Starting phenix.real_space_refine on Thu Jun 19 07:21:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cl5_45662/06_2025/9cl5_45662.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cl5_45662/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cl5_45662/06_2025/9cl5_45662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cl5_45662/06_2025/9cl5_45662.map" model { file = "/net/cci-nas-00/data/ceres_data/9cl5_45662/06_2025/9cl5_45662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cl5_45662/06_2025/9cl5_45662.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: "Cc" 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: "Db" 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: "Cc" 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: Ac, Ab, Dc, Da, Bb, Bc, Cb, Ca Time building chain proxies: 11.83, per 1000 atoms: 0.53 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: 4.97 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.21 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: 7.91 Time building geometry restraints manager: 5.92 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: 0.13 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ac' selection = chain 'Ab' } ncs_group { reference = chain 'Db' selection = chain 'Dc' selection = chain 'Da' } ncs_group { reference = chain 'Ba' selection = chain 'Bb' selection = chain 'Bc' } ncs_group { reference = chain 'Cc' selection = chain 'Cb' selection = chain 'Ca' } 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 47.600 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (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 TRP 0.016 0.001 TRPAb 198 HIS 0.008 0.001 HISCc 204 PHE 0.010 0.001 PHEBc 193 TYR 0.022 0.002 TYRCc 157 ARG 0.004 0.000 ARGAc 81 Details of bonding type rmsd hydrogen bonds : bond 0.14194 ( 1212) hydrogen bonds : angle 6.56989 ( 3519) covalent geometry : bond 0.00396 (22128) covalent geometry : angle 0.68358 (30219) *********************** 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 : 2.152 Fit side-chains REVERT: Aa 302 ILE cc_start: 0.7059 (pt) cc_final: 0.6789 (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: 1.1177 time to fit residues: 696.8375 Evaluate side-chains 300 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 292 time to evaluate : 2.809 ------------------------------------------------------------------------------- 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 222 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 239 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 Bb 81 GLN Bb 178 GLN Bc 164 ASN Bc 178 GLN Ab 44 ASN Ab 68 HIS ** Ab 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 178 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110822 restraints weight = 25705.100| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.66 r_work: 0.3254 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22128 Z= 0.235 Angle : 0.796 12.080 30219 Z= 0.424 Chirality : 0.049 0.173 3327 Planarity : 0.007 0.140 3756 Dihedral : 6.051 51.101 2911 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.68 % Favored : 96.10 % Rotamer: Outliers : 6.33 % Allowed : 16.87 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2664 helix: 0.94 (0.14), residues: 1311 sheet: 0.16 (0.26), residues: 372 loop : -0.77 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRPAb 198 HIS 0.012 0.002 HISAa 178 PHE 0.032 0.003 PHECc 224 TYR 0.033 0.003 TYRCb 157 ARG 0.010 0.001 ARGDb 22 Details of bonding type rmsd hydrogen bonds : bond 0.05238 ( 1212) hydrogen bonds : angle 5.38913 ( 3519) covalent geometry : bond 0.00509 (22128) covalent geometry : angle 0.79604 (30219) *********************** 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 500 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 359 time to evaluate : 2.341 Fit side-chains revert: symmetry clash REVERT: Aa 160 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8525 (ttmt) REVERT: Aa 221 ASP cc_start: 0.6645 (OUTLIER) cc_final: 0.6428 (m-30) REVERT: Aa 256 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7165 (mmt180) REVERT: Aa 287 GLU cc_start: 0.7901 (tp30) cc_final: 0.7330 (tm-30) REVERT: Aa 400 LYS cc_start: 0.7682 (ttmt) cc_final: 0.7099 (tttm) REVERT: Ca 92 VAL cc_start: 0.7203 (OUTLIER) cc_final: 0.6888 (p) REVERT: Ca 101 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.6224 (tpt) REVERT: Bc 198 MET cc_start: 0.8355 (mmt) cc_final: 0.8143 (tpt) REVERT: Bc 211 ARG cc_start: 0.7649 (tpt-90) cc_final: 0.7334 (mtt180) REVERT: Ab 53 THR cc_start: 0.7749 (OUTLIER) cc_final: 0.7504 (t) REVERT: Ab 287 GLU cc_start: 0.8048 (tt0) cc_final: 0.7847 (tm-30) REVERT: Ab 400 LYS cc_start: 0.8120 (tttm) cc_final: 0.7445 (tmtt) REVERT: Ac 274 GLU cc_start: 0.7624 (pp20) cc_final: 0.7422 (pp20) REVERT: Ac 368 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8439 (tp40) REVERT: Ac 400 LYS cc_start: 0.7418 (ttmt) cc_final: 0.7067 (ttmm) REVERT: Cb 63 MET cc_start: 0.8356 (mmm) cc_final: 0.8148 (mmm) REVERT: Cb 67 TRP cc_start: 0.7642 (m100) cc_final: 0.6005 (m-10) REVERT: Cc 24 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7658 (ptp) REVERT: Cc 86 LYS cc_start: 0.6991 (tttt) cc_final: 0.6788 (tmmt) REVERT: Db 1 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6626 (mmp) outliers start: 141 outliers final: 31 residues processed: 442 average time/residue: 1.2511 time to fit residues: 638.9159 Evaluate side-chains 316 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 278 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 33 SER Chi-restraints excluded: chain Aa residue 42 THR Chi-restraints excluded: chain Aa residue 47 ASP Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 63 LEU Chi-restraints excluded: chain Aa residue 95 VAL Chi-restraints excluded: chain Aa residue 97 THR Chi-restraints excluded: chain Aa residue 204 VAL Chi-restraints excluded: chain Aa residue 221 ASP Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 353 THR Chi-restraints excluded: chain Ca residue 92 VAL Chi-restraints excluded: chain Ca residue 101 MET Chi-restraints excluded: chain Ca residue 183 PHE Chi-restraints excluded: chain Ca residue 196 ASN Chi-restraints excluded: chain Ca residue 253 LEU Chi-restraints excluded: chain Bb residue 33 LEU Chi-restraints excluded: chain Bc residue 176 THR 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 334 THR Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 140 VAL Chi-restraints excluded: chain Ac residue 173 THR Chi-restraints excluded: chain Ac residue 224 ILE 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 Cb residue 186 VAL Chi-restraints excluded: chain Cc residue 24 MET Chi-restraints excluded: chain Cc residue 217 LEU Chi-restraints excluded: chain Db residue 1 MET Chi-restraints excluded: chain Dc residue 18 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 101 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ba 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 164 ASN Ba 174 GLN Ca 146 HIS Bb 164 ASN Bc 164 ASN Ab 265 GLN Ab 303 ASN Ac 309 ASN Cb 196 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096440 restraints weight = 25657.186| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.51 r_work: 0.3033 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.7906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22128 Z= 0.140 Angle : 0.589 9.099 30219 Z= 0.307 Chirality : 0.043 0.161 3327 Planarity : 0.005 0.063 3756 Dihedral : 5.213 49.144 2900 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.73 % Rotamer: Outliers : 3.41 % Allowed : 20.01 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 2664 helix: 1.59 (0.14), residues: 1317 sheet: 0.27 (0.25), residues: 396 loop : -0.40 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPBc 65 HIS 0.004 0.001 HISCc 133 PHE 0.018 0.002 PHEAc 200 TYR 0.025 0.002 TYRCb 157 ARG 0.013 0.001 ARGAc 298 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 1212) hydrogen bonds : angle 4.87196 ( 3519) covalent geometry : bond 0.00309 (22128) covalent geometry : angle 0.58895 (30219) *********************** 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 367 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 291 time to evaluate : 2.282 Fit side-chains revert: symmetry clash REVERT: Ba 64 MET cc_start: 0.8662 (tpp) cc_final: 0.8296 (mmp) REVERT: Ba 198 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7917 (tpt) REVERT: Ba 247 LYS cc_start: 0.8303 (tttt) cc_final: 0.7705 (ttmt) REVERT: Aa 63 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7984 (tp) REVERT: Aa 256 ARG cc_start: 0.7567 (mtm110) cc_final: 0.6952 (mmt180) REVERT: Aa 274 GLU cc_start: 0.8123 (tp30) cc_final: 0.7827 (tp30) REVERT: Aa 279 VAL cc_start: 0.6378 (OUTLIER) cc_final: 0.6085 (m) REVERT: Aa 287 GLU cc_start: 0.8177 (tp30) cc_final: 0.7488 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7070 (mtm110) cc_final: 0.6618 (ptp-170) REVERT: Aa 400 LYS cc_start: 0.7722 (ttmt) cc_final: 0.7012 (tttm) REVERT: Ca 67 TRP cc_start: 0.6751 (m100) cc_final: 0.6027 (m100) REVERT: Ca 196 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.7249 (t0) REVERT: Ca 208 PHE cc_start: 0.5503 (m-10) cc_final: 0.5291 (m-80) REVERT: Bb 247 LYS cc_start: 0.6999 (tttt) cc_final: 0.6559 (ttmm) REVERT: Bc 177 GLU cc_start: 0.8294 (tt0) cc_final: 0.8077 (tt0) REVERT: Bc 181 GLN cc_start: 0.7609 (mt0) cc_final: 0.7359 (mt0) REVERT: Ab 160 LYS cc_start: 0.8291 (pttt) cc_final: 0.7694 (mmtm) REVERT: Ab 287 GLU cc_start: 0.8038 (tt0) cc_final: 0.7478 (tm-30) REVERT: Ab 315 ARG cc_start: 0.6912 (mtm110) cc_final: 0.6446 (mtm180) REVERT: Ab 400 LYS cc_start: 0.7860 (tttm) cc_final: 0.7119 (tmtt) REVERT: Ab 413 LYS cc_start: 0.8177 (tttp) cc_final: 0.7975 (tptt) REVERT: Ac 274 GLU cc_start: 0.7996 (pp20) cc_final: 0.7617 (pp20) REVERT: Ac 298 ARG cc_start: 0.6913 (mtm110) cc_final: 0.6701 (ptp-170) REVERT: Ac 330 ASP cc_start: 0.8205 (m-30) cc_final: 0.7962 (m-30) REVERT: Ac 400 LYS cc_start: 0.7528 (ttmt) cc_final: 0.6908 (mtpp) REVERT: Cb 63 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8104 (mmm) REVERT: Cb 67 TRP cc_start: 0.7604 (m100) cc_final: 0.6047 (m-10) REVERT: Cb 210 GLU cc_start: 0.6535 (mt-10) cc_final: 0.5587 (mm-30) REVERT: Cb 213 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7400 (m-10) REVERT: Cc 78 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7479 (mp) REVERT: Cc 86 LYS cc_start: 0.7502 (tttt) cc_final: 0.7084 (ttmt) REVERT: Db 1 MET cc_start: 0.7561 (mmm) cc_final: 0.7090 (mmp) REVERT: Db 4 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7171 (tt) outliers start: 76 outliers final: 23 residues processed: 337 average time/residue: 1.3477 time to fit residues: 518.0841 Evaluate side-chains 301 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 164 ASN Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Aa residue 54 THR Chi-restraints excluded: chain Aa residue 63 LEU Chi-restraints excluded: chain Aa residue 279 VAL Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 353 THR Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 196 ASN Chi-restraints excluded: chain Ca residue 253 LEU Chi-restraints excluded: chain Da residue 4 LEU Chi-restraints excluded: chain Bb residue 44 VAL 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 95 VAL Chi-restraints excluded: chain Ab residue 282 GLU Chi-restraints excluded: chain Ab residue 320 THR Chi-restraints excluded: chain Ab residue 367 ILE Chi-restraints excluded: chain Ac residue 59 GLU Chi-restraints excluded: chain Ac residue 140 VAL Chi-restraints excluded: chain Ac residue 169 LEU Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Cb residue 63 MET Chi-restraints excluded: chain Cb residue 213 PHE Chi-restraints excluded: chain Cb residue 253 LEU Chi-restraints excluded: chain Cc residue 78 LEU Chi-restraints excluded: chain Cc residue 118 ILE Chi-restraints excluded: chain Cc residue 217 LEU Chi-restraints excluded: chain Db residue 4 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 255 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 123 optimal weight: 0.0170 chunk 247 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 195 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ba 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 164 ASN Ca 146 HIS Bb 173 HIS Bc 164 ASN Ab 75 GLN ** Ac 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.095404 restraints weight = 25756.677| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.48 r_work: 0.3011 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.8514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22128 Z= 0.121 Angle : 0.555 9.197 30219 Z= 0.288 Chirality : 0.043 0.201 3327 Planarity : 0.005 0.076 3756 Dihedral : 5.021 47.386 2900 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 2.78 % Allowed : 20.28 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.16), residues: 2664 helix: 1.97 (0.14), residues: 1293 sheet: 0.73 (0.27), residues: 348 loop : -0.34 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPAa 198 HIS 0.004 0.001 HISAc 135 PHE 0.019 0.001 PHECb 221 TYR 0.024 0.002 TYRCb 157 ARG 0.009 0.000 ARGCb 90 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 1212) hydrogen bonds : angle 4.73840 ( 3519) covalent geometry : bond 0.00267 (22128) covalent geometry : angle 0.55509 (30219) *********************** 