Starting phenix.real_space_refine on Wed Jun 18 10:07:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl1_45658/06_2025/9cl1_45658.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl1_45658/06_2025/9cl1_45658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cl1_45658/06_2025/9cl1_45658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl1_45658/06_2025/9cl1_45658.map" model { file = "/net/cci-nas-00/data/ceres_data/9cl1_45658/06_2025/9cl1_45658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl1_45658/06_2025/9cl1_45658.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.145 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 Cu 9 5.60 5 S 90 5.16 5 C 13614 2.51 5 N 3348 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20772 Number of models: 1 Model: "" Number of chains: 14 Chain: "Aa" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 24, 'TRANS': 357} Chain: "Ba" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "Cc" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1958 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 12, 'TRANS': 225} Chain: "Aa" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Ba" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "Aa" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "Ca" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Ba" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "Bb" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "Bc" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "Ab" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "Ac" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "Cb" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "Cc" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Restraints were copied for chains: Ac, Ab, Cb, Ca, Bb, Bc Time building chain proxies: 11.25, per 1000 atoms: 0.54 Number of scatterers: 20772 At special positions: 0 Unit cell: (109.038, 111.176, 120.797, 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) Cu 9 28.99 S 90 16.00 O 3711 8.00 N 3348 7.00 C 13614 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: 5.21 Conformation dependent library (CDL) restraints added in 2.6 seconds 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4698 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 24 sheets defined 55.7% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'Aa' and resid 41 through 46 Processing helix chain 'Aa' and resid 162 through 166 Processing helix chain 'Aa' and resid 185 through 208 removed outlier: 3.866A pdb=" N TRPAa 206 " --> pdb=" O TRPAa 202 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 211 through 221 removed outlier: 4.303A pdb=" N ARGAa 215 " --> pdb=" O ILEAa 211 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 229 through 258 Processing helix chain 'Aa' and resid 337 through 339 No H-bonds generated for 'chain 'Aa' and resid 337 through 339' Processing helix chain 'Aa' and resid 369 through 374 Processing helix chain 'Aa' and resid 376 through 382 removed outlier: 3.661A pdb=" N ILEAa 379 " --> pdb=" O LEUAa 376 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 20 through 58 removed outlier: 7.576A pdb=" N ASPCa 54 " --> pdb=" O LEUCa 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TRPCa 55 " --> pdb=" O THRCa 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASPCa 56 " --> pdb=" O METCa 52 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRPCa 58 " --> pdb=" O ASPCa 54 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 65 through 75 Proline residue: Ca 72 - end of helix Processing helix chain 'Ca' and resid 76 through 89 removed outlier: 3.503A pdb=" N ALACa 81 " --> pdb=" O THRCa 77 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 94 through 114 removed outlier: 3.858A pdb=" N CYSCa 99 " --> pdb=" O GLYCa 95 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 122 through 127 Processing helix chain 'Ca' and resid 131 through 146 Processing helix chain 'Ca' and resid 147 through 162 removed outlier: 4.269A pdb=" N ALACa 156 " --> pdb=" O ALACa 152 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 162 through 172 Proline residue: Ca 169 - end of helix Processing helix chain 'Ca' and resid 173 through 175 No H-bonds generated for 'chain 'Ca' and resid 173 through 175' Processing helix chain 'Ca' and resid 187 through 195 Processing helix chain 'Ca' and resid 201 through 205 removed outlier: 3.547A pdb=" N ILECa 204 " --> pdb=" O PROCa 201 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 215 through 217 No H-bonds generated for 'chain 'Ca' and resid 215 through 217' Processing helix chain 'Ca' and resid 218 through 245 removed outlier: 3.540A pdb=" N VALCa 222 " --> pdb=" O ASPCa 218 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHECa 236 " --> pdb=" O ILECa 232 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 47 through 76 removed outlier: 3.842A pdb=" N LEUBa 51 " --> pdb=" O ASPBa 47 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TRPBa 74 " --> pdb=" O GLYBa 70 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SERBa 75 " --> pdb=" O VALBa 71 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 82 through 89 removed outlier: 3.578A pdb=" N GLUBa 86 " --> pdb=" O ALABa 82 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 89 through 114 Processing helix chain 'Ba' and resid 123 through 150 Processing helix chain 'Ba' and resid 151 through 161 removed outlier: 3.547A pdb=" N GLNBa 161 " --> pdb=" O GLYBa 157 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 170 through 177 Processing helix chain 'Ba' and resid 179 through 199 Processing helix chain 'Ba' and resid 201 through 205 removed outlier: 3.975A pdb=" N LYSBa 204 " --> pdb=" O PHEBa 201 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLYBa 205 " --> pdb=" O PHEBa 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ba' and resid 201 through 205' Processing helix chain 'Ba' and resid 208 through 232 Proline residue: Ba 217 - end of helix removed outlier: 3.524A pdb=" N ILEBa 220 " --> pdb=" O GLYBa 216 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEUBa 221 " --> pdb=" O PROBa 217 " (cutoff:3.500A) Proline residue: Ba 222 - end of helix removed outlier: 4.877A pdb=" N GLYBa 225 " --> pdb=" O LEUBa 221 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEUBa 226 " --> pdb=" O PROBa 222 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 242 through 244 No H-bonds generated for 'chain 'Ba' and resid 242 through 244' Processing helix chain 'Ba' and resid 245 through 254 removed outlier: 3.682A pdb=" N VALBa 249 " --> pdb=" O HISBa 245 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEUBa 254 " --> pdb=" O ILEBa 250 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 257 through 273 removed outlier: 3.629A pdb=" N THRBa 263 " --> pdb=" O METBa 259 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLYBa 272 " --> pdb=" O SERBa 268 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLYBa 273 " --> pdb=" O PHEBa 269 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 273 through 279 Processing helix chain 'Bb' and resid 47 through 76 removed outlier: 3.841A pdb=" N LEUBb 51 " --> pdb=" O ASPBb 47 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRPBb 74 " --> pdb=" O GLYBb 70 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SERBb 75 " --> pdb=" O VALBb 71 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 82 through 89 removed outlier: 3.578A pdb=" N GLUBb 86 " --> pdb=" O ALABb 82 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 89 through 114 Processing helix chain 'Bb' and resid 123 through 150 Processing helix chain 'Bb' and resid 151 through 161 removed outlier: 3.547A pdb=" N GLNBb 161 " --> pdb=" O GLYBb 157 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 170 through 177 Processing helix chain 'Bb' and resid 179 through 199 Processing helix chain 'Bb' and resid 201 through 205 removed outlier: 3.975A pdb=" N LYSBb 204 " --> pdb=" O PHEBb 201 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLYBb 205 " --> pdb=" O PHEBb 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 201 through 205' Processing helix chain 'Bb' and resid 208 through 232 Proline residue: Bb 217 - end of helix removed outlier: 3.524A pdb=" N ILEBb 220 " --> pdb=" O GLYBb 216 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEUBb 221 " --> pdb=" O PROBb 217 " (cutoff:3.500A) Proline residue: Bb 222 - end of helix removed outlier: 4.878A pdb=" N GLYBb 225 " --> pdb=" O LEUBb 221 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEUBb 226 " --> pdb=" O PROBb 222 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 242 through 244 No H-bonds generated for 'chain 'Bb' and resid 242 through 244' Processing helix chain 'Bb' and resid 245 through 254 removed outlier: 3.683A pdb=" N VALBb 249 " --> pdb=" O HISBb 245 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEUBb 254 " --> pdb=" O ILEBb 250 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 257 through 273 removed outlier: 3.628A pdb=" N THRBb 263 " --> pdb=" O METBb 259 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLYBb 272 " --> pdb=" O SERBb 268 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLYBb 273 " --> pdb=" O PHEBb 269 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 273 through 279 Processing helix chain 'Bc' and resid 47 through 76 removed outlier: 3.841A pdb=" N LEUBc 51 " --> pdb=" O ASPBc 47 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRPBc 74 " --> pdb=" O GLYBc 70 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SERBc 75 " --> pdb=" O VALBc 71 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 82 through 89 removed outlier: 3.578A pdb=" N GLUBc 86 " --> pdb=" O ALABc 82 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 89 through 114 Processing helix chain 'Bc' and resid 123 through 150 Processing helix chain 'Bc' and resid 151 through 161 removed outlier: 3.548A pdb=" N GLNBc 161 " --> pdb=" O GLYBc 157 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 170 through 177 Processing helix chain 'Bc' and resid 179 through 199 Processing helix chain 'Bc' and resid 201 through 205 removed outlier: 3.975A pdb=" N LYSBc 204 " --> pdb=" O PHEBc 201 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLYBc 205 " --> pdb=" O PHEBc 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bc' and resid 201 through 205' Processing helix chain 'Bc' and resid 208 through 232 Proline residue: Bc 217 - end of helix removed outlier: 3.524A pdb=" N ILEBc 220 " --> pdb=" O GLYBc 216 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEUBc 221 " --> pdb=" O PROBc 217 " (cutoff:3.500A) Proline residue: Bc 222 - end of helix removed outlier: 4.877A pdb=" N GLYBc 225 " --> pdb=" O LEUBc 221 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEUBc 226 " --> pdb=" O PROBc 222 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 242 through 244 No H-bonds generated for 'chain 'Bc' and resid 242 through 244' Processing helix chain 'Bc' and resid 245 through 254 removed outlier: 3.683A pdb=" N VALBc 249 " --> pdb=" O HISBc 245 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEUBc 254 " --> pdb=" O ILEBc 250 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 257 through 273 removed outlier: 3.628A pdb=" N THRBc 263 " --> pdb=" O