Starting phenix.real_space_refine on Mon Aug 10 04:48:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v1j_64695/08_2026/9v1j_64695.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v1j_64695/08_2026/9v1j_64695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v1j_64695/08_2026/9v1j_64695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v1j_64695/08_2026/9v1j_64695.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v1j_64695/08_2026/9v1j_64695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v1j_64695/08_2026/9v1j_64695.map" } resolution = 3.1 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 1062 5.49 5 S 100 5.16 5 C 22342 2.51 5 N 7718 2.21 5 O 10695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41917 Number of models: 1 Model: "" Number of chains: 20 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: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 641 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "sH" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1593 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 63} Chain breaks: 1 Chain: "sK" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 5} Chain: "sa" Number of atoms: 20995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 20995 Classifications: {'RNA': 981} Modifications used: {'rna2p_pur': 100, 'rna2p_pyr': 53, 'rna3p_pur': 470, 'rna3p_pyr': 358} Link IDs: {'rna2p': 152, 'rna3p': 828} Chain breaks: 10 Chain: "sb" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1327 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 6, 'TRANS': 161} Chain breaks: 1 Chain: "sc" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1642 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 9, 'TRANS': 205} Chain: "se" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1717 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 3, 'TRANS': 208} Chain: "sf" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2031 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 15, 'TRANS': 240} Chain: "sh" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1345 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain breaks: 3 Chain: "si" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 615 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain breaks: 1 Chain: "sj" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1329 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Chain: "sk" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1293 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "sm" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1263 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 4, 'TRANS': 149} Chain: "so" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1184 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 6, 'TRANS': 143} 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: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 560 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain breaks: 1 Chain: "sy" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1010 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} 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: 8.07, per 1000 atoms: 0.19 Number of scatterers: 41917 At special positions: 0 Unit cell: (165.85, 196.88, 175.48, 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 100 16.00 P 1062 15.00 O 10695 8.00 N 7718 7.00 C 22342 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: 3.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 28 sheets defined 30.5% alpha, 21.6% beta 317 base pairs and 528 stacking pairs defined. Time for finding SS restraints: 5.75 Creating SS restraints... Processing helix chain 'sB' and resid 49 through 56 removed outlier: 3.639A pdb=" N ASNsB 56 " --> pdb=" O ASPsB 52 " (cutoff:3.500A) Processing helix chain 'sB' and resid 74 through 81 Processing helix chain 'sC' and resid 12 through 19 Processing helix chain 'sb' and resid 36 through 40 removed outlier: 3.766A pdb=" N GLUsb 40 " --> pdb=" O PHEsb 37 " (cutoff:3.500A) Processing helix chain 'sb' and resid 55 through 75 Processing helix chain 'sb' and resid 77 through 79 No H-bonds generated for 'chain 'sb' and resid 77 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 144 Processing helix chain 'sb' and resid 174 through 190 Processing helix chain 'sc' and resid 41 through 49 Processing helix chain 'sc' and resid 54 through 62 removed outlier: 3.996A pdb=" N ILEsc 58 " --> pdb=" O SERsc 54 " (cutoff:3.500A) Processing helix chain 'sc' and resid 67 through 75 removed outlier: 4.151A pdb=" N VALsc 71 " --> pdb=" O GLUsc 67 " (cutoff:3.500A) Processing helix chain 'sc' and resid 122 through 137 removed outlier: 3.564A pdb=" N LYSsc 135 " --> pdb=" O METsc 131 " (cutoff:3.500A) Processing helix chain 'sc' and resid 183 through 193 removed outlier: 3.680A pdb=" N PHEsc 189 " --> pdb=" O THRsc 185 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEUsc 192 " --> pdb=" O LYSsc 188 " (cutoff:3.500A) Processing helix chain 'sc' and resid 208 through 222 Processing helix chain 'sc' and resid 240 through 245 Processing helix chain 'sc' and resid 245 through 251 Processing helix chain 'se' and resid 25 through 27 No H-bonds generated for 'chain 'se' and resid 25 through 27' Processing helix chain 'se' and resid 58 through 63 Processing helix chain 'se' and resid 72 through 76 Processing helix chain 'se' and resid 78 through 82 removed outlier: 3.693A pdb=" N PHEse 81 " --> pdb=" O ASNse 78 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLYse 82 " --> pdb=" O GLUse 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'se' and resid 78 through 82' Processing helix chain 'se' and resid 108 through 115 Processing helix chain 'se' and resid 159 through 180 removed outlier: 3.617A pdb=" N SERse 180 " --> pdb=" O LYSse 176 " (cutoff:3.500A) Processing helix chain 'se' and resid 182 through 192 removed outlier: 3.722A pdb=" N GLUse 192 " --> pdb=" O ASPse 188 " (cutoff:3.500A) Processing helix chain 'se' and resid 193 through 204 Processing helix chain 'se' and resid 226 through 234 Processing helix chain 'sf' and resid 8 through 12 Processing helix chain 'sf' and resid 13 through 17 Processing helix chain 'sf' and resid 42 through 48 Processing helix chain 'sf' and resid 55 through 64 removed outlier: 3.589A pdb=" N METsf 61 " --> pdb=" O ARGsf 57 " (cutoff:3.500A) Processing helix chain 'sf' and resid 221 through 223 No H-bonds generated for 'chain 'sf' and resid 221 through 223' Processing helix chain 'sf' and resid 246 through 255 Processing helix chain 'sh' and resid 234 through 242 Processing helix chain 'sh' and resid 250 through 254 removed outlier: 3.504A pdb=" N VALsh 254 " --> pdb=" O LYSsh 251 " (cutoff:3.500A) Processing helix chain 'sh' and resid 275 through 279 removed outlier: 3.553A pdb=" N LEUsh 279 " --> pdb=" O PROsh 276 " (cutoff:3.500A) Processing helix chain 'sh' and resid 298 through 314 removed outlier: 3.820A pdb=" N ALAsh 304 " --> pdb=" O ALAsh 300 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARGsh 309 " --> pdb=" O ALAsh 305 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYRsh 310 " --> pdb=" O ILEsh 306 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYSsh 314 " --> pdb=" O TYRsh 310 " (cutoff:3.500A) Processing helix chain 'si' and resid 123 through 137 Processing helix chain 'sj' and resid 25 through 29 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: 3.697A pdb=" N ARGsj 92 " --> pdb=" O ASNsj 88 " (cutoff:3.500A) Processing helix chain 'sj' and resid 106 through 118 Processing helix chain 'sj' and resid 189 through 199 removed outlier: 3.525A pdb=" N LEUsj 193 " --> pdb=" O ASPsj 189 " (cutoff:3.500A) Processing helix chain 'sj' and resid 208 through 213 Processing helix chain 'sj' and resid 221 through 231 removed outlier: 3.522A pdb=" N PHEsj 227 " --> pdb=" O LYSsj 223 " (cutoff:3.500A) Processing helix chain 'sk' and resid 20 through 35 removed outlier: 3.583A pdb=" N ALAsk 26 " --> pdb=" O GLUsk 22 " (cutoff:3.500A) Processing helix chain 'sk' and resid 38 through 61 removed outlier: 3.998A pdb=" N ILEsk 42 " --> pdb=" O ASNsk 38 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VALsk 45 " --> pdb=" O GLUsk 41 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N METsk 61 " --> pdb=" O LYSsk 57 " (cutoff:3.500A) Processing helix chain 'sk' and resid 66 through 83 Processing helix chain 'sk' and resid 93 through 98 removed outlier: 4.029A pdb=" N LEUsk 97 " --> pdb=" O LEUsk 93 " (cutoff:3.500A) removed outlier: 3.880A 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: 3.817A pdb=" N LEUsk 104 " --> pdb=" O LYSsk 100 " (cutoff:3.500A) Processing helix chain 'sk' and resid 108 through 116 Processing helix chain 'sk' and resid 121 through 131 removed outlier: 3.522A pdb=" N ARGsk 126 " --> pdb=" O ILEsk 122 " (cutoff:3.500A) Processing helix chain 'sk' and resid 152 through 154 No H-bonds generated for 'chain 'sk' and resid 152 through 154' Processing helix chain 'sm' and resid 45 through 50 Processing helix chain 'so' and resid 29 through 43 Processing helix chain 'so' and resid 46 through 58 removed outlier: 3.521A pdb=" N ALAso 52 " --> pdb=" O SERso 48 " (cutoff:3.500A) Processing helix chain 'so' and resid 63 through 68 Processing helix chain 'so' and resid 70 through 78 Processing helix chain 'so' and resid 85 through 105 removed outlier: 4.114A pdb=" N LYSso 104 " --> pdb=" O LYSso 100 " (cutoff:3.500A) Processing helix chain 'so' and resid 108 through 132 removed outlier: 3.637A pdb=" N LYSso 112 " --> pdb=" O ASPso 108 " (cutoff:3.500A) Processing helix chain 'so' and resid 142 through 151 removed outlier: 3.993A pdb=" N SERso 147 " --> pdb=" O ALAso 143 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALAso 148 " --> pdb=" O ASNso 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILEso 149 " --> pdb=" O THRso 145 " (cutoff:3.500A) Processing helix chain 'sp' and resid 54 through 57 removed outlier: 3.896A 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 65 through 83 Processing helix chain 'sp' and resid 105 through 117 removed outlier: 4.045A 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: 3.519A 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: 3.501A pdb=" N ASNsr 92 " --> pdb=" O LYSsr 88 " (cutoff:3.500A) Processing helix chain 'sr' and resid 113 through 120 Processing helix chain 'sx' and resid 53 through 59 Processing helix chain 'sx' and resid 61 through 73 Processing helix chain 'sx' and resid 81 through 85 Processing helix chain 'sy' and resid 8 through 19 removed outlier: 3.595A pdb=" N ARGsy 15 " --> pdb=" O METsy 11 " (cutoff:3.500A) Processing helix chain 'sy' and resid 22 through 28 removed outlier: 3.862A pdb=" N GLYsy 28 " --> pdb=" O GLUsy 24 " (cutoff:3.500A) Processing helix chain 'sz' and resid 84 through 89 removed outlier: 3.667A pdb=" N LYSsz 88 " --> pdb=" O SERsz 84 " (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 'sC' and resid 44 through 48 removed outlier: 3.649A pdb=" N GLUsC 35 " --> pdb=" O ARGsC 81 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARGsC 81 " --> pdb=" O GLUsC 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'sC' and resid 65 through 68 removed outlier: 3.656A pdb=" N THRsC 68 " --> pdb=" O LYSsC 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'sb' and resid 104 through 106 removed outlier: 6.274A pdb=" N VALsb 81 " --> pdb=" O THRsb 104 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VALsb 106 " --> pdb=" O VALsb 81 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALAsb 83 " --> pdb=" O VALsb 106 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VALsb 82 " --> pdb=" O ILEsb 130 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILEsb 129 " --> pdb=" O ILEsb 152 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N PHEsb 154 " --> pdb=" O ILEsb 129 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VALsb 131 " --> pdb=" O PHEsb 154 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THRsb 151 " --> pdb=" O ILEsb 166 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ILEsb 168 " --> pdb=" O THRsb 151 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALAsb 153 " --> pdb=" O ILEsb 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'sc' and