restraints excluded: chain sf residue 36 MET Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 82 VAL Chi-restraints excluded: chain sf residue 87 VAL Chi-restraints excluded: chain sf residue 127 ARG Chi-restraints excluded: chain sf residue 128 VAL Chi-restraints excluded: chain sf residue 198 VAL Chi-restraints excluded: chain sh residue 73 VAL Chi-restraints excluded: chain sh residue 101 ILE Chi-restraints excluded: chain sh residue 121 ILE Chi-restraints excluded: chain sh residue 159 ARG Chi-restraints excluded: chain sh residue 185 THR Chi-restraints excluded: chain si residue 155 VAL Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 165 VAL Chi-restraints excluded: chain si residue 188 ILE Chi-restraints excluded: chain sj residue 35 ASN Chi-restraints excluded: chain sj residue 82 VAL Chi-restraints excluded: chain sj residue 93 THR Chi-restraints excluded: chain sk residue 3 ARG Chi-restraints excluded: chain sk residue 52 MET Chi-restraints excluded: chain sk residue 105 LEU Chi-restraints excluded: chain sk residue 128 LEU Chi-restraints excluded: chain sk residue 143 VAL Chi-restraints excluded: chain sk residue 158 LEU Chi-restraints excluded: chain sm residue 18 SER Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 143 THR Chi-restraints excluded: chain sm residue 144 SER Chi-restraints excluded: chain so residue 126 THR Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 60 ASP Chi-restraints excluded: chain sp residue 81 LYS Chi-restraints excluded: chain sr residue 53 VAL Chi-restraints excluded: chain sr residue 114 THR Chi-restraints excluded: chain sr residue 119 LYS Chi-restraints excluded: chain sx residue 37 VAL Chi-restraints excluded: chain sx residue 61 ILE Chi-restraints excluded: chain sx residue 84 MET Chi-restraints excluded: chain sx residue 86 ILE Chi-restraints excluded: chain sy residue 19 LYS Chi-restraints excluded: chain sy residue 86 ASP Chi-restraints excluded: chain sy residue 92 VAL Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sz residue 26 VAL Chi-restraints excluded: chain sz residue 28 VAL Chi-restraints excluded: chain sz residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 236 optimal weight: 10.0000 chunk 307 optimal weight: 1.9990 chunk 177 optimal weight: 20.0000 chunk 68 optimal weight: 40.0000 chunk 214 optimal weight: 2.9990 chunk 254 optimal weight: 0.0370 chunk 103 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 overall best weight: 4.8068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sr 66 ASN ** sz 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.065662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.053738 restraints weight = 211259.681| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.41 r_work: 0.3285 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 44361 Z= 0.153 Angle : 0.550 8.950 65326 Z= 0.286 Chirality : 0.036 0.264 8254 Planarity : 0.004 0.095 4046 Dihedral : 22.533 178.308 19480 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.93 % Favored : 94.78 % Rotamer: Outliers : 4.63 % Allowed : 27.02 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.18), residues: 2069 helix: 0.33 (0.23), residues: 521 sheet: -0.41 (0.27), residues: 391 loop : -1.46 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGsr 78 TYR 0.014 0.001 TYRsy 34 PHE 0.011 0.001 PHEsf 224 TRP 0.010 0.001 TRPsb 183 HIS 0.005 0.001 HISsh 191 Details of bonding type rmsd covalent geometry : bond 0.00296 (44361) covalent geometry : angle 0.54955 (65326) hydrogen bonds : bond 0.05664 ( 1294) hydrogen bonds : angle 3.96687 ( 2667) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 195 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sb 18 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6806 (tm-30) REVERT: sb 21 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7725 (tttm) REVERT: sc 247 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8283 (tptt) REVERT: sf 58 GLU cc_start: 0.8951 (mp0) cc_final: 0.8208 (mt-10) REVERT: sf 125 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6731 (mp0) REVERT: sf 151 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7436 (mp0) REVERT: sh 64 MET cc_start: 0.7611 (tmm) cc_final: 0.7308 (tpt) REVERT: sh 106 ILE cc_start: 0.7874 (mm) cc_final: 0.7635 (mm) REVERT: sh 159 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6702 (mtp85) REVERT: sh 212 ARG cc_start: 0.8899 (ttp-110) cc_final: 0.8616 (ptt90) REVERT: sh 217 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5884 (tp) REVERT: si 100 LYS cc_start: 0.7739 (tptp) cc_final: 0.6684 (tppt) REVERT: sk 3 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.5912 (mtm-85) REVERT: sk 152 SER cc_start: 0.8254 (t) cc_final: 0.7433 (m) REVERT: sm 46 GLU cc_start: 0.8283 (tp30) cc_final: 0.7727 (mt-10) REVERT: sp 81 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8299 (mtmm) REVERT: sx 84 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7368 (ttm) REVERT: sz 23 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6826 (ttp-170) REVERT: sz 68 TYR cc_start: 0.5893 (t80) cc_final: 0.5670 (t80) outliers start: 85 outliers final: 52 residues processed: 268 average time/residue: 0.2476 time to fit residues: 111.3193 Evaluate side-chains 238 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 178 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 42 LYS Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 59 LEU Chi-restraints excluded: chain sB residue 76 SER Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 28 THR Chi-restraints excluded: chain sb residue 18 GLU Chi-restraints excluded: chain sb residue 174 SER Chi-restraints excluded: chain sb residue 199 ASP Chi-restraints excluded: chain sb residue 204 VAL Chi-restraints excluded: chain sc residue 203 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain sc residue 247 LYS Chi-restraints excluded: chain se residue 45 VAL Chi-restraints excluded: chain se residue 48 ILE Chi-restraints excluded: chain se residue 70 VAL Chi-restraints excluded: chain se residue 121 THR Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 87 VAL Chi-restraints excluded: chain sf residue 128 VAL Chi-restraints excluded: chain sh residue 73 VAL Chi-restraints excluded: chain sh residue 159 ARG Chi-restraints excluded: chain sh residue 184 VAL Chi-restraints excluded: chain sh residue 185 THR Chi-restraints excluded: chain sh residue 209 GLU Chi-restraints excluded: chain sh residue 217 LEU Chi-restraints excluded: chain si residue 102 VAL Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 163 VAL Chi-restraints excluded: chain si residue 199 VAL Chi-restraints excluded: chain sj residue 93 THR Chi-restraints excluded: chain sk residue 3 ARG Chi-restraints excluded: chain sk residue 89 ASP Chi-restraints excluded: chain sk residue 128 LEU Chi-restraints excluded: chain sk residue 143 VAL Chi-restraints excluded: chain sk residue 158 LEU Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 144 SER Chi-restraints excluded: chain sp residue 52 THR Chi-restraints excluded: chain sp residue 81 LYS Chi-restraints excluded: chain sp residue 85 VAL Chi-restraints excluded: chain sr residue 2 VAL Chi-restraints excluded: chain sr residue 53 VAL Chi-restraints excluded: chain sr residue 60 LYS Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sr residue 114 THR Chi-restraints excluded: chain sx residue 37 VAL Chi-restraints excluded: chain sx residue 84 MET Chi-restraints excluded: chain sx residue 86 ILE Chi-restraints excluded: chain sy residue 79 ILE Chi-restraints excluded: chain sy residue 86 ASP Chi-restraints excluded: chain sy residue 92 VAL Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sz residue 14 ASN Chi-restraints excluded: chain sz residue 20 LEU Chi-restraints excluded: chain sz residue 23 ARG Chi-restraints excluded: chain sz residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 300 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 268 optimal weight: 9.9990 chunk 315 optimal weight: 40.0000 chunk 154 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 258 optimal weight: 9.9990 chunk 126 optimal weight: 30.