METBc 259 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLYBc 272 " --> pdb=" O SERBc 268 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLYBc 273 " --> pdb=" O PHEBc 269 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 273 through 279 Processing helix chain 'Ab' and resid 41 through 46 Processing helix chain 'Ab' and resid 162 through 166 Processing helix chain 'Ab' and resid 185 through 208 removed outlier: 3.867A pdb=" N TRPAb 206 " --> pdb=" O TRPAb 202 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 211 through 221 removed outlier: 4.303A pdb=" N ARGAb 215 " --> pdb=" O ILEAb 211 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 229 through 258 Processing helix chain 'Ab' and resid 337 through 339 No H-bonds generated for 'chain 'Ab' and resid 337 through 339' Processing helix chain 'Ab' and resid 369 through 374 Processing helix chain 'Ab' and resid 376 through 382 removed outlier: 3.661A pdb=" N ILEAb 379 " --> pdb=" O LEUAb 376 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 41 through 46 Processing helix chain 'Ac' and resid 162 through 166 Processing helix chain 'Ac' and resid 185 through 208 removed outlier: 3.867A pdb=" N TRPAc 206 " --> pdb=" O TRPAc 202 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 211 through 221 removed outlier: 4.303A pdb=" N ARGAc 215 " --> pdb=" O ILEAc 211 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 229 through 258 Processing helix chain 'Ac' and resid 337 through 339 No H-bonds generated for 'chain 'Ac' and resid 337 through 339' Processing helix chain 'Ac' and resid 369 through 374 Processing helix chain 'Ac' and resid 376 through 382 removed outlier: 3.660A pdb=" N ILEAc 379 " --> pdb=" O LEUAc 376 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 20 through 58 removed outlier: 7.575A pdb=" N ASPCb 54 " --> pdb=" O LEUCb 50 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRPCb 55 " --> pdb=" O THRCb 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASPCb 56 " --> pdb=" O METCb 52 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRPCb 58 " --> pdb=" O ASPCb 54 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 65 through 75 Proline residue: Cb 72 - end of helix Processing helix chain 'Cb' and resid 76 through 89 removed outlier: 3.503A pdb=" N ALACb 81 " --> pdb=" O THRCb 77 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 94 through 114 removed outlier: 3.857A pdb=" N CYSCb 99 " --> pdb=" O GLYCb 95 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 122 through 127 Processing helix chain 'Cb' and resid 131 through 146 Processing helix chain 'Cb' and resid 147 through 162 removed outlier: 4.268A pdb=" N ALACb 156 " --> pdb=" O ALACb 152 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 162 through 172 Proline residue: Cb 169 - end of helix Processing helix chain 'Cb' and resid 173 through 175 No H-bonds generated for 'chain 'Cb' and resid 173 through 175' Processing helix chain 'Cb' and resid 187 through 195 Processing helix chain 'Cb' and resid 201 through 205 removed outlier: 3.546A pdb=" N ILECb 204 " --> pdb=" O PROCb 201 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 215 through 217 No H-bonds generated for 'chain 'Cb' and resid 215 through 217' Processing helix chain 'Cb' and resid 218 through 245 removed outlier: 3.540A pdb=" N VALCb 222 " --> pdb=" O ASPCb 218 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHECb 236 " --> pdb=" O ILECb 232 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 20 through 58 removed outlier: 7.576A pdb=" N ASPCc 54 " --> pdb=" O LEUCc 50 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TRPCc 55 " --> pdb=" O THRCc 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASPCc 56 " --> pdb=" O METCc 52 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRPCc 58 " --> pdb=" O ASPCc 54 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 65 through 75 Proline residue: Cc 72 - end of helix Processing helix chain 'Cc' and resid 76 through 89 removed outlier: 3.502A pdb=" N ALACc 81 " --> pdb=" O THRCc 77 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 94 through 114 removed outlier: 3.857A pdb=" N CYSCc 99 " --> pdb=" O GLYCc 95 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 122 through 127 Processing helix chain 'Cc' and resid 131 through 146 Processing helix chain 'Cc' and resid 147 through 162 removed outlier: 4.269A pdb=" N ALACc 156 " --> pdb=" O ALACc 152 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 162 through 172 Proline residue: Cc 169 - end of helix Processing helix chain 'Cc' and resid 173 through 175 No H-bonds generated for 'chain 'Cc' and resid 173 through 175' Processing helix chain 'Cc' and resid 187 through 195 Processing helix chain 'Cc' and resid 201 through 205 removed outlier: 3.546A pdb=" N ILECc 204 " --> pdb=" O PROCc 201 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 215 through 217 No H-bonds generated for 'chain 'Cc' and resid 215 through 217' Processing helix chain 'Cc' and resid 218 through 245 removed outlier: 3.540A pdb=" N VALCc 222 " --> pdb=" O ASPCc 218 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHECc 236 " --> pdb=" O ILECc 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Aa' and resid 50 through 54 removed outlier: 4.490A pdb=" N LEUAa 52 " --> pdb=" O LYSAa 68 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYSAa 68 " --> pdb=" O LEUAa 52 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRPAa 54 " --> pdb=" O GLUAa 66 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLUAa 66 " --> pdb=" O TRPAa 54 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASPAa 123 " --> pdb=" O ILEAa 105 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILEAa 105 " --> pdb=" O ASPAa 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARGAa 125 " --> pdb=" O SERAa 103 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SERAa 103 " --> pdb=" O ARGAa 125 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VALAa 127 " --> pdb=" O LYSAa 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Aa' and resid 58 through 60 removed outlier: 6.899A pdb=" N VALAa 59 " --> pdb=" O GLUAa 160 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VALAa 144 " --> pdb=" O PROAa 149 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILEAa 151 " --> pdb=" O METAa 142 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N METAa 142 " --> pdb=" O ILEAa 151 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THRAa 140 " --> pdb=" O PROAa 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Aa' and resid 113 through 114 removed outlier: 6.746A pdb=" N SERAa 113 " --> pdb=" O METAa 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Aa' and resid 169 through 171 Processing sheet with id=AA5, first strand: chain 'Aa' and resid 346 through 348 removed outlier: 7.903A pdb=" N ALAAa 297 " --> pdb=" O TYRAa 291 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYRAa 291 " --> pdb=" O ALAAa 297 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARGAa 299 " --> pdb=" O ALAAa 289 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALAAa 289 " --> pdb=" O ARGAa 299 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYSAa 301 " --> pdb=" O GLUAa 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Aa' and resid 341 through 342 removed outlier: 5.199A pdb=" N LEUAa 314 " --> pdb=" O PHEAa 394 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHEAa 394 " --> pdb=" O LEUAa 314 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLUAa 316 " --> pdb=" O PHEAa 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Ca' and resid 177 through 180 Processing sheet with id=AA8, first strand: chain 'Ca' and resid 250 through 251 Processing sheet with id=AA9, first strand: chain 'Ba' and resid 206 through 207 Processing sheet with id=AB1, first strand: chain 'Bc' and resid 206 through 207 Processing sheet with id=AB2, first strand: chain 'Ab' and resid 50 through 54 removed outlier: 4.490A pdb=" N LEUAb 52 " --> pdb=" O LYSAb 68 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYSAb 68 " --> pdb=" O LEUAb 52 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRPAb 54 " --> pdb=" O GLUAb 66 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLUAb 66 " --> pdb=" O TRPAb 54 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASPAb 123 " --> pdb=" O ILEAb 105 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILEAb 105 " --> pdb=" O ASPAb 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARGAb 125 " --> pdb=" O SERAb 103 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SERAb 103 " --> pdb=" O ARGAb 125 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VALAb 127 " --> pdb=" O LYSAb 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Ab' and resid 58 through 60 removed outlier: 6.899A pdb=" N VALAb 59 " --> pdb=" O GLUAb 160 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VALAb 144 " --> pdb=" O PROAb 149 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILEAb 151 " --> pdb=" O METAb 142 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N METAb 142 " --> pdb=" O ILEAb 151 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THRAb 140 " --> pdb=" O PROAb 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ab' and resid 113 through 114 removed outlier: 6.747A pdb=" N SERAb 113 " --> pdb=" O METAb 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'Ab' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'Ab' and resid 346 through 348 removed outlier: 7.903A pdb=" N ALAAb 297 " --> pdb=" O TYRAb 291 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYRAb 291 " --> pdb=" O ALAAb 297 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARGAb 299 " --> pdb=" O ALAAb 289 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALAAb 289 " --> pdb=" O ARGAb 299 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYSAb 301 " --> pdb=" O GLUAb 287 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ab' and resid 341 through 342 removed outlier: 5.198A pdb=" N LEUAb 314 " --> pdb=" O PHEAb 394 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHEAb 394 " --> pdb=" O LEUAb 314 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLUAb 316 " --> pdb=" O PHEAb 392 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Ac' and resid 50 through 54 removed outlier: 4.490A pdb=" N LEUAc 52 " --> pdb=" O LYSAc 68 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYSAc 68 " --> pdb=" O LEUAc 52 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRPAc 54 " --> pdb=" O GLUAc 66 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLUAc 66 " --> pdb=" O TRPAc 54 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASPAc 123 " --> pdb=" O ILEAc 105 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILEAc 105 " --> pdb=" O ASPAc 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARGAc 125 " --> pdb=" O SERAc 103 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SERAc 103 " --> pdb=" O ARGAc 125 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VALAc 127 " --> pdb=" O LYSAc 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Ac' and resid 58 through 60 removed outlier: 6.899A pdb=" N VALAc 59 " --> pdb=" O GLUAc 160 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VALAc 144 " --> pdb=" O PROAc 149 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ILEAc 151 " --> pdb=" O METAc 142 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N METAc 142 " --> pdb=" O ILEAc 151 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THRAc 140 " --> pdb=" O PROAc 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Ac' and resid 113 through 114 removed outlier: 6.747A pdb=" N SERAc 113 " --> pdb=" O METAc 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'Ac' and resid 169 through 171 Processing sheet with id=AC3, first strand: chain 'Ac' and resid 346 through 348 removed outlier: 7.902A pdb=" N ALAAc 297 " --> pdb=" O TYRAc 291 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N TYRAc 291 " --> pdb=" O ALAAc 297 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARGAc 299 " --> pdb=" O ALAAc 289 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALAAc 289 " --> pdb=" O ARGAc 299 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYSAc 301 " --> pdb=" O GLUAc 287 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Ac' and resid 341 through 342 removed outlier: 5.199A pdb=" N LEUAc 314 " --> pdb=" O PHEAc 394 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHEAc 394 " --> pdb=" O LEUAc 314 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLUAc 316 " --> pdb=" O PHEAc 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Cb' and resid 177 through 180 Processing sheet with id=AC6, first strand: chain 'Cc' and resid 177 through 180 1116 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.81 Time building geometry restraints manager: 6.