resid 80 through 91 removed outlier: 5.422A pdb=" N VALsc 82 " --> pdb=" O ALAsc 105 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALAsc 105 " --> pdb=" O VALsc 82 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THRsc 84 " --> pdb=" O TYRsc 103 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYRsc 103 " --> pdb=" O THRsc 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'sc' and resid 160 through 161 Processing sheet with id=AA8, first strand: chain 'se' and resid 44 through 51 removed outlier: 4.697A pdb=" N GLYse 46 " --> pdb=" O VALse 34 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N CYSse 98 " --> pdb=" O TRPse 31 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASNse 33 " --> pdb=" O CYSse 98 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N METse 100 " --> pdb=" O ASNse 33 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYSse 35 " --> pdb=" O METse 100 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHEse 102 " --> pdb=" O LYSse 35 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N CYSse 98 " --> pdb=" O VALse 93 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VALse 93 " --> pdb=" O CYSse 98 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N METse 100 " --> pdb=" O GLUse 91 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLUse 91 " --> pdb=" O METse 100 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHEse 102 " --> pdb=" O LYSse 89 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LYSse 89 " --> pdb=" O PHEse 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'se' and resid 44 through 51 removed outlier: 4.697A pdb=" N GLYse 46 " --> pdb=" O VALse 34 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N CYSse 98 " --> pdb=" O TRPse 31 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASNse 33 " --> pdb=" O CYSse 98 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N METse 100 " --> pdb=" O ASNse 33 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYSse 35 " --> pdb=" O METse 100 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N PHEse 102 " --> pdb=" O LYSse 35 " (cutoff:3.500A) removed outlier: 13.619A pdb=" N ILEse 101 " --> pdb=" O LYSse 221 " (cutoff:3.500A) removed outlier: 13.369A pdb=" N LYSse 221 " --> pdb=" O ILEse 101 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N HISse 103 " --> pdb=" O ILEse 219 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILEse 219 " --> pdb=" O HISse 103 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ARGse 215 " --> pdb=" O LEUse 107 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VALse 212 " --> pdb=" O PHEse 144 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHEse 144 " --> pdb=" O VALse 212 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILEse 214 " --> pdb=" O ILEse 142 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILEse 142 " --> pdb=" O ILEse 214 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYSse 216 " --> pdb=" O PHEse 140 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARGse 138 " --> pdb=" O LYSse 218 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEUse 136 " --> pdb=" O LEUse 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'sf' and resid 40 through 41 Processing sheet with id=AB2, first strand: chain 'sf' and resid 73 through 74 removed outlier: 4.374A pdb=" N ASNsf 96 " --> pdb=" O LEUsf 112 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARGsf 106 " --> pdb=" O ASNsf 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'sf' and resid 144 through 145 removed outlier: 6.781A pdb=" N TYRsf 136 " --> pdb=" O ARGsf 127 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARGsf 127 " --> pdb=" O TYRsf 136 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VALsf 138 " --> pdb=" O GLUsf 125 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASPsf 169 " --> pdb=" O LYSsf 159 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASNsf 161 " --> pdb=" O ILEsf 167 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILEsf 167 " --> pdb=" O ASNsf 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'sf' and resid 215 through 219 removed outlier: 6.673A pdb=" N ILEsf 205 " --> pdb=" O ARGsf 196 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARGsf 196 " --> pdb=" O ILEsf 205 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HISsf 207 " --> pdb=" O VALsf 194 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASNsf 177 " --> pdb=" O ILEsf 193 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THRsf 178 " --> pdb=" O ILEsf 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'sh' and resid 169 through 174 Processing sheet with id=AB6, first strand: chain 'sh' and resid 257 through 258 Processing sheet with id=AB7, first strand: chain 'si' and resid 154 through 165 removed outlier: 7.214A pdb=" N ALAsi 164 " --> pdb=" O VALsi 141 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VALsi 141 " --> pdb=" O ALAsi 164 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEUsi 150 " --> pdb=" O THRsr 48 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N THRsr 48 " --> pdb=" O LEUsi 150 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASPsr 49 " --> pdb=" O ASNsr 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'sj' and resid 37 through 38 removed outlier: 6.521A pdb=" N ARGsj 42 " --> pdb=" O LEUsj 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'sj' and resid 62 through 67 removed outlier: 6.943A pdb=" N ILEsj 101 " --> pdb=" O VALsj 82 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALAsj 100 " --> pdb=" O ILEsj 205 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N GLYsj 217 " --> pdb=" O ASNsj 62 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASNsj 64 " --> pdb=" O GLYsj 217 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILEsj 219 " --> pdb=" O ASNsj 64 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SERsj 66 " --> pdb=" O ILEsj 219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'sk' and resid 139 through 140 removed outlier: 3.636A pdb=" N GLNsk 139 " --> pdb=" O VALsk 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'sm' and resid 66 through 76 removed outlier: 26.663A pdb=" N GLYsm 67 " --> pdb=" O TYRsm 92 " (cutoff:3.500A) removed outlier: 22.842A pdb=" N TYRsm 92 " --> pdb=" O GLYsm 67 " (cutoff:3.500A) removed outlier: 17.459A pdb=" N THRsm 69 " --> pdb=" O PHEsm 90 " (cutoff:3.500A) removed outlier: 14.717A pdb=" N PHEsm 90 " --> pdb=" O THRsm 69 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N SERsm 71 " --> pdb=" O ASPsm 88 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASPsm 88 " --> pdb=" O SERsm 71 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILEsm 84 " --> pdb=" O LYSsm 75 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARGsm 98 " --> pdb=" O VALsm 93 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N PHEsm 137 " --> pdb=" O ASNsm 105 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALAsm 107 " --> pdb=" O PHEsm 137 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N VALsm 139 " --> pdb=" O ALAsm 107 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N HISsm 109 " --> pdb=" O VALsm 139 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LYSsm 141 " --> pdb=" O HISsm 109 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VALsm 124 " --> pdb=" O LEUsm 140 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHEsm 142 " --> pdb=" O HISsm 122 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N HISsm 122 " --> pdb=" O PHEsm 142 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VALsm 123 " --> pdb=" O LEUsm 70 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEUsm 70 " --> pdb=" O VALsm 123 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILEsm 125 " --> pdb=" O ARGsm 68 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ARGsm 68 " --> pdb=" O ILEsm 125 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLNsm 127 " --> pdb=" O ARGsm 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'sp' and resid 29 through 30 removed outlier: 6.766A pdb=" N THRsp 35 " --> pdb=" O THRsp 52 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THRsp 52 " --> pdb=" O THRsp 35 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VALsp 37 " --> pdb=" O ARGsp 50 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARGsp 50 " --> pdb=" O VALsp 37 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VALsp 39 " --> pdb=" O ILEsp 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'sp' and resid 29 through 30 removed outlier: 6.291A pdb=" N ALAsp 22 " --> pdb=" O VALsp 85 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SERsp 87 " --> pdb=" O ALAsp 22 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THRsp 86 " --> pdb=" O LYSsp 120 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLYsp 122 " --> pdb=" O THRsp 86 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEUsp 88 " --> pdb=" O GLYsp 122 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILEsp 124 " --> pdb=" O LEUsp 88 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILEsp 90 " --> pdb=" O ILEsp 124 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASPsp 126 " --> pdb=" O ILEsp 90 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N METsp 92 " --> pdb=" O ASPsp 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'sr' and resid 72 through 74 Processing sheet with id=AC6, first strand: chain 'sr' and resid 72 through 74 removed outlier: 6.692A pdb=" N VALsr 103 " --> pdb=" O LEUsr 126 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHEsr 128 " --> pdb=" O ALAsr 101 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALAsr 101 " --> pdb=" O PHEsr 128 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'sx' and resid 30 through 33 removed outlier: 3.505A pdb=" N VALsx 52 " --> pdb=" O VALsx 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'sy' and resid 78 through 82 removed outlier: 3.801A pdb=" N GLUsy 51 " --> pdb=" O ARGsy 69 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARGsy 71 " --> pdb=" O VALsy 49 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VALsy 49 " --> pdb=" O ARGsy 71 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEUsy 99 " --> pdb=" O VALsy 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'sz' and resid 16 through 18 removed outlier: 3.528A pdb=" N ILEsz 16 " --> pdb=" O GLNsz 25 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLNsz 25 " --> pdb=" O ILEsz 16 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'sz' and resid 16 through 18 removed outlier: 3.528A pdb=" N ILEsz 16 " --> pdb=" O GLNsz 25 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLNsz 25 " --> pdb=" O ILEsz 16 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHEsz 76 " --> pdb=" O GLYsz 63 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLYsz 63 " --> pdb=" O PHEsz 76 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEUsz 78 " --> pdb=" O LEUsz 61 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEUsz 61 " --> pdb=" O LEUsz 78 " (cutoff:3.500A) 658 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 754 hydrogen bonds 1204 hydrogen bond angles 0 basepair planarities 317 basepair parallelities 528 stacking parallelities Total time for adding SS restraints: 16.17 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 3998 1.26 - 1.40: 13126 1.40 - 1.53: 25059 1.53 - 1.67: 2621 1.67 - 1.81: 155 Bond restraints: 44959 Sorted by residual: bond pdb=" CA LYSsi 118 " pdb=" C LYSsi 118 " ideal model delta sigma weight residual 1.522 1.345 0.177 1.14e-02 7.69e+03 2.41e+02 bond pdb=" CA ALAsh 283 " pdb=" C ALAsh 283 " ideal model delta sigma weight residual 1.524 1.339 0.185 1.24e-02 6.50e+03 2.23e+02 bond pdb=" CA LYSsh 282 " pdb=" C LYSsh 282 " ideal model delta sigma weight residual 1.523 1.340 0.183 1.34e-02 5.57e+03 1.86e+02 bond pdb=" N GLNsh 284 " pdb=" CA GLNsh 284 " ideal model delta sigma weight residual 1.457 1.287 0.170 1.29e-02 6.01e+03 1.73e+02 bond pdb=" CA ILEsh 218 " pdb=" C ILEsh 218 " ideal model delta sigma weight residual 1.523 1.361 0.162 1.27e-02 6.20e+03 1.63e+02 ... (remaining 44954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.99: 65712 8.99 - 17.98: 72 17.98 - 26.97: 17 26.97 - 35.96: 3 35.96 - 44.95: 1 Bond angle restraints: 