Starting phenix.real_space_refine on Fri Sep 19 02:09:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl5_45662/09_2025/9cl5_45662.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl5_45662/09_2025/9cl5_45662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cl5_45662/09_2025/9cl5_45662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl5_45662/09_2025/9cl5_45662.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cl5_45662/09_2025/9cl5_45662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl5_45662/09_2025/9cl5_45662.map" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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 6 5.60 5 S 81 5.16 5 C 14193 2.51 5 N 3510 2.21 5 O 4482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22272 Number of models: 1 Model: "" Number of chains: 18 Chain: "Ba" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1974 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 11, 'TRANS': 232} Chain: "Aa" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3026 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 364} Chain: "Ca" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1982 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 9, 'TRANS': 231} Chain: "Da" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 167 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "Aa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "Ca" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "Ba" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "Aa" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 167 Classifications: {'water': 167} Link IDs: {None: 166} Chain: "Ca" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "Da" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Bb" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "Bc" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "Ab" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 166 Classifications: {'water': 166} Link IDs: {None: 165} Chain: "Ac" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 167 Classifications: {'water': 167} Link IDs: {None: 166} Chain: "Cb" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "Cc" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "Db" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Dc" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: Bb, Bc, Ab, Ac, Cb, Cc, Db, Dc Time building chain proxies: 4.70, per 1000 atoms: 0.21 Number of scatterers: 22272 At special positions: 0 Unit cell: (117.86, 112.88, 121.18, 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 6 28.99 S 81 16.00 O 4482 8.00 N 3510 7.00 C 14193 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: 1.80 Conformation dependent library (CDL) restraints added in 952.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 21 sheets defined 56.7% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'Ba' and resid 15 through 50 Processing helix chain 'Ba' and resid 50 through 56 removed outlier: 3.697A pdb=" N ASPBa 54 " --> pdb=" O ALABa 50 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRPBa 56 " --> pdb=" O ASPBa 52 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 57 through 60 Processing helix chain 'Ba' and resid 63 through 89 Proline residue: Ba 70 - end of helix removed outlier: 4.462A pdb=" N THRBa 75 " --> pdb=" O ILEBa 71 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N PHEBa 76 " --> pdb=" O LEUBa 72 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYSBa 77 " --> pdb=" O GLYBa 73 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 92 through 112 Processing helix chain 'Ba' and resid 129 through 144 Processing helix chain 'Ba' and resid 145 through 160 removed outlier: 4.214A pdb=" N SERBa 154 " --> pdb=" O ALABa 150 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 160 through 166 Processing helix chain 'Ba' and resid 167 through 173 removed outlier: 4.537A pdb=" N ALABa 170 " --> pdb=" O PROBa 167 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALABa 171 " --> pdb=" O ALABa 168 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 185 through 193 Processing helix chain 'Ba' and resid 216 through 244 removed outlier: 3.663A pdb=" N METBa 231 " --> pdb=" O PHEBa 227 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHEBa 238 " --> pdb=" O PHEBa 234 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 30 through 34 Processing helix chain 'Aa' and resid 35 through 41 Processing helix chain 'Aa' and resid 158 through 162 Processing helix chain 'Aa' and resid 180 through 207 Proline residue: Aa 190 - end of helix Processing helix chain 'Aa' and resid 208 through 217 Processing helix chain 'Aa' and resid 219 through 224 removed outlier: 3.896A pdb=" N VALAa 223 " --> pdb=" O LYSAa 219 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILEAa 224 " --> pdb=" O ALAAa 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aa' and resid 219 through 224' Processing helix chain 'Aa' and resid 225 through 254 Processing helix chain 'Aa' and resid 370 through 375 Processing helix chain 'Aa' and resid 376 through 383 removed outlier: 3.509A pdb=" N ASPAa 379 " --> pdb=" O ARGAa 376 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEUAa 380 " --> pdb=" O LEUAa 377 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALAAa 381 " --> pdb=" O SERAa 378 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 21 through 46 Processing helix chain 'Ca' and resid 55 through 62 removed outlier: 3.659A pdb=" N GLNCa 59 " --> pdb=" O ALACa 55 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 62 through 87 removed outlier: 3.652A pdb=" N LEUCa 66 " --> pdb=" O TRPCa 62 " (cutoff:3.500A) Proline residue: Ca 71 - end of helix Processing helix chain 'Ca' and resid 91 through 95 removed outlier: 3.601A pdb=" N ALACa 94 " --> pdb=" O ASNCa 91 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 96 through 123 Processing helix chain 'Ca' and resid 123 through 136 removed outlier: 3.525A pdb=" N GLUCa 127 " --> pdb=" O SERCa 123 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLYCa 130 " --> pdb=" O THRCa 126 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 143 through 150 Processing helix chain 'Ca' and resid 152 through 172 Processing helix chain 'Ca' and resid 172 through 177 Processing helix chain 'Ca' and resid 181 through 189 Processing helix chain 'Ca' and resid 192 through 204 removed outlier: 4.604A pdb=" N GLYCa 198 " --> pdb=" O ILECa 194 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEUCa 199 " --> pdb=" O PROCa 195 " (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 227 removed outlier: 3.825A pdb=" N METCa 227 " --> pdb=" O PHECa 223 " (cutoff:3.500A) Processing helix chain 'Ca' and resid 230 through 255 removed outlier: 3.559A pdb=" N ARGCa 241 " --> pdb=" O GLNCa 237 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYSCa 248 " --> pdb=" O ALACa 244 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLUCa 249 " --> pdb=" O LEUCa 245 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLYCa 250 " --> pdb=" O VALCa 246 " (cutoff:3.500A) Processing helix chain 'Da' and resid 3 through 23 Processing helix chain 'Bb' and resid 15 through 50 Processing helix chain 'Bb' and resid 50 through 56 removed outlier: 3.697A pdb=" N ASPBb 54 " --> pdb=" O ALABb 50 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRPBb 56 " --> pdb=" O ASPBb 52 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 57 through 60 Processing helix chain 'Bb' and resid 63 through 89 Proline residue: Bb 70 - end of helix removed outlier: 4.462A pdb=" N THRBb 75 " --> pdb=" O ILEBb 71 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N PHEBb 76 " --> pdb=" O LEUBb 72 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYSBb 77 " --> pdb=" O GLYBb 73 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 92 through 112 Processing helix chain 'Bb' and resid 129 through 144 Processing helix chain 'Bb' and resid 145 through 160 removed outlier: 4.213A pdb=" N SERBb 154 " --> pdb=" O ALABb 150 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 160 through 166 Processing helix chain 'Bb' and resid 167 through 173 removed outlier: 4.536A pdb=" N ALABb 170 " --> pdb=" O PROBb 167 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALABb 171 " --> pdb=" O ALABb 168 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 185 through 193 Processing helix chain 'Bb' and resid 216 through 244 removed outlier: 3.663A pdb=" N METBb 231 " --> pdb=" O PHEBb 227 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHEBb 238 " --> pdb=" O PHEBb 234 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 15 through 50 Processing helix chain 'Bc' and resid 50 through 56 removed outlier: 3.697A pdb=" N ASPBc 54 " --> pdb=" O ALABc 50 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRPBc 56 " --> pdb=" O ASPBc 52 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 57 through 60 Processing helix chain 'Bc' and resid 63 through 89 Proline residue: Bc 70 - end of helix removed outlier: 4.462A pdb=" N THRBc 75 " --> pdb=" O ILEBc 71 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHEBc 76 " --> pdb=" O LEUBc 72 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYSBc 77 " --> pdb=" O GLYBc 73 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 92 through 112 Processing helix chain 'Bc' and resid 129 through 144 Processing helix chain 'Bc' and resid 145 through 160 removed outlier: 4.213A pdb=" N SERBc 154 " --> pdb=" O ALABc 150 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 160 through 166 Processing helix chain 'Bc' and resid 167 through 173 removed outlier: 4.536A pdb=" N ALABc 170 " --> pdb=" O PROBc 167 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ALABc 171 " --> pdb=" O ALABc 168 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 185 through 193 Processing helix chain 'Bc' and resid 216 through 244 removed outlier: 3.664A pdb=" N METBc 231 " --> pdb=" O PHEBc 227 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHEBc 238 " --> pdb=" O PHEBc 234 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 30 through 34 Processing helix chain 'Ab' and resid 35 through 41 Processing helix chain 'Ab' and resid 158 through 162 Processing helix chain 'Ab' and resid 180 through 207 Proline residue: Ab 190 - end of helix Processing helix chain 'Ab' and resid 208 through 217 Processing helix chain 'Ab' and resid 219 through 224 removed outlier: 3.895A pdb=" N VALAb 223 " --> pdb=" O LYSAb 219 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILEAb 224 " --> pdb=" O ALAAb 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ab' and resid 219 through 224' Processing helix chain 'Ab' and resid 225 through 254 Processing helix chain 'Ab' and resid 370 through 375 Processing helix chain 'Ab' and resid 376 through 383 removed outlier: 3.510A pdb=" N ASPAb 379 " --> pdb=" O ARGAb 376 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEUAb 380 " --> pdb=" O LEUAb 377 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALAAb 381 " --> pdb=" O SERAb 378 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 30 through 34 Processing helix chain 'Ac' and resid 35 through 41 Processing helix chain 'Ac' and resid 158 through 162 Processing helix chain 'Ac' and resid 180 through 207 Proline residue: Ac 190 - end of helix Processing helix chain 'Ac' and resid 208 through 217 Processing helix chain 'Ac' and resid 219 through 224 removed outlier: 3.896A pdb=" N VALAc 223 " --> pdb=" O LYSAc 219 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILEAc 224 " --> pdb=" O ALAAc 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 219 through 224' Processing helix chain 'Ac' and resid 225 through 254 Processing helix chain 'Ac' and resid 370 through 375 Processing helix chain 'Ac' and resid 376 through 383 removed outlier: 3.510A pdb=" N ASPAc 379 " --> pdb=" O ARGAc 376 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEUAc 380 " --> pdb=" O LEUAc 377 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALAAc 381 " --> pdb=" O SERAc 378 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 21 through 46 Processing helix chain 'Cb' and resid 55 through 62 removed outlier: 3.659A pdb=" N GLNCb 59 " --> pdb=" O ALACb 55 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 62 through 87 removed outlier: 3.651A pdb=" N LEUCb 66 " --> pdb=" O TRPCb 62 " (cutoff:3.500A) Proline residue: Cb 71 - end of helix Processing helix chain 'Cb' and resid 91 through 95 removed outlier: 3.601A pdb=" N ALACb 94 " --> pdb=" O ASNCb 91 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 96 through 123 Processing helix chain 'Cb' and resid 123 through 136 removed outlier: 3.525A pdb=" N GLUCb 127 " --> pdb=" O SERCb 123 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLYCb 130 " --> pdb=" O THRCb 126 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 143 through 150 Processing helix chain 'Cb' and resid 152 through 172 Processing helix chain 'Cb' and resid 172 through 177 Processing helix chain 'Cb' and resid 181 through 189 Processing helix chain 'Cb' and resid 192 through 204 removed outlier: 4.604A pdb=" N GLYCb 198 " --> pdb=" O ILECb 194 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEUCb 199 " --> pdb=" O PROCb 195 " (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 227 removed outlier: 3.826A pdb=" N METCb 227 " --> pdb=" O PHECb 223 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 230 through 255 removed outlier: 3.558A pdb=" N ARGCb 241 " --> pdb=" O GLNCb 237 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYSCb 248 " --> pdb=" O ALACb 244 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLUCb 249 " --> pdb=" O LEUCb 245 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLYCb 250 " --> pdb=" O VALCb 246 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 21 through 46 Processing helix chain 'Cc' and resid 55 through 62 removed outlier: 3.659A pdb=" N GLNCc 59 " --> pdb=" O ALACc 55 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 62 through 87 removed outlier: 3.652A pdb=" N LEUCc 66 " --> pdb=" O TRPCc 62 " (cutoff:3.500A) Proline residue: Cc 71 - end of helix Processing helix chain 'Cc' and resid 91 through 95 removed outlier: 3.601A pdb=" N ALACc 94 " --> pdb=" O ASNCc 91 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 96 through 123 Processing helix chain 'Cc' and resid 123 through 136 removed outlier: 3.525A pdb=" N GLUCc 127 " --> pdb=" O SERCc 123 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLYCc 130 " --> pdb=" O THRCc 126 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 143 through 150 Processing helix chain 'Cc' and resid 152 through 172 Processing helix chain 'Cc' and resid 172 through 177 Processing helix chain 'Cc' and resid 181 through 189 Processing helix chain 'Cc' and resid 192 through 204 removed outlier: 4.603A pdb=" N GLYCc 198 " --> pdb=" O ILECc 194 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEUCc 199 " --> pdb=" O PROCc 195 " (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 227 removed outlier: 3.825A pdb=" N METCc 227 " --> pdb=" O PHECc 223 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 230 through 255 removed outlier: 3.559A pdb=" N ARGCc 241 " --> pdb=" O GLNCc 237 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYSCc 248 " --> pdb=" O ALACc 244 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLUCc 249 " --> pdb=" O LEUCc 245 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLYCc 250 " --> pdb=" O VALCc 246 " (cutoff:3.500A) Processing helix chain 'Db' and resid 3 through 23 Processing helix chain 'Dc' and resid 3 through 23 Processing sheet with id=AA1, first strand: chain 'Ba' and resid 175 through 177 Processing sheet with id=AA2, first strand: chain 'Ba' and resid 248 through 249 Processing sheet with id=AA3, first strand: chain 'Aa' and resid 43 through 50 removed outlier: 4.381A pdb=" N VALAa 48 " --> pdb=" O SERAa 64 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SERAa 64 " --> pdb=" O VALAa 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TRPAa 50 " --> pdb=" O VALAa 62 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VALAa 62 " --> pdb=" O TRPAa 50 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALAAa 119 " --> pdb=" O ILEAa 101 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILEAa 101 " --> pdb=" O ALAAa 119 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SERAa 121 " --> pdb=" O GLNAa 99 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLNAa 99 " --> pdb=" O SERAa 121 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASNAa 123 " --> pdb=" O THRAa 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Aa' and resid 54 through 56 removed outlier: 4.454A pdb=" N ALAAa 136 " --> pdb=" O GLYAa 148 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLYAa 150 " --> pdb=" O VALAa 134 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VALAa 134 " --> pdb=" O GLYAa 150 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TRPAa 152 " --> pdb=" O TRPAa 132 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TRPAa 132 " --> pdb=" O TRPAa 152 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLUAa 154 " --> pdb=" O GLYAa 130 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLYAa 130 " --> pdb=" O GLUAa 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Aa' and resid 165 through 167 Processing sheet with id=AA6, first strand: chain 'Aa' and resid 348 through 349 removed outlier: 5.302A pdb=" N GLUAa 299 " --> pdb=" O LYSAa 294 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLYAa 290 " --> pdb=" O ASNAa 303 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYSAa 305 " --> pdb=" O LEUAa 288 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEUAa 288 " --> pdb=" O LYSAa 305 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYSAa 307 " --> pdb=" O THRAa 286 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THRAa 286 " --> pdb=" O LYSAa 307 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ILEAa 411 " --> pdb=" O ASNAa 289 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLYAa 291 " --> pdb=" O ILEAa 411 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYSAa 413 " --> pdb=" O GLYAa 291 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYRAa 293 " --> pdb=" O LYSAa 413 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Aa' and resid 343 through 344 removed outlier: 5.657A pdb=" N LEUAa 316 " --> pdb=" O PHEAa 395 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHEAa 395 " --> pdb=" O LEUAa 316 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLUAa 318 " --> pdb=" O PHEAa 393 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Ca' and resid 179 through 180 Processing sheet with id=AA9, first strand: chain 'Bb' and resid 175 through 177 Processing sheet with id=AB1, first strand: chain 'Bc' and resid 175 through 177 Processing sheet with id=AB2, first strand: chain 'Bc' and resid 248 through 249 Processing sheet with id=AB3, first strand: chain 'Ab' and resid 43 through 50 removed outlier: 4.381A pdb=" N VALAb 48 " --> pdb=" O SERAb 64 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SERAb 64 " --> pdb=" O VALAb 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TRPAb 50 " --> pdb=" O VALAb 62 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VALAb 62 " --> pdb=" O TRPAb 50 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALAAb 119 " --> pdb=" O ILEAb 101 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILEAb 101 " --> pdb=" O ALAAb 119 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SERAb 121 " --> pdb=" O GLNAb 99 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLNAb 99 " --> pdb=" O SERAb 121 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASNAb 123 " --> pdb=" O THRAb 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ab' and resid 54 through 56 removed outlier: 4.454A pdb=" N ALAAb 136 " --> pdb=" O GLYAb 148 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLYAb 150 " --> pdb=" O VALAb 134 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VALAb 134 " --> pdb=" O GLYAb 150 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TRPAb 152 " --> pdb=" O TRPAb 132 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TRPAb 132 " --> pdb=" O TRPAb 152 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLUAb 154 " --> pdb=" O GLYAb 130 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLYAb 130 " --> pdb=" O GLUAb 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Ab' and resid 165 through 167 Processing sheet with id=AB6, first strand: chain 'Ab' and resid 348 through 349 removed outlier: 5.302A pdb=" N GLUAb 299 " --> pdb=" O LYSAb 294 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLYAb 290 " --> pdb=" O ASNAb 303 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYSAb 305 " --> pdb=" O LEUAb 288 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEUAb 288 " --> pdb=" O LYSAb 305 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYSAb 307 " --> pdb=" O THRAb 286 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THRAb 286 " --> pdb=" O LYSAb 307 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ILEAb 411 " --> pdb=" O ASNAb 289 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLYAb 291 " --> pdb=" O ILEAb 411 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYSAb 413 " --> pdb=" O GLYAb 291 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYRAb 293 " --> pdb=" O LYSAb 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ab' and resid 343 through 344 removed outlier: 5.657A pdb=" N LEUAb 316 " --> pdb=" O PHEAb 395 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHEAb 395 " --> pdb=" O LEUAb 316 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLUAb 318 " --> pdb=" O PHEAb 393 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Ac' and resid 43 through 50 removed outlier: 4.381A pdb=" N VALAc 48 " --> pdb=" O SERAc 64 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SERAc 64 " --> pdb=" O VALAc 48 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TRPAc 