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6267 1.34 - 1.46: 5377 1.46 - 1.58: 9485 1.58 - 1.69: 0 1.69 - 1.81: 174 Bond restraints: 21303 Sorted by residual: bond pdb=" CA SERAb 37 " pdb=" CB SERAb 37 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.39e-02 5.18e+03 1.27e+01 bond pdb=" N LEUBb 221 " pdb=" CA LEUBb 221 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.26e+01 bond pdb=" CA SERAc 37 " pdb=" CB SERAc 37 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.39e-02 5.18e+03 1.25e+01 bond pdb=" N LEUBa 221 " pdb=" CA LEUBa 221 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.23e+01 bond pdb=" CA SERAa 37 " pdb=" CB SERAa 37 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.39e-02 5.18e+03 1.22e+01 ... (remaining 21298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 28547 3.40 - 6.79: 518 6.79 - 10.19: 17 10.19 - 13.59: 3 13.59 - 16.99: 3 Bond angle restraints: 29088 Sorted by residual: angle pdb=" C HISAa 139 " pdb=" CA HISAa 139 " pdb=" CB HISAa 139 " ideal model delta sigma weight residual 109.35 92.36 16.99 1.98e+00 2.55e-01 7.36e+01 angle pdb=" C HISAb 139 " pdb=" CA HISAb 139 " pdb=" CB HISAb 139 " ideal model delta sigma weight residual 109.35 92.38 16.97 1.98e+00 2.55e-01 7.34e+01 angle pdb=" C HISAc 139 " pdb=" CA HISAc 139 " pdb=" CB HISAc 139 " ideal model delta sigma weight residual 109.35 92.40 16.95 1.98e+00 2.55e-01 7.33e+01 angle pdb=" CA PHEAc 71 " pdb=" CB PHEAc 71 " pdb=" CG PHEAc 71 " ideal model delta sigma weight residual 113.80 121.20 -7.40 1.00e+00 1.00e+00 5.47e+01 angle pdb=" CA PHEAa 71 " pdb=" CB PHEAa 71 " pdb=" CG PHEAa 71 " ideal model delta sigma weight residual 113.80 121.17 -7.37 1.00e+00 1.00e+00 5.43e+01 ... (remaining 29083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10214 17.94 - 35.88: 1315 35.88 - 53.83: 417 53.83 - 71.77: 93 71.77 - 89.71: 24 Dihedral angle restraints: 12063 sinusoidal: 4704 harmonic: 7359 Sorted by residual: dihedral pdb=" CA VALAc 293 " pdb=" C VALAc 293 " pdb=" N PROAc 294 " pdb=" CA PROAc 294 " ideal model delta harmonic sigma weight residual 180.00 133.18 46.82 0 5.00e+00 4.00e-02 8.77e+01 dihedral pdb=" CA VALAa 293 " pdb=" C VALAa 293 " pdb=" N PROAa 294 " pdb=" CA PROAa 294 " ideal model delta harmonic sigma weight residual 180.00 133.18 46.82 0 5.00e+00 4.00e-02 8.77e+01 dihedral pdb=" CA VALAb 293 " pdb=" C VALAb 293 " pdb=" N PROAb 294 " pdb=" CA PROAb 294 " ideal model delta harmonic sigma weight residual 180.00 133.19 46.81 0 5.00e+00 4.00e-02 8.76e+01 ... (remaining 12060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2581 0.078 - 0.157: 433 0.157 - 0.235: 95 0.235 - 0.313: 14 0.313 - 0.391: 9 Chirality restraints: 3132 Sorted by residual: chirality pdb=" CB ILEAc 211 " pdb=" CA ILEAc 211 " pdb=" CG1 ILEAc 211 " pdb=" CG2 ILEAc 211 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CB ILEAa 211 " pdb=" CA ILEAa 211 " pdb=" CG1 ILEAa 211 " pdb=" CG2 ILEAa 211 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILEAb 211 " pdb=" CA ILEAb 211 " pdb=" CG1 ILEAb 211 " pdb=" CG2 ILEAb 211 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 3129 not shown) Planarity restraints: 3609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGCb 16 " -0.513 9.50e-02 1.11e+02 2.30e-01 3.24e+01 pdb=" NE ARGCb 16 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARGCb 16 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARGCb 16 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGCb 16 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGCa 16 " -0.513 9.50e-02 1.11e+02 2.30e-01 3.23e+01 pdb=" NE ARGCa 16 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARGCa 16 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARGCa 16 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGCa 16 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGCc 16 " -0.512 9.50e-02 1.11e+02 2.30e-01 3.23e+01 pdb=" NE ARGCc 16 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARGCc 16 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARGCc 16 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGCc 16 " -0.018 2.00e-02 2.50e+03 ... (remaining 3606 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 161 2.50 - 3.10: 14888 3.10 - 3.70: 32428 3.70 - 4.30: 48440 4.30 - 4.90: 82631 Nonbonded interactions: 178548 Sorted by model distance: nonbonded pdb=" ND1 HISAc 48 " pdb="CU CUAc 502 " model vdw 1.899 2.320 nonbonded pdb=" ND1 HISAa 48 " pdb="CU CUAa 502 " model vdw 1.899 2.320 nonbonded pdb=" ND1 HISAb 48 " pdb="CU CUAb 502 " model vdw 1.899 2.320 nonbonded pdb=" ND1 HISAa 72 " pdb="CU CUAa 502 " model vdw 1.964 2.320 nonbonded pdb=" ND1 HISAc 72 " pdb="CU CUAc 502 " model vdw 1.965 2.320 ... (remaining 178543 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: 0.14 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ac' selection = chain 'Ab' } ncs_group { reference = chain 'Cc' selection = chain 'Cb' selection = chain 'Ca' } ncs_group { reference = chain 'Ba' selection = chain 'Bb' selection = chain 'Bc' } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 45.710 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 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:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5129 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 21303 Z= 0.435 Angle : 1.040 16.986 29088 Z= 0.692 Chirality : 0.065 0.391 3132 Planarity : 0.011 0.230 3609 Dihedral : 18.436 89.710 7365 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.19 % Favored : 94.21 % Rotamer: Outliers : 6.95 % Allowed : 22.86 % Favored : 70.19 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2523 helix: 0.67 (0.15), residues: 1161 sheet: -0.04 (0.27), residues: 381 loop : -1.56 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPCc 159 HIS 0.005 0.002 HISAb 33 PHE 0.027 0.002 PHEAa 212 TYR 0.022 0.002 TYRBa 184 ARG 0.009 0.001 ARGAb 299 Details of bonding type rmsd hydrogen bonds : bond 0.14410 ( 1116) hydrogen bonds : angle 7.26145 ( 3240) covalent geometry : bond 0.00644 (21303) covalent geometry : angle 1.04028 (29088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 422 time to evaluate : 2.293 Fit side-chains REVERT: Aa 65 VAL cc_start: 0.7029 (OUTLIER) cc_final: 0.6713 (p) REVERT: Aa 103 SER cc_start: 0.8187 (t) cc_final: 0.7902 (t) REVERT: Aa 117 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6876 (mp0) REVERT: Aa 141 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7723 (ptp) REVERT: Aa 160 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6563 (pt0) REVERT: Aa 167 ARG cc_start: 0.6077 (mtp85) cc_final: 0.5856 (mmt-90) REVERT: Aa 211 ILE cc_start: 0.3519 (OUTLIER) cc_final: 0.2812 (tp) REVERT: Aa 249 MET cc_start: 0.5133 (mtm) cc_final: 0.4898 (tmm) REVERT: Aa 273 LYS cc_start: 0.7471 (mtpm) cc_final: 0.7085 (mptp) REVERT: Aa 283 SER cc_start: 0.6872 (t) cc_final: 0.6393 (p) REVERT: Aa 285 LYS cc_start: 0.6476 (tttt) cc_final: 0.6116 (tttp) REVERT: Aa 287 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7707 (mt-10) REVERT: Aa 296 ARG cc_start: 0.6621 (mtm-85) cc_final: 0.6294 (ptp90) REVERT: Aa 375 ARG cc_start: 0.5896 (mtt180) cc_final: 0.5078 (mpt180) REVERT: Aa 382 ASP cc_start: 0.6757 (m-30) cc_final: 0.6393 (m-30) REVERT: Aa 414 MET cc_start: 0.6041 (mmt) cc_final: 0.5794 (mtp) REVERT: Ca 37 PHE cc_start: 0.3042 (t80) cc_final: 0.2796 (t80) REVERT: Ca 157 MET cc_start: 0.3301 (ttp) cc_final: 0.2899 (ttt) REVERT: Ca 213 ARG cc_start: 0.5565 (mtt180) cc_final: 0.4782 (mtm180) REVERT: Ca 237 MET cc_start: 0.6234 (ttm) cc_final: 0.5056 (mmt) REVERT: Ba 84 GLU cc_start: 0.5900 (mt-10) cc_final: 0.5604 (mt-10) REVERT: Ba 279 CYS cc_start: 0.3504 (OUTLIER) cc_final: 0.2705 (m) REVERT: Bb 84 GLU cc_start: 0.5839 (mt-10) cc_final: 0.5561 (tt0) REVERT: Bc 84 GLU cc_start: 0.6181 (mt-10) cc_final: 0.5850 (mt-10) REVERT: Bc 227 ASN cc_start: 0.4526 (OUTLIER) cc_final: 0.4211 (p0) REVERT: Ab 65 VAL cc_start: 0.6898 (OUTLIER) cc_final: 0.6445 (p) REVERT: Ab 93 MET cc_start: 0.7609 (ptp) cc_final: 0.7349 (ptm) REVERT: Ab 103 SER cc_start: 0.7999 (t) cc_final: 0.7630 (t) REVERT: Ab 104 TYR cc_start: 0.7262 (m-80) cc_final: 0.6960 (m-80) REVERT: Ab 108 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: Ab 117 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7009 (mp0) REVERT: Ab 165 GLU cc_start: 0.6145 (mm-30) cc_final: 0.5935 (mt-10) REVERT: Ab 167 ARG cc_start: 0.6096 (mtp85) cc_final: 0.5685 (mmt-90) REVERT: Ab 211 ILE cc_start: 0.3451 (OUTLIER) cc_final: 0.2790 (tp) REVERT: Ab 249 MET cc_start: 0.5468 (mtm) cc_final: 0.5169 (tmm) REVERT: Ab 273 LYS cc_start: 0.7356 (mtpm) cc_final: 0.7062 (mptp) REVERT: Ab 283 SER cc_start: 0.6931 (t) cc_final: 0.6588 (p) REVERT: Ab 292 ARG cc_start: 0.6244 (mtp85) cc_final: 0.5944 (mmt180) REVERT: Ab 323 ARG cc_start: 0.7460 (mtm180) cc_final: 0.7218 (mtp-110) REVERT: Ab 375 ARG cc_start: 0.5765 (mtt180) cc_final: 0.5469 (mtt90) REVERT: Ab 414 MET cc_start: 0.5713 (mmt) cc_final: 0.5481 (mtp) REVERT: Ac 50 TYR cc_start: 0.6142 (p90) cc_final: 0.5489 (p90) REVERT: Ac 70 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6710 (ptpt) REVERT: Ac 103 SER cc_start: 0.8053 (t) cc_final: 0.7524 (t) REVERT: Ac 108 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6835 (tp40) REVERT: Ac 117 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6944 (mp0) REVERT: Ac 140 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7572 (p) REVERT: Ac 160 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6581 (pt0) REVERT: Ac 165 GLU cc_start: 0.6212 (mm-30) cc_final: 0.5994 (mt-10) REVERT: Ac 211 ILE cc_start: 0.3621 (OUTLIER) cc_final: 0.2916 (tp) REVERT: Ac 249 MET cc_start: 0.5357 (mtm) cc_final: 0.4951 (tmm) REVERT: Ac 251 MET cc_start: 