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sr 66 ASN ** sz 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.064036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.051945 restraints weight = 210204.518| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.41 r_work: 0.3232 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 44361 Z= 0.274 Angle : 0.660 8.676 65326 Z= 0.339 Chirality : 0.040 0.338 8254 Planarity : 0.005 0.111 4046 Dihedral : 22.682 178.637 19472 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.38 % Favored : 93.23 % Rotamer: Outliers : 6.05 % Allowed : 25.82 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2069 helix: 0.24 (0.23), residues: 521 sheet: -0.51 (0.26), residues: 406 loop : -1.59 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGso 124 TYR 0.014 0.002 TYRsm 96 PHE 0.013 0.002 PHEsz 89 TRP 0.013 0.002 TRPsb 183 HIS 0.005 0.001 HISsp 38 Details of bonding type rmsd covalent geometry : bond 0.00543 (44361) covalent geometry : angle 0.65971 (65326) hydrogen bonds : bond 0.06624 ( 1294) hydrogen bonds : angle 4.05614 ( 2667) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 182 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sb 18 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6708 (tm-30) REVERT: sc 108 ASP cc_start: 0.7580 (p0) cc_final: 0.7294 (p0) REVERT: sc 247 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8184 (tptt) REVERT: sf 36 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8341 (tpp) REVERT: sf 58 GLU cc_start: 0.8855 (mp0) cc_final: 0.8265 (mt-10) REVERT: sf 187 MET cc_start: 0.7633 (ttt) cc_final: 0.7316 (ttt) REVERT: sh 159 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6667 (mtp85) REVERT: sh 188 ARG cc_start: 0.4433 (tpp-160) cc_final: 0.3404 (tpp-160) REVERT: sh 212 ARG cc_start: 0.8910 (ttp-110) cc_final: 0.8659 (ptt90) REVERT: sh 217 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5683 (tp) REVERT: si 134 GLU cc_start: 0.5702 (OUTLIER) cc_final: 0.5499 (mt-10) REVERT: sk 3 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6342 (mtm-85) REVERT: sk 115 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5684 (mtm110) REVERT: sm 46 GLU cc_start: 0.8193 (tp30) cc_final: 0.7683 (mt-10) REVERT: sp 81 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8318 (mtmm) REVERT: sr 112 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7987 (p0) REVERT: sr 115 GLU cc_start: 0.8307 (pm20) cc_final: 0.7836 (pm20) REVERT: sr 119 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8916 (mttt) REVERT: sx 84 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7446 (ttm) REVERT: sy 43 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8048 (p) REVERT: sz 18 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7639 (t0) outliers start: 111 outliers final: 65 residues processed: 275 average time/residue: 0.2522 time to fit residues: 116.2449 Evaluate side-chains 249 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 170 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 29 CYS Chi-restraints excluded: chain sB residue 42 LYS Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 59 LEU Chi-restraints excluded: chain sB residue 60 THR Chi-restraints excluded: chain sB residue 76 SER Chi-restraints excluded: chain sC residue 10 ASN Chi-restraints excluded: chain sb residue 18 GLU Chi-restraints excluded: chain sb residue 174 SER Chi-restraints excluded: chain sb residue 176 LEU Chi-restraints excluded: chain sb residue 199 ASP Chi-restraints excluded: chain sb residue 204 VAL Chi-restraints excluded: chain sb residue 206 VAL Chi-restraints excluded: chain sc residue 203 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain sc residue 247 LYS Chi-restraints excluded: chain se residue 45 VAL Chi-restraints excluded: chain se residue 48 ILE Chi-restraints excluded: chain se residue 70 VAL Chi-restraints excluded: chain se residue 121 THR Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain sf residue 24 THR Chi-restraints excluded: chain sf residue 36 MET Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 82 VAL Chi-restraints excluded: chain sf residue 128 VAL Chi-restraints excluded: chain sh residue 73 VAL Chi-restraints excluded: chain sh residue 114 VAL Chi-restraints excluded: chain sh residue 159 ARG Chi-restraints excluded: chain sh residue 185 THR Chi-restraints excluded: chain sh residue 209 GLU Chi-restraints excluded: chain sh residue 217 LEU Chi-restraints excluded: chain si residue 102 VAL Chi-restraints excluded: chain si residue 134 GLU Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 163 VAL Chi-restraints excluded: chain si residue 188 ILE Chi-restraints excluded: chain sj residue 82 VAL Chi-restraints excluded: chain sj residue 93 THR Chi-restraints excluded: chain sk residue 3 ARG Chi-restraints excluded: chain sk residue 89 ASP Chi-restraints excluded: chain sk residue 103 ASN Chi-restraints excluded: chain sk residue 115 ARG Chi-restraints excluded: chain sk residue 128 LEU Chi-restraints excluded: chain sk residue 158 LEU Chi-restraints excluded: chain sm residue 18 SER Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 138 ASN Chi-restraints excluded: chain sm residue 143 THR Chi-restraints excluded: chain sm residue 144 SER Chi-restraints excluded: chain so residue 126 THR Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 40 THR Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 52 THR Chi-restraints excluded: chain sp residue 81 LYS Chi-restraints excluded: chain sp residue 118 ASN Chi-restraints excluded: chain sp residue 127 VAL Chi-restraints excluded: chain sr residue 2 VAL Chi-restraints excluded: chain sr residue 53 VAL Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 112 ASP Chi-restraints excluded: chain sr residue 114 THR Chi-restraints excluded: chain sr residue 119 LYS Chi-restraints excluded: chain sx residue 37 VAL Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sx residue 84 MET Chi-restraints excluded: chain sx residue 86 ILE Chi-restraints excluded: chain sy residue 12 LEU Chi-restraints excluded: chain sy residue 31 VAL Chi-restraints excluded: chain sy residue 43 SER Chi-restraints excluded: chain sy residue 79 ILE Chi-restraints excluded: chain sy residue 86 ASP Chi-restraints excluded: chain sy residue 92 VAL Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sz residue 18 ASN Chi-restraints excluded: chain sz residue 23 ARG Chi-restraints excluded: chain sz residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 295 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 14 optimal weight: 50.0000 chunk 315 optimal weight: 50.0000 chunk 8 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 25 optimal weight: 40.0000 chunk 196 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sr 66 ASN ** sz 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.063889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.051842 restraints weight = 209064.941| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.45 r_work: 0.3230 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 44361 Z= 0.282 Angle : 0.652 8.760 65326 Z= 0.335 Chirality : 0.041 0.323 8254 Planarity : 0.005 0.113 4046 Dihedral : 22.666 179.399 19471 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.94 % Favored : 93.72 % Rotamer: Outliers : 6.15 % Allowed : 26.42 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.18), residues: 2069 helix: 0.22 (0.23), residues: 524 sheet: -0.77 (0.25), residues: 421 loop : -1.58 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGsh 88 TYR 0.013 0.002 TYRsm 96 PHE 0.014 0.002 PHEsf 224 TRP 0.011 0.002 TRPsb 183 HIS 0.007 0.001 HISsh 191 Details of bonding type rmsd covalent geometry : bond 