50 " --> pdb=" O VALAc 62 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VALAc 62 " --> pdb=" O TRPAc 50 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALAAc 119 " --> pdb=" O ILEAc 101 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILEAc 101 " --> pdb=" O ALAAc 119 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SERAc 121 " --> pdb=" O GLNAc 99 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLNAc 99 " --> pdb=" O SERAc 121 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASNAc 123 " --> pdb=" O THRAc 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Ac' and resid 54 through 56 removed outlier: 4.454A pdb=" N ALAAc 136 " --> pdb=" O GLYAc 148 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLYAc 150 " --> pdb=" O VALAc 134 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VALAc 134 " --> pdb=" O GLYAc 150 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TRPAc 152 " --> pdb=" O TRPAc 132 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TRPAc 132 " --> pdb=" O TRPAc 152 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLUAc 154 " --> pdb=" O GLYAc 130 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLYAc 130 " --> pdb=" O GLUAc 154 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Ac' and resid 165 through 167 Processing sheet with id=AC2, first strand: chain 'Ac' and resid 348 through 349 removed outlier: 5.302A pdb=" N GLUAc 299 " --> pdb=" O LYSAc 294 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLYAc 290 " --> pdb=" O ASNAc 303 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYSAc 305 " --> pdb=" O LEUAc 288 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEUAc 288 " --> pdb=" O LYSAc 305 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYSAc 307 " --> pdb=" O THRAc 286 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THRAc 286 " --> pdb=" O LYSAc 307 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ILEAc 411 " --> pdb=" O ASNAc 289 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLYAc 291 " --> pdb=" O ILEAc 411 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LYSAc 413 " --> pdb=" O GLYAc 291 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYRAc 293 " --> pdb=" O LYSAc 413 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Ac' and resid 343 through 344 removed outlier: 5.657A pdb=" N LEUAc 316 " --> pdb=" O PHEAc 395 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHEAc 395 " --> pdb=" O LEUAc 316 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLUAc 318 " --> pdb=" O PHEAc 393 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3519 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: 4.40 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6572 1.34 - 1.46: 4678 1.46 - 1.58: 10722 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 22128 Sorted by residual: bond pdb=" N LEUCc 199 " pdb=" CA LEUCc 199 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 1.02e+01 bond pdb=" N LEUCa 199 " pdb=" CA LEUCa 199 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" N LEUCb 199 " pdb=" CA LEUCb 199 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 9.95e+00 bond pdb=" CA ALAAc 136 " pdb=" CB ALAAc 136 " ideal model delta sigma weight residual 1.529 1.490 0.040 1.43e-02 4.89e+03 7.73e+00 bond pdb=" CA ALAAa 136 " pdb=" CB ALAAa 136 " ideal model delta sigma weight residual 1.529 1.490 0.040 1.43e-02 4.89e+03 7.64e+00 ... (remaining 22123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 29491 2.01 - 4.02: 591 4.02 - 6.03: 116 6.03 - 8.04: 15 8.04 - 10.05: 6 Bond angle restraints: 30219 Sorted by residual: angle pdb=" CA ASPCa 129 " pdb=" CB ASPCa 129 " pdb=" CG ASPCa 129 " ideal model delta sigma weight residual 112.60 122.65 -10.05 1.00e+00 1.00e+00 1.01e+02 angle pdb=" CA ASPCb 129 " pdb=" CB ASPCb 129 " pdb=" CG ASPCb 129 " ideal model delta sigma weight residual 112.60 122.63 -10.03 1.00e+00 1.00e+00 1.01e+02 angle pdb=" CA ASPCc 129 " pdb=" CB ASPCc 129 " pdb=" CG ASPCc 129 " ideal model delta sigma weight residual 112.60 122.62 -10.02 1.00e+00 1.00e+00 1.00e+02 angle pdb=" N GLNCa 128 " pdb=" CA GLNCa 128 " pdb=" C GLNCa 128 " ideal model delta sigma weight residual 112.38 105.46 6.92 1.22e+00 6.72e-01 3.22e+01 angle pdb=" N GLNCc 128 " pdb=" CA GLNCc 128 " pdb=" C GLNCc 128 " ideal model delta sigma weight residual 112.38 105.47 6.91 1.22e+00 6.72e-01 3.21e+01 ... (remaining 30214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 10809 16.95 - 33.90: 1221 33.90 - 50.85: 351 50.85 - 67.80: 102 67.80 - 84.74: 9 Dihedral angle restraints: 12492 sinusoidal: 4827 harmonic: 7665 Sorted by residual: dihedral pdb=" CA TYRAc 46 " pdb=" C TYRAc 46 " pdb=" N ASPAc 47 " pdb=" CA ASPAc 47 " ideal model delta harmonic sigma weight residual -180.00 -133.04 -46.96 0 5.00e+00 4.00e-02 8.82e+01 dihedral pdb=" CA TYRAb 46 " pdb=" C TYRAb 46 " pdb=" N ASPAb 47 " pdb=" CA ASPAb 47 " ideal model delta harmonic sigma weight residual -180.00 -133.05 -46.95 0 5.00e+00 4.00e-02 8.82e+01 dihedral pdb=" CA TYRAa 46 " pdb=" C TYRAa 46 " pdb=" N ASPAa 47 " pdb=" CA ASPAa 47 " ideal model delta harmonic sigma weight residual -180.00 -133.08 -46.92 0 5.00e+00 4.00e-02 8.81e+01 ... (remaining 12489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2450 0.047 - 0.094: 647 0.094 - 0.141: 206 0.141 - 0.188: 12 0.188 - 0.234: 12 Chirality restraints: 3327 Sorted by residual: chirality pdb=" CA ALAAa 136 " pdb=" N ALAAa 136 " pdb=" C ALAAa 136 " pdb=" CB ALAAa 136 " both_signs ideal model delta sigma weight residual False 2.48 2.72 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ALAAb 136 " pdb=" N ALAAb 136 " pdb=" C ALAAb 136 " pdb=" CB ALAAb 136 " both_signs ideal model delta sigma weight residual False 2.48 2.72 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ALAAc 136 " pdb=" N ALAAc 136 " pdb=" C ALAAc 136 " pdb=" CB ALAAc 136 " both_signs ideal model delta sigma weight residual False 2.48 2.72 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3324 not shown) Planarity restraints: 3756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGDb 22 " 0.765 9.50e-02 1.11e+02 3.43e-01 7.15e+01 pdb=" NE ARGDb 22 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARGDb 22 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARGDb 22 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGDb 22 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGDa 22 " 0.764 9.50e-02 1.11e+02 3.43e-01 7.15e+01 pdb=" NE ARGDa 22 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARGDa 22 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARGDa 22 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGDa 22 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGDc 22 " 0.764 9.50e-02 1.11e+02 3.43e-01 7.14e+01 pdb=" NE ARGDc 22 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARGDc 22 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARGDc 22 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARGDc 22 " 0.023 2.00e-02 2.50e+03 ... (remaining 3753 not shown) Histogram of nonbonded interaction distances: 0.06 - 1.02: 12 1.02 - 1.99: 3 1.99 - 2.96: 10925 2.96 - 3.93: 64611 3.93 - 4.90: 128878 Warning: very small nonbonded interaction distances. Nonbonded interactions: 204429 Sorted by model distance: nonbonded pdb=" O HOHBa 326 " pdb=" O HOHBa 329 " model vdw 0.056 3.040 nonbonded pdb=" O HOHBb 326 " pdb=" O HOHBb 329 " model vdw 0.073 3.040 nonbonded pdb=" O HOHBc 326 " pdb=" O HOHBc 329 " model vdw 0.075 3.040 nonbonded pdb=" O HOHAb 656 " pdb=" O HOHAb 716 " model vdw 0.437 3.040 nonbonded pdb=" O HOHAa 655 " pdb=" O HOHAa 718 " model vdw 0.446 3.040 ... (remaining 204424 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: 0.04 Found NCS groups: ncs_group { reference = chain 'Ba' selection = chain 'Bb' selection = chain 'Bc' } ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' } ncs_group { reference = chain 'Ca' selection = chain 'Cb' selection = chain 'Cc' } ncs_group { reference = chain 'Da' selection = chain 'Db' selection = chain 'Dc' } 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22128 Z= 0.245 Angle : 0.684 10.047 30219 Z= 0.427 Chirality : 0.047 0.234 3327 Planarity : 0.011 0.343 3756 Dihedral : 16.195 84.745 7596 Min Nonbonded Distance : 0.056 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.04 % Favored : 96.73 % Rotamer: Outliers : 2.15 % Allowed : 14.94 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.16), residues: 2664 helix: 1.14 (0.14), residues: 1332 sheet: 0.82 (0.26), residues: 354 loop : -0.44 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAc 81 TYR 0.022 0.002 TYRCc 157 PHE 0.010 0.001 PHEBc 193 TRP 0.016 0.001 TRPAb 198 HIS 0.008 0.001 HISCc 204 Details of bonding type rmsd covalent geometry : bond 0.00396 (22128) covalent geometry : angle 0.68358 (30219) hydrogen bonds : bond 0.14194 ( 1212) hydrogen bonds : angle 6.56989 ( 3519) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 507 time to evaluate : 0.810 Fit side-chains REVERT: Aa 302 ILE cc_start: 0.7059 (pt) cc_final: 0.6790 (pt) REVERT: Aa 373 ASP cc_start: 0.7150 (t0) cc_final: 0.6807 (t0) outliers start: 48 outliers final: 8 residues processed: 535 average time/residue: 0.5636 time to fit residues: 350.4443 Evaluate side-chains 301 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 293 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 276 THR Chi-restraints excluded: chain Ca residue 147 ILE Chi-restraints excluded: chain Da residue 19 THR Chi-restraints excluded: chain Ab residue 209 ILE Chi-restraints excluded: chain Cb residue 157 TYR Chi-restraints excluded: chain Cb residue 183 PHE Chi-restraints excluded: chain Cc residue 217 LEU Chi-restraints excluded: chain Db residue 19 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.0010 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 45 HIS ** Ba 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 109 GLN Bc 164 ASN Bc 178 GLN Ab 44 ASN Ab 68 HIS Ab 188 HIS ** Ab 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 308 ASN Ac 308 ASN Ac 309 ASN Ac 387 GLN Cb 109 GLN ** Cb 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 109 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109029 restraints weight = 25498.171| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.65 r_work: 0.3230 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22128 Z= 0.197 Angle : 0.740 11.619 30219 Z= 0.387 Chirality : 0.047 0.172 3327 Planarity : 0.007 0.183 3756 Dihedral : 5.739 49.661 2911 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.75 % Favored : 96.06 % Rotamer: Outliers : 6.24 % Allowed : 16.60 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.16), residues: 2664 helix: 1.10 (0.14), residues: 1335 sheet: 0.21 (0.25), residues: 387 loop : -0.58 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARGDc 22 TYR 0.030 0.002 TYRCb 157 PHE 0.030 0.002 PHECc 224 TRP 0.035 0.002 TRPAb 198 HIS 0.012 0.002 HISBa 45 Details of bonding type rmsd covalent geometry : bond 0.00434 (22128) covalent geometry : angle 0.74006 (30219) hydrogen bonds : bond 0.04551 ( 1212) hydrogen bonds : angle 5.19422 ( 3519) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 360 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 60 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7068 (mm-30) REVERT: Aa 160 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8288 (ttmt) REVERT: Aa 256 ARG cc_start: 0.7164 (mtm110) cc_final: 0.6715 (mmt180) REVERT: Aa 282 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6428 (mt-10) REVERT: Aa 287 GLU cc_start: 0.7642 (tp30) cc_final: 0.7048 (tm-30) REVERT: Aa 345 ASP cc_start: 0.7414 (p0) cc_final: 0.6070 (t0) REVERT: Ca 43 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6463 (tp40) REVERT: Ca 92 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6673 (p) REVERT: Da 15 ILE cc_start: 0.8428 (mm) cc_final: 0.8197 (mt) REVERT: Bb 14 ASN cc_start: 0.7147 (t0) cc_final: 0.6933 (m-40) REVERT: Bb 61 ASP cc_start: 0.8430 (p0) cc_final: 0.8227 (p0) REVERT: Bb 108 ASN cc_start: 0.6967 (t0) cc_final: 0.6493 (t0) REVERT: Bc 211 ARG cc_start: 0.7161 (tpt-90) cc_final: 0.6852 (mmm160) REVERT: Ab 400 LYS cc_start: 0.7963 (tttm) cc_final: 0.7426 (tmtt) REVERT: Ac 368 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8317 (tp40) REVERT: Cb 213 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.7012 (m-10) REVERT: Cc 242 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5961 (mt) REVERT: Db 1 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6009 (mmp) REVERT: Dc 19 THR cc_start: 0.7769 (t) cc_final: 0.7554 (p) outliers start: 139 outliers final: 27 residues processed: 446 average time/residue: 0.5602 time to fit residues: 289.9751 Evaluate side-chains 302 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 33 SER Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 60 GLU Chi-restraints excluded: chain Aa residue 63 LEU Chi-restraints excluded: chain Aa residue 97 THR Chi-restraints excluded: chain Aa residue 204 VAL Chi-restraints excluded: chain Aa residue 282 GLU Chi-restraints excluded: chain Aa residue 353 THR Chi-restraints excluded: chain Ca residue 43 GLN Chi-restraints excluded: chain Ca residue 92 VAL Chi-restraints excluded: chain Ca residue 196 ASN Chi-restraints excluded: chain Ca residue 253 LEU Chi-restraints excluded: chain Bc residue 49 THR Chi-restraints excluded: chain Bc residue 176 THR Chi-restraints excluded: chain Ab residue 57 VAL Chi-restraints excluded: chain Ab residue 95 VAL Chi-restraints excluded: chain Ab residue 276 THR Chi-restraints excluded: chain Ab residue 320 THR Chi-restraints excluded: chain Ab residue 334 THR Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 54 THR Chi-restraints excluded: chain Ac residue 140 VAL Chi-restraints excluded: chain Ac residue 173 THR Chi-restraints excluded: chain Ac residue 252 SER Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Ac residue 368 GLN Chi-restraints excluded: chain Ac residue 415 VAL Chi-restraints excluded: chain Cb residue 118 ILE Chi-restraints excluded: chain Cb residue 183 PHE Chi-restraints excluded: chain Cb residue 213 PHE Chi-restraints excluded: chain Cc residue 70 ILE Chi-restraints excluded: chain Cc residue 217 LEU Chi-restraints excluded: chain Cc residue 242 ILE Chi-restraints excluded: chain Db residue 1 MET Chi-restraints excluded: chain Db residue 4 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 27 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 204 optimal weight: 0.5980 chunk 226 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ba 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 174 GLN ** Aa 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 109 GLN Ca 146 HIS ** Bc 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 164 ASN Ab 139 ASN Ab 265 GLN Ab 303 ASN Ab 308 ASN Ab 368 GLN Ac 44 ASN Ac 123 ASN Ac 151 GLN Ac 251 ASN Ac 309 ASN Cb 237 GLN Cc 109 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.090222 restraints weight = 25945.028| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.49 r_work: 0.2938 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.9195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 22128 Z= 0.225 Angle : 0.723 9.952 30219 Z= 0.383 Chirality : 0.048 0.180 3327 Planarity : 0.007 0.071 3756 Dihedral : 5.739 54.276 2902 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 4.44 % Allowed : 19.02 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.16), residues: 2664 helix: 1.22 (0.14), residues: 1323 sheet: 0.68 (0.27), residues: 321 loop : -0.55 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARGAb 214 TYR 0.033 0.002 TYRCb 157 PHE 0.028 0.002 PHEBb 92 TRP 0.055 0.002 TRPCb 219 HIS 0.007 0.002 HISBb 173 Details of bonding type rmsd covalent geometry : bond 0.00519 (22128) covalent geometry : angle 0.72347 (30219) hydrogen bonds : bond 0.06231 ( 1212) hydrogen bonds : angle 5.16966 ( 3519) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 324 time to evaluate : 0.897 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8178 (tpt) REVERT: Ba 247 LYS cc_start: 0.8459 (tttt) cc_final: 0.7984 (ttmm) REVERT: Aa 60 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: Aa 256 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7092 (mmt180) REVERT: Aa 287 GLU cc_start: 0.8241 (tp30) cc_final: 0.7583 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7282 (mtm110) cc_final: 0.7028 (ptp-170) REVERT: Aa 400 LYS cc_start: 0.7947 (ttmt) cc_final: 0.7191 (tttm) REVERT: Ca 43 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7632 (tp40) REVERT: Ca 59 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7592 (mp10) REVERT: Ca 67 TRP cc_start: 0.6698 (m100) cc_final: 0.6042 (m100) REVERT: Bb 247 LYS cc_start: 0.7643 (tttt) cc_final: 0.7182 (ttmm) REVERT: Bc 177 GLU cc_start: 0.8699 (tt0) cc_final: 0.8483 (tt0) REVERT: Bc 247 LYS cc_start: 0.8170 (tttt) cc_final: 0.7946 (ttmm) REVERT: Ab 61 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8311 (ppp) REVERT: Ab 113 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8105 (mm-30) REVERT: Ab 160 LYS cc_start: 0.8443 (pttt) cc_final: 0.8221 (ptmm) REVERT: Ab 287 GLU cc_start: 0.8003 (tt0) cc_final: 0.7539 (tm-30) REVERT: Ab 353 THR cc_start: 0.8622 (m) cc_final: 0.8338 (t) REVERT: Ab 366 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7665 (mtpp) REVERT: Ac 256 ARG cc_start: 0.7893 (mpp-170) cc_final: 0.6874 (mmt180) REVERT: Ac 312 GLN cc_start: 0.8046 (pt0) cc_final: 0.7838 (pt0) REVERT: Ac 330 ASP cc_start: 0.8339 (m-30) cc_final: 0.8136 (m-30) REVERT: Ac 400 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7549 (mtpp) REVERT: Cb 67 TRP cc_start: 0.7742 (m100) cc_final: 0.6288 (m-10) REVERT: Cb 87 THR cc_start: 0.8499 (m) cc_final: 0.8183 (p) REVERT: Cc 57 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6836 (pm20) REVERT: Cc 240 MET cc_start: 0.7933 (ttm) cc_final: 0.7720 (mtp) REVERT: Db 4 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7680 (tm) REVERT: Db 22 ARG cc_start: 0.7053 (tpp80) cc_final: 0.6835 (tpp-160) REVERT: Dc 20 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7521 (mp) outliers start: 99 outliers final: 26 residues processed: 386 average time/residue: 0.6631 time to fit residues: 291.9649 Evaluate side-chains 304 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Ba residue 239 MET Chi-restraints excluded: chain Aa residue 47 ASP Chi-restraints excluded: chain Aa residue 54 THR Chi-restraints excluded: chain Aa residue 60 GLU Chi-restraints excluded: chain Aa residue 97 THR Chi-restraints excluded: chain Aa residue 274 GLU Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Ca residue 43 GLN Chi-restraints excluded: chain Ca residue 213 PHE Chi-restraints excluded: chain Ca residue 253 LEU Chi-restraints excluded: chain Da residue 4 LEU Chi-restraints excluded: chain Da residue 21 THR Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Bc residue 49 THR Chi-restraints excluded: chain Bc residue 164 ASN Chi-restraints excluded: chain Bc residue 184 THR Chi-restraints excluded: chain Bc residue 197 SER Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 57 VAL Chi-restraints excluded: chain Ab residue 61 MET Chi-restraints excluded: chain Ab residue 95 VAL Chi-restraints excluded: chain Ab residue 276 THR Chi-restraints excluded: chain Ab residue 295 VAL Chi-restraints excluded: chain Ab residue 320 THR Chi-restraints excluded: chain Ab residue 350 VAL Chi-restraints excluded: chain Ab residue 366 LYS Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Cc residue 95 VAL Chi-restraints excluded: chain Db residue 4 LEU Chi-restraints excluded: chain Dc residue 20 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 173 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 233 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 256 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 172 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 164 ASN Aa 44 ASN Aa 68 HIS ** Aa 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 109 GLN Ca 196 ASN Bb 108 ASN Bb 173 HIS Bc 14 ASN Bc 87 ASN Bc 108 ASN Bc 164 ASN Ab 139 ASN Ac 34 GLN Ac 68 HIS Ac 104 GLN Ac 308 ASN ** Cb 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 109 GLN Cc 237 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.110163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.087398 restraints weight = 26092.335| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.67 r_work: 0.2900 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.9461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22128 Z= 0.156 Angle : 0.605 9.625 30219 Z= 0.315 Chirality : 0.045 0.197 3327 Planarity : 0.005 0.071 3756 Dihedral : 5.340 53.011 2898 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.55 % Rotamer: Outliers : 3.01 % Allowed : 19.16 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.16), residues: 2664 helix: 1.55 (0.14), residues: 1329 sheet: 0.45 (0.25), residues: 366 loop : -0.27 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAa 298 TYR 0.026 0.002 TYRCb 157 PHE 0.021 0.002 PHECb 221 TRP 0.019 0.001 TRPAa 198 HIS 0.004 0.001 HISAc 135 Details of bonding type rmsd covalent geometry : bond 0.00365 (22128) covalent geometry : angle 0.60483 (30219) hydrogen bonds : bond 0.05053 ( 1212) hydrogen bonds : angle 4.89051 ( 3519) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 283 time to evaluate : 0.828 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8362 (tpt) REVERT: Ba 247 LYS cc_start: 0.8571 (tttt) cc_final: 0.8182 (ttmm) REVERT: Aa 60 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: Aa 256 ARG cc_start: 0.7671 (mtm110) cc_final: 0.7236 (mmt180) REVERT: Aa 287 GLU cc_start: 0.8454 (tp30) cc_final: 0.7894 (tm-30) REVERT: Aa 350 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8588 (m) REVERT: Aa 400 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7342 (tttm) REVERT: Ca 43 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7864 (tp40) REVERT: Ca 59 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7948 (mp10) REVERT: Ca 67 TRP cc_start: 0.6901 (m100) cc_final: 0.6173 (m100) REVERT: Ca 68 THR cc_start: 0.8790 (m) cc_final: 0.8533 (m) REVERT: Da 1 MET cc_start: 0.8498 (mmm) cc_final: 0.8038 (tpp) REVERT: Da 4 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8207 (tt) REVERT: Bb 247 LYS cc_start: 0.8160 (tttt) cc_final: 0.7807 (ttmm) REVERT: Bc 247 LYS cc_start: 0.8385 (tttt) cc_final: 0.8167 (ttmm) REVERT: Bc 248 VAL cc_start: 0.8464 (m) cc_final: 0.8230 (t) REVERT: Ab 61 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8529 (ppp) REVERT: Ab 160 LYS cc_start: 0.8677 (pttt) cc_final: 0.8417 (ptmm) REVERT: Ab 256 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7152 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8189 (tt0) cc_final: 0.7768 (tm-30) REVERT: Ab 353 THR cc_start: 0.8756 (m) cc_final: 0.8529 (t) REVERT: Ab 366 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7826 (mtpp) REVERT: Ac 59 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: Ac 116 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8552 (mttm) REVERT: Ac 256 ARG cc_start: 0.8092 (mpp-170) cc_final: 0.7233 (mmt180) REVERT: Ac 299 GLU cc_start: 0.7727 (mp0) cc_final: 0.7347 (mt-10) REVERT: Ac 400 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7753 (mtpp) REVERT: Ac 415 VAL cc_start: 0.8198 (p) cc_final: 0.7799 (m) REVERT: Cb 22 ARG cc_start: 0.8421 (mtp180) cc_final: 0.8220 (mpp80) REVERT: Cb 87 THR cc_start: 0.8569 (m) cc_final: 0.8334 (p) REVERT: Cb 210 GLU cc_start: 0.7169 (mp0) cc_final: 0.6539 (mp0) REVERT: Cb 214 VAL cc_start: 0.7448 (t) cc_final: 0.7179 (m) REVERT: Cc 57 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7147 (pm20) REVERT: Cc 86 LYS cc_start: 0.8379 (tmmt) cc_final: 0.8012 (tmmt) REVERT: Cc 210 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6822 (mp0) REVERT: Db 1 MET cc_start: 0.8176 (mmm) cc_final: 0.7795 (mmm) REVERT: Db 4 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7911 (tt) REVERT: Db 19 THR cc_start: 0.7577 (m) cc_final: 0.7115 (p) outliers start: 67 outliers final: 27 residues processed: 322 average time/residue: 0.6596 time to fit residues: 240.9849 Evaluate side-chains 307 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 164 ASN Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Ba residue 239 MET Chi-restraints excluded: chain Aa residue 54 THR Chi-restraints excluded: chain Aa residue 60 GLU Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Ca residue 43 GLN Chi-restraints excluded: chain Ca residue 118 ILE Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Da residue 4 LEU Chi-restraints excluded: chain Bb residue 58 ASP Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Ab residue 47 ASP Chi-restraints excluded: chain Ab residue 61 MET Chi-restraints excluded: chain Ab residue 256 ARG Chi-restraints excluded: chain Ab residue 276 THR Chi-restraints excluded: chain Ab residue 320 THR Chi-restraints excluded: chain Ab residue 366 LYS Chi-restraints excluded: chain Ac residue 47 ASP Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 54 THR Chi-restraints excluded: chain Ac residue 59 GLU Chi-restraints excluded: chain Ac residue 116 LYS Chi-restraints excluded: chain Ac residue 287 GLU Chi-restraints excluded: chain Ac residue 292 VAL Chi-restraints excluded: chain Ac residue 320 THR Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Cb residue 186 VAL Chi-restraints excluded: chain Cb residue 212 LEU Chi-restraints excluded: chain Cb residue 217 LEU Chi-restraints excluded: chain Cb residue 219 TRP Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cc residue 118 ILE Chi-restraints excluded: chain Cc residue 246 VAL Chi-restraints excluded: chain Db residue 4 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 169 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 308 ASN Aa 368 GLN Ca 196 ASN Bc 14 ASN Bc 164 ASN Ac 104 GLN ** Cb 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.085222 restraints weight = 26074.933| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.65 r_work: 0.2883 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.9743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 22128 Z= 0.163 Angle : 0.608 10.128 30219 Z= 0.316 Chirality : 0.045 0.170 3327 Planarity : 0.005 0.058 3756 Dihedral : 5.291 54.490 2898 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 3.23 % Allowed : 18.30 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.16), residues: 2664 helix: 1.68 (0.14), residues: 1326 sheet: 0.37 (0.25), residues: 399 loop : -0.31 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGAa 298 TYR 0.026 0.002 TYRCb 157 PHE 0.024 0.002 PHECb 221 TRP 0.017 0.001 TRPAc 198 HIS 0.006 0.001 HISBb 173 Details of bonding type rmsd covalent geometry : bond 0.00388 (22128) covalent geometry : angle 0.60772 (30219) hydrogen bonds : bond 0.05309 ( 1212) hydrogen bonds : angle 4.89955 ( 3519) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 0.925 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8327 (tpt) REVERT: Ba 247 LYS cc_start: 0.8502 (tttt) cc_final: 0.8162 (ttmm) REVERT: Aa 60 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: Aa 256 ARG cc_start: 0.7680 (mtm110) cc_final: 0.7156 (mtp180) REVERT: Aa 287 GLU cc_start: 0.8453 (tp30) cc_final: 0.7937 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7801 (mtm110) cc_final: 0.7424 (ptp-170) REVERT: Aa 350 VAL cc_start: 0.8881 (OUTLIER) cc_final: 0.8582 (m) REVERT: Aa 400 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7404 (tttm) REVERT: Ca 43 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7848 (tp40) REVERT: Ca 59 GLN cc_start: 0.8311 (mm-40) cc_final: 0.8014 (mp10) REVERT: Ca 67 TRP cc_start: 0.6801 (m100) cc_final: 0.6045 (m100) REVERT: Ca 68 THR cc_start: 0.8882 (m) cc_final: 0.8665 (m) REVERT: Ca 87 THR cc_start: 0.8457 (m) cc_final: 0.8116 (p) REVERT: Ca 92 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7516 (p) REVERT: Ca 213 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7662 (m-10) REVERT: Da 1 MET cc_start: 0.8763 (mmm) cc_final: 0.8417 (tpp) REVERT: Da 4 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8204 (tt) REVERT: Bb 206 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8642 (pt0) REVERT: Bb 247 LYS cc_start: 0.8322 (tttt) cc_final: 0.7977 (ttmm) REVERT: Bc 247 LYS cc_start: 0.8423 (tttt) cc_final: 0.8177 (ttmm) REVERT: Bc 248 VAL cc_start: 0.8465 (m) cc_final: 0.8210 (t) REVERT: Ab 61 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8549 (ppp) REVERT: Ab 158 ASP cc_start: 0.8222 (t0) cc_final: 0.7943 (t0) REVERT: Ab 160 LYS cc_start: 0.8687 (pttt) cc_final: 0.8427 (ttpp) REVERT: Ab 256 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7051 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8228 (tt0) cc_final: 0.7793 (tm-30) REVERT: Ab 353 THR cc_start: 0.8713 (m) cc_final: 0.8486 (t) REVERT: Ab 366 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7768 (mtpp) REVERT: Ac 59 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: Ac 256 ARG cc_start: 0.8084 (mpp-170) cc_final: 0.7229 (mmt180) REVERT: Ac 299 GLU cc_start: 0.7607 (mp0) cc_final: 0.7237 (mt-10) REVERT: Ac 362 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: Ac 400 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7771 (mtpp) REVERT: Ac 415 VAL cc_start: 0.8183 (p) cc_final: 0.7913 (m) REVERT: Cb 87 THR cc_start: 0.8545 (m) cc_final: 0.8311 (p) REVERT: Cb 210 GLU cc_start: 0.7333 (mp0) cc_final: 0.6485 (mp0) REVERT: Cb 214 VAL cc_start: 0.7705 (t) cc_final: 0.7398 (m) REVERT: Cc 57 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7058 (pm20) REVERT: Cc 59 GLN cc_start: 0.8426 (tp40) cc_final: 0.7689 (mm-40) REVERT: Cc 86 LYS cc_start: 0.8482 (tmmt) cc_final: 0.8088 (ttmt) REVERT: Cc 210 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6843 (mp0) REVERT: Db 1 MET cc_start: 0.8249 (mmm) cc_final: 0.8001 (mmm) REVERT: Db 19 THR cc_start: 0.7751 (m) cc_final: 0.7306 (p) outliers start: 72 outliers final: 33 residues processed: 316 average time/residue: 0.6814 time to fit residues: 244.7921 Evaluate side-chains 296 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Ba residue 239 MET Chi-restraints excluded: chain Aa residue 54 THR Chi-restraints excluded: chain Aa residue 60 GLU Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 406 ILE Chi-restraints excluded: chain Ca residue 43 GLN Chi-restraints excluded: chain Ca residue 92 VAL Chi-restraints excluded: chain Ca residue 118 ILE Chi-restraints excluded: chain Ca residue 134 MET Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 213 PHE Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Da residue 4 LEU Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Bb residue 206 GLU Chi-restraints excluded: chain Bb residue 239 MET Chi-restraints excluded: chain Bc residue 197 SER Chi-restraints excluded: chain Ab residue 47 ASP Chi-restraints excluded: chain Ab residue 61 MET Chi-restraints excluded: chain Ab residue 95 VAL Chi-restraints excluded: chain Ab residue 256 ARG Chi-restraints excluded: chain Ab residue 276 THR Chi-restraints excluded: chain Ab residue 314 LEU Chi-restraints excluded: chain Ab residue 320 THR Chi-restraints excluded: chain Ab residue 350 VAL Chi-restraints excluded: chain Ab residue 366 LYS Chi-restraints excluded: chain Ac residue 47 ASP Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 54 THR Chi-restraints excluded: chain Ac residue 59 GLU Chi-restraints excluded: chain Ac residue 287 GLU Chi-restraints excluded: chain Ac residue 292 VAL Chi-restraints excluded: chain Ac residue 312 GLN Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Ac residue 362 GLU Chi-restraints excluded: chain Cb residue 118 ILE Chi-restraints excluded: chain Cb residue 212 LEU Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cb residue 253 LEU Chi-restraints excluded: chain Cc residue 118 ILE Chi-restraints excluded: chain Cc residue 246 VAL Chi-restraints excluded: chain Dc residue 12 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 257 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 368 GLN Bb 14 ASN Bc 164 ASN Ac 104 GLN Ac 368 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.085104 restraints weight = 25765.365| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.54 r_work: 0.2855 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.9942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22128 Z= 0.151 Angle : 0.587 10.148 30219 Z= 0.305 Chirality : 0.044 0.150 3327 Planarity : 0.005 0.057 3756 Dihedral : 5.239 53.558 2898 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Rotamer: Outliers : 2.92 % Allowed : 18.53 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.16), residues: 2664 helix: 1.74 (0.14), residues: 1332 sheet: 0.38 (0.25), residues: 399 loop : -0.25 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGAa 298 TYR 0.024 0.002 TYRCb 157 PHE 0.024 0.002 PHECb 221 TRP 0.017 0.001 TRPAc 198 HIS 0.005 