0.5450 (ttt) cc_final: 0.4944 (tpt) REVERT: Ac 272 MET cc_start: 0.6990 (mmp) cc_final: 0.6725 (mmt) REVERT: Ac 273 LYS cc_start: 0.7439 (mtpm) cc_final: 0.7002 (mptp) REVERT: Ac 283 SER cc_start: 0.6997 (t) cc_final: 0.6581 (p) REVERT: Ac 285 LYS cc_start: 0.6542 (tttt) cc_final: 0.6034 (tptp) REVERT: Ac 287 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7837 (mt-10) REVERT: Ac 323 ARG cc_start: 0.7396 (mtm180) cc_final: 0.7145 (mtm180) REVERT: Ac 330 TYR cc_start: 0.6892 (t80) cc_final: 0.6598 (t80) REVERT: Ac 382 ASP cc_start: 0.6569 (m-30) cc_final: 0.6366 (m-30) REVERT: Cb 37 PHE cc_start: 0.3217 (t80) cc_final: 0.2954 (t80) REVERT: Cb 157 MET cc_start: 0.3373 (ttp) cc_final: 0.2897 (ttm) REVERT: Cb 183 MET cc_start: 0.7498 (ttp) cc_final: 0.7096 (mtp) REVERT: Cb 213 ARG cc_start: 0.5920 (mtt180) cc_final: 0.5048 (mtm180) REVERT: Cb 230 MET cc_start: 0.4788 (tpt) cc_final: 0.4562 (mmm) REVERT: Cb 237 MET cc_start: 0.6267 (ttm) cc_final: 0.5795 (ttt) REVERT: Cb 249 ARG cc_start: 0.4253 (OUTLIER) cc_final: 0.3916 (mtm110) REVERT: Cc 37 PHE cc_start: 0.3254 (t80) cc_final: 0.3031 (t80) REVERT: Cc 65 ARG cc_start: 0.5728 (OUTLIER) cc_final: 0.4389 (tmt170) REVERT: Cc 114 ASN cc_start: 0.6864 (m-40) cc_final: 0.6293 (m-40) REVERT: Cc 157 MET cc_start: 0.2919 (ttp) cc_final: 0.2578 (ttt) REVERT: Cc 179 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7178 (tt0) REVERT: Cc 209 LYS cc_start: 0.6107 (mttt) cc_final: 0.5716 (mmtt) REVERT: Cc 213 ARG cc_start: 0.5919 (mtt180) cc_final: 0.4967 (mtm180) REVERT: Cc 237 MET cc_start: 0.6214 (ttm) cc_final: 0.5846 (ttt) REVERT: Cc 245 PHE cc_start: 0.6523 (m-80) cc_final: 0.6287 (m-10) REVERT: Cc 249 ARG cc_start: 0.5114 (OUTLIER) cc_final: 0.4661 (mtm110) outliers start: 150 outliers final: 10 residues processed: 539 average time/residue: 1.3113 time to fit residues: 799.5434 Evaluate side-chains 321 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 296 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 65 VAL Chi-restraints excluded: chain Aa residue 118 ILE Chi-restraints excluded: chain Aa residue 141 MET Chi-restraints excluded: chain Aa residue 211 ILE Chi-restraints excluded: chain Ca residue 76 VAL Chi-restraints excluded: chain Ba residue 279 CYS Chi-restraints excluded: chain Bc residue 132 PHE Chi-restraints excluded: chain Bc residue 227 ASN Chi-restraints excluded: chain Ab residue 46 THR Chi-restraints excluded: chain Ab residue 65 VAL Chi-restraints excluded: chain Ab residue 80 THR Chi-restraints excluded: chain Ab residue 108 GLN Chi-restraints excluded: chain Ab residue 140 THR Chi-restraints excluded: chain Ab residue 211 ILE Chi-restraints excluded: chain Ac residue 65 VAL Chi-restraints excluded: chain Ac residue 70 LYS Chi-restraints excluded: chain Ac residue 80 THR Chi-restraints excluded: chain Ac residue 108 GLN Chi-restraints excluded: chain Ac residue 140 THR Chi-restraints excluded: chain Ac residue 211 ILE Chi-restraints excluded: chain Cb residue 76 VAL Chi-restraints excluded: chain Cb residue 249 ARG Chi-restraints excluded: chain Cc residue 65 ARG Chi-restraints excluded: chain Cc residue 76 VAL Chi-restraints excluded: chain Cc residue 249 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 0.9980 chunk 188 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 195 optimal weight: 0.0060 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 306 ASN Ca 23 GLN ** Ca 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 223 ASN Bb 223 ASN Bb 227 ASN Bc 223 ASN Ab 143 ASN Ab 182 ASN Ac 33 HIS Ac 38 GLN Ac 143 ASN Cb 18 HIS Cb 23 GLN ** Cb 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 175 HIS Cb 252 GLN ** Cc 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 181 ASN Cc 239 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.197171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.167623 restraints weight = 23178.967| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.36 r_work: 0.3643 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21303 Z= 0.147 Angle : 0.660 8.613 29088 Z= 0.342 Chirality : 0.047 0.397 3132 Planarity : 0.006 0.103 3609 Dihedral : 6.638 61.133 2842 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.66 % Favored : 97.23 % Rotamer: Outliers : 5.42 % Allowed : 22.53 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2523 helix: 1.54 (0.15), residues: 1170 sheet: 0.54 (0.27), residues: 351 loop : -0.89 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPAc 77 HIS 0.007 0.001 HISAa 48 PHE 0.026 0.002 PHEBa 269 TYR 0.023 0.002 TYRBa 184 ARG 0.010 0.001 ARGCa 249 Details of bonding type rmsd hydrogen bonds : bond 0.04762 ( 1116) hydrogen bonds : angle 5.08550 ( 3240) covalent geometry : bond 0.00331 (21303) covalent geometry : angle 0.66012 (29088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 290 time to evaluate : 2.194 Fit side-chains revert: symmetry clash REVERT: Aa 93 MET cc_start: 0.8657 (ptp) cc_final: 0.8229 (ptm) REVERT: Aa 100 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8704 (ttm110) REVERT: Aa 328 ASP cc_start: 0.7976 (m-30) cc_final: 0.7775 (m-30) REVERT: Ca 37 PHE cc_start: 0.5343 (t80) cc_final: 0.4883 (t80) REVERT: Ca 66 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8488 (mm) REVERT: Ca 157 MET cc_start: 0.4448 (ttp) cc_final: 0.4089 (ttt) REVERT: Ca 202 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: Ca 213 ARG cc_start: 0.7702 (mtt180) cc_final: 0.6849 (mtm180) REVERT: Ca 219 VAL cc_start: 0.6820 (OUTLIER) cc_final: 0.6490 (t) REVERT: Ca 237 MET cc_start: 0.6939 (ttm) cc_final: 0.6237 (mmt) REVERT: Ba 219 MET cc_start: 0.7661 (mmm) cc_final: 0.7400 (mmt) REVERT: Bb 88 TYR cc_start: 0.6707 (m-80) cc_final: 0.6488 (m-80) REVERT: Bb 192 PHE cc_start: 0.6844 (t80) cc_final: 0.6598 (t80) REVERT: Bb 259 MET cc_start: 0.6372 (mtm) cc_final: 0.4834 (mmp) REVERT: Bc 69 GLU cc_start: 0.7452 (pt0) cc_final: 0.7147 (pt0) REVERT: Bc 145 ILE cc_start: 0.6528 (OUTLIER) cc_final: 0.6326 (pp) REVERT: Bc 259 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.3771 (mtm) REVERT: Ab 108 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8486 (tm-30) REVERT: Ab 160 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7611 (pt0) REVERT: Ab 249 MET cc_start: 0.7204 (mtm) cc_final: 0.6991 (tmm) REVERT: Ab 360 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.6530 (ptp90) REVERT: Ac 218 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5472 (mtt) REVERT: Ac 285 LYS cc_start: 0.8845 (tttt) cc_final: 0.8460 (tptp) REVERT: Ac 375 ARG cc_start: 0.8333 (mtp85) cc_final: 0.8099 (mtt-85) REVERT: Ac 401 GLN cc_start: 0.8519 (mt0) cc_final: 0.8317 (mt0) REVERT: Cb 31 MET cc_start: 0.4723 (OUTLIER) cc_final: 0.4265 (mtm) REVERT: Cb 37 PHE cc_start: 0.5125 (t80) cc_final: 0.4711 (t80) REVERT: Cb 157 MET cc_start: 0.4455 (ttp) cc_final: 0.4054 (ttt) REVERT: Cb 213 ARG cc_start: 0.7638 (mtt180) cc_final: 0.6959 (mtm180) REVERT: Cb 230 MET cc_start: 0.6934 (tpt) cc_final: 0.6683 (mmm) REVERT: Cb 237 MET cc_start: 0.7007 (ttm) cc_final: 0.6275 (mmt) REVERT: Cb 249 ARG cc_start: 0.5947 (mtm-85) cc_final: 0.5192 (mtt180) REVERT: Cc 20 GLU cc_start: 0.4764 (OUTLIER) cc_final: 0.4558 (mm-30) REVERT: Cc 37 PHE cc_start: 0.5372 (t80) cc_final: 0.5062 (t80) REVERT: Cc 65 ARG cc_start: 0.7695 (ttm110) cc_final: 0.7003 (ttt180) REVERT: Cc 157 MET cc_start: 0.4412 (ttp) cc_final: 0.3975 (ttt) REVERT: Cc 183 MET cc_start: 0.8827 (ttm) cc_final: 0.8434 (ttt) REVERT: Cc 202 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: Cc 213 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7145 (mtm180) REVERT: Cc 237 MET cc_start: 0.7040 (ttm) cc_final: 0.6657 (ttt) REVERT: Cc 249 ARG cc_start: 0.6876 (mtm-85) cc_final: 0.6506 (mtm110) outliers start: 117 outliers final: 19 residues processed: 379 average time/residue: 1.3926 time to fit residues: 594.8555 Evaluate side-chains 283 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 252 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 100 ARG Chi-restraints excluded: chain Aa residue 344 ASP Chi-restraints excluded: chain Ca residue 66 LEU Chi-restraints excluded: chain Ca residue 76 VAL Chi-restraints excluded: chain Ca residue 202 GLU Chi-restraints excluded: chain Ca residue 219 VAL Chi-restraints excluded: chain Ca residue 246 SER Chi-restraints excluded: chain Ba residue 132 PHE Chi-restraints excluded: chain Bb residue 132 PHE Chi-restraints excluded: chain Bb residue 271 GLN Chi-restraints excluded: chain Bc residue 145 ILE Chi-restraints excluded: chain Bc residue 227 ASN Chi-restraints excluded: chain Bc residue 259 MET Chi-restraints excluded: chain Ab residue 108 GLN Chi-restraints excluded: chain Ab residue 110 VAL Chi-restraints excluded: chain Ab residue 162 SER Chi-restraints excluded: chain Ab residue 252 SER Chi-restraints excluded: chain Ab residue 256 SER Chi-restraints excluded: chain Ab residue 360 ARG Chi-restraints excluded: chain Ac residue 110 VAL Chi-restraints excluded: chain Ac residue 145 GLN Chi-restraints excluded: chain Ac residue 162 SER Chi-restraints excluded: chain Ac residue 218 MET Chi-restraints excluded: chain Ac residue 252 SER Chi-restraints excluded: chain Ac residue 256 SER Chi-restraints excluded: chain Cb residue 31 MET Chi-restraints excluded: chain Cb residue 76 VAL Chi-restraints excluded: chain Cb residue 91 ARG Chi-restraints excluded: chain Cc residue 20 GLU Chi-restraints excluded: chain Cc residue 76 VAL Chi-restraints excluded: chain Cc residue 202 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 161 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 151 optimal weight: 0.0170 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 255 ASN Aa 306 ASN Aa 404 GLN ** Ca 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 227 ASN Ba 271 GLN ** Bb 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 404 GLN Ac 404 GLN Cb 181 ASN Cc 23 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.170559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.137462 restraints weight = 22171.598| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.36 r_work: 0.3274 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21303 Z= 0.201 Angle : 0.745 10.846 29088 Z= 0.384 Chirality : 0.051 0.413 3132 Planarity : 0.007 0.103 3609 Dihedral : 5.577 53.116 2801 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.05 % Favored : 96.83 % Rotamer: Outliers : 4.87 % Allowed : 21.79 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2523 helix: 1.08 (0.14), residues: 1200 sheet: 0.91 (0.27), residues: 354 loop : -0.79 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPCa 94 HIS 0.007 0.002 HISCa 239 PHE 0.103 0.002 PHEBb 132 TYR 0.027 0.002 TYRBb 184 ARG 0.013 0.001 ARGAa 296 Details of bonding type rmsd hydrogen bonds : bond 0.05380 ( 1116) hydrogen bonds : angle 5.14401 ( 3240) covalent geometry : bond 0.00463 (21303) covalent geometry : angle 0.74527 (29088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 270 time to evaluate : 2.303 Fit side-chains REVERT: Aa 131 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.8112 (ttt180) REVERT: Aa 249 MET cc_start: 0.7277 (tmm) cc_final: 0.6920 (mtm) REVERT: Aa 360 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7564 (ptp-170) REVERT: Aa 414 MET cc_start: 