65805 Sorted by residual: angle pdb=" C VALsh 210 " pdb=" CA VALsh 210 " pdb=" CB VALsh 210 " ideal model delta sigma weight residual 111.40 66.45 44.95 1.90e+00 2.77e-01 5.60e+02 angle pdb=" N LYSsh 289 " pdb=" CA LYSsh 289 " pdb=" C LYSsh 289 " ideal model delta sigma weight residual 113.97 85.24 28.73 1.28e+00 6.10e-01 5.04e+02 angle pdb=" N ILEsh 209 " pdb=" CA ILEsh 209 " pdb=" C ILEsh 209 " ideal model delta sigma weight residual 110.21 135.28 -25.07 1.13e+00 7.83e-01 4.92e+02 angle pdb=" N ALAsh 283 " pdb=" CA ALAsh 283 " pdb=" C ALAsh 283 " ideal model delta sigma weight residual 110.97 89.13 21.84 1.09e+00 8.42e-01 4.01e+02 angle pdb=" C GLYsh 231 " pdb=" N PROsh 232 " pdb=" CA PROsh 232 " ideal model delta sigma weight residual 120.11 99.09 21.02 1.12e+00 7.97e-01 3.52e+02 ... (remaining 65800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 25348 35.99 - 71.99: 2450 71.99 - 107.98: 227 107.98 - 143.98: 8 143.98 - 179.97: 19 Dihedral angle restraints: 28052 sinusoidal: 21091 harmonic: 6961 Sorted by residual: dihedral pdb=" C VALsh 210 " pdb=" N VALsh 210 " pdb=" CA VALsh 210 " pdb=" CB VALsh 210 " ideal model delta harmonic sigma weight residual -122.00 -45.26 -76.74 0 2.50e+00 1.60e-01 9.42e+02 dihedral pdb=" N VALsh 210 " pdb=" C VALsh 210 " pdb=" CA VALsh 210 " pdb=" CB VALsh 210 " ideal model delta harmonic sigma weight residual 123.40 50.78 72.62 0 2.50e+00 1.60e-01 8.44e+02 dihedral pdb=" C LYSsh 289 " pdb=" N LYSsh 289 " pdb=" CA LYSsh 289 " pdb=" CB LYSsh 289 " ideal model delta harmonic sigma weight residual -122.60 -93.10 -29.50 0 2.50e+00 1.60e-01 1.39e+02 ... (remaining 28049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.241: 8233 0.241 - 0.482: 16 0.482 - 0.723: 5 0.723 - 0.964: 1 0.964 - 1.205: 1 Chirality restraints: 8256 Sorted by residual: chirality pdb=" CA VALsh 210 " pdb=" N VALsh 210 " pdb=" C VALsh 210 " pdb=" CB VALsh 210 " both_signs ideal model delta sigma weight residual False 2.44 1.24 1.20 2.00e-01 2.50e+01 3.63e+01 chirality pdb=" CA TYRsi 137 " pdb=" N TYRsi 137 " pdb=" C TYRsi 137 " pdb=" CB TYRsi 137 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA LYSsh 285 " pdb=" N LYSsh 285 " pdb=" C LYSsh 285 " pdb=" CB LYSsh 285 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.06e+00 ... (remaining 8253 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THRsh 208 " 0.048 2.00e-02 2.50e+03 1.14e-01 1.30e+02 pdb=" C THRsh 208 " -0.196 2.00e-02 2.50e+03 pdb=" O THRsh 208 " 0.082 2.00e-02 2.50e+03 pdb=" N ILEsh 209 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHEsy 103 " 0.034 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C PHEsy 103 " -0.104 2.00e-02 2.50e+03 pdb=" O PHEsy 103 " 0.034 2.00e-02 2.50e+03 pdb=" N GLYsy 104 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLNsh 284 " -0.028 2.00e-02 2.50e+03 5.66e-02 3.20e+01 pdb=" C GLNsh 284 " 0.098 2.00e-02 2.50e+03 pdb=" O GLNsh 284 " -0.036 2.00e-02 2.50e+03 pdb=" N LYSsh 285 " -0.034 2.00e-02 2.50e+03 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 4 2.06 - 2.77: 8062 2.77 - 3.48: 53780 3.48 - 4.19: 126474 4.19 - 4.90: 180665 Nonbonded interactions: 368985 Sorted by model distance: nonbonded pdb=" O ILEsh 203 " pdb=" OE2 GLUsh 217 " model vdw 1.348 3.040 nonbonded pdb=" C ILEsh 203 " pdb=" OE2 GLUsh 217 " model vdw 1.729 3.270 nonbonded pdb=" O4' Usa 147 " pdb=" OD1 ASNsh 223 " model vdw 1.835 3.040 nonbonded pdb=" O ILEsh 203 " pdb=" CD GLUsh 217 " model vdw 1.842 3.270 nonbonded pdb=" O ILEsh 203 " pdb=" OE1 GLUsh 217 " model vdw 2.066 3.040 ... (remaining 368980 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 46.660 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.007 0.185 44959 Z= 0.531 Angle : 1.028 44.953 65805 Z= 0.723 Chirality : 0.064 1.205 8256 Planarity : 0.006 0.138 4362 Dihedral : 22.278 179.970 23564 Min Nonbonded Distance : 1.348 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 1.18 % Allowed : 5.13 % Favored : 93.69 % Rotamer: Outliers : 3.47 % Allowed : 27.81 % Favored : 68.72 % Cbeta Deviations : 1.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.17), residues: 2378 helix: -0.04 (0.20), residues: 651 sheet: -0.62 (0.24), residues: 473 loop : -1.32 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARGsy 106 TYR 0.046 0.001 TYRsi 117 PHE 0.015 0.001 PHEsz 89 TRP 0.032 0.002 TRPsb 183 HIS 0.029 0.001 HISsh 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.53 (44959) covalent geometry : angle 1.02784 / 0.72 (65805) hydrogen bonds : bond 0.17638 / 11.96 ( 1397) hydrogen bonds : angle 6.93181 / 4.85 ( 3067) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 297 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sB 6 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7425 (ttm-80) REVERT: sB 44 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8560 (mt) REVERT: sC 81 ARG cc_start: 0.7875 (ptt-90) cc_final: 0.7635 (ptm-80) REVERT: sb 44 TYR cc_start: 0.8495 (t80) cc_final: 0.8050 (t80) REVERT: sb 51 GLU cc_start: 0.7006 (pm20) cc_final: 0.6557 (pm20) REVERT: sb 55 ASN cc_start: 0.8716 (t0) cc_final: 0.8391 (m-40) REVERT: sc 245 TYR cc_start: 0.8187 (m-80) cc_final: 0.7876 (m-80) REVERT: sh 145 TYR cc_start: 0.5586 (m-80) cc_final: 0.4180 (t80) REVERT: sh 281 HIS cc_start: 0.5728 (OUTLIER) cc_final: 0.5083 (m90) REVERT: si 140 GLU cc_start: 0.5970 (tt0) cc_final: 0.5643 (tt0) REVERT: si 153 LYS cc_start: 0.8387 (mppt) cc_final: 0.8070 (mttp) REVERT: sj 189 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6932 (p0) REVERT: sk 63 ASP cc_start: 0.8118 (t0) cc_final: 0.7807 (t0) REVERT: sk 66 ASP cc_start: 0.8376 (m-30) cc_final: 0.8025 (m-30) REVERT: sk 155 LEU cc_start: 0.8999 (mp) cc_final: 0.8781 (mp) REVERT: sk 157 GLN cc_start: 0.7912 (pm20) cc_final: 0.7297 (pm20) REVERT: sm 24 GLU cc_start: 0.7627 (tp30) cc_final: 0.7295 (mp0) REVERT: sm 26 ASP cc_start: 0.8240 (t0) cc_final: 0.7869 (p0) REVERT: sz 23 ARG cc_start: 0.6348 (ttp-170) cc_final: 0.6120 (ttp-170) REVERT: sz 67 LYS cc_start: 0.7491 (mmpt) cc_final: 0.6982 (ttpt) outliers start: 72 outliers final: 26 residues processed: 350 average time/residue: 0.2664 time to fit residues: 150.5544 Evaluate side-chains 257 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 6 ARG Chi-restraints excluded: chain sB residue 44 ILE Chi-restraints excluded: chain sc residue 213 VAL Chi-restraints excluded: chain sf residue 244 LYS Chi-restraints excluded: chain sh residue 209 ILE Chi-restraints excluded: chain sh residue 229 ARG Chi-restraints excluded: chain sh residue 281 HIS Chi-restraints excluded: chain sh residue 289 LYS Chi-restraints excluded: chain sh residue 291 LEU Chi-restraints excluded: chain sh residue 299 GLU Chi-restraints excluded: chain sh residue 309 ARG Chi-restraints excluded: chain sh residue 310 TYR Chi-restraints excluded: chain si residue 111 GLN Chi-restraints excluded: chain si residue 115 THR Chi-restraints excluded: chain si residue 116 ASP Chi-restraints excluded: chain si residue 139 VAL Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 165 VAL Chi-restraints excluded: chain sj residue 27 ASN Chi-restraints excluded: chain sj residue 189 ASP Chi-restraints excluded: chain sm residue 108 VAL Chi-restraints excluded: chain so residue 87 ASP Chi-restraints excluded: chain so residue 150 VAL Chi-restraints excluded: chain sy residue 83 VAL Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sy residue 113 ILE Chi-restraints excluded: chain sy residue 117 ARG Chi-restraints excluded: chain sy residue 121 VAL Chi-restraints excluded: chain sy residue 126 VAL Chi-restraints excluded: chain sz residue 83 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sb 48 ASN sc 57 GLN sc 227 GLN se 39 ASN sf 149 HIS sf 155 ASN sf 249 GLN sh 186 ASN so 105 ASN ** sp 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** sr 80 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.054590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.044255 restraints weight = 220257.540| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.93 r_work: 0.3050 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 44959 Z= 0.219 Angle : 0.689 14.358 65805 Z= 0.377 Chirality : 0.044 0.487 8256 Planarity : 0.006 0.105 4362 Dihedral : 22.316 178.757 18761 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.47 % Favored : 94.03 % Rotamer: Outliers : 6.46 % Allowed : 22.55 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.26 % 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: -1.13 (0.17), residues: 2378 helix: 0.01 (0.20), residues: 654 sheet: -0.63 (0.25), residues: 430 loop : -1.17 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGsh 302 TYR 0.028 0.002 TYRsr 50 PHE 0.025 0.002 PHEsf 84 TRP 0.019 0.002 TRPsb 183 HIS 0.007 0.001 HISsc 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.22 (44959) covalent geometry : angle 0.68875 / 0.38 (65805) hydrogen bonds : bond 0.07260 / 5.02 ( 1397) hydrogen bonds : angle 4.76422 / 3.50 ( 3067) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 244 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: sB 44 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8798 (mt) REVERT: sB 69 MET cc_start: 0.8918 (ptt) cc_final: 0.8505 (ptt) REVERT: sC 35 GLU cc_start: 0.7855 (pm20) cc_final: 0.7229 (pm20) REVERT: sb 44 TYR cc_start: 0.8400 (t80) cc_final: 0.7771 (t80) REVERT: sb 55 ASN cc_start: 0.8721 (t0) cc_final: 0.8170 (m-40) REVERT: sb 125 GLU cc_start: 0.7985 (mp0) cc_final: 0.7155 (pp20) REVERT: sc 196 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8233 (mt-10) REVERT: se 228 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8542 (pp) REVERT: sh 145 TYR cc_start: 0.5672 (m-80) cc_final: 0.4041 (t80) REVERT: sh 296 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.6805 (tpp) REVERT: sh 303 TYR cc_start: 0.6983 (m-80) cc_final: 0.6762 (t80) REVERT: si 100 LYS cc_start: 0.6393 (tptp) cc_final: 0.4629 (pptt) REVERT: si 153 LYS cc_start: 0.8375 (mppt) cc_final: 0.8130 (mttp) REVERT: sj 189 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6639 (p0) REVERT: sk 66 ASP cc_start: 0.8890 (m-30) cc_final: 0.8550 (m-30) REVERT: sk 157 GLN cc_start: 0.8035 (pm20) cc_final: 0.7266 (pm20) REVERT: sm 26 ASP cc_start: 0.8317 (t0) cc_final: 0.7413 (p0) REVERT: sm 39 MET cc_start: 0.8933 (mtm) cc_final: 0.8450 (mtm) REVERT: so 36 GLU cc_start: 0.8753 (tp30) cc_final: 0.8421 (mm-30) REVERT: so 39 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8456 (ptpt) REVERT: sp 60 ASP cc_start: 0.6325 (OUTLIER) cc_final: 0.6030 (t0) REVERT: sr 50 TYR cc_start: 0.8498 (p90) cc_final: 0.8264 (p90) REVERT: sx 73 ASP cc_start: 0.8637 (m-30) cc_final: 0.8328 (m-30) REVERT: sx 86 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.7109 (pp) REVERT: sy 103 PHE cc_start: 0.4444 (OUTLIER) cc_final: 0.4050 (m-80) REVERT: sz 13 ARG cc_start: 0.5084 (mmt90) cc_final: 0.4791 (mmt90) REVERT: sz 67 LYS cc_start: 0.7218 (mmpt) cc_final: 0.6768 (ttpt) outliers start: 134 outliers final: 55 residues processed: 354 average time/residue: 0.2527 time to fit residues: 146.2142 Evaluate side-chains 284 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 221 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 37 LYS Chi-restraints excluded: chain sB residue 44 ILE Chi-restraints excluded: chain sB residue 50 VAL Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sC residue 9 LEU Chi-restraints excluded: chain sC residue 45 THR Chi-restraints excluded: chain sC residue 75 THR Chi-restraints excluded: chain sb residue 64 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 249 LEU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain se residue 228 LEU Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 82 VAL Chi-restraints excluded: chain sf residue 156 ASP Chi-restraints excluded: chain sf residue 244 LYS Chi-restraints excluded: chain sh residue 287 GLU Chi-restraints excluded: chain sh residue 291 LEU Chi-restraints excluded: chain sh residue 296 MET Chi-restraints excluded: chain sh residue 309 ARG Chi-restraints excluded: chain sh residue 310 TYR Chi-restraints excluded: chain si residue 115 THR Chi-restraints excluded: chain si residue 158 SER Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 165 VAL