0.001 HISBb 173 Details of bonding type rmsd covalent geometry : bond 0.00356 (22128) covalent geometry : angle 0.58657 (30219) hydrogen bonds : bond 0.05132 ( 1212) hydrogen bonds : angle 4.86572 ( 3519) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 271 time to evaluate : 0.877 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8159 (tpt) REVERT: Ba 247 LYS cc_start: 0.8252 (tttt) cc_final: 0.7882 (ttmm) REVERT: Aa 60 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: Aa 159 MET cc_start: 0.8218 (ttt) cc_final: 0.7689 (ttt) REVERT: Aa 160 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8310 (pttm) REVERT: Aa 172 SER cc_start: 0.8770 (m) cc_final: 0.8484 (p) REVERT: Aa 256 ARG cc_start: 0.7611 (mtm110) cc_final: 0.6925 (mmt180) REVERT: Aa 287 GLU cc_start: 0.8348 (tp30) cc_final: 0.7698 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7368 (ptp-170) REVERT: Aa 350 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8452 (m) REVERT: Aa 366 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7674 (tmtm) REVERT: Aa 400 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7518 (mtpp) REVERT: Ca 43 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7576 (tp40) REVERT: Ca 59 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7874 (mp10) REVERT: Ca 67 TRP cc_start: 0.6580 (m100) cc_final: 0.5823 (m100) REVERT: Ca 87 THR cc_start: 0.8303 (m) cc_final: 0.8024 (p) REVERT: Ca 201 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7207 (mm-30) REVERT: Ca 213 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: Da 1 MET cc_start: 0.8785 (mmm) cc_final: 0.8489 (tpp) REVERT: Da 4 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7881 (tt) REVERT: Bb 164 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8305 (t0) REVERT: Bb 247 LYS cc_start: 0.8169 (tttt) cc_final: 0.7787 (ttmm) REVERT: Bc 247 LYS cc_start: 0.8265 (tttt) cc_final: 0.7934 (ttmm) REVERT: Bc 248 VAL cc_start: 0.8226 (m) cc_final: 0.8004 (t) REVERT: Ab 53 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7771 (p) REVERT: Ab 61 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8417 (ppp) REVERT: Ab 158 ASP cc_start: 0.8053 (t0) cc_final: 0.7713 (t0) REVERT: Ab 160 LYS cc_start: 0.8544 (pttt) cc_final: 0.8246 (ttpp) REVERT: Ab 256 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6849 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8073 (tt0) cc_final: 0.7610 (tm-30) REVERT: Ab 305 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8432 (mtpt) REVERT: Ab 330 ASP cc_start: 0.8405 (m-30) cc_final: 0.8161 (m-30) REVERT: Ab 353 THR cc_start: 0.8554 (m) cc_final: 0.8317 (t) REVERT: Ab 366 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7644 (mtpp) REVERT: Ac 59 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: Ac 116 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8161 (mttm) REVERT: Ac 256 ARG cc_start: 0.7930 (mpp-170) cc_final: 0.6963 (mmt180) REVERT: Ac 299 GLU cc_start: 0.7467 (mp0) cc_final: 0.7097 (mt-10) REVERT: Ac 400 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7494 (mtpp) REVERT: Ac 415 VAL cc_start: 0.7971 (p) cc_final: 0.7579 (m) REVERT: Cb 87 THR cc_start: 0.8373 (m) cc_final: 0.8086 (p) REVERT: Cb 210 GLU cc_start: 0.7135 (mp0) cc_final: 0.6398 (mp0) REVERT: Cb 214 VAL cc_start: 0.7714 (t) cc_final: 0.7470 (m) REVERT: Cb 253 LEU cc_start: 0.7789 (mm) cc_final: 0.7359 (tm) REVERT: Cc 57 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6892 (pm20) REVERT: Cc 59 GLN cc_start: 0.8207 (tp40) cc_final: 0.7530 (mm-40) REVERT: Cc 86 LYS cc_start: 0.8307 (tmmt) cc_final: 0.8040 (ttmt) REVERT: Cc 210 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6925 (mp0) REVERT: Db 1 MET cc_start: 0.8071 (mmm) cc_final: 0.7793 (mmm) REVERT: Db 19 THR cc_start: 0.7703 (m) cc_final: 0.7382 (p) outliers start: 65 outliers final: 33 residues processed: 314 average time/residue: 0.6482 time to fit residues: 231.3943 Evaluate side-chains 304 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Ba residue 239 MET Chi-restraints excluded: chain Aa residue 60 GLU Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 366 LYS Chi-restraints excluded: chain Aa residue 406 ILE Chi-restraints excluded: chain Ca residue 43 GLN Chi-restraints excluded: chain Ca residue 118 ILE Chi-restraints excluded: chain Ca residue 134 MET Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 213 PHE Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Da residue 4 LEU Chi-restraints excluded: chain Bb residue 164 ASN Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Ab residue 47 ASP Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 61 MET Chi-restraints excluded: chain Ab residue 95 VAL Chi-restraints excluded: chain Ab residue 256 ARG Chi-restraints excluded: chain Ab residue 276 THR Chi-restraints excluded: chain Ab residue 314 LEU Chi-restraints excluded: chain Ab residue 320 THR Chi-restraints excluded: chain Ab residue 350 VAL Chi-restraints excluded: chain Ab residue 366 LYS Chi-restraints excluded: chain Ac residue 47 ASP Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 54 THR Chi-restraints excluded: chain Ac residue 59 GLU Chi-restraints excluded: chain Ac residue 116 LYS Chi-restraints excluded: chain Ac residue 287 GLU Chi-restraints excluded: chain Ac residue 292 VAL Chi-restraints excluded: chain Ac residue 312 GLN Chi-restraints excluded: chain Ac residue 320 THR Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Cb residue 118 ILE Chi-restraints excluded: chain Cb residue 183 PHE Chi-restraints excluded: chain Cb residue 186 VAL Chi-restraints excluded: chain Cb residue 212 LEU Chi-restraints excluded: chain Cb residue 217 LEU Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cc residue 118 ILE Chi-restraints excluded: chain Cc residue 246 VAL Chi-restraints excluded: chain Dc residue 12 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 171 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 245 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 308 ASN Ca 200 ASN Bb 14 ASN Bc 164 ASN Ac 104 GLN Cb 59 GLN Cb 196 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.084560 restraints weight = 25670.387| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.53 r_work: 0.2847 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 1.0018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22128 Z= 0.153 Angle : 0.590 10.247 30219 Z= 0.306 Chirality : 0.045 0.151 3327 Planarity : 0.005 0.057 3756 Dihedral : 5.227 54.402 2898 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.55 % Rotamer: Outliers : 2.83 % Allowed : 18.62 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.16), residues: 2664 helix: 1.77 (0.14), residues: 1332 sheet: 0.36 (0.24), residues: 399 loop : -0.30 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAa 298 TYR 0.024 0.002 TYRCb 157 PHE 0.024 0.002 PHECb 221 TRP 0.017 0.001 TRPAc 198 HIS 0.005 0.001 HISCa 133 Details of bonding type rmsd covalent geometry : bond 0.00362 (22128) covalent geometry : angle 0.58984 (30219) hydrogen bonds : bond 0.05212 ( 1212) hydrogen bonds : angle 4.86909 ( 3519) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 260 time to evaluate : 0.877 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8210 (tpt) REVERT: Ba 247 LYS cc_start: 0.8282 (tttt) cc_final: 0.7932 (ttmm) REVERT: Aa 60 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: Aa 159 MET cc_start: 0.8403 (ttt) cc_final: 0.7860 (ttt) REVERT: Aa 172 SER cc_start: 0.8779 (m) cc_final: 0.8519 (p) REVERT: Aa 256 ARG cc_start: 0.7664 (mtm110) cc_final: 0.6926 (mtp180) REVERT: Aa 272 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8107 (mm-30) REVERT: Aa 287 GLU cc_start: 0.8380 (tp30) cc_final: 0.7740 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7813 (mtm110) cc_final: 0.7441 (ptp-170) REVERT: Aa 350 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8498 (m) REVERT: Aa 366 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7740 (tttm) REVERT: Aa 400 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7543 (mtpp) REVERT: Ca 43 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7671 (tp40) REVERT: Ca 59 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7939 (mp10) REVERT: Ca 67 TRP cc_start: 0.6621 (m100) cc_final: 0.5916 (m100) REVERT: Ca 87 THR cc_start: 0.8367 (m) cc_final: 0.8126 (p) REVERT: Da 4 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7912 (tt) REVERT: Bb 164 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8347 (t0) REVERT: Bb 247 LYS cc_start: 0.8210 (tttt) cc_final: 0.7845 (ttmm) REVERT: Bc 247 LYS cc_start: 0.8278 (tttt) cc_final: 0.7952 (ttmm) REVERT: Bc 248 VAL cc_start: 0.8269 (m) cc_final: 0.8041 (t) REVERT: Ab 53 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7784 (p) REVERT: Ab 61 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8462 (ppp) REVERT: Ab 158 ASP cc_start: 0.8095 (t0) cc_final: 0.7703 (t0) REVERT: Ab 160 LYS cc_start: 0.8589 (pttt) cc_final: 0.8276 (pttp) REVERT: Ab 256 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6888 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8135 (tt0) cc_final: 0.7622 (tm-30) REVERT: Ab 305 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8479 (mtpt) REVERT: Ab 330 ASP cc_start: 0.8404 (m-30) cc_final: 0.8122 (m-30) REVERT: Ab 366 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7702 (mtpp) REVERT: Ac 59 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: Ac 116 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8236 (mttm) REVERT: Ac 256 ARG cc_start: 0.7959 (mpp-170) cc_final: 0.7022 (mmt180) REVERT: Ac 299 GLU cc_start: 0.7357 (mp0) cc_final: 0.7062 (mt-10) REVERT: Ac 400 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7544 (mtpp) REVERT: Ac 415 VAL cc_start: 0.8013 (p) cc_final: 0.7771 (m) REVERT: Cb 87 THR cc_start: 0.8367 (m) cc_final: 0.8124 (p) REVERT: Cb 210 GLU cc_start: 0.7217 (mp0) cc_final: 0.6573 (mp0) REVERT: Cb 214 VAL cc_start: 0.7740 (t) cc_final: 0.7509 (m) REVERT: Cb 253 LEU cc_start: 0.7886 (mm) cc_final: 0.7441 (tm) REVERT: Cc 57 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6933 (pm20) REVERT: Cc 59 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7504 (mm-40) REVERT: Cc 86 LYS cc_start: 0.8350 (tmmt) cc_final: 0.8102 (ttmt) REVERT: Cc 210 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6879 (mp0) REVERT: Db 19 THR cc_start: 0.7806 (m) cc_final: 0.7507 (p) outliers start: 63 outliers final: 36 residues processed: 298 average time/residue: 0.7024 time to fit residues: 237.5001 Evaluate side-chains 302 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 164 ASN Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Ba residue 239 MET Chi-restraints excluded: chain Aa residue 60 GLU Chi-restraints excluded: chain Aa residue 167 THR Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 366 LYS Chi-restraints excluded: chain Aa residue 406 ILE Chi-restraints excluded: chain Ca residue 43 GLN Chi-restraints excluded: chain Ca residue 91 ASN Chi-restraints excluded: chain Ca residue 118 ILE Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 217 LEU Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Da residue 4 LEU Chi-restraints excluded: chain Bb residue 58 ASP Chi-restraints excluded: chain Bb residue 164 ASN Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Bc residue 164 ASN Chi-restraints excluded: chain Ab residue 47 ASP Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 61 MET Chi-restraints excluded: chain Ab residue 95 VAL Chi-restraints excluded: chain Ab residue 256 ARG Chi-restraints excluded: chain Ab residue 276 THR Chi-restraints excluded: chain Ab residue 312 GLN Chi-restraints excluded: chain Ab residue 314 LEU Chi-restraints excluded: chain Ab residue 320 THR Chi-restraints excluded: chain Ab residue 350 VAL Chi-restraints excluded: chain Ab residue 366 LYS Chi-restraints excluded: chain Ac residue 47 ASP Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 54 THR Chi-restraints excluded: chain Ac residue 59 GLU Chi-restraints excluded: chain Ac residue 116 LYS Chi-restraints excluded: chain Ac residue 287 GLU Chi-restraints excluded: chain Ac residue 292 VAL Chi-restraints excluded: chain Ac residue 312 GLN Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Cb residue 118 ILE Chi-restraints excluded: chain Cb residue 186 VAL Chi-restraints excluded: chain Cb residue 217 LEU Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cc residue 59 GLN Chi-restraints excluded: chain Cc residue 118 ILE Chi-restraints excluded: chain Cc residue 246 VAL Chi-restraints excluded: chain Dc residue 12 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 114 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 228 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 104 GLN Cb 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.084677 restraints weight = 25575.367| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.53 r_work: 0.2852 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 1.0059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22128 Z= 0.150 Angle : 0.594 10.225 30219 Z= 0.306 Chirality : 0.044 0.150 3327 Planarity : 0.005 0.057 3756 Dihedral : 5.216 53.818 2898 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.92 % Allowed : 18.80 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.16), residues: 2664 helix: 1.77 (0.14), residues: 1302 sheet: 0.43 (0.25), residues: 384 loop : -0.31 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAa 298 TYR 0.024 0.002 TYRCb 157 PHE 0.024 0.002 PHECb 221 TRP 0.017 0.001 TRPAc 198 HIS 0.007 0.001 HISCa 133 Details of bonding type rmsd covalent geometry : bond 0.00353 (22128) covalent geometry : angle 0.59362 (30219) hydrogen bonds : bond 0.05158 ( 1212) hydrogen bonds : angle 4.86750 ( 3519) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 258 time to evaluate : 0.892 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8139 (tpt) REVERT: Ba 247 LYS cc_start: 0.8210 (tttt) cc_final: 0.7855 (ttmm) REVERT: Aa 60 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: Aa 159 MET cc_start: 0.8312 (ttt) cc_final: 0.7789 (ttt) REVERT: Aa 160 LYS cc_start: 0.8471 (pttm) cc_final: 0.8120 (ptmm) REVERT: Aa 172 SER cc_start: 0.8677 (m) cc_final: 0.8401 (p) REVERT: Aa 256 ARG cc_start: 0.7683 (mtm110) cc_final: 0.6855 (mtp180) REVERT: Aa 272 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8074 (mm-30) REVERT: Aa 287 GLU cc_start: 0.8309 (tp30) cc_final: 0.7641 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7415 (ptp-170) REVERT: Aa 350 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8442 (m) REVERT: Aa 366 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7675 (tttm) REVERT: Aa 400 LYS cc_start: 0.7802 (ttmt) cc_final: 0.7398 (mtpp) REVERT: Ca 43 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7563 (tp40) REVERT: Ca 59 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7587 (mm-40) REVERT: Ca 67 TRP cc_start: 0.6526 (m100) cc_final: 0.5824 (m100) REVERT: Ca 87 THR cc_start: 0.8307 (m) cc_final: 0.8065 (p) REVERT: Ca 252 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7956 (tmtp) REVERT: Bb 164 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8278 (t0) REVERT: Bb 247 LYS cc_start: 0.8149 (tttt) cc_final: 0.7781 (ttmm) REVERT: Bc 247 LYS cc_start: 0.8211 (tttt) cc_final: 0.7865 (ttmm) REVERT: Bc 248 VAL cc_start: 0.8199 (m) cc_final: 0.7968 (t) REVERT: Ab 53 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7672 (p) REVERT: Ab 61 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8392 (ppp) REVERT: Ab 158 ASP cc_start: 0.8074 (t0) cc_final: 0.7665 (t0) REVERT: Ab 160 LYS cc_start: 0.8555 (pttt) cc_final: 0.8238 (pttp) REVERT: Ab 256 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6827 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8042 (tt0) cc_final: 0.7537 (tm-30) REVERT: Ab 305 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8402 (mtpt) REVERT: Ab 315 ARG cc_start: 0.7207 (mtm180) cc_final: 0.6969 (mtm180) REVERT: Ab 330 ASP cc_start: 0.8340 (m-30) cc_final: 0.8035 (m-30) REVERT: Ab 366 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7651 (mtpp) REVERT: Ac 59 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: Ac 116 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8152 (mttm) REVERT: Ac 256 ARG cc_start: 0.7895 (mpp-170) cc_final: 0.6953 (mmt180) REVERT: Ac 299 GLU cc_start: 0.7288 (mp0) cc_final: 0.6957 (mt-10) REVERT: Ac 400 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7411 (mtpp) REVERT: Ac 415 VAL cc_start: 0.7933 (p) cc_final: 0.7702 (m) REVERT: Cb 87 THR cc_start: 0.8293 (m) cc_final: 0.8046 (p) REVERT: Cb 210 GLU cc_start: 0.7121 (mp0) cc_final: 0.6504 (mp0) REVERT: Cb 214 VAL cc_start: 0.7740 (t) cc_final: 0.7509 (m) REVERT: Cb 253 LEU cc_start: 0.7857 (mm) cc_final: 0.7436 (tm) REVERT: Cc 57 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6871 (pm20) REVERT: Cc 59 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7424 (mm-40) REVERT: Cc 86 LYS cc_start: 0.8259 (tmmt) cc_final: 0.8013 (ttmt) REVERT: Cc 210 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6781 (mp0) REVERT: Db 19 THR cc_start: 0.7770 (m) cc_final: 0.7484 (p) outliers start: 65 outliers final: 38 residues processed: 301 average time/residue: 0.6608 time to fit residues: 225.7043 Evaluate side-chains 303 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 164 ASN Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Ba residue 239 MET Chi-restraints excluded: chain Aa residue 60 GLU Chi-restraints excluded: chain Aa residue 167 THR Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 366 LYS Chi-restraints excluded: chain Aa residue 406 ILE Chi-restraints excluded: chain Ca residue 43 GLN Chi-restraints excluded: chain Ca residue 91 ASN Chi-restraints excluded: chain Ca residue 118 ILE Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 217 LEU Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Bb residue 58 ASP Chi-restraints excluded: chain Bb residue 164 ASN Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Bc residue 15 SER Chi-restraints excluded: chain Ab residue 47 ASP Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 61 MET Chi-restraints excluded: chain Ab residue 95 VAL Chi-restraints excluded: chain Ab residue 256 ARG Chi-restraints excluded: chain Ab residue 276 THR Chi-restraints excluded: chain Ab residue 312 GLN Chi-restraints excluded: chain Ab residue 314 LEU Chi-restraints excluded: chain Ab residue 320 THR Chi-restraints excluded: chain Ab residue 350 VAL Chi-restraints excluded: chain Ab residue 366 LYS Chi-restraints excluded: chain Ac residue 47 ASP Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 54 THR Chi-restraints excluded: chain Ac residue 59 GLU Chi-restraints excluded: chain Ac residue 116 LYS Chi-restraints excluded: chain Ac residue 287 GLU Chi-restraints excluded: chain Ac residue 292 VAL Chi-restraints excluded: chain Ac residue 312 GLN Chi-restraints excluded: chain Ac residue 320 THR Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Cb residue 118 ILE Chi-restraints excluded: chain Cb residue 186 VAL Chi-restraints excluded: chain Cb residue 217 LEU Chi-restraints excluded: chain Cb residue 219 TRP Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cc residue 59 GLN Chi-restraints excluded: chain Cc residue 118 ILE Chi-restraints excluded: chain Cc residue 246 VAL Chi-restraints excluded: chain Dc residue 12 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 229 optimal weight: 0.0870 chunk 110 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Bc 164 ASN Cb 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.107818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.086242 restraints weight = 25660.688| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.53 r_work: 0.2876 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 1.0101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22128 Z= 0.126 Angle : 0.564 10.108 30219 Z= 0.291 Chirality : 0.043 0.144 3327 Planarity : 0.005 0.057 3756 Dihedral : 5.076 53.128 2898 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 2.47 % Allowed : 19.20 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.16), residues: 2664 helix: 1.89 (0.14), residues: 1299 sheet: 0.39 (0.25), residues: 399 loop : -0.30 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAa 298 TYR 0.022 0.001 TYRCb 157 PHE 0.022 0.001 PHECb 221 TRP 0.018 0.001 TRPAc 198 HIS 0.007 0.001 HISCa 133 Details of bonding type rmsd covalent geometry : bond 0.00286 (22128) covalent geometry : angle 0.56393 (30219) hydrogen bonds : bond 0.04715 ( 1212) hydrogen bonds : angle 4.78454 ( 3519) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 0.602 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8171 (tpt) REVERT: Ba 247 LYS cc_start: 0.8237 (tttt) cc_final: 0.7893 (ttmm) REVERT: Aa 60 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: Aa 159 MET cc_start: 0.8171 (ttt) cc_final: 0.7664 (ttt) REVERT: Aa 160 LYS cc_start: 0.8423 (pttm) cc_final: 0.8098 (pttp) REVERT: Aa 172 SER cc_start: 0.8807 (m) cc_final: 0.8559 (p) REVERT: Aa 256 ARG cc_start: 0.7722 (mtm110) cc_final: 0.6902 (mtp180) REVERT: Aa 272 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8061 (mm-30) REVERT: Aa 287 GLU cc_start: 0.8348 (tp30) cc_final: 0.7694 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7797 (mtm110) cc_final: 0.7436 (ptp-170) REVERT: Aa 350 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8467 (m) REVERT: Aa 400 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7489 (mtpp) REVERT: Ca 43 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7633 (tp40) REVERT: Ca 52 ASP cc_start: 0.7241 (p0) cc_final: 0.6621 (t0) REVERT: Ca 59 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7650 (mm-40) REVERT: Ca 67 TRP cc_start: 0.6584 (m100) cc_final: 0.5928 (m100) REVERT: Ca 87 THR cc_start: 0.8354 (m) cc_final: 0.8134 (p) REVERT: Ca 252 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7961 (tmtp) REVERT: Bb 247 LYS cc_start: 