0.6908 (mtm) cc_final: 0.6458 (mmp) REVERT: Ca 30 TRP cc_start: 0.5436 (OUTLIER) cc_final: 0.4886 (m100) REVERT: Ca 157 MET cc_start: 0.5649 (ttp) cc_final: 0.5253 (ttm) REVERT: Ca 179 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: Ca 213 ARG cc_start: 0.8008 (mtt180) cc_final: 0.6899 (mtm180) REVERT: Ca 237 MET cc_start: 0.7084 (ttm) cc_final: 0.6729 (ttt) REVERT: Ba 111 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5783 (tp) REVERT: Bc 250 ILE cc_start: 0.7487 (mm) cc_final: 0.7174 (mt) REVERT: Bc 259 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.5318 (mtm) REVERT: Ab 93 MET cc_start: 0.9206 (ptp) cc_final: 0.8777 (ptm) REVERT: Ab 108 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8663 (tm-30) REVERT: Ab 249 MET cc_start: 0.7749 (mtm) cc_final: 0.7204 (tmm) REVERT: Ab 288 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7619 (t70) REVERT: Ab 300 MET cc_start: 0.8814 (mtm) cc_final: 0.8408 (mtm) REVERT: Ab 375 ARG cc_start: 0.8560 (mtt-85) cc_final: 0.8250 (mtp85) REVERT: Ac 120 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8628 (mtpt) REVERT: Ac 249 MET cc_start: 0.7303 (tmm) cc_final: 0.7049 (mtm) REVERT: Ac 260 ILE cc_start: 0.8639 (mt) cc_final: 0.8425 (mp) REVERT: Ac 299 ARG cc_start: 0.8178 (mtp-110) cc_final: 0.7895 (ttp80) REVERT: Ac 328 ASP cc_start: 0.8702 (m-30) cc_final: 0.8405 (m-30) REVERT: Ac 375 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8154 (mtp85) REVERT: Cb 30 TRP cc_start: 0.5031 (OUTLIER) cc_final: 0.4521 (m100) REVERT: Cb 62 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8563 (mttp) REVERT: Cb 157 MET cc_start: 0.5923 (ttp) cc_final: 0.5410 (mmt) REVERT: Cb 213 ARG cc_start: 0.7850 (mtt180) cc_final: 0.6934 (mtm180) REVERT: Cb 237 MET cc_start: 0.7539 (ttm) cc_final: 0.7058 (ttp) REVERT: Cc 157 MET cc_start: 0.5452 (ttp) cc_final: 0.5001 (mmt) REVERT: Cc 205 ARG cc_start: 0.8787 (mtm180) cc_final: 0.8433 (mtm180) REVERT: Cc 213 ARG cc_start: 0.7854 (mtt180) cc_final: 0.6899 (mtm180) REVERT: Cc 237 MET cc_start: 0.7450 (ttm) cc_final: 0.6912 (ttt) outliers start: 105 outliers final: 33 residues processed: 358 average time/residue: 1.3682 time to fit residues: 553.8821 Evaluate side-chains 280 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 47 ILE Chi-restraints excluded: chain Aa residue 131 ARG Chi-restraints excluded: chain Aa residue 145 GLN Chi-restraints excluded: chain Aa residue 213 ILE Chi-restraints excluded: chain Aa residue 283 SER Chi-restraints excluded: chain Aa residue 334 THR Chi-restraints excluded: chain Aa residue 360 ARG Chi-restraints excluded: chain Ca residue 30 TRP Chi-restraints excluded: chain Ca residue 62 LYS Chi-restraints excluded: chain Ca residue 74 VAL Chi-restraints excluded: chain Ca residue 179 GLU Chi-restraints excluded: chain Ca residue 246 SER Chi-restraints excluded: chain Ba residue 111 LEU Chi-restraints excluded: chain Ba residue 132 PHE Chi-restraints excluded: chain Bc residue 232 THR Chi-restraints excluded: chain Bc residue 259 MET Chi-restraints excluded: chain Ab residue 80 THR Chi-restraints excluded: chain Ab residue 108 GLN Chi-restraints excluded: chain Ab residue 137 HIS Chi-restraints excluded: chain Ab residue 252 SER Chi-restraints excluded: chain Ab residue 283 SER Chi-restraints excluded: chain Ab residue 288 ASP Chi-restraints excluded: chain Ab residue 296 ARG Chi-restraints excluded: chain Ab residue 334 THR Chi-restraints excluded: chain Ab residue 405 ILE Chi-restraints excluded: chain Ac residue 120 LYS Chi-restraints excluded: chain Ac residue 140 THR Chi-restraints excluded: chain Ac residue 162 SER Chi-restraints excluded: chain Ac residue 256 SER Chi-restraints excluded: chain Ac residue 283 SER Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 405 ILE Chi-restraints excluded: chain Cb residue 30 TRP Chi-restraints excluded: chain Cb residue 62 LYS Chi-restraints excluded: chain Cb residue 74 VAL Chi-restraints excluded: chain Cb residue 91 ARG Chi-restraints excluded: chain Cb residue 162 ILE Chi-restraints excluded: chain Cb residue 227 SER Chi-restraints excluded: chain Cb residue 255 SER Chi-restraints excluded: chain Cc residue 68 VAL Chi-restraints excluded: chain Cc residue 74 VAL Chi-restraints excluded: chain Cc residue 222 VAL Chi-restraints excluded: chain Cc residue 227 SER Chi-restraints excluded: chain Cc residue 246 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 149 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 227 ASN Ab 306 ASN ** Cb 45 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 = 0.3839 r_free = 0.3839 target = 0.169060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.135900 restraints weight = 22669.350| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.38 r_work: 0.3270 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21303 Z= 0.137 Angle : 0.602 8.626 29088 Z= 0.311 Chirality : 0.047 0.367 3132 Planarity : 0.006 0.091 3609 Dihedral : 5.087 50.432 2796 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.66 % Favored : 97.23 % Rotamer: Outliers : 3.29 % Allowed : 23.27 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2523 helix: 1.45 (0.15), residues: 1203 sheet: 0.91 (0.27), residues: 351 loop : -0.49 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPCb 94 HIS 0.003 0.001 HISCc 45 PHE 0.025 0.001 PHEBa 201 TYR 0.021 0.001 TYRBa 184 ARG 0.006 0.001 ARGAa 375 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 1116) hydrogen bonds : angle 4.85191 ( 3240) covalent geometry : bond 0.00316 (21303) covalent geometry : angle 0.60229 (29088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 244 time to evaluate : 2.241 Fit side-chains REVERT: Aa 79 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8231 (pp20) REVERT: Aa 249 MET cc_start: 0.7240 (tmm) cc_final: 0.6838 (mtm) REVERT: Aa 414 MET cc_start: 0.7113 (mtm) cc_final: 0.6326 (mmp) REVERT: Ca 157 MET cc_start: 0.6150 (ttp) cc_final: 0.5672 (mtt) REVERT: Ca 213 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7007 (mtm180) REVERT: Ca 237 MET cc_start: 0.7246 (ttm) cc_final: 0.6827 (ttt) REVERT: Bc 259 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5370 (mtm) REVERT: Ab 93 MET cc_start: 0.9115 (ptp) cc_final: 0.8720 (ptm) REVERT: Ab 273 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8534 (mptp) REVERT: Ab 375 ARG cc_start: 0.8662 (mtt-85) cc_final: 0.8363 (mtp85) REVERT: Ac 299 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7860 (ttp80) REVERT: Ac 328 ASP cc_start: 0.8713 (m-30) cc_final: 0.8426 (m-30) REVERT: Ac 375 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8127 (mtp85) REVERT: Cb 30 TRP cc_start: 0.5151 (OUTLIER) cc_final: 0.4823 (m100) REVERT: Cb 157 MET cc_start: 0.5976 (ttp) cc_final: 0.5660 (mmt) REVERT: Cb 213 ARG cc_start: 0.8056 (mtt180) cc_final: 0.7067 (mtm180) REVERT: Cb 237 MET cc_start: 0.7499 (ttm) cc_final: 0.6946 (ttt) REVERT: Cc 157 MET cc_start: 0.5582 (ttp) cc_final: 0.5161 (mmt) REVERT: Cc 213 ARG cc_start: 0.7951 (mtt180) cc_final: 0.6663 (mpp-170) REVERT: Cc 237 MET cc_start: 0.7424 (ttm) cc_final: 0.6889 (ttt) outliers start: 71 outliers final: 26 residues processed: 301 average time/residue: 1.3229 time to fit residues: 452.7949 Evaluate side-chains 257 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 79 GLU Chi-restraints excluded: chain Aa residue 80 THR Chi-restraints excluded: chain Aa residue 145 GLN Chi-restraints excluded: chain Aa residue 181 GLU Chi-restraints excluded: chain Aa residue 213 ILE Chi-restraints excluded: chain Aa residue 283 SER Chi-restraints excluded: chain Ca residue 74 VAL Chi-restraints excluded: chain Ca residue 183 MET Chi-restraints excluded: chain Ca residue 246 SER Chi-restraints excluded: chain Ba residue 132 PHE Chi-restraints excluded: chain Ba residue 145 ILE Chi-restraints excluded: chain Bb residue 132 PHE Chi-restraints excluded: chain Bc residue 249 VAL Chi-restraints excluded: chain Bc residue 259 MET Chi-restraints excluded: chain Ab residue 80 THR Chi-restraints excluded: chain Ab residue 273 LYS Chi-restraints excluded: chain Ab residue 283 SER Chi-restraints excluded: chain Ab residue 296 ARG Chi-restraints excluded: chain Ab residue 334 THR Chi-restraints excluded: chain Ab residue 405 ILE Chi-restraints excluded: chain Ac residue 283 SER Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 344 ASP Chi-restraints excluded: chain Ac residue 405 ILE Chi-restraints excluded: chain Cb residue 30 TRP Chi-restraints excluded: chain Cb residue 74 VAL Chi-restraints excluded: chain Cc residue 60 ASP Chi-restraints excluded: chain Cc residue 68 VAL Chi-restraints excluded: chain Cc residue 74 VAL Chi-restraints excluded: chain Cc residue 246 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 110 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 78 optimal weight: 0.0060 chunk 139 optimal weight: 0.0770 overall best weight: 0.8356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 306 ASN ** Ca 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 161 GLN Ab 306 ASN Cc 114 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.169151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.136101 restraints weight = 22387.569| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.29 r_work: 0.3256 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21303 Z= 0.130 Angle : 0.587 8.417 29088 Z= 0.304 Chirality : 0.046 0.399 3132 Planarity : 0.006 0.088 3609 Dihedral : 4.822 47.139 2793 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.97 % Favored : 96.91 % Rotamer: Outliers : 3.15 % Allowed : 23.09 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2523 helix: 1.64 (0.15), residues: 1197 sheet: 1.07 (0.26), residues: 345 loop : -0.45 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPCb 159 HIS 0.005 0.001 HISBc 245 PHE 0.057 0.002 PHEBb 132 TYR 0.020 0.001 TYRBa 184 ARG 0.005 0.000 ARGAa 375 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1116) hydrogen bonds : angle 4.75719 ( 3240) covalent geometry : bond 0.00302 (21303) covalent geometry : angle 0.58680 (29088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 245 time to evaluate : 2.250 Fit side-chains REVERT: Aa 79 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8222 (pp20) REVERT: Aa 100 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8927 (ttm110) REVERT: Aa 414 MET cc_start: 0.6980 (mtm) cc_final: 0.6394 (mmp) REVERT: Ca 52 MET cc_start: 0.8174 (pp-130) cc_final: 0.7681 (pp-130) REVERT: Ca 157 MET cc_start: 0.6474 (ttp) cc_final: 0.6047 (mtt) REVERT: Ca 213 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7234 (mtm180) REVERT: Ca 237 MET cc_start: 0.7432 (ttm) cc_final: 0.6977 (ttt) REVERT: Bb 69 GLU cc_start: 0.8385 (pt0) cc_final: 0.8138 (pt0) REVERT: Bc 259 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5603 (mtm) REVERT: Ab 93 MET cc_start: 0.9134 (ptp) cc_final: 0.8735 (ptm) REVERT: Ab 251 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7643 (ttm) REVERT: Ab 375 ARG cc_start: 0.8661 (mtt-85) cc_final: 0.8382 (mtp85) REVERT: Ac 299 ARG cc_start: 0.8208 (mtp-110) cc_final: 0.7979 (ttp80) REVERT: Ac 328 ASP cc_start: 0.8577 (m-30) cc_final: 0.8334 (m-30) REVERT: Ac 375 ARG cc_start: 0.8469 (mtp85) cc_final: 0.8185 (mtp85) REVERT: Ac 414 MET cc_start: 0.7546 (mtm) cc_final: 0.6581 (mmp) REVERT: Cb 30 TRP cc_start: 0.5077 (OUTLIER) cc_final: 0.4817 (m100) REVERT: Cb 86 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5912 (mp) REVERT: Cb 157 MET cc_start: 0.6225 (ttp) cc_final: 0.5960 (mmt) REVERT: Cb 213 ARG cc_start: 0.8236 (mtt180) cc_final: 0.7316 (mtm180) REVERT: Cb 237 MET cc_start: 0.7372 (ttm) cc_final: 0.6863 (ttt) REVERT: Cc 157 MET cc_start: 0.6091 (ttp) cc_final: 0.5686 (mmt) REVERT: Cc 213 ARG cc_start: 0.8040 (mtt180) cc_final: 0.6987 (mtm180) REVERT: Cc 237 MET cc_start: 0.7528 (ttm) cc_final: 0.6979 (ttt) outliers start: 68 outliers final: 24 residues processed: 297 average time/residue: 1.3169 time to fit residues: 443.9346 Evaluate side-chains 267 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 79 GLU Chi-restraints excluded: chain Aa residue 80 THR Chi-restraints excluded: chain Aa residue 100 ARG Chi-restraints excluded: chain Aa residue 137 HIS Chi-restraints excluded: chain Aa residue 145 GLN Chi-restraints excluded: chain Aa residue 181 GLU Chi-restraints excluded: chain Aa residue 283 SER Chi-restraints excluded: chain Aa residue 334 THR Chi-restraints excluded: chain Ca residue 74 VAL Chi-restraints excluded: chain Ca residue 227 SER Chi-restraints excluded: chain Ca residue 246 SER Chi-restraints excluded: chain Ba residue 132 PHE Chi-restraints excluded: chain Bc residue 259 MET Chi-restraints excluded: chain Ab residue 80 THR Chi-restraints excluded: chain Ab residue 251 MET Chi-restraints excluded: chain Ab residue 283 SER Chi-restraints excluded: chain Ab residue 296 ARG Chi-restraints excluded: chain Ab residue 334 THR Chi-restraints excluded: chain Ab residue 405 ILE Chi-restraints excluded: chain Ac residue 283 SER Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 344 ASP Chi-restraints excluded: chain Cb residue 30 TRP Chi-restraints excluded: chain Cb residue 74 VAL Chi-restraints excluded: chain Cb residue 86 LEU Chi-restraints excluded: chain Cc residue 60 ASP Chi-restraints excluded: chain Cc residue 68 VAL Chi-restraints excluded: chain Cc residue 74 VAL Chi-restraints excluded: chain Cc residue 131 LEU Chi-restraints excluded: chain Cc residue 246 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 12 optimal weight: 0.0770 chunk 225 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 134 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 247 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ca 110 ASN Ba 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.167534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134611 restraints weight = 22115.221| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.35 r_work: 0.3253 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21303 Z= 0.122 Angle : 0.570 8.420 29088 Z= 0.294 Chirality : 0.046 0.447 3132 Planarity : 0.006 0.082 3609 Dihedral : 4.677 45.944 2793 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.89 % Favored : 96.99 % Rotamer: Outliers : 3.29 % Allowed : 22.86 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2523 helix: 1.82 (0.15), residues: 1191 sheet: 1.02 (0.25), residues: 375 loop : -0.30 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPCc 94 HIS 0.004 0.001 HISBc 245 PHE 0.026 0.001 PHEBa 201 TYR 0.019 0.001 TYRBa 184 ARG 0.006 0.000 ARGAa 375 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 1116) hydrogen bonds : angle 4.66791 ( 3240) covalent geometry : bond 0.00281 (21303) covalent geometry : angle 0.57031 (29088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 261 time to evaluate : 1.990 Fit side-chains REVERT: Aa 79 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8220 (pp20) REVERT: Aa 93 MET cc_start: 0.8607 (ptp) cc_final: 0.8394 (ptm) REVERT: Aa 100 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8995 (ttm110) REVERT: Aa 108 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8804 (tp40) REVERT: Aa 117 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: Aa 375 ARG cc_start: 0.8502 (mtt90) cc_final: 0.8193 (mtp85) REVERT: Aa 414 MET cc_start: 0.6963 (mtm) cc_final: 0.6275 (mmp) REVERT: Ca 157 MET cc_start: 0.6592 (ttp) cc_final: 0.6211 (mtt) REVERT: Ca 202 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: Ca 213 ARG cc_start: 0.8298 (mtt180) cc_final: 0.7325 (mtm180) REVERT: Ca 237 MET cc_start: 0.7370 (ttm) cc_final: 0.6774 (ttt) REVERT: Bb 177 PHE cc_start: 0.8800 (m-10) cc_final: 0.8479 (m-10) REVERT: Bb 218 PHE cc_start: 0.7083 (t80) cc_final: 0.6703 (t80) REVERT: Bc 90 MET cc_start: 0.8081 (mmm) cc_final: 0.7771 (tpt) REVERT: Bc 259 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.5878 (mtm) REVERT: Ab 93 MET cc_start: 0.9156 (ptp) cc_final: 0.8745 (ptm) REVERT: Ab 273 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8512 (mptp) REVERT: Ab 375 ARG cc_start: 0.8624 (mtt-85) cc_final: 0.8334 (mtp85) REVERT: Ac 120 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8560 (mtpt) REVERT: Ac 141 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8765 (ptp) REVERT: Ac 145 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: Ac 299 ARG cc_start: 0.8168 (mtp-110) cc_final: 0.7937 (ttp80) REVERT: Ac 328 ASP cc_start: 0.8583 (m-30) cc_final: 0.8350 (m-30) REVERT: Ac 375 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8155 (mtp85) REVERT: Ac 405 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8013 (pt) REVERT: Ac 414 MET cc_start: 0.7614 (mtm) cc_final: 0.6516 (mmp) REVERT: Cb 157 MET cc_start: 0.6456 (ttp) cc_final: 0.6214 (mmt) REVERT: Cb 213 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7348 (mtm180) REVERT: Cb 236 PHE cc_start: 0.5976 (t80) cc_final: 0.5738 (t80) REVERT: Cb 237 MET cc_start: 0.7543 (ttm) cc_final: 0.6936 (ttt) REVERT: Cb 249 ARG cc_start: 0.6508 (mtm-85) cc_final: 0.5774 (mtt180) REVERT: Cc 157 MET cc_start: 0.6057 (ttp) cc_final: 0.5703 (mmt) REVERT: Cc 213 ARG cc_start: 0.8136 (mtt180) cc_final: 0.6928 (mtm180) REVERT: Cc 237 MET cc_start: 0.7405 (ttm) cc_final: 0.6774 (ttt) outliers start: 71 outliers final: 30 residues processed: 312 average time/residue: 1.2615 time to fit residues: 448.7200 Evaluate side-chains 288 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 79 GLU Chi-restraints excluded: chain Aa residue 80 THR Chi-restraints excluded: chain Aa residue 100 ARG Chi-restraints excluded: chain Aa residue 108 GLN Chi-restraints excluded: chain Aa residue 117 GLU Chi-restraints excluded: chain Aa residue 137 HIS Chi-restraints excluded: chain Aa residue 145 GLN Chi-restraints excluded: chain Aa residue 283 SER Chi-restraints excluded: chain Aa residue 290 THR Chi-restraints excluded: chain Aa residue 334 THR Chi-restraints excluded: chain Ca residue 30 TRP Chi-restraints excluded: chain Ca residue 62 LYS Chi-restraints excluded: chain Ca residue 76 VAL Chi-restraints excluded: chain Ca residue 202 GLU Chi-restraints excluded: chain Ca residue 227 SER Chi-restraints excluded: chain Ca residue 246 SER Chi-restraints excluded: chain Ba residue 132 PHE Chi-restraints excluded: chain Bb residue 106 ILE Chi-restraints excluded: chain Bc residue 259 MET Chi-restraints excluded: chain Ab residue 80 THR Chi-restraints excluded: chain Ab residue 203 ILE Chi-restraints excluded: chain Ab residue 273 LYS Chi-restraints excluded: chain Ab residue 283 SER Chi-restraints excluded: chain Ab residue 334 THR Chi-restraints excluded: chain Ab residue 405 ILE Chi-restraints excluded: chain Ac residue 64 THR Chi-restraints excluded: chain Ac residue 120 LYS Chi-restraints excluded: chain Ac residue 137 HIS Chi-restraints excluded: chain Ac residue 141 MET Chi-restraints excluded: chain Ac residue 145 GLN Chi-restraints excluded: chain Ac residue 162 SER Chi-restraints excluded: chain Ac residue 283 SER Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 344 ASP Chi-restraints excluded: chain Ac residue 405 ILE Chi-restraints excluded: chain Cb residue 74 VAL Chi-restraints excluded: chain Cc residue 40 ILE Chi-restraints excluded: chain Cc residue 68 VAL Chi-restraints excluded: chain Cc residue 74 VAL Chi-restraints excluded: chain Cc residue 131 LEU Chi-restraints excluded: chain Cc residue 246 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 63 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 122 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 233 optimal weight: 0.0870 chunk 178 optimal weight: 0.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 306 ASN Ab 306 ASN Cc 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.168409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134992 restraints weight = 22233.825| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.26 r_work: 0.3259 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.6384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21303 Z= 0.117 Angle : 0.564 7.764 29088 Z= 0.291 Chirality : 0.046 0.421 3132 Planarity : 0.006 0.080 3609 Dihedral : 4.601 45.983 2793 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.73 % Favored : 97.19 % Rotamer: Outliers : 2.69 % Allowed : 23.60 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.17), residues: 2523 helix: 1.85 (0.15), residues: 1197 sheet: 1.28 (0.26), residues: 345 loop : -0.35 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPAc 202 HIS 0.004 0.001 HISCc 45 PHE 0.025 0.001 PHEBc 201 TYR 0.019 0.001 TYRBa 184 ARG 0.005 0.000 ARGAa 375 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 1116) hydrogen bonds : angle 4.62443 ( 3240) covalent geometry : bond 0.00270 (21303) covalent geometry : angle 0.56378 (29088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 2.083 Fit side-chains REVERT: Aa 93 MET cc_start: 0.8646 (ptp) cc_final: 0.8418 (ptm) REVERT: Aa 100 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8988 (ttm110) REVERT: Aa 108 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8794 (tp40) REVERT: Aa 117 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: Aa 375 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8213 (mtp85) REVERT: Aa 414 MET cc_start: 0.6839 (mtm) cc_final: 0.6268 (mmp) REVERT: Ca 157 MET cc_start: 0.6420 (ttp) cc_final: 0.6132 (mtt) REVERT: Ca 202 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8209 (tm-30) REVERT: Ca 213 ARG cc_start: 0.8307 (mtt180) cc_final: 0.7356 (mtm180) REVERT: Ca 237 MET cc_start: 0.7369 (ttm) cc_final: 0.6793 (ttp) REVERT: Bb 218 PHE cc_start: 0.7141 (t80) cc_final: 0.6849 (t80) REVERT: Bc 90 MET cc_start: 0.8207 (mmm) cc_final: 0.7894 (tpt) REVERT: Bc 259 MET cc_start: 0.6538 (OUTLIER) cc_final: 0.6021 (mtm) REVERT: Ab 93 MET cc_start: 0.9155 (ptp) cc_final: 0.8596 (ptm) REVERT: Ab 273 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8493 (mptp) REVERT: Ab 375 ARG cc_start: 0.8616 (mtt-85) cc_final: 0.8322 (mtp85) REVERT: Ac 145 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: Ac 299 ARG cc_start: 0.8161 (mtp-110) cc_final: 0.7940 (ttp80) REVERT: Ac 375 ARG cc_start: 0.8399 (mtp85) cc_final: 0.8109 (mtp85) REVERT: Ac 405 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8009 (pt) REVERT: Ac 414 MET cc_start: 0.7604 (mtm) cc_final: 0.6561 (mmp) REVERT: Cb 60 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6889 (m-30) REVERT: Cb 62 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8788 (mttm) REVERT: Cb 213 