0.00557 (44361) covalent geometry : angle 0.65173 (65326) hydrogen bonds : bond 0.06523 ( 1294) hydrogen bonds : angle 4.03973 ( 2667) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 172 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sB 28 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8029 (ttt-90) REVERT: sb 18 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: sc 108 ASP cc_start: 0.7720 (p0) cc_final: 0.7446 (p0) REVERT: sc 247 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8243 (tptt) REVERT: sf 58 GLU cc_start: 0.8917 (mp0) cc_final: 0.8297 (mt-10) REVERT: sf 146 ARG cc_start: 0.7440 (mmp-170) cc_final: 0.6903 (mmp80) REVERT: sf 187 MET cc_start: 0.7810 (ttt) cc_final: 0.7532 (ttt) REVERT: sh 159 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6939 (mtp85) REVERT: sh 197 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7448 (mm-30) REVERT: sk 3 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6335 (mtm-85) REVERT: sk 115 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.5750 (mtm110) REVERT: sk 152 SER cc_start: 0.8107 (t) cc_final: 0.7321 (m) REVERT: sm 46 GLU cc_start: 0.8182 (tp30) cc_final: 0.7719 (mt-10) REVERT: sp 81 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8402 (mtmm) REVERT: sr 112 ASP cc_start: 0.8333 (p0) cc_final: 0.7469 (p0) REVERT: sr 115 GLU cc_start: 0.8025 (pm20) cc_final: 0.7585 (pm20) REVERT: sr 119 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8903 (mttt) REVERT: sx 84 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7346 (ttm) REVERT: sx 85 MET cc_start: 0.8784 (mmm) cc_final: 0.8390 (mmm) REVERT: sz 18 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7617 (t0) outliers start: 113 outliers final: 79 residues processed: 272 average time/residue: 0.2367 time to fit residues: 107.4130 Evaluate side-chains 258 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 169 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 28 ARG Chi-restraints excluded: chain sB residue 29 CYS Chi-restraints excluded: chain sB residue 42 LYS Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 59 LEU Chi-restraints excluded: chain sB residue 60 THR Chi-restraints excluded: chain sB residue 76 SER Chi-restraints excluded: chain sC residue 10 ASN Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 31 SER Chi-restraints excluded: chain sb residue 18 GLU Chi-restraints excluded: chain sb residue 174 SER Chi-restraints excluded: chain sb residue 199 ASP Chi-restraints excluded: chain sb residue 204 VAL Chi-restraints excluded: chain sb residue 206 VAL Chi-restraints excluded: chain sc residue 203 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain sc residue 247 LYS Chi-restraints excluded: chain se residue 45 VAL Chi-restraints excluded: chain se residue 48 ILE Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 70 VAL Chi-restraints excluded: chain se residue 121 THR Chi-restraints excluded: chain se residue 122 LEU Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain sf residue 21 LEU Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 82 VAL Chi-restraints excluded: chain sf residue 128 VAL Chi-restraints excluded: chain sh residue 63 MET Chi-restraints excluded: chain sh residue 108 VAL Chi-restraints excluded: chain sh residue 114 VAL Chi-restraints excluded: chain sh residue 121 ILE Chi-restraints excluded: chain sh residue 159 ARG Chi-restraints excluded: chain sh residue 184 VAL Chi-restraints excluded: chain sh residue 185 THR Chi-restraints excluded: chain sh residue 209 GLU Chi-restraints excluded: chain sh residue 216 ILE Chi-restraints excluded: chain si residue 102 VAL Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 163 VAL Chi-restraints excluded: chain si residue 188 ILE Chi-restraints excluded: chain si residue 199 VAL Chi-restraints excluded: chain sj residue 3 ILE Chi-restraints excluded: chain sj residue 35 ASN Chi-restraints excluded: chain sj residue 82 VAL Chi-restraints excluded: chain sj residue 93 THR Chi-restraints excluded: chain sk residue 3 ARG Chi-restraints excluded: chain sk residue 89 ASP Chi-restraints excluded: chain sk residue 103 ASN Chi-restraints excluded: chain sk residue 115 ARG Chi-restraints excluded: chain sk residue 128 LEU Chi-restraints excluded: chain sk residue 147 LEU Chi-restraints excluded: chain sk residue 158 LEU Chi-restraints excluded: chain sm residue 18 SER Chi-restraints excluded: chain sm residue 85 VAL Chi-restraints excluded: chain sm residue 138 ASN Chi-restraints excluded: chain sm residue 143 THR Chi-restraints excluded: chain sm residue 144 SER Chi-restraints excluded: chain so residue 126 THR Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 40 THR Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 55 MET Chi-restraints excluded: chain sp residue 81 LYS Chi-restraints excluded: chain sp residue 118 ASN Chi-restraints excluded: chain sp residue 124 ILE Chi-restraints excluded: chain sr residue 2 VAL Chi-restraints excluded: chain sr residue 42 MET Chi-restraints excluded: chain sr residue 53 VAL Chi-restraints excluded: chain sr residue 60 LYS Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 105 THR Chi-restraints excluded: chain sr residue 114 THR Chi-restraints excluded: chain sr residue 119 LYS Chi-restraints excluded: chain sx residue 37 VAL Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sx residue 84 MET Chi-restraints excluded: chain sy residue 12 LEU Chi-restraints excluded: chain sy residue 79 ILE Chi-restraints excluded: chain sy residue 86 ASP Chi-restraints excluded: chain sy residue 92 VAL Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sz residue 18 ASN Chi-restraints excluded: chain sz residue 23 ARG Chi-restraints excluded: chain sz residue 65 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 191 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 299 optimal weight: 6.9990 chunk 259 optimal weight: 30.0000 chunk 199 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 262 optimal weight: 40.0000 chunk 29 optimal weight: 20.0000 chunk 65 optimal weight: 30.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sB 25 HIS sr 66 ASN ** sz 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.064477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.052763 restraints weight = 209397.773| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.45 r_work: 0.3248 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 44361 Z= 0.205 Angle : 0.593 8.795 65326 Z= 0.308 Chirality : 0.038 0.285 8254 Planarity : 0.004 0.100 4046 Dihedral : 22.596 179.811 19470 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.90 % Favored : 93.86 % Rotamer: Outliers : 5.61 % Allowed : 26.91 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2069 helix: 0.33 (0.23), residues: 531 sheet: -0.70 (0.26), residues: 419 loop : -1.56 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsr 78 TYR 0.012 0.001 TYRsz 68 PHE 0.013 0.001 PHEsz 89 TRP 0.009 0.001 TRPsb 183 HIS 0.007 0.001 HISsh 191 Details of bonding type rmsd covalent geometry : bond 0.00402 (44361) covalent geometry : angle 0.59349 (65326) hydrogen bonds : bond 0.05933 ( 1294) hydrogen bonds : angle 3.89583 ( 2667) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 176 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sB 28 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8059 (ttt-90) REVERT: sb 18 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6670 (tm-30) REVERT: sb 89 MET cc_start: 0.8660 (tpp) cc_final: 0.8420 (tpp) REVERT: sc 108 ASP cc_start: 0.7540 (p0) cc_final: 0.7249 (p0) REVERT: sc 247 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8208 (tptt) REVERT: sf 36 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8084 (tpp) REVERT: sf 58 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8346 (mt-10) REVERT: sf 94 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8357 (tppt) REVERT: sf 146 ARG cc_start: 0.7256 (mmp-170) cc_final: 0.6714 (mmp80) REVERT: sf 187 MET cc_start: 0.7944 (ttt) cc_final: 0.7689 (ttt) REVERT: sh 159 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6831 (mtp85) REVERT: sh 197 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7481 (mm-30) REVERT: sk 3 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6153 (mtm-85) REVERT: sk 115 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.5842 (mtm110) REVERT: sk 152 SER cc_start: 0.8131 (t) cc_final: 0.7357 (m) REVERT: sm 46 GLU cc_start: 0.8119 (tp30) cc_final: 0.7680 (mt-10) REVERT: sp 81 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8423 (mtmm) REVERT: sr 112 ASP cc_start: 0.8246 (p0) cc_final: 0.7833 (p0) REVERT: sr 119 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8891 (mttt) REVERT: sx 84 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7596 (mtt) REVERT: sx 85 MET cc_start: 0.8790 (mmm) cc_final: 0.8342 (mmm) REVERT: sy 43 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.7996 (p) REVERT: sz 18 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7468 (t0) outliers start: 103 outliers final: 75 residues processed: 264 average time/residue: 0.2215 time to fit residues: 97.4974 Evaluate side-chains 261 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 172 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 26 CYS Chi-restraints excluded: chain sB residue 28 ARG Chi-restraints excluded: chain sB residue 29 CYS Chi-restraints excluded: chain sB residue 42 LYS Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 59 LEU Chi-restraints excluded: chain sB residue 76 SER Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 31 SER Chi-restraints excluded: chain sb residue 18 GLU Chi-restraints excluded: chain sb residue 174 SER Chi-restraints excluded: chain sb residue 176 LEU Chi-restraints excluded: chain sb residue 199 ASP Chi-restraints excluded: chain sb residue 204 VAL Chi-restraints excluded: chain sb residue 206 VAL Chi-restraints excluded: chain sc residue 86 GLN Chi-restraints excluded: chain sc residue 93 SER Chi-restraints excluded: chain sc residue 203 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain sc residue 247 LYS Chi-restraints excluded: chain se residue 45 VAL Chi-restraints excluded: chain se residue 48 ILE Chi-restraints excluded: chain se residue 70 VAL Chi-restraints excluded: chain se residue 121 THR Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain sf residue 21 LEU Chi-restraints excluded: chain sf residue 36 MET Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 58 GLU Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 82 VAL Chi-restraints excluded: chain sf residue 94 LYS Chi-restraints excluded: chain sf residue 128 VAL Chi-restraints excluded: chain sh residue 63 MET Chi-restraints excluded: chain sh residue 121 ILE Chi-restraints excluded: chain sh residue 157 VAL Chi-restraints excluded: chain sh residue 159 ARG Chi-restraints excluded: chain sh residue 184 VAL Chi-restraints excluded: chain sh residue 185 THR Chi-restraints excluded: chain sh residue 188 ARG Chi-restraints excluded: chain sh residue 209 GLU Chi-restraints excluded: chain sh residue 216 ILE Chi-restraints excluded: chain sh residue 219 ARG Chi-restraints excluded: chain si residue 102 VAL Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 163 VAL Chi-restraints excluded: chain si residue 188 ILE Chi-restraints excluded: chain sj residue 3 ILE Chi-restraints excluded: chain sj residue 82 VAL Chi-restraints excluded: chain sj residue 93 THR Chi-restraints excluded: chain sk residue 3 ARG Chi-restraints excluded: chain sk residue 89 ASP Chi-restraints excluded: chain sk residue 103 ASN Chi-restraints excluded: chain sk residue 115 ARG Chi-restraints excluded: chain sk residue 128 LEU Chi-restraints excluded: chain sk residue 147 LEU Chi-restraints excluded: chain sk residue 158 LEU Chi-restraints excluded: chain sm residue 18 SER Chi-restraints excluded: chain sm residue 138 ASN Chi-restraints excluded: chain sm residue 143 THR Chi-restraints excluded: chain sm residue 144 SER Chi-restraints excluded: chain so residue 126 THR Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 40 THR Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 52 THR Chi-restraints excluded: chain sp residue 55 MET Chi-restraints excluded: chain sp residue 81 LYS Chi-restraints excluded: chain sp residue 124 ILE Chi-restraints excluded: chain sr residue 2 VAL Chi-restraints excluded: chain sr residue 42 MET Chi-restraints excluded: chain sr residue 53 VAL Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 114 THR Chi-restraints excluded: chain sr residue 119 LYS Chi-restraints excluded: chain sx residue 37 VAL Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sx residue 84 MET Chi-restraints excluded: chain sy residue 41 THR Chi-restraints excluded: chain sy residue 43 SER Chi-restraints excluded: chain sy residue 79 ILE Chi-restraints excluded: chain sy residue 86 ASP Chi-restraints excluded: chain sy residue 92 VAL Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sz residue 18 ASN Chi-restraints excluded: chain sz residue 20 LEU Chi-restraints excluded: chain sz residue 23 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 126 optimal weight: 30.0000 chunk 213 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 205 optimal weight: 30.0000 chunk 254 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 282 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 279 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: se 71 ASN sr 66 ASN ** sz 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.064277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.052205 restraints weight = 209178.213| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.39 r_work: 0.3241 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 44361 Z= 0.227 Angle : 0.607 8.834 65326 Z= 0.314 Chirality : 0.038 0.301 8254 Planarity : 0.005 0.103 4046 Dihedral : 22.594 179.315 19469 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.99 % Favored : 93.77 % Rotamer: Outliers : 5.99 % Allowed : 26.20 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 2069 helix: 0.42 (0.23), residues: 524 sheet: -0.69 (0.26), residues: 407 loop : -1.51 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGso 124 TYR 0.014 0.001 TYRsc 103 PHE 0.012 0.001 PHEsz 89 TRP 0.011 0.002 TRPsb 183 HIS 0.007 0.001 HISsh 191 Details of bonding type rmsd covalent geometry : bond 0.00447 (44361) covalent geometry : angle 0.60654 (65326) hydrogen bonds : bond 0.06100 ( 1294) hydrogen bonds : angle 3.89769 ( 2667) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 175 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sB 6 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8054 (ttm-80) REVERT: sB 28 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8127 (ttt-90) REVERT: sb 14 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8729 (mmtt) REVERT: sb 18 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6357 (tm-30) REVERT: sc 108 ASP cc_start: 0.7688 (p0) cc_final: 0.7428 (p0) REVERT: sc 247 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8196 (tptt) REVERT: sf 36 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8109 (tpp) REVERT: sf 58 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8359 (mt-10) REVERT: sf 94 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8330 (tppt) REVERT: sf 146 ARG cc_start: 0.7350 (mmp-170) cc_final: 0.6854 (mmp80) REVERT: sf 170 PHE cc_start: 0.8644 (p90) cc_final: 0.8329 (p90) REVERT: sf 187 MET cc_start: 0.8014 (ttt) cc_final: 0.7757 (ttt) REVERT: sh 159 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6921 (mtp85) REVERT: sh 197 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7635 (mm-30) REVERT: si 162 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6461 (t80) REVERT: sk 3 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6242 (mtm-85) REVERT: sk 115 