Chi-restraints excluded: chain sj residue 27 ASN Chi-restraints excluded: chain sj residue 89 ASP Chi-restraints excluded: chain sj residue 189 ASP Chi-restraints excluded: chain sj residue 193 LEU Chi-restraints excluded: chain sk residue 21 ARG Chi-restraints excluded: chain sk residue 31 VAL Chi-restraints excluded: chain sm residue 18 SER Chi-restraints excluded: chain sm residue 73 ILE Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 108 VAL Chi-restraints excluded: chain so residue 31 LEU Chi-restraints excluded: chain so residue 39 LYS Chi-restraints excluded: chain so residue 71 VAL Chi-restraints excluded: chain so residue 87 ASP Chi-restraints excluded: chain so residue 97 SER Chi-restraints excluded: chain so residue 150 VAL Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 57 VAL Chi-restraints excluded: chain sp residue 60 ASP Chi-restraints excluded: chain sp residue 62 ASP Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sr residue 74 VAL Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 107 SER Chi-restraints excluded: chain sx residue 86 ILE Chi-restraints excluded: chain sy residue 57 THR Chi-restraints excluded: chain sy residue 71 ARG Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sy residue 121 VAL Chi-restraints excluded: chain sy residue 122 CYS Chi-restraints excluded: chain sy residue 123 VAL Chi-restraints excluded: chain sz residue 66 THR Chi-restraints excluded: chain sz residue 74 SER Chi-restraints excluded: chain sz residue 83 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 201 optimal weight: 8.9990 chunk 219 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 285 optimal weight: 0.9980 chunk 168 optimal weight: 20.0000 chunk 259 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 60 optimal weight: 50.0000 chunk 242 optimal weight: 9.9990 chunk 97 optimal weight: 30.0000 chunk 260 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sf 207 HIS sk 91 ASN ** sp 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** sy 44 HIS ** 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 = 0.3469 r_free = 0.3469 target = 0.054146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.043796 restraints weight = 219476.286| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.91 r_work: 0.3031 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 44959 Z= 0.216 Angle : 0.658 15.183 65805 Z= 0.358 Chirality : 0.046 0.514 8256 Planarity : 0.006 0.118 4362 Dihedral : 22.256 178.326 18727 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.42 % Favored : 94.03 % Rotamer: Outliers : 5.06 % Allowed : 24.53 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.09 % 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: -0.96 (0.17), residues: 2378 helix: 0.58 (0.21), residues: 653 sheet: -0.62 (0.25), residues: 429 loop : -1.29 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGsh 278 TYR 0.028 0.002 TYRse 189 PHE 0.025 0.002 PHEsf 84 TRP 0.019 0.002 TRPsb 183 HIS 0.016 0.001 HISsh 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.22 (44959) covalent geometry : angle 0.65833 / 0.36 (65805) hydrogen bonds : bond 0.07829 / 5.31 ( 1397) hydrogen bonds : angle 4.49782 / 3.31 ( 3067) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 238 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: sB 37 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8695 (mtpt) REVERT: sB 44 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8880 (mt) REVERT: sC 35 GLU cc_start: 0.7851 (pm20) cc_final: 0.6874 (pm20) REVERT: sC 81 ARG cc_start: 0.8219 (ptm-80) cc_final: 0.7991 (ptm-80) REVERT: sb 68 ARG cc_start: 0.9434 (OUTLIER) cc_final: 0.9052 (ttp-170) REVERT: sb 100 TYR cc_start: 0.9285 (m-80) cc_final: 0.8969 (m-80) REVERT: sb 125 GLU cc_start: 0.8190 (mp0) cc_final: 0.7437 (pp20) REVERT: sb 187 ARG cc_start: 0.8916 (ttp-170) cc_final: 0.7774 (tpp-160) REVERT: sc 110 ASN cc_start: 0.9450 (OUTLIER) cc_final: 0.9222 (m110) REVERT: sc 131 MET cc_start: 0.8719 (mmm) cc_final: 0.8491 (tpp) REVERT: se 188 ASP cc_start: 0.9134 (m-30) cc_final: 0.8929 (m-30) REVERT: sf 181 MET cc_start: 0.8831 (mmt) cc_final: 0.8440 (mpp) REVERT: sf 239 ASP cc_start: 0.8337 (p0) cc_final: 0.8100 (p0) REVERT: si 100 LYS cc_start: 0.6375 (tptp) cc_final: 0.5024 (pptt) REVERT: si 153 LYS cc_start: 0.8463 (mppt) cc_final: 0.8194 (mttp) REVERT: sj 116 PHE cc_start: 0.8968 (t80) cc_final: 0.8098 (t80) REVERT: sk 66 ASP cc_start: 0.8980 (m-30) cc_final: 0.8675 (m-30) REVERT: sk 118 PHE cc_start: 0.8678 (m-80) cc_final: 0.8457 (m-80) REVERT: sk 157 GLN cc_start: 0.8337 (pm20) cc_final: 0.7521 (pm20) REVERT: sm 26 ASP cc_start: 0.8440 (t0) cc_final: 0.8235 (t0) REVERT: sr 111 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8570 (mt) REVERT: sx 8 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8363 (mm-30) REVERT: sx 73 ASP cc_start: 0.8917 (m-30) cc_final: 0.8471 (m-30) REVERT: sy 49 VAL cc_start: 0.7013 (OUTLIER) cc_final: 0.6594 (p) REVERT: sy 127 SER cc_start: 0.7160 (OUTLIER) cc_final: 0.6849 (p) REVERT: sz 67 LYS cc_start: 0.7438 (mmpt) cc_final: 0.6923 (ttpt) outliers start: 105 outliers final: 58 residues processed: 325 average time/residue: 0.2486 time to fit residues: 132.9006 Evaluate side-chains 282 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 11 SER Chi-restraints excluded: chain sB residue 37 LYS Chi-restraints excluded: chain sB residue 44 ILE Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sC residue 6 VAL Chi-restraints excluded: chain sC residue 9 LEU Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 15 SER Chi-restraints excluded: chain sC residue 34 LEU Chi-restraints excluded: chain sC residue 45 THR Chi-restraints excluded: chain sC residue 46 THR Chi-restraints excluded: chain sb residue 28 VAL Chi-restraints excluded: chain sb residue 68 ARG Chi-restraints excluded: chain sb residue 99 LYS Chi-restraints excluded: chain sb residue 124 MET Chi-restraints excluded: chain sb residue 151 THR Chi-restraints excluded: chain sc residue 73 HIS Chi-restraints excluded: chain sc residue 110 ASN Chi-restraints excluded: chain sc residue 249 LEU Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 85 MET Chi-restraints excluded: chain sf residue 218 THR Chi-restraints excluded: chain sf residue 220 LEU Chi-restraints excluded: chain sf residue 232 THR Chi-restraints excluded: chain sf residue 244 LYS Chi-restraints excluded: chain sh residue 275 THR Chi-restraints excluded: chain sh residue 291 LEU Chi-restraints excluded: chain sh residue 309 ARG Chi-restraints excluded: chain sh residue 310 TYR Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 165 VAL Chi-restraints excluded: chain si residue 192 LYS Chi-restraints excluded: chain sj residue 27 ASN Chi-restraints excluded: chain sj residue 189 ASP Chi-restraints excluded: chain sj residue 193 LEU Chi-restraints excluded: chain sk residue 112 LEU Chi-restraints excluded: chain sm residue 1 MET Chi-restraints excluded: chain sm residue 13 VAL Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 108 VAL Chi-restraints excluded: chain so residue 31 LEU Chi-restraints excluded: chain so residue 72 LEU Chi-restraints excluded: chain so residue 87 ASP Chi-restraints excluded: chain so residue 91 LEU Chi-restraints excluded: chain sp residue 14 VAL Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 57 VAL Chi-restraints excluded: chain sr residue 74 VAL Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sr residue 107 SER Chi-restraints excluded: chain sr residue 111 LEU Chi-restraints excluded: chain sy residue 29 LYS Chi-restraints excluded: chain sy residue 49 VAL Chi-restraints excluded: chain sy residue 57 THR Chi-restraints excluded: chain sy residue 77 LYS Chi-restraints excluded: chain sy residue 83 VAL Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sy residue 116 VAL Chi-restraints excluded: chain sy residue 127 SER Chi-restraints excluded: chain sz residue 74 SER Chi-restraints excluded: chain sz residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 59 optimal weight: 50.0000 chunk 286 optimal weight: 0.8980 chunk 262 optimal weight: 20.0000 chunk 111 optimal weight: 50.0000 chunk 225 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 328 optimal weight: 20.0000 chunk 179 optimal weight: 40.0000 chunk 256 optimal weight: 20.0000 chunk 263 optimal weight: 8.9990 overall best weight: 7.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sC 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sc 57 GLN se 62 GLN sk 91 ASN so 101 HIS sp 27 HIS ** sy 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.053913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.043595 restraints weight = 219076.546| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.89 r_work: 0.3024 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 44959 Z= 0.206 Angle : 0.583 11.792 65805 Z= 0.322 Chirality : 0.042 0.505 8256 Planarity : 0.005 0.106 4362 Dihedral : 22.239 177.694 18724 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.09 % Favored : 94.41 % Rotamer: Outliers : 4.58 % Allowed : 24.58 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.09 % 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: -0.87 (0.17), residues: 2378 helix: 0.74 (0.21), residues: 661 sheet: -0.66 (0.25), residues: 441 loop : -1.25 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGsz 13 TYR 0.016 0.001 TYRsr 50 PHE 0.023 0.001 PHEsf 84 TRP 0.011 0.001 TRPsy 25 HIS 0.006 0.001 HISsh 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.21 (44959) covalent geometry : angle 0.58266 / 0.32 (65805) hydrogen bonds : bond 0.06926 / 4.74 ( 1397) hydrogen bonds : angle 4.29469 / 3.18 ( 3067) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 218 time to evaluate : 0.814 Fit side-chains REVERT: sB 37 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8782 (mppt) REVERT: sB 44 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8898 (mt) REVERT: sB 69 MET cc_start: 0.9030 (ptt) cc_final: 0.8785 (ptp) REVERT: sC 35 GLU cc_start: 0.8053 (pm20) cc_final: 0.7010 (pm20) REVERT: sC 62 GLN cc_start: 0.8542 (tp40) cc_final: 0.8285 (tp-100) REVERT: sC 81 ARG cc_start: 0.8245 (ptm-80) cc_final: 0.7805 (ptm-80) REVERT: sb 68 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.8802 (ttp-170) REVERT: sb 125 GLU cc_start: 0.8263 (mp0) cc_final: 0.7719 (pp20) REVERT: sb 187 ARG cc_start: 0.8944 (ttp-170) cc_final: 0.7771 (tpp-160) REVERT: sc 42 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8079 (mmmm) REVERT: sc 110 ASN cc_start: 0.9465 (OUTLIER) cc_final: 0.9241 (m110) REVERT: sc 244 LYS cc_start: 0.9019 (ptmm) cc_final: 0.8806 (ptmm) REVERT: sf 181 MET cc_start: 0.9011 (mmt) cc_final: 0.8600 (mpp) REVERT: sf 239 ASP cc_start: 0.8355 (p0) cc_final: 0.8075 (p0) REVERT: si 100 LYS cc_start: 0.6360 (tptp) cc_final: 0.5134 (pptt) REVERT: si 153 LYS cc_start: 0.8488 (mppt) cc_final: 0.8229 (mttp) REVERT: sj 116 PHE cc_start: 0.8863 (t80) cc_final: 0.8070 (t80) REVERT: sj 189 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7023 (p0) REVERT: sk 66 ASP cc_start: 0.9039 (m-30) cc_final: 0.8613 (m-30) REVERT: sk 157 GLN cc_start: 0.8342 (pm20) cc_final: 0.7551 (pm20) REVERT: so 91 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8783 (mp) REVERT: sp 123 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.6884 (mtt180) REVERT: sx 73 ASP cc_start: 0.8915 (m-30) cc_final: 0.8402 (m-30) REVERT: sy 49 VAL cc_start: 0.7126 (OUTLIER) cc_final: 0.6665 (p) REVERT: sz 67 LYS cc_start: 0.7464 (mmpt) cc_final: 0.6939 (mtpt) REVERT: sz 72 LYS cc_start: 0.6377 (tptm) cc_final: 0.6171 (tptp) outliers start: 95 outliers final: 61 residues processed: 295 average time/residue: 0.2399 time to fit residues: 117.2961 Evaluate side-chains 277 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 207 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 11 SER Chi-restraints excluded: chain sB residue 37 LYS Chi-restraints excluded: chain sB residue 44 ILE Chi-restraints excluded: chain sB residue 50 VAL Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sC residue 9 LEU Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 34 LEU Chi-restraints excluded: chain sC residue 45 THR Chi-restraints excluded: chain sb residue 64 SER