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7326 (mtm180) REVERT: Cb 236 PHE cc_start: 0.5881 (t80) cc_final: 0.5671 (t80) REVERT: Cb 237 MET cc_start: 0.7600 (ttm) cc_final: 0.7042 (ttt) REVERT: Cb 249 ARG cc_start: 0.6552 (mtm-85) cc_final: 0.5809 (mtt180) REVERT: Cc 157 MET cc_start: 0.6236 (ttp) cc_final: 0.5937 (mmt) REVERT: Cc 213 ARG cc_start: 0.8155 (mtt180) cc_final: 0.6930 (mtm180) REVERT: Cc 237 MET cc_start: 0.7411 (ttm) cc_final: 0.6738 (ttt) outliers start: 58 outliers final: 29 residues processed: 291 average time/residue: 1.3282 time to fit residues: 442.0363 Evaluate side-chains 280 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 80 THR Chi-restraints excluded: chain Aa residue 100 ARG Chi-restraints excluded: chain Aa residue 108 GLN Chi-restraints excluded: chain Aa residue 117 GLU Chi-restraints excluded: chain Aa residue 137 HIS Chi-restraints excluded: chain Aa residue 145 GLN Chi-restraints excluded: chain Aa residue 252 SER Chi-restraints excluded: chain Aa residue 283 SER Chi-restraints excluded: chain Aa residue 334 THR Chi-restraints excluded: chain Ca residue 60 ASP Chi-restraints excluded: chain Ca residue 62 LYS Chi-restraints excluded: chain Ca residue 202 GLU Chi-restraints excluded: chain Ba residue 90 MET Chi-restraints excluded: chain Ba residue 132 PHE Chi-restraints excluded: chain Ba residue 145 ILE Chi-restraints excluded: chain Bb residue 106 ILE Chi-restraints excluded: chain Bb residue 153 THR Chi-restraints excluded: chain Bb residue 249 VAL Chi-restraints excluded: chain Bc residue 259 MET Chi-restraints excluded: chain Ab residue 80 THR Chi-restraints excluded: chain Ab residue 203 ILE Chi-restraints excluded: chain Ab residue 273 LYS Chi-restraints excluded: chain Ab residue 283 SER Chi-restraints excluded: chain Ab residue 334 THR Chi-restraints excluded: chain Ab residue 405 ILE Chi-restraints excluded: chain Ac residue 145 GLN Chi-restraints excluded: chain Ac residue 283 SER Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 344 ASP Chi-restraints excluded: chain Ac residue 405 ILE Chi-restraints excluded: chain Cb residue 60 ASP Chi-restraints excluded: chain Cb residue 62 LYS Chi-restraints excluded: chain Cb residue 74 VAL Chi-restraints excluded: chain Cb residue 171 ILE Chi-restraints excluded: chain Cc residue 40 ILE Chi-restraints excluded: chain Cc residue 68 VAL Chi-restraints excluded: chain Cc residue 74 VAL Chi-restraints excluded: chain Cc residue 131 LEU Chi-restraints excluded: chain Cc residue 246 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 247 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 177 optimal weight: 0.0870 chunk 80 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ca 175 HIS Bc 227 ASN Bc 245 HIS Ab 33 HIS ** Cb 45 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 = 0.3703 r_free = 0.3703 target = 0.156631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123620 restraints weight = 22443.794| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.33 r_work: 0.3121 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 21303 Z= 0.251 Angle : 0.721 11.068 29088 Z= 0.375 Chirality : 0.053 0.433 3132 Planarity : 0.007 0.092 3609 Dihedral : 5.193 50.277 2793 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.47 % Rotamer: Outliers : 3.62 % Allowed : 23.09 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.16), residues: 2523 helix: 1.08 (0.14), residues: 1215 sheet: 1.15 (0.26), residues: 336 loop : -0.46 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPAc 202 HIS 0.009 0.002 HISCc 45 PHE 0.029 0.003 PHEBa 201 TYR 0.030 0.003 TYRCc 195 ARG 0.007 0.001 ARGBa 66 Details of bonding type rmsd hydrogen bonds : bond 0.05282 ( 1116) hydrogen bonds : angle 5.06299 ( 3240) covalent geometry : bond 0.00623 (21303) covalent geometry : angle 0.72146 (29088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 246 time to evaluate : 2.172 Fit side-chains REVERT: Aa 79 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8320 (pp20) REVERT: Aa 100 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.9014 (ttm110) REVERT: Aa 108 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8576 (tp40) REVERT: Aa 117 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: Aa 163 MET cc_start: 0.9006 (ttm) cc_final: 0.8804 (ttm) REVERT: Aa 264 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8542 (mt) REVERT: Aa 414 MET cc_start: 0.7125 (mtm) cc_final: 0.6435 (mmp) REVERT: Ca 30 TRP cc_start: 0.6136 (OUTLIER) cc_final: 0.5755 (m100) REVERT: Ca 157 MET cc_start: 0.6932 (ttp) cc_final: 0.6606 (mtt) REVERT: Ca 202 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: Ca 213 ARG cc_start: 0.8417 (mtt180) cc_final: 0.7296 (mtm180) REVERT: Ca 237 MET cc_start: 0.7561 (ttm) cc_final: 0.6991 (ttt) REVERT: Ca 243 ARG cc_start: 0.4992 (mmt90) cc_final: 0.4509 (mtm-85) REVERT: Bb 113 LYS cc_start: 0.6186 (OUTLIER) cc_final: 0.5469 (mttp) REVERT: Bc 90 MET cc_start: 0.8472 (mmm) cc_final: 0.8238 (tpt) REVERT: Bc 250 ILE cc_start: 0.7782 (mm) cc_final: 0.7460 (mt) REVERT: Bc 259 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6261 (mtm) REVERT: Bc 271 GLN cc_start: 0.5835 (OUTLIER) cc_final: 0.5203 (pp30) REVERT: Ab 264 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8678 (mt) REVERT: Ab 273 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8516 (mptp) REVERT: Ac 120 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8612 (mtpt) REVERT: Ac 273 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8780 (mptp) REVERT: Ac 299 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.7924 (ttp80) REVERT: Ac 375 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8296 (mtp85) REVERT: Cb 30 TRP cc_start: 0.6349 (OUTLIER) cc_final: 0.5819 (m100) REVERT: Cb 31 MET cc_start: 0.6799 (mtm) cc_final: 0.6452 (mtt) REVERT: Cb 62 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8833 (mttm) REVERT: Cb 157 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6737 (mmm) REVERT: Cb 213 ARG cc_start: 0.8206 (mtt180) cc_final: 0.7364 (mtm180) REVERT: Cb 236 PHE cc_start: 0.5956 (t80) cc_final: 0.5737 (t80) REVERT: Cb 237 MET cc_start: 0.7700 (ttm) cc_final: 0.6997 (ttt) REVERT: Cb 243 ARG cc_start: 0.5598 (mmt90) cc_final: 0.4855 (mtm-85) REVERT: Cb 249 ARG cc_start: 0.6695 (mtm-85) cc_final: 0.6091 (mtp-110) REVERT: Cc 43 SER cc_start: 0.8345 (t) cc_final: 0.8060 (p) REVERT: Cc 157 MET cc_start: 0.7048 (ttp) cc_final: 0.6570 (mmt) REVERT: Cc 202 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: Cc 213 ARG cc_start: 0.8147 (mtt180) cc_final: 0.6918 (mtm180) REVERT: Cc 227 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8109 (p) REVERT: Cc 237 MET cc_start: 0.7520 (ttm) cc_final: 0.6840 (ttt) REVERT: Cc 249 ARG cc_start: 0.7159 (mtm-85) cc_final: 0.6578 (mtp-110) outliers start: 78 outliers final: 34 residues processed: 311 average time/residue: 1.3969 time to fit residues: 490.8108 Evaluate side-chains 282 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 229 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 79 GLU Chi-restraints excluded: chain Aa residue 80 THR Chi-restraints excluded: chain Aa residue 100 ARG Chi-restraints excluded: chain Aa residue 108 GLN Chi-restraints excluded: chain Aa residue 117 GLU Chi-restraints excluded: chain Aa residue 137 HIS Chi-restraints excluded: chain Aa residue 145 GLN Chi-restraints excluded: chain Aa residue 264 LEU Chi-restraints excluded: chain Aa residue 283 SER Chi-restraints excluded: chain Ca residue 30 TRP Chi-restraints excluded: chain Ca residue 60 ASP Chi-restraints excluded: chain Ca residue 62 LYS Chi-restraints excluded: chain Ca residue 123 ILE Chi-restraints excluded: chain Ca residue 202 GLU Chi-restraints excluded: chain Ca residue 227 SER Chi-restraints excluded: chain Ba residue 132 PHE Chi-restraints excluded: chain Ba residue 249 VAL Chi-restraints excluded: chain Bb residue 113 LYS Chi-restraints excluded: chain Bb residue 153 THR Chi-restraints excluded: chain Bb residue 249 VAL Chi-restraints excluded: chain Bc residue 158 THR Chi-restraints excluded: chain Bc residue 259 MET Chi-restraints excluded: chain Bc residue 271 GLN Chi-restraints excluded: chain Ab residue 80 THR Chi-restraints excluded: chain Ab residue 140 THR Chi-restraints excluded: chain Ab residue 162 SER Chi-restraints excluded: chain Ab residue 203 ILE Chi-restraints excluded: chain Ab residue 264 LEU Chi-restraints excluded: chain Ab residue 273 LYS Chi-restraints excluded: chain Ab residue 283 SER Chi-restraints excluded: chain Ab residue 305 THR Chi-restraints excluded: chain Ab residue 334 THR Chi-restraints excluded: chain Ab residue 405 ILE Chi-restraints excluded: chain Ac residue 80 THR Chi-restraints excluded: chain Ac residue 120 LYS Chi-restraints excluded: chain Ac residue 140 THR Chi-restraints excluded: chain Ac residue 273 LYS Chi-restraints excluded: chain Ac residue 283 SER Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 405 ILE Chi-restraints excluded: chain Cb residue 30 TRP Chi-restraints excluded: chain Cb residue 62 LYS Chi-restraints excluded: chain Cb residue 74 VAL Chi-restraints excluded: chain Cb residue 157 MET Chi-restraints excluded: chain Cb residue 202 GLU Chi-restraints excluded: chain Cc residue 40 ILE Chi-restraints excluded: chain Cc residue 60 ASP Chi-restraints excluded: chain Cc residue 74 VAL Chi-restraints excluded: chain Cc residue 131 LEU Chi-restraints excluded: chain Cc residue 202 GLU Chi-restraints excluded: chain Cc residue 222 VAL Chi-restraints excluded: chain Cc residue 227 SER Chi-restraints excluded: chain Cc residue 246 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 63 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.159829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126529 restraints weight = 22226.455| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.31 r_work: 0.3157 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.7145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21303 Z= 0.155 Angle : 0.614 8.364 29088 Z= 0.319 Chirality : 0.048 0.414 3132 Planarity : 0.006 0.085 3609 Dihedral : 4.903 47.817 2793 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 2.60 % Allowed : 24.43 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.16), residues: 2523 helix: 1.23 (0.15), residues: 1245 sheet: 0.85 (0.25), residues: 375 loop : -0.34 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPCa 159 HIS 0.006 0.001 HISCc 45 PHE 0.025 0.002 PHEBc 201 TYR 0.020 0.002 TYRBc 184 ARG 0.008 0.001 ARGCc 243 Details of bonding type rmsd hydrogen bonds : bond 0.04426 ( 1116) hydrogen bonds : angle 4.86082 ( 3240) covalent geometry : bond 0.00370 (21303) covalent geometry : angle 0.61441 (29088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 2.629 Fit side-chains REVERT: Aa 79 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8323 (pp20) REVERT: Aa 100 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8974 (ttm110) REVERT: Aa 108 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8688 (tp40) REVERT: Aa 117 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: Aa 414 MET cc_start: 0.7064 (mtm) cc_final: 0.6415 (mmp) REVERT: Ca 157 MET cc_start: 0.6822 (ttp) cc_final: 0.6580 (mtt) REVERT: Ca 202 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: Ca 213 ARG cc_start: 0.8513 (mtt180) cc_final: 0.7441 (mtm180) REVERT: Ca 237 MET cc_start: 0.7539 (ttm) cc_final: 0.6963 (ttt) REVERT: Ca 243 ARG cc_start: 0.4955 (mmt90) cc_final: 0.4481 (mtm-85) REVERT: Bc 90 MET cc_start: 0.8469 (mmm) cc_final: 0.8217 (tpt) REVERT: Bc 259 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6317 (mtm) REVERT: Ab 264 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8447 (mt) REVERT: Ab 273 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8506 (mptp) REVERT: Ab 300 MET cc_start: 0.8805 (mtm) cc_final: 0.8568 (mtm) REVERT: Ac 213 ILE cc_start: 0.4051 (OUTLIER) cc_final: 0.3718 (tp) REVERT: Ac 299 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7760 (ttp80) REVERT: Ac 375 ARG cc_start: 0.8594 (mtp85) cc_final: 0.8300 (mtp85) REVERT: Cb 31 MET cc_start: 0.6772 (mtm) cc_final: 0.6441 (mtt) REVERT: Cb 62 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8810 (mttm) REVERT: Cb 157 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6826 (mmm) REVERT: Cb 213 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7418 (mtm180) REVERT: Cb 236 PHE cc_start: 0.6108 (t80) cc_final: 0.5903 (t80) REVERT: Cb 237 MET cc_start: 0.7685 (ttm) cc_final: 0.7012 (ttt) REVERT: Cb 243 ARG cc_start: 0.5288 (mmt90) cc_final: 0.4543 (mtm-85) REVERT: Cb 249 ARG cc_start: 0.6706 (mtm-85) cc_final: 0.6147 (mtp-110) REVERT: Cc 52 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7809 (pp-130) REVERT: Cc 157 MET cc_start: 0.6988 (ttp) cc_final: 0.6574 (mmt) REVERT: Cc 185 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8865 (mtm) REVERT: Cc 213 ARG cc_start: 0.8196 (mtt180) cc_final: 0.6995 (mtm180) REVERT: Cc 237 MET cc_start: 0.7440 (ttm) cc_final: 0.6777 (ttt) REVERT: Cc 249 ARG cc_start: 0.7192 (mtm-85) cc_final: 0.6669 (mtp-110) outliers start: 56 outliers final: 30 residues processed: 287 average time/residue: 1.5009 time to fit residues: 483.7212 Evaluate side-chains 279 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 79 GLU Chi-restraints excluded: chain Aa residue 80 THR Chi-restraints excluded: chain Aa residue 100 ARG Chi-restraints excluded: chain Aa residue 108 GLN Chi-restraints excluded: chain Aa residue 117 GLU Chi-restraints excluded: chain Aa residue 137 HIS Chi-restraints excluded: chain Aa residue 145 GLN Chi-restraints excluded: chain Aa residue 252 SER Chi-restraints excluded: chain Aa residue 283 SER Chi-restraints excluded: chain Ca residue 60 ASP Chi-restraints excluded: chain Ca residue 62 LYS Chi-restraints excluded: chain Ca residue 202 GLU Chi-restraints excluded: chain Ba residue 132 PHE Chi-restraints excluded: chain Bb residue 153 THR Chi-restraints excluded: chain Bb residue 249 VAL Chi-restraints excluded: chain Bc residue 158 THR Chi-restraints excluded: chain Bc residue 259 MET Chi-restraints excluded: chain Ab residue 80 THR Chi-restraints excluded: chain Ab residue 140 THR Chi-restraints excluded: chain Ab residue 162 SER Chi-restraints excluded: chain Ab residue 264 LEU Chi-restraints excluded: chain Ab residue 273 LYS Chi-restraints excluded: chain Ab residue 283 SER Chi-restraints excluded: chain Ab residue 305 THR Chi-restraints excluded: chain Ab residue 334 THR Chi-restraints excluded: chain Ab residue 405 ILE Chi-restraints excluded: chain Ac residue 137 HIS Chi-restraints excluded: chain Ac residue 162 SER Chi-restraints excluded: chain Ac residue 213 ILE Chi-restraints excluded: chain Ac residue 283 SER Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 405 ILE Chi-restraints excluded: chain Cb residue 62 LYS Chi-restraints excluded: chain Cb residue 74 VAL Chi-restraints excluded: chain Cb residue 157 MET Chi-restraints excluded: chain Cb residue 202 GLU Chi-restraints excluded: chain Cc residue 40 ILE Chi-restraints excluded: chain Cc residue 52 MET Chi-restraints excluded: chain Cc residue 60 ASP Chi-restraints excluded: chain Cc residue 74 VAL Chi-restraints excluded: chain Cc residue 131 LEU Chi-restraints excluded: chain Cc residue 185 MET Chi-restraints excluded: chain Cc residue 246 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 181 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 192 optimal weight: 7.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.159659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.126387 restraints weight = 22068.702| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.30 r_work: 0.3159 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.7389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21303 Z= 0.149 Angle : 0.609 8.374 29088 Z= 0.315 Chirality : 0.047 0.435 3132 Planarity : 0.006 0.083 3609 Dihedral : 4.811 47.605 2793 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.21 % Favored : 96.67 % Rotamer: Outliers : 2.32 % Allowed : 24.80 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.17), residues: 2523 helix: 1.39 (0.15), residues: 1218 sheet: 0.89 (0.25), residues: 375 loop : -0.39 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPCc 159 HIS 0.006 0.001 HISCc 45 PHE 0.034 0.002 PHEBc 192 TYR 0.021 0.002 TYRBa 184 ARG 0.007 0.000 ARGAa 375 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 1116) hydrogen bonds : angle 4.80924 ( 3240) covalent geometry : bond 0.00355 (21303) covalent geometry : angle 0.60901 (29088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5046 Ramachandran restraints generated. 2523 Oldfield, 0 Emsley, 2523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 2.903 Fit side-chains REVERT: Aa 79 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8311 (pp20) REVERT: Aa 108 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8720 (tp40) REVERT: Aa 117 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: Aa 163 MET cc_start: 0.8945 (ttm) cc_final: 0.8683 (ttm) REVERT: Aa 249 MET cc_start: 0.7889 (mtp) cc_final: 0.7629 (mmm) REVERT: Aa 414 MET cc_start: 0.7120 (mtm) cc_final: 0.6454 (mmp) REVERT: Ca 213 ARG cc_start: 0.8498 (mtt180) cc_final: 0.7405 (mtm180) REVERT: Ca 237 MET cc_start: 0.7581 (ttm) cc_final: 0.7006 (ttt) REVERT: Ca 243 ARG cc_start: 0.5114 (mmt90) cc_final: 0.4590 (mtm-85) REVERT: Ba 90 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.6933 (mpt) REVERT: Ba 245 HIS cc_start: 0.8154 (m170) cc_final: 0.7888 (m-70) REVERT: Bc 90 MET cc_start: 0.8488 (mmm) cc_final: 0.8248 (tpt) REVERT: Bc 259 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.6363 (mtm) REVERT: Ab 93 MET cc_start: 0.9118 (ptp) cc_final: 0.8791 (ptm) REVERT: Ab 264 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8409 (mt) REVERT: Ab 273 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8480 (mptp) REVERT: Ab 300 MET cc_start: 0.8766 (mtm) cc_final: 0.8536 (mtm) REVERT: Ac 239 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.5878 (t80) REVERT: Ac 299 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7642 (ttp80) REVERT: Ac 328 ASP cc_start: 0.8643 (m-30) cc_final: 0.8358 (t0) REVERT: Ac 375 ARG cc_start: 0.8600 (mtp85) cc_final: 0.8320 (mtp85) REVERT: Cb 31 MET cc_start: 0.6884 (mtm) cc_final: 0.6523 (mtt) REVERT: Cb 62 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8824 (mttm) REVERT: Cb 213 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7385 (mtm180) REVERT: Cb 237 MET cc_start: 0.7600 (ttm) cc_final: 0.6941 (ttt) REVERT: Cb 243 ARG cc_start: 0.5210 (mmt90) cc_final: 0.4439 (mtm-85) REVERT: Cb 249 ARG cc_start: 0.6671 (mtm-85) cc_final: 0.6289 (mtm110) REVERT: Cc 52 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7862 (pp-130) REVERT: Cc 157 MET cc_start: 0.6990 (ttp) cc_final: 0.6650 (mmt) REVERT: Cc 185 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8851 (mtm) REVERT: Cc 213 ARG cc_start: 0.8163 (mtt180) cc_final: 0.6991 (mtm180) REVERT: Cc 237 MET cc_start: 0.7467 (ttm) cc_final: 0.6762 (ttt) REVERT: Cc 249 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.6879 (mtm110) outliers start: 50 outliers final: 27 residues processed: 281 average time/residue: 1.7622 time to fit residues: 575.2616 Evaluate side-chains 275 residues out of total 2157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 79 GLU Chi-restraints excluded: chain Aa residue 80 THR Chi-restraints excluded: chain Aa residue 108 GLN Chi-restraints excluded: chain Aa residue 117 GLU Chi-restraints excluded: chain Aa residue 137 HIS Chi-restraints excluded: chain Aa residue 145 GLN Chi-restraints excluded: chain Aa residue 252 SER Chi-restraints excluded: chain Aa residue 283 SER Chi-restraints excluded: chain Ca residue 60 ASP Chi-restraints excluded: chain Ca residue 62 LYS Chi-restraints excluded: chain Ba residue 90 MET Chi-restraints excluded: chain Ba residue 132 PHE Chi-restraints excluded: chain Bb residue 153 THR Chi-restraints excluded: chain Bb residue 249 VAL Chi-restraints excluded: chain Bc residue 158 THR Chi-restraints excluded: chain Bc residue 259 MET Chi-restraints excluded: chain Ab residue 80 THR Chi-restraints excluded: chain Ab residue 140 THR Chi-restraints excluded: chain Ab residue 162 SER Chi-restraints excluded: chain Ab residue 264 LEU Chi-restraints excluded: chain Ab residue 273 LYS Chi-restraints excluded: chain Ab residue 283 SER Chi-restraints excluded: chain Ab residue 305 THR Chi-restraints excluded: chain Ab residue 334 THR Chi-restraints excluded: chain Ab residue 405 ILE Chi-restraints excluded: chain Ac residue 162 SER Chi-restraints excluded: chain Ac residue 239 PHE Chi-restraints excluded: chain Ac residue 283 SER Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Cb residue 62 LYS Chi-restraints excluded: chain Cb residue 74 VAL Chi-restraints excluded: chain Cb residue 131 LEU Chi-restraints excluded: chain Cb residue 171 ILE Chi-restraints excluded: chain Cc residue 40 ILE Chi-restraints excluded: chain Cc residue 52 MET Chi-restraints excluded: chain Cc residue 74 VAL Chi-restraints excluded: chain Cc residue 131 LEU Chi-restraints excluded: chain Cc residue 185 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 95 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 189 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Bc 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.160642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.127527 restraints weight = 22310.154| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.28 r_work: 0.3175 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.7483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21303 Z= 0.130 Angle : 0.583 8.081 29088 Z= 0.302 Chirality : 0.046 0.411 3132 Planarity : 0.006 0.080 3609 Dihedral : 4.714 46.968 2793 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.75 % Rotamer: Outliers : 1.95 % Allowed : 24.90 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2523 helix: 1.52 (0.15), residues: 1218 sheet: 0.97 (0.24), residues: 375 loop : -0.37 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPCc 159 HIS 0.006 0.001 HISCc 45 PHE 0.036 0.001 PHECc 226 TYR 0.020 0.001 TYRBa 184 ARG 0.007 0.000 ARGAa 375 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 1116) hydrogen bonds : angle 4.73350 ( 3240) covalent geometry : bond 0.00305 (21303) covalent geometry : angle 0.58311 (29088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15647.85 seconds wall clock time: 268 minutes 50.70 seconds (16130.70 seconds total)