0.8200 (tttt) cc_final: 0.7835 (ttmm) REVERT: Bc 247 LYS cc_start: 0.8320 (tttt) cc_final: 0.7972 (ttmm) REVERT: Bc 248 VAL cc_start: 0.8232 (m) cc_final: 0.8031 (t) REVERT: Ab 53 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7651 (p) REVERT: Ab 61 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8391 (ppp) REVERT: Ab 158 ASP cc_start: 0.8137 (t0) cc_final: 0.7717 (t0) REVERT: Ab 160 LYS cc_start: 0.8583 (pttt) cc_final: 0.8279 (pttp) REVERT: Ab 256 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6888 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8091 (tt0) cc_final: 0.7599 (tm-30) REVERT: Ab 315 ARG cc_start: 0.7287 (mtm180) cc_final: 0.7044 (mtm180) REVERT: Ab 330 ASP cc_start: 0.8357 (m-30) cc_final: 0.8082 (m-30) REVERT: Ac 59 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: Ac 116 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8202 (mttm) REVERT: Ac 256 ARG cc_start: 0.7914 (mpp-170) cc_final: 0.7003 (mmt180) REVERT: Ac 299 GLU cc_start: 0.7223 (mp0) cc_final: 0.6953 (mt-10) REVERT: Ac 400 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7518 (mtpp) REVERT: Cb 87 THR cc_start: 0.8333 (m) cc_final: 0.8101 (p) REVERT: Cb 210 GLU cc_start: 0.7144 (mp0) cc_final: 0.6545 (mp0) REVERT: Cb 214 VAL cc_start: 0.7661 (t) cc_final: 0.7390 (m) REVERT: Cb 253 LEU cc_start: 0.7907 (mm) cc_final: 0.7536 (tt) REVERT: Cc 57 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6947 (pm20) REVERT: Cc 59 GLN cc_start: 0.8188 (tp40) cc_final: 0.7410 (mm-40) REVERT: Cc 86 LYS cc_start: 0.8293 (tmmt) cc_final: 0.7949 (ttmt) REVERT: Cc 210 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6731 (mp0) REVERT: Db 19 THR cc_start: 0.7871 (m) cc_final: 0.7597 (p) outliers start: 55 outliers final: 33 residues processed: 299 average time/residue: 0.6500 time to fit residues: 220.8691 Evaluate side-chains 293 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 164 ASN Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Ba residue 239 MET Chi-restraints excluded: chain Aa residue 60 GLU Chi-restraints excluded: chain Aa residue 95 VAL Chi-restraints excluded: chain Aa residue 167 THR Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 406 ILE Chi-restraints excluded: chain Ca residue 43 GLN Chi-restraints excluded: chain Ca residue 91 ASN Chi-restraints excluded: chain Ca residue 118 ILE Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 217 LEU Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Bc residue 164 ASN Chi-restraints excluded: chain Bc residue 197 SER Chi-restraints excluded: chain Ab residue 47 ASP Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 61 MET Chi-restraints excluded: chain Ab residue 95 VAL Chi-restraints excluded: chain Ab residue 256 ARG Chi-restraints excluded: chain Ab residue 276 THR Chi-restraints excluded: chain Ab residue 312 GLN Chi-restraints excluded: chain Ab residue 314 LEU Chi-restraints excluded: chain Ab residue 320 THR Chi-restraints excluded: chain Ab residue 350 VAL Chi-restraints excluded: chain Ac residue 47 ASP Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 54 THR Chi-restraints excluded: chain Ac residue 59 GLU Chi-restraints excluded: chain Ac residue 116 LYS Chi-restraints excluded: chain Ac residue 292 VAL Chi-restraints excluded: chain Ac residue 312 GLN Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Cb residue 118 ILE Chi-restraints excluded: chain Cb residue 217 LEU Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cc residue 246 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 241 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Bc 178 GLN Ac 104 GLN Cb 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.086299 restraints weight = 25793.570| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.53 r_work: 0.2876 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 1.0097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 22128 Z= 0.146 Angle : 0.711 59.179 30219 Z= 0.401 Chirality : 0.044 0.485 3327 Planarity : 0.005 0.057 3756 Dihedral : 5.087 53.151 2898 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 2.06 % Allowed : 19.78 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.16), residues: 2664 helix: 1.90 (0.14), residues: 1299 sheet: 0.39 (0.25), residues: 399 loop : -0.29 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAa 298 TYR 0.022 0.001 TYRCb 157 PHE 0.021 0.001 PHECb 221 TRP 0.018 0.001 TRPAc 198 HIS 0.007 0.001 HISCa 133 Details of bonding type rmsd covalent geometry : bond 0.00311 (22128) covalent geometry : angle 0.71134 (30219) hydrogen bonds : bond 0.04746 ( 1212) hydrogen bonds : angle 4.79367 ( 3519) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 0.614 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8190 (tpt) REVERT: Ba 247 LYS cc_start: 0.8254 (tttt) cc_final: 0.7915 (ttmm) REVERT: Aa 60 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: Aa 159 MET cc_start: 0.8179 (ttt) cc_final: 0.7675 (ttt) REVERT: Aa 160 LYS cc_start: 0.8389 (pttm) cc_final: 0.8122 (pttp) REVERT: Aa 172 SER cc_start: 0.8828 (m) cc_final: 0.8588 (p) REVERT: Aa 256 ARG cc_start: 0.7729 (mtm110) cc_final: 0.6913 (mtp180) REVERT: Aa 272 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8010 (mm-30) REVERT: Aa 287 GLU cc_start: 0.8360 (tp30) cc_final: 0.7714 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7447 (ptp-170) REVERT: Aa 350 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8479 (m) REVERT: Aa 400 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7512 (mtpp) REVERT: Ca 43 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7648 (tp40) REVERT: Ca 52 ASP cc_start: 0.7250 (p0) cc_final: 0.6644 (t0) REVERT: Ca 59 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7664 (mm-40) REVERT: Ca 67 TRP cc_start: 0.6603 (m100) cc_final: 0.5946 (m100) REVERT: Ca 87 THR cc_start: 0.8368 (m) cc_final: 0.8157 (p) REVERT: Ca 252 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7972 (tmtp) REVERT: Bb 247 LYS cc_start: 0.8208 (tttt) cc_final: 0.7853 (ttmm) REVERT: Bc 247 LYS cc_start: 0.8329 (tttt) cc_final: 0.7987 (ttmm) REVERT: Ab 53 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7670 (p) REVERT: Ab 61 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8411 (ppp) REVERT: Ab 158 ASP cc_start: 0.8145 (t0) cc_final: 0.7727 (t0) REVERT: Ab 160 LYS cc_start: 0.8591 (pttt) cc_final: 0.8288 (pttp) REVERT: Ab 256 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6901 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8045 (tt0) cc_final: 0.7600 (tm-30) REVERT: Ab 315 ARG cc_start: 0.7300 (mtm180) cc_final: 0.7061 (mtm180) REVERT: Ab 330 ASP cc_start: 0.8365 (m-30) cc_final: 0.8066 (m-30) REVERT: Ac 59 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: Ac 116 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8221 (mttm) REVERT: Ac 256 ARG cc_start: 0.7924 (mpp-170) cc_final: 0.7025 (mmt180) REVERT: Ac 299 GLU cc_start: 0.7228 (mp0) cc_final: 0.6959 (mt-10) REVERT: Ac 400 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7538 (mtpp) REVERT: Cb 87 THR cc_start: 0.8355 (m) cc_final: 0.8131 (p) REVERT: Cb 210 GLU cc_start: 0.7155 (mp0) cc_final: 0.6562 (mp0) REVERT: Cb 214 VAL cc_start: 0.7658 (t) cc_final: 0.7410 (m) REVERT: Cb 253 LEU cc_start: 0.7920 (mm) cc_final: 0.7547 (tt) REVERT: Cc 57 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6972 (pm20) REVERT: Cc 59 GLN cc_start: 0.8207 (tp40) cc_final: 0.7434 (mm-40) REVERT: Cc 86 LYS cc_start: 0.8309 (tmmt) cc_final: 0.7967 (ttmt) REVERT: Cc 210 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6744 (mp0) REVERT: Db 19 THR cc_start: 0.7883 (m) cc_final: 0.7607 (p) outliers start: 46 outliers final: 36 residues processed: 280 average time/residue: 0.6552 time to fit residues: 207.5693 Evaluate side-chains 295 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 164 ASN Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Ba residue 239 MET Chi-restraints excluded: chain Aa residue 60 GLU Chi-restraints excluded: chain Aa residue 95 VAL Chi-restraints excluded: chain Aa residue 167 THR Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 406 ILE Chi-restraints excluded: chain Ca residue 43 GLN Chi-restraints excluded: chain Ca residue 91 ASN Chi-restraints excluded: chain Ca residue 118 ILE Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 217 LEU Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Bb residue 198 MET Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Bc residue 164 ASN Chi-restraints excluded: chain Bc residue 197 SER Chi-restraints excluded: chain Ab residue 47 ASP Chi-restraints excluded: chain Ab residue 53 THR Chi-restraints excluded: chain Ab residue 61 MET Chi-restraints excluded: chain Ab residue 95 VAL Chi-restraints excluded: chain Ab residue 256 ARG Chi-restraints excluded: chain Ab residue 276 THR Chi-restraints excluded: chain Ab residue 312 GLN Chi-restraints excluded: chain Ab residue 314 LEU Chi-restraints excluded: chain Ab residue 320 THR Chi-restraints excluded: chain Ab residue 350 VAL Chi-restraints excluded: chain Ac residue 47 ASP Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 54 THR Chi-restraints excluded: chain Ac residue 59 GLU Chi-restraints excluded: chain Ac residue 116 LYS Chi-restraints excluded: chain Ac residue 292 VAL Chi-restraints excluded: chain Ac residue 312 GLN Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Cb residue 118 ILE Chi-restraints excluded: chain Cb residue 217 LEU Chi-restraints excluded: chain Cb residue 219 TRP Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cc residue 63 MET Chi-restraints excluded: chain Cc residue 246 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 199 optimal weight: 8.9990 chunk 229 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 209 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Cb 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.085990 restraints weight = 25726.682| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.53 r_work: 0.2872 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 1.0095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22128 Z= 0.155 Angle : 0.718 59.200 30219 Z= 0.392 Chirality : 0.044 0.153 3327 Planarity : 0.005 0.057 3756 Dihedral : 5.084 53.133 2898 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.42 % Favored : 96.47 % Rotamer: Outliers : 2.15 % Allowed : 19.47 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.16), residues: 2664 helix: 1.89 (0.14), residues: 1299 sheet: 0.39 (0.25), residues: 399 loop : -0.29 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAa 298 TYR 0.022 0.002 TYRCb 157 PHE 0.021 0.001 PHECb 221 TRP 0.018 0.001 TRPAc 198 HIS 0.008 0.001 HISCa 133 Details of bonding type rmsd covalent geometry : bond 0.00373 (22128) covalent geometry : angle 0.71762 (30219) hydrogen bonds : bond 0.04816 ( 1212) hydrogen bonds : angle 4.79019 ( 3519) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8013.34 seconds wall clock time: 136 minutes 53.22 seconds (8213.22 seconds total)