Chi-restraints excluded: chain sb residue 68 ARG Chi-restraints excluded: chain sb residue 98 MET Chi-restraints excluded: chain sb residue 99 LYS Chi-restraints excluded: chain sb residue 101 THR Chi-restraints excluded: chain sb residue 151 THR Chi-restraints excluded: chain sc residue 42 LYS Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 73 HIS Chi-restraints excluded: chain sc residue 110 ASN Chi-restraints excluded: chain sc residue 249 LEU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 184 THR Chi-restraints excluded: chain se residue 228 LEU Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 220 LEU Chi-restraints excluded: chain sf residue 232 THR Chi-restraints excluded: chain sf residue 244 LYS Chi-restraints excluded: chain sh residue 275 THR Chi-restraints excluded: chain sh residue 291 LEU Chi-restraints excluded: chain sh residue 309 ARG Chi-restraints excluded: chain sh residue 310 TYR Chi-restraints excluded: chain si residue 139 VAL Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 165 VAL Chi-restraints excluded: chain sj residue 27 ASN Chi-restraints excluded: chain sj residue 189 ASP Chi-restraints excluded: chain sj residue 193 LEU Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 31 VAL Chi-restraints excluded: chain sk residue 112 LEU Chi-restraints excluded: chain sk residue 150 VAL Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 108 VAL Chi-restraints excluded: chain so residue 31 LEU Chi-restraints excluded: chain so residue 72 LEU Chi-restraints excluded: chain so residue 87 ASP Chi-restraints excluded: chain so residue 91 LEU Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 57 VAL Chi-restraints excluded: chain sp residue 62 ASP Chi-restraints excluded: chain sp residue 123 ARG Chi-restraints excluded: chain sr residue 74 VAL Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sr residue 107 SER Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sy residue 49 VAL Chi-restraints excluded: chain sy residue 57 THR Chi-restraints excluded: chain sy residue 77 LYS Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sy residue 116 VAL Chi-restraints excluded: chain sy residue 123 VAL Chi-restraints excluded: chain sz residue 66 THR Chi-restraints excluded: chain sz residue 74 SER Chi-restraints excluded: chain sz residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 175 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 76 optimal weight: 50.0000 chunk 41 optimal weight: 50.0000 chunk 92 optimal weight: 40.0000 chunk 37 optimal weight: 50.0000 chunk 59 optimal weight: 50.0000 chunk 211 optimal weight: 10.0000 chunk 18 optimal weight: 70.0000 chunk 202 optimal weight: 9.9990 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sB 25 HIS ** sC 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sc 227 GLN sf 248 GLN sk 91 ASN ** sy 44 HIS ** 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 = 0.3439 r_free = 0.3439 target = 0.053288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.042983 restraints weight = 218723.309| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.90 r_work: 0.2997 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 44959 Z= 0.250 Angle : 0.637 12.130 65805 Z= 0.345 Chirality : 0.046 0.572 8256 Planarity : 0.005 0.100 4362 Dihedral : 22.218 179.431 18724 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.97 % Favored : 93.48 % Rotamer: Outliers : 6.02 % Allowed : 23.90 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.09 % 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: -0.94 (0.17), residues: 2378 helix: 0.74 (0.21), residues: 659 sheet: -0.73 (0.24), residues: 454 loop : -1.33 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGsf 146 TYR 0.020 0.002 TYRsf 147 PHE 0.025 0.002 PHEsf 84 TRP 0.013 0.002 TRPsy 25 HIS 0.009 0.001 HISsc 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.25 (44959) covalent geometry : angle 0.63741 / 0.35 (65805) hydrogen bonds : bond 0.07417 / 5.06 ( 1397) hydrogen bonds : angle 4.33727 / 3.23 ( 3067) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 220 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: sB 37 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8796 (mtpt) REVERT: sB 44 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.8897 (mt) REVERT: sC 35 GLU cc_start: 0.8199 (pm20) cc_final: 0.7426 (pm20) REVERT: sC 81 ARG cc_start: 0.8362 (ptm-80) cc_final: 0.7978 (ptm-80) REVERT: sb 27 ARG cc_start: 0.7097 (ptm160) cc_final: 0.6633 (ptp-110) REVERT: sb 30 ILE cc_start: 0.8772 (tt) cc_final: 0.8215 (pt) REVERT: sb 68 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.8736 (ttp-170) REVERT: sb 187 ARG cc_start: 0.8885 (ttp-170) cc_final: 0.7486 (tpp-160) REVERT: sc 110 ASN cc_start: 0.9495 (OUTLIER) cc_final: 0.9276 (m110) REVERT: sc 131 MET cc_start: 0.8787 (mmm) cc_final: 0.8460 (tpp) REVERT: sc 244 LYS cc_start: 0.8982 (ptmm) cc_final: 0.8676 (ptmm) REVERT: se 233 GLN cc_start: 0.8379 (tt0) cc_final: 0.8165 (mt0) REVERT: sf 94 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8036 (mmmt) REVERT: sf 181 MET cc_start: 0.9064 (mmt) cc_final: 0.8705 (mpp) REVERT: sf 239 ASP cc_start: 0.8367 (p0) cc_final: 0.8082 (p0) REVERT: sh 148 LYS cc_start: 0.4289 (OUTLIER) cc_final: 0.3458 (tptt) REVERT: sh 306 ILE cc_start: 0.8331 (pt) cc_final: 0.8087 (mt) REVERT: si 100 LYS cc_start: 0.6464 (tptp) cc_final: 0.5341 (pptt) REVERT: si 122 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.4919 (mmt180) REVERT: si 153 LYS cc_start: 0.8423 (mppt) cc_final: 0.8157 (mttp) REVERT: sj 116 PHE cc_start: 0.8901 (t80) cc_final: 0.8031 (t80) REVERT: sj 197 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8392 (tm-30) REVERT: sj 221 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: sk 66 ASP cc_start: 0.9042 (m-30) cc_final: 0.8609 (m-30) REVERT: sk 157 GLN cc_start: 0.8451 (pm20) cc_final: 0.7602 (pm20) REVERT: so 91 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8833 (mp) REVERT: sp 60 ASP cc_start: 0.6856 (OUTLIER) cc_final: 0.6373 (t0) REVERT: sp 123 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.6927 (mtt180) REVERT: sx 73 ASP cc_start: 0.8965 (m-30) cc_final: 0.8594 (m-30) REVERT: sy 127 SER cc_start: 0.7779 (OUTLIER) cc_final: 0.7440 (p) REVERT: sz 67 LYS cc_start: 0.7602 (mmpt) cc_final: 0.7055 (mtpt) outliers start: 125 outliers final: 81 residues processed: 320 average time/residue: 0.2350 time to fit residues: 122.9423 Evaluate side-chains 305 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 212 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 11 SER Chi-restraints excluded: chain sB residue 37 LYS Chi-restraints excluded: chain sB residue 44 ILE Chi-restraints excluded: chain sB residue 50 VAL Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sC residue 6 VAL Chi-restraints excluded: chain sC residue 9 LEU Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 15 SER Chi-restraints excluded: chain sC residue 34 LEU Chi-restraints excluded: chain sC residue 44 THR Chi-restraints excluded: chain sC residue 45 THR Chi-restraints excluded: chain sC residue 46 THR Chi-restraints excluded: chain sb residue 55 ASN Chi-restraints excluded: chain sb residue 64 SER Chi-restraints excluded: chain sb residue 68 ARG Chi-restraints excluded: chain sb residue 98 MET Chi-restraints excluded: chain sb residue 101 THR Chi-restraints excluded: chain sb residue 124 MET Chi-restraints excluded: chain sb residue 151 THR Chi-restraints excluded: chain sc residue 73 HIS Chi-restraints excluded: chain sc residue 110 ASN Chi-restraints excluded: chain sc residue 248 ILE Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 126 SER Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain se residue 184 THR Chi-restraints excluded: chain se residue 214 ILE Chi-restraints excluded: chain se residue 228 LEU Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 94 LYS Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 232 THR Chi-restraints excluded: chain sf residue 244 LYS Chi-restraints excluded: chain sh residue 148 LYS Chi-restraints excluded: chain sh residue 208 THR Chi-restraints excluded: chain sh residue 261 LYS Chi-restraints excluded: chain sh residue 265 SER Chi-restraints excluded: chain sh residue 275 THR Chi-restraints excluded: chain sh residue 291 LEU Chi-restraints excluded: chain sh residue 299 GLU Chi-restraints excluded: chain si residue 122 ARG Chi-restraints excluded: chain si residue 139 VAL Chi-restraints excluded: chain si residue 158 SER Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 192 LYS Chi-restraints excluded: chain sj residue 27 ASN Chi-restraints excluded: chain sj residue 189 ASP Chi-restraints excluded: chain sj residue 193 LEU Chi-restraints excluded: chain sj residue 201 VAL Chi-restraints excluded: chain sj residue 221 GLU Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 21 ARG Chi-restraints excluded: chain sk residue 31 VAL Chi-restraints excluded: chain sk residue 112 LEU Chi-restraints excluded: chain sk residue 140 VAL Chi-restraints excluded: chain sk residue 150 VAL Chi-restraints excluded: chain sm residue 1 MET Chi-restraints excluded: chain sm residue 76 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 108 VAL Chi-restraints excluded: chain sm residue 143 THR Chi-restraints excluded: chain so residue 31 LEU Chi-restraints excluded: chain so residue 72 LEU Chi-restraints excluded: chain so residue 87 ASP Chi-restraints excluded: chain so residue 91 LEU Chi-restraints excluded: chain so residue 110 ASP Chi-restraints excluded: chain sp residue 14 VAL Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 57 VAL Chi-restraints excluded: chain sp residue 60 ASP Chi-restraints excluded: chain sp residue 62 ASP Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 119 MET Chi-restraints excluded: chain sp residue 123 ARG Chi-restraints excluded: chain sr residue 74 VAL Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 107 SER Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sy residue 57 THR Chi-restraints excluded: chain sy residue 77 LYS Chi-restraints excluded: chain sy residue 83 VAL Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sy residue 116 VAL Chi-restraints excluded: chain sy residue 123 VAL Chi-restraints excluded: chain sy residue 127 SER Chi-restraints excluded: chain sz residue 66 THR Chi-restraints excluded: chain sz residue 74 SER Chi-restraints excluded: chain sz residue 83 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 57 optimal weight: 50.0000 chunk 171 optimal weight: 10.0000 chunk 77 optimal weight: 50.0000 chunk 183 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 42 optimal weight: 50.0000 chunk 26 optimal weight: 40.0000 chunk 294 optimal weight: 8.9990 chunk 28 optimal weight: 40.