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.5726 (mtm110) REVERT: sk 152 SER cc_start: 0.8107 (t) cc_final: 0.7344 (m) REVERT: sm 46 GLU cc_start: 0.8153 (tp30) cc_final: 0.7717 (mt-10) REVERT: sp 81 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8436 (mtmm) REVERT: sr 112 ASP cc_start: 0.8149 (p0) cc_final: 0.7873 (p0) REVERT: sr 119 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8932 (mttt) REVERT: sx 84 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7423 (mmm) REVERT: sy 43 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.7981 (p) REVERT: sy 65 ARG cc_start: 0.5403 (OUTLIER) cc_final: 0.1936 (mtp180) REVERT: sz 18 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7456 (t0) outliers start: 110 outliers final: 83 residues processed: 265 average time/residue: 0.2548 time to fit residues: 111.9046 Evaluate side-chains 273 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 173 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 6 ARG Chi-restraints excluded: chain sB residue 26 CYS Chi-restraints excluded: chain sB residue 28 ARG Chi-restraints excluded: chain sB residue 29 CYS Chi-restraints excluded: chain sB residue 42 LYS Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 59 LEU Chi-restraints excluded: chain sB residue 60 THR Chi-restraints excluded: chain sB residue 76 SER Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 31 SER Chi-restraints excluded: chain sb residue 18 GLU Chi-restraints excluded: chain sb residue 174 SER Chi-restraints excluded: chain sb residue 176 LEU Chi-restraints excluded: chain sb residue 199 ASP Chi-restraints excluded: chain sb residue 204 VAL Chi-restraints excluded: chain sb residue 206 VAL Chi-restraints excluded: chain sc residue 86 GLN Chi-restraints excluded: chain sc residue 93 SER Chi-restraints excluded: chain sc residue 203 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain sc residue 247 LYS Chi-restraints excluded: chain se residue 45 VAL Chi-restraints excluded: chain se residue 48 ILE Chi-restraints excluded: chain se residue 70 VAL Chi-restraints excluded: chain se residue 121 THR Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain se residue 200 VAL Chi-restraints excluded: chain sf residue 21 LEU Chi-restraints excluded: chain sf residue 36 MET Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 58 GLU Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 82 VAL Chi-restraints excluded: chain sf residue 94 LYS Chi-restraints excluded: chain sf residue 128 VAL Chi-restraints excluded: chain sh residue 63 MET Chi-restraints excluded: chain sh residue 121 ILE Chi-restraints excluded: chain sh residue 157 VAL Chi-restraints excluded: chain sh residue 159 ARG Chi-restraints excluded: chain sh residue 184 VAL Chi-restraints excluded: chain sh residue 185 THR Chi-restraints excluded: chain sh residue 188 ARG Chi-restraints excluded: chain sh residue 209 GLU Chi-restraints excluded: chain sh residue 216 ILE Chi-restraints excluded: chain si residue 102 VAL Chi-restraints excluded: chain si residue 135 MET Chi-restraints excluded: chain si residue 155 VAL Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 162 PHE Chi-restraints excluded: chain si residue 163 VAL Chi-restraints excluded: chain si residue 188 ILE Chi-restraints excluded: chain si residue 199 VAL Chi-restraints excluded: chain sj residue 3 ILE Chi-restraints excluded: chain sj residue 82 VAL Chi-restraints excluded: chain sj residue 93 THR Chi-restraints excluded: chain sk residue 3 ARG Chi-restraints excluded: chain sk residue 89 ASP Chi-restraints excluded: chain sk residue 103 ASN Chi-restraints excluded: chain sk residue 115 ARG Chi-restraints excluded: chain sk residue 128 LEU Chi-restraints excluded: chain sk residue 147 LEU Chi-restraints excluded: chain sk residue 158 LEU Chi-restraints excluded: chain sm residue 18 SER Chi-restraints excluded: chain sm residue 138 ASN Chi-restraints excluded: chain sm residue 143 THR Chi-restraints excluded: chain sm residue 144 SER Chi-restraints excluded: chain so residue 126 THR Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 40 THR Chi-restraints excluded: chain sp residue 52 THR Chi-restraints excluded: chain sp residue 55 MET Chi-restraints excluded: chain sp residue 81 LYS Chi-restraints excluded: chain sp residue 118 ASN Chi-restraints excluded: chain sp residue 124 ILE Chi-restraints excluded: chain sr residue 2 VAL Chi-restraints excluded: chain sr residue 42 MET Chi-restraints excluded: chain sr residue 53 VAL Chi-restraints excluded: chain sr residue 60 LYS Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 105 THR Chi-restraints excluded: chain sr residue 114 THR Chi-restraints excluded: chain sr residue 119 LYS Chi-restraints excluded: chain sx residue 37 VAL Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sx residue 84 MET Chi-restraints excluded: chain sy residue 41 THR Chi-restraints excluded: chain sy residue 43 SER Chi-restraints excluded: chain sy residue 65 ARG Chi-restraints excluded: chain sy residue 79 ILE Chi-restraints excluded: chain sy residue 86 ASP Chi-restraints excluded: chain sy residue 92 VAL Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sz residue 17 VAL Chi-restraints excluded: chain sz residue 18 ASN Chi-restraints excluded: chain sz residue 20 LEU Chi-restraints excluded: chain sz residue 23 ARG Chi-restraints excluded: chain sz residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 133 optimal weight: 6.9990 chunk 80 optimal weight: 40.0000 chunk 312 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 273 optimal weight: 20.0000 chunk 159 optimal weight: 0.0870 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 284 optimal weight: 10.0000 overall best weight: 6.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: se 71 ASN sr 66 ASN ** sz 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.064747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.053094 restraints weight = 209341.847| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.43 r_work: 0.3252 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 44361 Z= 0.185 Angle : 0.579 11.313 65326 Z= 0.300 Chirality : 0.037 0.280 8254 Planarity : 0.004 0.103 4046 Dihedral : 22.560 179.981 19469 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.36 % Favored : 94.39 % Rotamer: Outliers : 5.77 % Allowed : 26.42 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.18), residues: 2069 helix: 0.53 (0.23), residues: 524 sheet: -0.67 (0.26), residues: 412 loop : -1.44 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGso 124 TYR 0.015 0.001 TYRsz 68 PHE 0.013 0.001 PHEsz 89 TRP 0.010 0.001 TRPsb 60 HIS 0.008 0.001 HISsh 191 Details of bonding type rmsd covalent geometry : bond 0.00363 (44361) covalent geometry : angle 0.57903 (65326) hydrogen bonds : bond 0.05763 ( 1294) hydrogen bonds : angle 3.83129 ( 2667) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 180 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sB 6 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8046 (ttm-80) REVERT: sb 18 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6353 (tm-30) REVERT: sc 75 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8697 (mt) REVERT: sc 108 ASP cc_start: 0.7622 (p0) cc_final: 0.7311 (p0) REVERT: sc 244 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8486 (mttp) REVERT: sc 247 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8230 (tptt) REVERT: sf 58 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8276 (mt-10) REVERT: sf 94 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8310 (tppt) REVERT: sf 146 ARG cc_start: 0.7260 (mmp-170) cc_final: 0.6759 (mmp80) REVERT: sf 170 PHE cc_start: 0.8651 (p90) cc_final: 0.8349 (p90) REVERT: sf 187 MET cc_start: 0.8042 (ttt) cc_final: 0.7795 (ttt) REVERT: sh 64 MET cc_start: 0.7761 (tpt) cc_final: 0.7493 (mmm) REVERT: sh 159 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6863 (mtp85) REVERT: sh 197 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7654 (mm-30) REVERT: sk 3 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6003 (mtm-85) REVERT: sm 46 GLU cc_start: 0.8086 (tp30) cc_final: 0.7677 (mt-10) REVERT: sm 98 ARG cc_start: 0.9529 (OUTLIER) cc_final: 0.9319 (mtt-85) REVERT: sp 81 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8420 (mtmm) REVERT: sr 119 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8939 (mttt) REVERT: sx 84 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7467 (mmm) REVERT: sy 43 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.7982 (p) REVERT: sz 18 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7394 (t0) outliers start: 106 outliers final: 79 residues processed: 270 average time/residue: 0.2348 time to fit residues: 105.6468 Evaluate side-chains 267 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 173 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 6 ARG Chi-restraints excluded: chain sB residue 26 CYS Chi-restraints excluded: chain sB residue 29 CYS Chi-restraints excluded: chain sB residue 42 LYS Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 59 LEU Chi-restraints excluded: chain sB residue 60 THR Chi-restraints excluded: chain sB residue 76 SER Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 31 SER Chi-restraints excluded: chain sb residue 18 GLU Chi-restraints excluded: chain sb residue 174 SER Chi-restraints excluded: chain sb residue 176 LEU Chi-restraints excluded: chain sb residue 199 ASP Chi-restraints excluded: chain sb residue 204 VAL Chi-restraints excluded: chain sb residue 206 VAL Chi-restraints excluded: chain sc residue 75 LEU Chi-restraints excluded: chain sc residue 86 GLN Chi-restraints excluded: chain sc residue 203 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain sc residue 244 LYS Chi-restraints excluded: chain sc residue 247 LYS Chi-restraints excluded: chain se residue 45 VAL Chi-restraints excluded: chain se residue 48 ILE Chi-restraints excluded: chain se residue 53 THR Chi-restraints excluded: chain se residue 70 VAL Chi-restraints excluded: chain se residue 121 THR Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain se residue 200 VAL Chi-restraints excluded: chain sf residue 21 LEU Chi-restraints excluded: chain sf residue 58 GLU Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 82 VAL Chi-restraints excluded: chain sf residue 94 LYS Chi-restraints excluded: chain sf residue 128 VAL Chi-restraints excluded: chain sh residue 63 MET Chi-restraints excluded: chain sh residue 108 VAL Chi-restraints excluded: chain sh residue 121 ILE Chi-restraints excluded: chain sh residue 157 VAL Chi-restraints excluded: chain sh residue 159 ARG Chi-restraints excluded: chain sh residue 184 VAL Chi-restraints excluded: chain sh residue 185 THR Chi-restraints excluded: chain sh residue 188 ARG Chi-restraints excluded: chain sh residue 216 ILE Chi-restraints excluded: chain si residue 102 VAL Chi-restraints excluded: chain si residue 135 MET Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 162 PHE Chi-restraints excluded: chain si residue 163 VAL Chi-restraints excluded: chain si residue 199 VAL Chi-restraints excluded: chain sj residue 3 ILE Chi-restraints excluded: chain sj residue 20 SER Chi-restraints excluded: chain sj residue 35 ASN Chi-restraints excluded: chain sj residue 82 VAL Chi-restraints excluded: chain sj residue 93 THR Chi-restraints excluded: chain sk residue 3 ARG Chi-restraints excluded: chain sk residue 103 ASN Chi-restraints excluded: chain sk residue 128 LEU Chi-restraints excluded: chain sk residue 147 LEU Chi-restraints excluded: chain sk residue 158 LEU Chi-restraints excluded: chain sm residue 18 SER Chi-restraints excluded: chain sm residue 98 ARG Chi-restraints excluded: chain sm residue 138 ASN Chi-restraints excluded: chain sm residue 143 THR Chi-restraints excluded: chain sm residue 144 SER Chi-restraints excluded: chain so residue 126 THR Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 52 THR Chi-restraints excluded: chain sp residue 55 MET Chi-restraints excluded: chain sp residue 81 LYS Chi-restraints excluded: chain sp residue 124 ILE Chi-restraints excluded: chain sp residue 127 VAL Chi-restraints excluded: chain sp residue 145 ARG Chi-restraints excluded: chain sr residue 2 VAL Chi-restraints excluded: chain sr residue 42 MET Chi-restraints excluded: chain sr residue 53 VAL Chi-restraints excluded: chain sr residue 60 LYS Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 105 THR Chi-restraints excluded: chain sr residue 119 LYS Chi-restraints excluded: chain sx residue 84 MET Chi-restraints excluded: chain sx residue 86 ILE Chi-restraints excluded: chain sy residue 41 THR Chi-restraints excluded: chain sy residue 43 SER Chi-restraints excluded: chain sy residue 79 ILE Chi-restraints excluded: chain sy residue 86 ASP Chi-restraints excluded: chain sy residue 92 VAL Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sz residue 17 VAL Chi-restraints excluded: chain sz residue 18 ASN Chi-restraints excluded: chain sz residue 20 LEU Chi-restraints excluded: chain sz residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 260 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 170 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 84 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: se 71 ASN sr 66 ASN ** sz 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.064288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.052204 restraints weight = 209562.788| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.39 r_work: 0.3239 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 44361 Z= 0.227 Angle : 0.608 12.489 65326 Z= 0.314 Chirality : 0.038 0.301 8254 Planarity : 0.004 0.103 4046 Dihedral : 22.569 179.364 19468 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.99 % Favored : 93.77 % Rotamer: Outliers : 5.99 % Allowed : 26.20 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.18), residues: 2069 helix: 0.45 (0.23), residues: 524 sheet: -0.66 (0.26), residues: 407 loop : -1.49 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGsr 78 TYR 0.014 0.001 TYRsz 68 PHE 0.019 0.001 PHEsz 89 TRP 0.009 0.002 TRPsb 60 HIS 0.010 0.001 HISsh 191 Details of bonding type rmsd covalent geometry : bond 0.00448 (44361) covalent geometry : angle 0.60841 (65326) hydrogen bonds : bond 0.06082 ( 1294) hydrogen bonds : angle 3.86926 ( 2667) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 177 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sB 6 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8059 (ttm-80) REVERT: sB 28 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8108 (ttt-90) REVERT: sb 18 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6450 (tm-30) REVERT: sb 89 MET cc_start: 0.8716 (tpp) cc_final: 0.8483 (tpp) REVERT: sc 75 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8724 (mt) REVERT: sc 108 ASP cc_start: 0.7735 (p0) cc_final: 0.7412 (p0) REVERT: sc 244 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8510 (mttp) REVERT: sc 247 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8209 (tptt) REVERT: sf 36 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8050 (tpp) REVERT: sf 58 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: sf 94 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8317 (tppt) REVERT: sf 146 ARG cc_start: 0.7245 (mmp-170) cc_final: 0.6743 (mmp80) REVERT: sf 147 TYR cc_start: 0.8043 (m-80) cc_final: 0.7748 (m-80) REVERT: sf 151 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7704 (mp0) REVERT: sf 170 PHE cc_start: 0.8631 (p90) cc_final: 0.8319 (p90) REVERT: sf 187 MET cc_start: 0.8037 (ttt) cc_final: 0.7773 (ttt) REVERT: sh 64 MET cc_start: 0.7900 (tpt) cc_final: 0.7633 (mmm) REVERT: sh 159 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6901 (mtp85) REVERT: sh 197 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7619 (mm-30) REVERT: sh 213 TYR cc_start: 0.8657 (m-80) cc_final: 0.8351 (m-80) REVERT: si 162 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6449 (t80) REVERT: sk 3 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6237 (mtm-85) REVERT: sk 115 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.5867 (mtm110) REVERT: sk 152 SER cc_start: 0.8115 (t) cc_final: 0.7337 (m) REVERT: sm 46 GLU cc_start: 0.8110 (tp30) cc_final: 0.7668 (mt-10) REVERT: sm 98 ARG cc_start: 0.9548 (OUTLIER) cc_final: 0.9325 (mtt-85) REVERT: sp 81 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8441 (mtmm) REVERT: sr 119 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8930 (mttt) REVERT: sx 84 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7401 (mmm) REVERT: sx 85 MET cc_start: 0.8843 (mmm) cc_final: 0.8503 (mmm) REVERT: sy 43 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.7968 (p) REVERT: sy 65 ARG cc_start: 0.5300 (OUTLIER) cc_final: 0.1866 (mtp180) REVERT: sz 18 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7495 (t0) outliers start: 110 outliers final: 81 residues processed: 269 average time/residue: 0.2311 time to fit residues: 102.8815 Evaluate side-chains 275 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 174 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 6 ARG Chi-restraints excluded: chain sB residue 26 CYS Chi-restraints excluded: chain sB residue 28 ARG Chi-restraints excluded: chain sB residue 29 CYS Chi-restraints excluded: chain sB residue 42 LYS Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 59 LEU Chi-restraints excluded: chain sB residue 76 SER Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 31 SER Chi-restraints excluded: chain sb residue 18 GLU Chi-restraints excluded: chain sb residue 174 SER Chi-restraints excluded: chain sb residue 176 LEU Chi-restraints excluded: chain sb residue 199 ASP Chi-restraints excluded: chain sb residue 204 VAL Chi-restraints excluded: chain sb residue 206 VAL Chi-restraints excluded: chain sc residue 75 LEU Chi-restraints excluded: chain sc residue 86 GLN Chi-restraints excluded: chain sc residue 203 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain sc residue 244 LYS Chi-restraints excluded: chain sc residue 247 LYS Chi-restraints excluded: chain se residue 45 VAL Chi-restraints excluded: chain se residue 48 ILE Chi-restraints excluded: chain se residue 53 THR Chi-restraints excluded: chain se residue 70 VAL Chi-restraints excluded: chain se residue 121 THR Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain se residue 200 VAL Chi-restraints excluded: chain sf residue 21 LEU Chi-restraints excluded: chain sf residue 36 MET Chi-restraints excluded: chain sf residue 58 GLU Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 82 VAL Chi-restraints excluded: chain sf residue 94 LYS Chi-restraints excluded: chain sf residue 128 VAL Chi-restraints excluded: chain sh residue 71 ASN Chi-restraints excluded: chain sh residue 108 VAL Chi-restraints excluded: chain sh residue 121 ILE Chi-restraints excluded: chain sh residue 157 VAL Chi-restraints excluded: chain sh residue 159 ARG Chi-restraints excluded: chain sh residue 184 VAL Chi-restraints excluded: chain sh residue 185 THR Chi-restraints excluded: chain sh residue 188 ARG Chi-restraints excluded: chain sh residue 216 ILE Chi-restraints excluded: chain si residue 102 VAL Chi-restraints excluded: chain si residue 135 MET Chi-restraints excluded: chain si residue 155 VAL Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 162 PHE Chi-restraints excluded: chain si residue 163 VAL Chi-restraints excluded: chain si residue 199 VAL Chi-restraints excluded: chain sj residue 3 ILE Chi-restraints excluded: chain sj residue 20 SER Chi-restraints excluded: chain sj residue 35 ASN Chi-restraints excluded: chain sj residue 82 VAL Chi-restraints excluded: chain sj residue 93 THR Chi-restraints excluded: chain sk residue 3 ARG Chi-restraints excluded: chain sk residue 103 ASN Chi-restraints excluded: chain sk residue 115 ARG Chi-restraints excluded: chain sk residue 128 LEU Chi-restraints excluded: chain sk residue 147 LEU Chi-restraints excluded: chain sk residue 158 LEU Chi-restraints excluded: chain sm residue 18 SER Chi-restraints excluded: chain sm residue 98 ARG Chi-restraints excluded: chain sm residue 138 ASN Chi-restraints excluded: chain sm residue 143 THR Chi-restraints excluded: chain sm residue 144 SER Chi-restraints excluded: chain so residue 126 THR Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 40 THR Chi-restraints excluded: chain sp residue 52 THR Chi-restraints excluded: chain sp residue 55 MET Chi-restraints excluded: chain sp residue 81 LYS Chi-restraints excluded: chain sp residue 124 ILE Chi-restraints excluded: chain sp residue 127 VAL Chi-restraints excluded: chain sp residue 145 ARG Chi-restraints excluded: chain sr residue 2 VAL Chi-restraints excluded: chain sr residue 36 GLU Chi-restraints excluded: chain sr residue 42 MET Chi-restraints excluded: chain sr residue 53 VAL Chi-restraints excluded: chain sr residue 60 LYS Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 105 THR Chi-restraints excluded: chain sr residue 119 LYS Chi-restraints excluded: chain sx residue 37 VAL Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sx residue 84 MET Chi-restraints excluded: chain sx residue 86 ILE Chi-restraints excluded: chain sy residue 41 THR Chi-restraints excluded: chain sy residue 43 SER Chi-restraints excluded: chain sy residue 65 ARG Chi-restraints excluded: chain sy residue 79 ILE Chi-restraints excluded: chain sy residue 86 ASP Chi-restraints excluded: chain sy residue 92 VAL Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sz residue 17 VAL Chi-restraints excluded: chain sz residue 18 ASN Chi-restraints excluded: chain sz residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 105 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 118 optimal weight: 30.0000 chunk 238 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 219 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: se 71 ASN sh 71 ASN sr 66 ASN ** sz 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.063978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.051959 restraints weight = 208956.263| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.38 r_work: 0.3231 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 44361 Z= 0.255 Angle : 0.639 14.929 65326 Z= 0.330 Chirality : 0.040 0.315 8254 Planarity : 0.005 0.107 4046 Dihedral : 22.611 179.005 19468 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.09 % Favored : 93.62 % Rotamer: Outliers : 5.94 % Allowed : 26.47 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.18), residues: 2069 helix: 0.35 (0.23), residues: 523 sheet: -0.69 (0.26), residues: 416 loop : -1.53 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGsr 78 TYR 0.019 0.002 TYRsz 68 PHE 0.018 0.002 PHEsz 89 TRP 0.010 0.002 TRPsb 183 HIS 0.010 0.001 HISsh 191 Details of bonding type rmsd covalent geometry : bond 0.00503 (44361) covalent geometry : angle 0.63898 (65326) hydrogen bonds : bond 0.06361 ( 1294) hydrogen bonds : angle 3.94352 ( 2667) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4138 Ramachandran restraints generated. 