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sb 49 ASN sk 91 ASN so 101 HIS so 105 ASN ** sy 44 HIS ** 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 = 0.3435 r_free = 0.3435 target = 0.053119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.042808 restraints weight = 220931.858| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.92 r_work: 0.2993 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 44959 Z= 0.258 Angle : 0.629 11.525 65805 Z= 0.341 Chirality : 0.046 0.565 8256 Planarity : 0.005 0.106 4362 Dihedral : 22.243 178.962 18717 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.63 % Favored : 93.86 % Rotamer: Outliers : 5.54 % Allowed : 24.96 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.17), residues: 2378 helix: 0.83 (0.21), residues: 660 sheet: -0.85 (0.24), residues: 470 loop : -1.37 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGsz 13 TYR 0.015 0.002 TYRsf 147 PHE 0.020 0.002 PHEsf 84 TRP 0.012 0.001 TRPsb 60 HIS 0.006 0.001 HISsh 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.26 (44959) covalent geometry : angle 0.62950 / 0.34 (65805) hydrogen bonds : bond 0.07313 / 5.01 ( 1397) hydrogen bonds : angle 4.29584 / 3.20 ( 3067) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 224 time to evaluate : 1.006 Fit side-chains REVERT: sB 6 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.8432 (ttm-80) REVERT: sB 37 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8806 (mtpt) REVERT: sB 44 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.8893 (mt) REVERT: sC 35 GLU cc_start: 0.8152 (pm20) cc_final: 0.7337 (pm20) REVERT: sC 81 ARG cc_start: 0.8370 (ptm-80) cc_final: 0.7832 (ptm-80) REVERT: sb 68 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.8792 (ttp-170) REVERT: sb 99 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9101 (mptt) REVERT: sb 111 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8917 (t) REVERT: sb 187 ARG cc_start: 0.8869 (ttp-170) cc_final: 0.7443 (tpp-160) REVERT: sc 110 ASN cc_start: 0.9520 (OUTLIER) cc_final: 0.9303 (m110) REVERT: sc 122 GLU cc_start: 0.8139 (mp0) cc_final: 0.7671 (mt-10) REVERT: sc 131 MET cc_start: 0.8891 (mmm) cc_final: 0.8546 (tpt) REVERT: sc 244 LYS cc_start: 0.9014 (ptmm) cc_final: 0.8514 (ptmm) REVERT: se 233 GLN cc_start: 0.8499 (tt0) cc_final: 0.8197 (mt0) REVERT: sf 94 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8104 (mmmt) REVERT: sf 181 MET cc_start: 0.9125 (mmt) cc_final: 0.8761 (mpp) REVERT: sf 239 ASP cc_start: 0.8402 (p0) cc_final: 0.8061 (p0) REVERT: sh 148 LYS cc_start: 0.4266 (OUTLIER) cc_final: 0.3310 (tptt) REVERT: sh 222 THR cc_start: 0.8164 (p) cc_final: 0.7862 (m) REVERT: sh 261 LYS cc_start: 0.1008 (OUTLIER) cc_final: 0.0723 (ptmm) REVERT: si 100 LYS cc_start: 0.6306 (tptp) cc_final: 0.5262 (pptt) REVERT: si 122 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.4753 (mmt180) REVERT: si 153 LYS cc_start: 0.8418 (mppt) cc_final: 0.8149 (mttp) REVERT: sj 197 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8332 (tm-30) REVERT: sk 66 ASP cc_start: 0.9043 (m-30) cc_final: 0.8693 (m-30) REVERT: sk 157 GLN cc_start: 0.8485 (pm20) cc_final: 0.7623 (pm20) REVERT: sp 123 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.6932 (mtt180) REVERT: sr 36 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8719 (mm-30) REVERT: sr 130 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7024 (m-80) REVERT: sx 73 ASP cc_start: 0.8910 (m-30) cc_final: 0.8439 (m-30) REVERT: sz 67 LYS cc_start: 0.7489 (mmpt) cc_final: 0.6953 (mtpt) outliers start: 115 outliers final: 82 residues processed: 312 average time/residue: 0.2402 time to fit residues: 123.3354 Evaluate side-chains 313 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 218 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 6 ARG Chi-restraints excluded: chain sB residue 11 SER Chi-restraints excluded: chain sB residue 37 LYS Chi-restraints excluded: chain sB residue 44 ILE Chi-restraints excluded: chain sB residue 50 VAL Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sC residue 6 VAL Chi-restraints excluded: chain sC residue 9 LEU Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 15 SER Chi-restraints excluded: chain sC residue 34 LEU Chi-restraints excluded: chain sC residue 44 THR Chi-restraints excluded: chain sC residue 45 THR Chi-restraints excluded: chain sC residue 75 THR Chi-restraints excluded: chain sb residue 28 VAL Chi-restraints excluded: chain sb residue 55 ASN Chi-restraints excluded: chain sb residue 64 SER Chi-restraints excluded: chain sb residue 68 ARG Chi-restraints excluded: chain sb residue 98 MET Chi-restraints excluded: chain sb residue 99 LYS Chi-restraints excluded: chain sb residue 101 THR Chi-restraints excluded: chain sb residue 111 THR Chi-restraints excluded: chain sb residue 124 MET Chi-restraints excluded: chain sb residue 151 THR Chi-restraints excluded: chain sc residue 63 ILE Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 73 HIS Chi-restraints excluded: chain sc residue 110 ASN Chi-restraints excluded: chain sc residue 248 ILE Chi-restraints excluded: chain sc residue 249 LEU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 110 ASP Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain se residue 184 THR Chi-restraints excluded: chain se residue 214 ILE Chi-restraints excluded: chain se residue 228 LEU Chi-restraints excluded: chain sf residue 37 LYS Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 94 LYS Chi-restraints excluded: chain sf residue 131 THR Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 232 THR Chi-restraints excluded: chain sf residue 244 LYS Chi-restraints excluded: chain sh residue 148 LYS Chi-restraints excluded: chain sh residue 208 THR Chi-restraints excluded: chain sh residue 261 LYS Chi-restraints excluded: chain sh residue 265 SER Chi-restraints excluded: chain sh residue 275 THR Chi-restraints excluded: chain sh residue 291 LEU Chi-restraints excluded: chain sh residue 299 GLU Chi-restraints excluded: chain si residue 122 ARG Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 192 LYS Chi-restraints excluded: chain sj residue 27 ASN Chi-restraints excluded: chain sj residue 189 ASP Chi-restraints excluded: chain sj residue 193 LEU Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 21 ARG Chi-restraints excluded: chain sk residue 31 VAL Chi-restraints excluded: chain sk residue 112 LEU Chi-restraints excluded: chain sk residue 140 VAL Chi-restraints excluded: chain sk residue 150 VAL Chi-restraints excluded: chain sm residue 13 VAL Chi-restraints excluded: chain sm residue 73 ILE Chi-restraints excluded: chain sm residue 76 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 108 VAL Chi-restraints excluded: chain so residue 31 LEU Chi-restraints excluded: chain so residue 72 LEU Chi-restraints excluded: chain so residue 87 ASP Chi-restraints excluded: chain sp residue 14 VAL Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 57 VAL Chi-restraints excluded: chain sp residue 62 ASP Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 119 MET Chi-restraints excluded: chain sp residue 123 ARG Chi-restraints excluded: chain sr residue 74 VAL Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sr residue 107 SER Chi-restraints excluded: chain sr residue 130 TYR Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sy residue 57 THR Chi-restraints excluded: chain sy residue 77 LYS Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sy residue 116 VAL Chi-restraints excluded: chain sy residue 123 VAL Chi-restraints excluded: chain sz residue 66 THR Chi-restraints excluded: chain sz residue 74 SER Chi-restraints excluded: chain sz residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 243 optimal weight: 5.9990 chunk 327 optimal weight: 8.9990 chunk 38 optimal weight: 50.0000 chunk 191 optimal weight: 0.1980 chunk 103 optimal weight: 30.0000 chunk 241 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 58 optimal weight: 40.0000 chunk 157 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sb 171 ASN sc 112 HIS sk 91 ASN so 105 ASN sr 80 ASN ** sy 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.053919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.043701 restraints weight = 218885.703| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.84 r_work: 0.3029 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 44959 Z= 0.151 Angle : 0.534 9.591 65805 Z= 0.302 Chirality : 0.039 0.468 8256 Planarity : 0.005 0.099 4362 Dihedral : 22.231 178.604 18717 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.21 % Favored : 94.45 % Rotamer: Outliers : 4.19 % Allowed : 26.17 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2378 helix: 0.99 (0.21), residues: 661 sheet: -0.82 (0.24), residues: 464 loop : -1.29 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGsh 302 TYR 0.014 0.001 TYRsr 50 PHE 0.016 0.001 PHEsf 216 TRP 0.011 0.001 TRPsb 60 HIS 0.005 0.001 HISsh 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (44959) covalent geometry : angle 0.53447 / 0.30 (65805) hydrogen bonds : bond 0.06702 / 4.57 ( 1397) hydrogen bonds : angle 4.12337 / 3.07 ( 3067) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 228 time to evaluate : 0.970 Fit side-chains REVERT: sB 6 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8406 (ttm-80) REVERT: sB 37 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8814 (mppt) REVERT: sB 44 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8886 (mt) REVERT: sC 22 MET cc_start: 0.9529 (OUTLIER) cc_final: 0.9303 (mmm) REVERT: sC 35 GLU cc_start: 0.8158 (pm20) cc_final: 0.7346 (pm20) REVERT: sC 81 ARG cc_start: 0.8333 (ptm-80) cc_final: 0.7822 (ptm-80) REVERT: sb 27 ARG cc_start: 0.6970 (ptm160) cc_final: 0.6484 (ptp-110) REVERT: sb 30 ILE cc_start: 0.8690 (tt) cc_final: 0.8128 (pt) REVERT: sb 68 ARG cc_start: 0.9417 (OUTLIER) cc_final: 0.8807 (ttp-170) REVERT: sb 99 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9088 (mptt) REVERT: sb 187 ARG cc_start: 0.8878 (ttp-170) cc_final: 0.7440 (tpp-160) REVERT: sc 80 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.5482 (tp30) REVERT: sc 81 GLU cc_start: 0.8829 (tt0) cc_final: 0.8590 (tt0) REVERT: sc 131 MET cc_start: 0.8825 (mmm) cc_final: 0.8131 (tpt) REVERT: sc 244 LYS cc_start: 0.9001 (ptmm) cc_final: 0.8490 (ptmm) REVERT: se 233 GLN cc_start: 0.8511 (tt0) cc_final: 0.8253 (mt0) REVERT: sf 181 MET cc_start: 0.9007 (mmt) cc_final: 0.8780 (mpp) REVERT: sf 239 ASP cc_start: 0.8257 (p0) cc_final: 0.8005 (p0) REVERT: sh 148 LYS cc_start: 0.4201 (OUTLIER) cc_final: 0.3393 (tptt) REVERT: sh 234 ARG cc_start: 0.4548 (OUTLIER) cc_final: 0.4228 (mtt180) REVERT: sh 270 ILE cc_start: 0.7559 (tt) cc_final: 0.7339 (tp) REVERT: si 100 LYS cc_start: 0.6329 (tptp) cc_final: 0.5312 (pptt) REVERT: si 120 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.4271 (mpt90) REVERT: si 153 LYS cc_start: 0.8473 (mppt) cc_final: 0.8178 (mttp) REVERT: sj 116 PHE cc_start: 0.8872 (t80) cc_final: 0.8107 (t80) REVERT: sk 66 ASP cc_start: 0.9006 (m-30) cc_final: 0.8602 (m-30) REVERT: sk 157 GLN cc_start: 0.8490 (pm20) cc_final: 0.8130 (pm20) REVERT: sp 123 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.6905 (mtt180) REVERT: sx 73 ASP cc_start: 0.8908 (m-30) cc_final: 0.8445 (m-30) REVERT: sy 11 MET cc_start: 0.9065 (mtp) cc_final: 0.8839 (mtp) REVERT: sz 67 LYS cc_start: 0.7440 (mmpt) cc_final: 0.6952 (mtpt) REVERT: sz 74 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8241 (t) REVERT: sz 87 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8324 (mtmm) outliers start: 87 outliers final: 61 residues processed: 295 average time/residue: 0.2271 time to fit residues: 110.2580 Evaluate side-chains 291 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 218 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 6 ARG Chi-restraints excluded: chain sB residue 11 SER Chi-restraints excluded: chain sB residue 37 LYS Chi-restraints excluded: chain sB residue 44 ILE Chi-restraints excluded: chain sB residue 50 VAL Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 60 THR Chi-restraints excluded: chain sC residue 9 LEU Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 22 MET Chi-restraints excluded: chain sC residue 45 THR Chi-restraints excluded: chain sC residue 75 THR Chi-restraints excluded: chain sb residue 68 ARG Chi-restraints excluded: chain sb residue 98 MET Chi-restraints excluded: chain sb residue 99 LYS Chi-restraints excluded: chain sb residue 101 THR Chi-restraints excluded: chain sb residue 151 THR Chi-restraints excluded: chain sc residue 63 ILE Chi-restraints excluded: chain sc residue 73 HIS Chi-restraints excluded: chain sc residue 80 GLU Chi-restraints excluded: chain sc residue 249 LEU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain se residue 228 LEU Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 131 THR Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 232 THR Chi-restraints excluded: chain sf residue 244 LYS Chi-restraints excluded: chain sh residue 148 LYS Chi-restraints excluded: chain sh residue 208 THR Chi-restraints excluded: chain sh residue 234 ARG Chi-restraints excluded: chain sh residue 265 SER Chi-restraints excluded: chain sh residue 275 THR Chi-restraints excluded: chain sh residue 291 LEU Chi-restraints excluded: chain sh residue 299 GLU Chi-restraints excluded: chain si residue 120 ARG Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 192 LYS Chi-restraints excluded: chain sj residue 27 ASN Chi-restraints excluded: chain sj residue 189 ASP Chi-restraints excluded: chain sj residue 193 LEU Chi-restraints excluded: chain sk residue 31 VAL Chi-restraints excluded: chain sk residue 112 LEU Chi-restraints excluded: chain sk residue 140 VAL Chi-restraints excluded: chain sk residue 150 VAL Chi-restraints excluded: chain sm residue 73 ILE Chi-restraints excluded: chain sm residue 76 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 108 VAL Chi-restraints excluded: chain sm residue 149 ASP Chi-restraints excluded: chain so residue 31 LEU Chi-restraints excluded: chain so residue 87 ASP Chi-restraints excluded: chain so residue 110 ASP Chi-restraints excluded: chain sp residue 14 VAL Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 57 VAL Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 123 ARG Chi-restraints excluded: chain sr residue 74 VAL Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sr residue 107 SER Chi-restraints excluded: chain sy residue 57 THR Chi-restraints excluded: chain sy residue 77 LYS Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sy residue 116 VAL Chi-restraints excluded: chain sy residue 123 VAL Chi-restraints excluded: chain sz residue 66 THR Chi-restraints excluded: chain sz residue 74 SER Chi-restraints excluded: chain sz residue 83 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 268 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 298 optimal weight: 20.0000 chunk 289 optimal weight: 40.0000 chunk 286 optimal weight: 3.9990 chunk 322 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 43 optimal weight: 60.0000 chunk 189 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 142 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... si 157 ASN sk 91 ASN so 101 HIS ** sy 44 HIS ** 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 = 0.3449 r_free = 0.3449 target = 0.053484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.043200 restraints weight = 219336.993| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.90 r_work: 0.3011 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 44959 Z= 0.202 Angle : 0.575 9.978 65805 Z= 0.316 Chirality : 0.042 0.534 8256 Planarity : 0.005 0.104 4362 Dihedral : 22.185 177.863 18717 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.68 % Favored : 93.94 % Rotamer: Outliers : 4.72 % Allowed : 25.83 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.17), residues: 2378 helix: 0.99 (0.21), residues: 660 sheet: -0.87 (0.24), residues: 471 loop : -1.29 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGsb 46 TYR 0.013 0.001 TYRsb 44 PHE 0.025 0.001 PHEsf 84 TRP 0.011 0.001 TRPsb 60 HIS 0.006 0.001 HISsh 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (44959) covalent geometry : angle 0.57471 / 0.32 (65805) hydrogen bonds : bond 0.06893 / 4.71 ( 1397) hydrogen bonds : angle 4.14781 / 3.09 ( 3067) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 219 time to evaluate : 0.941 Fit side-chains REVERT: sB 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.8488 (ttm-80) REVERT: sB 37 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8810 (mtpt) REVERT: sB 44 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.8892 (mt) REVERT: sC 35 GLU cc_start: 0.8229 (pm20) cc_final: 0.7342 (pm20) REVERT: sC 81 ARG cc_start: 0.8384 (ptm-80) cc_final: 0.7766 (ptm-80) REVERT: sb 27 ARG cc_start: 0.7007 (ptm160) cc_final: 0.6476 (ptp-110) REVERT: sb 30 ILE cc_start: 0.8713 (tt) cc_final: 0.8133 (pt) REVERT: sb 51 GLU cc_start: 0.7849 (pm20) cc_final: 0.7583 (pm20) REVERT: sb 68 ARG cc_start: 0.9401 (OUTLIER) cc_final: 0.8772 (ttp-170) REVERT: sb 99 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9098 (mptt) REVERT: sb 187 ARG cc_start: 0.8891 (ttp-170) cc_final: 0.7415 (tpp-160) REVERT: sc 244 LYS cc_start: 0.9041 (ptmm) cc_final: 0.8585 (ptmm) REVERT: se 233 GLN cc_start: 0.8533 (tt0) cc_final: 0.8289 (mt0) REVERT: sf 94 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8213 (mmtt) REVERT: sf 181 MET cc_start: 0.9022 (mmt) cc_final: 0.8762 (mpp) REVERT: sf 239 ASP cc_start: 0.8210 (p0) cc_final: 0.7962 (p0) REVERT: sh 222 THR cc_start: 0.8080 (p) cc_final: 0.7790 (m) REVERT: sh 234 ARG cc_start: 0.4716 (OUTLIER) cc_final: 0.4460 (mtt180) REVERT: si 100 LYS cc_start: 0.6415 (tptp) cc_final: 0.5318 (pptt) REVERT: si 112 SER cc_start: 0.8390 (m) cc_final: 0.8167 (p) REVERT: si 120 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.4351 (mpt90) REVERT: si 153 LYS cc_start: 0.8491 (mppt) cc_final: 0.8280 (mttp) REVERT: sk 66 ASP cc_start: 0.9010 (m-30) cc_final: 0.8597 (m-30) REVERT: sk 133 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8736 (mmm) REVERT: sk 157 GLN cc_start: 0.8472 (pm20) cc_final: 0.7871 (pm20) REVERT: sp 123 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.6924 (mtt180) REVERT: sx 73 ASP cc_start: 0.8923 (m-30) cc_final: 0.8441 (m-30) REVERT: sz 67 LYS cc_start: 0.7505 (mmpt) cc_final: 0.7020 (mtpt) REVERT: sz 74 SER cc_start: 0.8362 (OUTLIER) cc_final: 0.8146 (t) REVERT: sz 87 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8280 (mtmm) outliers start: 98 outliers final: 78 residues processed: 297 average time/residue: 0.2423 time to fit residues: 118.2771 Evaluate side-chains 303 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 214 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 6 ARG Chi-restraints excluded: chain sB residue 11 SER Chi-restraints excluded: chain sB residue 37 LYS Chi-restraints excluded: chain sB residue 44 ILE Chi-restraints excluded: chain sB residue 50 VAL Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sC residue 9 LEU Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 15 SER Chi-restraints excluded: chain sC residue 45 THR Chi-restraints excluded: chain sC residue 75 THR Chi-restraints excluded: chain sb residue 68 ARG Chi-restraints excluded: chain sb residue 98 MET Chi-restraints excluded: chain sb residue 99 LYS Chi-restraints excluded: chain sb residue 101 THR Chi-restraints excluded: chain sb residue 151 THR Chi-restraints excluded: chain sc residue 63 ILE Chi-restraints excluded: chain sc residue 73 HIS Chi-restraints excluded: chain sc residue 248 ILE Chi-restraints excluded: chain sc residue 249 LEU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 110 ASP Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 126 SER Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain se residue 184 THR Chi-restraints excluded: chain se residue 214 ILE Chi-restraints excluded: chain se residue 228 LEU Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 94 LYS Chi-restraints excluded: chain sf residue 131 THR Chi-restraints excluded: chain sf residue 175 ILE Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 232 THR Chi-restraints excluded: chain sf residue 244 LYS Chi-restraints excluded: chain sh residue 208 THR Chi-restraints excluded: chain sh residue 234 ARG Chi-restraints excluded: chain sh residue 265 SER Chi-restraints excluded: chain sh residue 275 THR Chi-restraints excluded: chain sh residue 291 LEU Chi-restraints excluded: chain sh residue 299 GLU Chi-restraints excluded: chain si residue 120 ARG Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 192 LYS Chi-restraints excluded: chain sj residue 27 ASN Chi-restraints excluded: chain sj residue 189 ASP Chi-restraints excluded: chain sj residue 193 LEU Chi-restraints excluded: chain sj residue 201 VAL Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 21 ARG Chi-restraints excluded: chain sk residue 112 LEU Chi-restraints excluded: chain sk residue 133 MET Chi-restraints excluded: chain sk residue 140 VAL Chi-restraints excluded: chain sk residue 150 VAL Chi-restraints excluded: chain sm residue 13 VAL Chi-restraints excluded: chain sm residue 73 ILE Chi-restraints excluded: chain sm residue 76 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 108 VAL Chi-restraints excluded: chain sm residue 149 ASP Chi-restraints excluded: chain so residue 31 LEU Chi-restraints excluded: chain so residue 72 LEU Chi-restraints excluded: chain so residue 87 ASP Chi-restraints excluded: chain sp residue 14 VAL Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 57 VAL Chi-restraints excluded: chain sp residue 62 ASP Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 119 MET Chi-restraints excluded: chain sp residue 123 ARG Chi-restraints excluded: chain sr residue 2 VAL Chi-restraints excluded: chain sr residue 74 VAL Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sr residue 107 SER Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sy residue 43 SER Chi-restraints excluded: chain sy residue 57 THR Chi-restraints excluded: chain sy residue 77 LYS Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sy residue 116 VAL Chi-restraints excluded: chain sy residue 123 VAL Chi-restraints excluded: chain sz residue 66 THR Chi-restraints excluded: chain sz residue 74 SER Chi-restraints excluded: chain sz residue 83 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 112 optimal weight: 40.0000 chunk 222 optimal weight: 40.0000 chunk 251 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 97 optimal weight: 30.0000 chunk 82 optimal weight: 40.0000 chunk 299 optimal weight: 0.8980 chunk 232 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sk 91 ASN ** sy 44 HIS ** 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 = 0.3473 r_free = 0.3473 target = 0.054172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043869 restraints weight = 218405.867| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.96 r_work: 0.3042 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 44959 Z= 0.132 Angle : 0.514 9.725 65805 Z= 0.292 Chirality : 0.038 0.456 8256 Planarity : 0.004 0.099 4362 Dihedral : 22.201 178.262 18717 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.51 % Favored : 94.24 % Rotamer: Outliers : 4.29 % Allowed : 26.22 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.17), residues: 2378 helix: 1.05 (0.21), residues: 661 sheet: -0.79 (0.24), residues: 462 loop : -1.17 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGsh 302 TYR 0.011 0.001 TYRsr 50 PHE 0.016 0.001 PHEsf 84 TRP 0.011 0.001 TRPsb 60 HIS 0.004 0.001 HISsy 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (44959) covalent geometry : angle 0.51436 / 0.29 (65805) hydrogen bonds : bond 0.06479 / 4.41 ( 1397) hydrogen bonds : angle 4.02295 / 3.00 ( 3067) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 222 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: sB 6 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.8410 (ttm-80) REVERT: sB 37 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8843 (mppt) REVERT: sB 44 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8887 (mt) REVERT: sC 35 GLU cc_start: 0.8247 (pm20) cc_final: 0.7385 (pm20) REVERT: sC 81 ARG cc_start: 0.8358 (ptm-80) cc_final: 0.7704 (ptm-80) REVERT: sb 27 ARG cc_start: 0.6999 (ptm160) cc_final: 0.6500 (ptp-110) REVERT: sb 30 ILE cc_start: 0.8686 (tt) cc_final: 0.8119 (pt) REVERT: sb 51 GLU cc_start: 0.7836 (pm20) cc_final: 0.7596 (pm20) REVERT: sb 68 ARG cc_start: 0.9405 (OUTLIER) cc_final: 0.8740 (ttp-170) REVERT: sb 99 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9065 (mptt) REVERT: sc 244 LYS cc_start: 0.9026 (ptmm) cc_final: 0.8578 (ptmm) REVERT: se 233 GLN cc_start: 0.8531 (tt0) cc_final: 0.8293 (mt0) REVERT: sh 148 LYS cc_start: 0.4324 (OUTLIER) cc_final: 0.3420 (tptt) REVERT: sh 296 MET cc_start: 0.7728 (tpp) cc_final: 0.7259 (tpp) REVERT: si 100 LYS cc_start: 0.6388 (tptp) cc_final: 0.5241 (pptt) REVERT: si 120 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.4158 (mpt90) REVERT: si 153 LYS cc_start: 0.8477 (mppt) cc_final: 0.8268 (mttp) REVERT: sk 59 MET cc_start: 0.8600 (mmm) cc_final: 0.8103 (mmm) REVERT: sk 66 ASP cc_start: 0.8999 (m-30) cc_final: 0.8650 (m-30) REVERT: sk 133 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8748 (mmm) REVERT: sk 157 GLN cc_start: 0.8462 (pm20) cc_final: 0.7852 (pm20) REVERT: sp 123 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.6900 (mtt180) REVERT: sx 73 ASP cc_start: 0.8927 (m-30) cc_final: 0.8472 (m-30) REVERT: sz 67 LYS cc_start: 0.7121 (mmpt) cc_final: 0.6594 (mtpt) REVERT: sz 87 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8246 (mtmm) outliers start: 89 outliers final: 70 residues processed: 289 average time/residue: 0.2477 time to fit residues: 117.1048 Evaluate side-chains 295 