2069 Oldfield, 0 Emsley, 2069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 174 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sB 6 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8071 (ttm-80) REVERT: sB 28 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8106 (ttt-90) REVERT: sb 18 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: sc 75 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8720 (mt) REVERT: sc 108 ASP cc_start: 0.7730 (p0) cc_final: 0.7404 (p0) REVERT: sc 244 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8446 (mttp) REVERT: sc 247 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8145 (tptt) REVERT: sf 36 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8081 (tpp) REVERT: sf 58 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8421 (mt-10) REVERT: sf 94 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8315 (tppt) REVERT: sf 146 ARG cc_start: 0.7148 (mmp-170) cc_final: 0.6643 (mmp80) REVERT: sf 151 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7719 (mp0) REVERT: sf 170 PHE cc_start: 0.8641 (p90) cc_final: 0.8377 (p90) REVERT: sf 187 MET cc_start: 0.8034 (ttt) cc_final: 0.7770 (ttt) REVERT: sh 197 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7493 (mm-30) REVERT: si 162 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6466 (t80) REVERT: sk 3 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6317 (mtm-85) REVERT: sk 115 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.5835 (mtm110) REVERT: sk 152 SER cc_start: 0.8126 (t) cc_final: 0.7388 (m) REVERT: sm 46 GLU cc_start: 0.8073 (tp30) cc_final: 0.7631 (mt-10) REVERT: sm 98 ARG cc_start: 0.9555 (OUTLIER) cc_final: 0.9314 (mtt-85) REVERT: sr 119 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8916 (mttt) REVERT: sx 84 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7394 (mmm) REVERT: sx 85 MET cc_start: 0.8838 (mmm) cc_final: 0.8490 (mmm) REVERT: sy 43 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.7976 (p) REVERT: sy 65 ARG cc_start: 0.5326 (OUTLIER) cc_final: 0.1879 (mtp180) REVERT: sy 103 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.6398 (t80) REVERT: sz 18 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7302 (t0) outliers start: 109 outliers final: 82 residues processed: 264 average time/residue: 0.2411 time to fit residues: 105.3125 Evaluate side-chains 272 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 171 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 6 ARG Chi-restraints excluded: chain sB residue 26 CYS Chi-restraints excluded: chain sB residue 28 ARG Chi-restraints excluded: chain sB residue 29 CYS Chi-restraints excluded: chain sB residue 42 LYS Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 59 LEU Chi-restraints excluded: chain sB residue 76 SER Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 31 SER Chi-restraints excluded: chain sb residue 18 GLU Chi-restraints excluded: chain sb residue 160 SER Chi-restraints excluded: chain sb residue 174 SER Chi-restraints excluded: chain sb residue 176 LEU Chi-restraints excluded: chain sb residue 199 ASP Chi-restraints excluded: chain sb residue 204 VAL Chi-restraints excluded: chain sb residue 206 VAL Chi-restraints excluded: chain sc residue 75 LEU Chi-restraints excluded: chain sc residue 86 GLN Chi-restraints excluded: chain sc residue 203 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain sc residue 244 LYS Chi-restraints excluded: chain sc residue 247 LYS Chi-restraints excluded: chain se residue 45 VAL Chi-restraints excluded: chain se residue 48 ILE Chi-restraints excluded: chain se residue 70 VAL Chi-restraints excluded: chain se residue 71 ASN Chi-restraints excluded: chain se residue 121 THR Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain se residue 200 VAL Chi-restraints excluded: chain sf residue 21 LEU Chi-restraints excluded: chain sf residue 36 MET Chi-restraints excluded: chain sf residue 58 GLU Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 82 VAL Chi-restraints excluded: chain sf residue 94 LYS Chi-restraints excluded: chain sf residue 128 VAL Chi-restraints excluded: chain sh residue 108 VAL Chi-restraints excluded: chain sh residue 121 ILE Chi-restraints excluded: chain sh residue 157 VAL Chi-restraints excluded: chain sh residue 184 VAL Chi-restraints excluded: chain sh residue 185 THR Chi-restraints excluded: chain sh residue 188 ARG Chi-restraints excluded: chain sh residue 216 ILE Chi-restraints excluded: chain si residue 102 VAL Chi-restraints excluded: chain si residue 135 MET Chi-restraints excluded: chain si residue 155 VAL Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 162 PHE Chi-restraints excluded: chain si residue 163 VAL Chi-restraints excluded: chain si residue 199 VAL Chi-restraints excluded: chain sj residue 3 ILE Chi-restraints excluded: chain sj residue 20 SER Chi-restraints excluded: chain sj residue 35 ASN Chi-restraints excluded: chain sj residue 82 VAL Chi-restraints excluded: chain sj residue 93 THR Chi-restraints excluded: chain sk residue 3 ARG Chi-restraints excluded: chain sk residue 103 ASN Chi-restraints excluded: chain sk residue 115 ARG Chi-restraints excluded: chain sk residue 128 LEU Chi-restraints excluded: chain sk residue 147 LEU Chi-restraints excluded: chain sk residue 158 LEU Chi-restraints excluded: chain sm residue 5 THR Chi-restraints excluded: chain sm residue 18 SER Chi-restraints excluded: chain sm residue 98 ARG Chi-restraints excluded: chain sm residue 138 ASN Chi-restraints excluded: chain sm residue 143 THR Chi-restraints excluded: chain sm residue 144 SER Chi-restraints excluded: chain so residue 126 THR Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 40 THR Chi-restraints excluded: chain sp residue 52 THR Chi-restraints excluded: chain sp residue 55 MET Chi-restraints excluded: chain sp residue 118 ASN Chi-restraints excluded: chain sp residue 124 ILE Chi-restraints excluded: chain sp residue 127 VAL Chi-restraints excluded: chain sp residue 145 ARG Chi-restraints excluded: chain sr residue 2 VAL Chi-restraints excluded: chain sr residue 36 GLU Chi-restraints excluded: chain sr residue 42 MET Chi-restraints excluded: chain sr residue 53 VAL Chi-restraints excluded: chain sr residue 60 LYS Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 105 THR Chi-restraints excluded: chain sr residue 119 LYS Chi-restraints excluded: chain sx residue 37 VAL Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sx residue 84 MET Chi-restraints excluded: chain sx residue 86 ILE Chi-restraints excluded: chain sy residue 41 THR Chi-restraints excluded: chain sy residue 43 SER Chi-restraints excluded: chain sy residue 65 ARG Chi-restraints excluded: chain sy residue 79 ILE Chi-restraints excluded: chain sy residue 86 ASP Chi-restraints excluded: chain sy residue 92 VAL Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sz residue 17 VAL Chi-restraints excluded: chain sz residue 18 ASN Chi-restraints excluded: chain sz residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 265 optimal weight: 8.9990 chunk 310 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 261 optimal weight: 6.9990 chunk 64 optimal weight: 30.0000 chunk 241 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 277 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 242 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: se 71 ASN sr 66 ASN ** sz 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.064208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.052188 restraints weight = 210297.241| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.38 r_work: 0.3241 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 44361 Z= 0.227 Angle : 0.618 15.298 65326 Z= 0.320 Chirality : 0.039 0.299 8254 Planarity : 0.004 0.102 4046 Dihedral : 22.600 179.112 19468 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.04 % Favored : 93.72 % Rotamer: Outliers : 5.61 % Allowed : 26.80 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.18), residues: 2069 helix: 0.40 (0.23), residues: 526 sheet: -0.68 (0.26), residues: 416 loop : -1.52 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGsr 78 TYR 0.015 0.001 TYRsz 68 PHE 0.019 0.001 PHEsz 89 TRP 0.011 0.002 TRPsb 60 HIS 0.010 0.001 HISsh 191 Details of bonding type rmsd covalent geometry : bond 0.00448 (44361) covalent geometry : angle 0.61812 (65326) hydrogen bonds : bond 0.06130 ( 1294) hydrogen bonds : angle 3.91518 ( 2667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11368.54 seconds wall clock time: 195 minutes 11.98 seconds (11711.98 seconds total)