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 216 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 6 ARG Chi-restraints excluded: chain sB residue 11 SER Chi-restraints excluded: chain sB residue 37 LYS Chi-restraints excluded: chain sB residue 44 ILE Chi-restraints excluded: chain sB residue 50 VAL Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sC residue 9 LEU Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 15 SER Chi-restraints excluded: chain sC residue 45 THR Chi-restraints excluded: chain sC residue 75 THR Chi-restraints excluded: chain sb residue 39 MET Chi-restraints excluded: chain sb residue 68 ARG Chi-restraints excluded: chain sb residue 98 MET Chi-restraints excluded: chain sb residue 99 LYS Chi-restraints excluded: chain sb residue 101 THR Chi-restraints excluded: chain sb residue 151 THR Chi-restraints excluded: chain sc residue 63 ILE Chi-restraints excluded: chain sc residue 73 HIS Chi-restraints excluded: chain sc residue 248 ILE Chi-restraints excluded: chain sc residue 249 LEU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 126 SER Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain se residue 228 LEU Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 131 THR Chi-restraints excluded: chain sf residue 175 ILE Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 232 THR Chi-restraints excluded: chain sf residue 244 LYS Chi-restraints excluded: chain sh residue 148 LYS Chi-restraints excluded: chain sh residue 208 THR Chi-restraints excluded: chain sh residue 275 THR Chi-restraints excluded: chain sh residue 291 LEU Chi-restraints excluded: chain sh residue 299 GLU Chi-restraints excluded: chain si residue 120 ARG Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 192 LYS Chi-restraints excluded: chain sj residue 27 ASN Chi-restraints excluded: chain sj residue 115 LYS Chi-restraints excluded: chain sj residue 189 ASP Chi-restraints excluded: chain sj residue 193 LEU Chi-restraints excluded: chain sj residue 201 VAL Chi-restraints excluded: chain sk residue 21 ARG Chi-restraints excluded: chain sk residue 112 LEU Chi-restraints excluded: chain sk residue 133 MET Chi-restraints excluded: chain sk residue 140 VAL Chi-restraints excluded: chain sk residue 150 VAL Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 73 ILE Chi-restraints excluded: chain sm residue 76 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 108 VAL Chi-restraints excluded: chain sm residue 149 ASP Chi-restraints excluded: chain so residue 31 LEU Chi-restraints excluded: chain so residue 87 ASP Chi-restraints excluded: chain sp residue 14 VAL Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 119 MET Chi-restraints excluded: chain sp residue 123 ARG Chi-restraints excluded: chain sr residue 74 VAL Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sr residue 107 SER Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sy residue 43 SER Chi-restraints excluded: chain sy residue 57 THR Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sy residue 116 VAL Chi-restraints excluded: chain sy residue 123 VAL Chi-restraints excluded: chain sz residue 66 THR Chi-restraints excluded: chain sz residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 156 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 69 optimal weight: 40.0000 chunk 291 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 40.0000 chunk 171 optimal weight: 7.9990 chunk 32 optimal weight: 50.0000 chunk 141 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sk 91 ASN so 101 HIS so 105 ASN ** sy 44 HIS ** 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 = 0.3450 r_free = 0.3450 target = 0.053506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.043282 restraints weight = 218582.333| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.84 r_work: 0.3014 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 44959 Z= 0.208 Angle : 0.579 9.677 65805 Z= 0.316 Chirality : 0.042 0.533 8256 Planarity : 0.005 0.103 4362 Dihedral : 22.169 178.977 18717 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.27 % Favored : 93.44 % Rotamer: Outliers : 4.24 % Allowed : 26.02 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.17), residues: 2378 helix: 1.03 (0.21), residues: 659 sheet: -0.87 (0.23), residues: 470 loop : -1.27 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGsz 13 TYR 0.011 0.001 TYRsp 99 PHE 0.019 0.001 PHEsi 162 TRP 0.010 0.001 TRPsy 25 HIS 0.006 0.001 HISsh 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.21 (44959) covalent geometry : angle 0.57853 / 0.32 (65805) hydrogen bonds : bond 0.06852 / 4.67 ( 1397) hydrogen bonds : angle 4.10043 / 3.06 ( 3067) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 218 time to evaluate : 1.048 Fit side-chains REVERT: sB 6 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.8422 (ttm-80) REVERT: sB 37 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8843 (mppt) REVERT: sB 44 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.8899 (mt) REVERT: sC 35 GLU cc_start: 0.8277 (pm20) cc_final: 0.7372 (pm20) REVERT: sC 81 ARG cc_start: 0.8403 (ptm-80) cc_final: 0.7813 (ptm-80) REVERT: sb 51 GLU cc_start: 0.7803 (pm20) cc_final: 0.7528 (pm20) REVERT: sb 68 ARG cc_start: 0.9400 (OUTLIER) cc_final: 0.8704 (ttp-170) REVERT: sb 99 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.9070 (mptt) REVERT: sc 244 LYS cc_start: 0.9005 (ptmm) cc_final: 0.8545 (ptmm) REVERT: se 233 GLN cc_start: 0.8560 (tt0) cc_final: 0.8328 (mt0) REVERT: sf 94 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8232 (mmtt) REVERT: sf 239 ASP cc_start: 0.8206 (p0) cc_final: 0.7877 (p0) REVERT: sh 148 LYS cc_start: 0.4470 (OUTLIER) cc_final: 0.3324 (tptt) REVERT: si 100 LYS cc_start: 0.6462 (tptp) cc_final: 0.5225 (pptt) REVERT: si 120 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.4332 (mpt90) REVERT: si 122 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.4704 (mmt180) REVERT: si 153 LYS cc_start: 0.8487 (mppt) cc_final: 0.8268 (mttp) REVERT: sk 66 ASP cc_start: 0.9002 (m-30) cc_final: 0.8630 (m-30) REVERT: sk 133 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8801 (mmm) REVERT: sk 157 GLN cc_start: 0.8454 (pm20) cc_final: 0.7845 (pm20) REVERT: sp 123 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.6930 (mtt180) REVERT: sx 73 ASP cc_start: 0.8914 (m-30) cc_final: 0.8425 (m-30) REVERT: sy 77 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.6197 (ttmm) REVERT: sz 67 LYS cc_start: 0.7414 (mmpt) cc_final: 0.6854 (mtpt) REVERT: sz 87 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8306 (mtmm) outliers start: 88 outliers final: 71 residues processed: 287 average time/residue: 0.2290 time to fit residues: 108.4685 Evaluate side-chains 300 residues out of total 2075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 217 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 6 ARG Chi-restraints excluded: chain sB residue 11 SER Chi-restraints excluded: chain sB residue 37 LYS Chi-restraints excluded: chain sB residue 44 ILE Chi-restraints excluded: chain sB residue 50 VAL Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sC residue 9 LEU Chi-restraints excluded: chain sC residue 12 THR Chi-restraints excluded: chain sC residue 15 SER Chi-restraints excluded: chain sC residue 45 THR Chi-restraints excluded: chain sC residue 75 THR Chi-restraints excluded: chain sb residue 68 ARG Chi-restraints excluded: chain sb residue 98 MET Chi-restraints excluded: chain sb residue 99 LYS Chi-restraints excluded: chain sb residue 101 THR Chi-restraints excluded: chain sb residue 151 THR Chi-restraints excluded: chain sc residue 63 ILE Chi-restraints excluded: chain sc residue 73 HIS Chi-restraints excluded: chain sc residue 248 ILE Chi-restraints excluded: chain sc residue 249 LEU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 126 SER Chi-restraints excluded: chain se residue 149 SER Chi-restraints excluded: chain se residue 184 THR Chi-restraints excluded: chain se residue 228 LEU Chi-restraints excluded: chain sf residue 43 ILE Chi-restraints excluded: chain sf residue 74 ILE Chi-restraints excluded: chain sf residue 94 LYS Chi-restraints excluded: chain sf residue 131 THR Chi-restraints excluded: chain sf residue 175 ILE Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 232 THR Chi-restraints excluded: chain sf residue 244 LYS Chi-restraints excluded: chain sh residue 148 LYS Chi-restraints excluded: chain sh residue 208 THR Chi-restraints excluded: chain sh residue 262 LYS Chi-restraints excluded: chain sh residue 275 THR Chi-restraints excluded: chain sh residue 291 LEU Chi-restraints excluded: chain sh residue 299 GLU Chi-restraints excluded: chain si residue 120 ARG Chi-restraints excluded: chain si residue 122 ARG Chi-restraints excluded: chain si residue 160 THR Chi-restraints excluded: chain si residue 192 LYS Chi-restraints excluded: chain sj residue 27 ASN Chi-restraints excluded: chain sj residue 189 ASP Chi-restraints excluded: chain sj residue 193 LEU Chi-restraints excluded: chain sj residue 201 VAL Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 21 ARG Chi-restraints excluded: chain sk residue 112 LEU Chi-restraints excluded: chain sk residue 133 MET Chi-restraints excluded: chain sk residue 140 VAL Chi-restraints excluded: chain sk residue 150 VAL Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 73 ILE Chi-restraints excluded: chain sm residue 76 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 108 VAL Chi-restraints excluded: chain sm residue 149 ASP Chi-restraints excluded: chain so residue 31 LEU Chi-restraints excluded: chain so residue 87 ASP Chi-restraints excluded: chain sp residue 14 VAL Chi-restraints excluded: chain sp residue 35 THR Chi-restraints excluded: chain sp residue 37 VAL Chi-restraints excluded: chain sp residue 47 THR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 119 MET Chi-restraints excluded: chain sp residue 123 ARG Chi-restraints excluded: chain sr residue 74 VAL Chi-restraints excluded: chain sr residue 83 LEU Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sr residue 107 SER Chi-restraints excluded: chain sx residue 48 THR Chi-restraints excluded: chain sy residue 43 SER Chi-restraints excluded: chain sy residue 57 THR Chi-restraints excluded: chain sy residue 77 LYS Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Chi-restraints excluded: chain sy residue 116 VAL Chi-restraints excluded: chain sy residue 123 VAL Chi-restraints excluded: chain sz residue 66 THR Chi-restraints excluded: chain sz residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 244 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 271 optimal weight: 8.9990 chunk 321 optimal weight: 9.9990 chunk 295 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 263 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 53 optimal weight: 40.0000 chunk 299 optimal weight: 7.9990 chunk 313 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sj 9 HIS sk 91 ASN so 101 HIS so 105 ASN ** sy 44 HIS ** 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 = 0.3459 r_free = 0.3459 target = 0.053728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.043521 restraints weight = 219297.487| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.85 r_work: 0.3025 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 44959 Z= 0.170 Angle : 0.548 9.886 65805 Z= 0.305 Chirality : 0.040 0.498 8256 Planarity : 0.005 0.105 4362 Dihedral : 22.184 179.999 18717 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.80 % Favored : 94.03 % Rotamer: Outliers : 4.14 % Allowed : 26.36 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 2378 helix: 1.03 (0.21), residues: 660 sheet: -0.80 (0.23), residues: 466 loop : -1.26 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGsz 13 TYR 0.011 0.001 TYRsh 310 PHE 0.014 0.001 PHEsf 84 TRP 0.010 0.001 TRPsb 60 HIS 0.005 0.001 HISsh 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (44959) covalent geometry : angle 0.54836 / 0.30 (65805) hydrogen bonds : bond 0.06661 / 4.54 ( 1397) hydrogen bonds : angle 4.05336 / 3.02 ( 3067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11682.56 seconds wall clock time: 200 minutes 31.93 seconds (12031.93 seconds total)