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 358 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 296 time to evaluate : 2.422 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.8037 (tpt) REVERT: Ba 247 LYS cc_start: 0.8514 (tttt) cc_final: 0.8096 (ttmm) REVERT: Aa 256 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7280 (mmt180) REVERT: Aa 274 GLU cc_start: 0.8191 (tp30) cc_final: 0.7975 (tp30) REVERT: Aa 287 GLU cc_start: 0.8420 (tp30) cc_final: 0.7811 (tm-30) REVERT: Aa 400 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7319 (tttm) REVERT: Ca 43 GLN cc_start: 0.8476 (tp40) cc_final: 0.8096 (tp-100) REVERT: Ca 67 TRP cc_start: 0.6851 (m100) cc_final: 0.6089 (m100) REVERT: Ca 180 SER cc_start: 0.8360 (m) cc_final: 0.8139 (t) REVERT: Da 9 MET cc_start: 0.8726 (ttt) cc_final: 0.8486 (ttp) REVERT: Bb 206 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: Bb 247 LYS cc_start: 0.7421 (tttt) cc_final: 0.7043 (ttmm) REVERT: Bc 181 GLN cc_start: 0.7772 (mt0) cc_final: 0.7558 (mt0) REVERT: Ab 160 LYS cc_start: 0.8528 (pttt) cc_final: 0.8315 (ptmm) REVERT: Ab 256 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7200 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8126 (tt0) cc_final: 0.7646 (tm-30) REVERT: Ab 315 ARG cc_start: 0.7357 (mtm110) cc_final: 0.7010 (mtm180) REVERT: Ab 353 THR cc_start: 0.8795 (m) cc_final: 0.8542 (t) REVERT: Ac 59 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: Ac 222 ASP cc_start: 0.7557 (t0) cc_final: 0.7155 (t0) REVERT: Ac 272 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: Ac 299 GLU cc_start: 0.7119 (mp0) cc_final: 0.6903 (mt-10) REVERT: Ac 330 ASP cc_start: 0.8328 (m-30) cc_final: 0.8087 (m-30) REVERT: Ac 362 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8646 (mm-30) REVERT: Ac 400 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7495 (mtpp) REVERT: Cb 67 TRP cc_start: 0.7762 (m100) cc_final: 0.6430 (m-10) REVERT: Cb 87 THR cc_start: 0.8362 (m) cc_final: 0.8049 (p) REVERT: Cb 210 GLU cc_start: 0.6667 (mt-10) cc_final: 0.6154 (mm-30) REVERT: Cb 214 VAL cc_start: 0.7732 (t) cc_final: 0.7321 (m) REVERT: Cc 57 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7055 (pm20) REVERT: Cc 86 LYS cc_start: 0.7855 (tttt) cc_final: 0.7529 (ttmt) REVERT: Db 1 MET cc_start: 0.7862 (mmm) cc_final: 0.7470 (mmm) outliers start: 62 outliers final: 29 residues processed: 334 average time/residue: 1.3900 time to fit residues: 530.6763 Evaluate side-chains 310 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 275 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Aa residue 47 ASP Chi-restraints excluded: chain Aa residue 53 THR Chi-restraints excluded: chain Aa residue 54 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 362 GLU Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 196 ASN Chi-restraints excluded: chain Ca residue 253 LEU Chi-restraints excluded: chain Da residue 4 LEU Chi-restraints excluded: chain Bb residue 44 VAL Chi-restraints excluded: chain Bb residue 58 ASP Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Bb residue 206 GLU 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 57 VAL Chi-restraints excluded: chain Ab residue 256 ARG Chi-restraints excluded: chain Ab residue 276 THR Chi-restraints excluded: chain Ab residue 282 GLU Chi-restraints excluded: chain Ab residue 350 VAL Chi-restraints excluded: chain Ab residue 367 ILE Chi-restraints excluded: chain Ac residue 59 GLU Chi-restraints excluded: chain Ac residue 169 LEU Chi-restraints excluded: chain Ac residue 272 GLU Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Ac residue 362 GLU Chi-restraints excluded: chain Cb residue 217 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 9 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 108 ASN Aa 188 HIS ** Aa 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 109 GLN Ac 34 GLN Ac 44 ASN ** Ac 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 123 ASN ** Cb 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 109 GLN Cc 237 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.106638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.085201 restraints weight = 25894.969| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.44 r_work: 0.2859 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.9679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22128 Z= 0.194 Angle : 0.653 9.898 30219 Z= 0.342 Chirality : 0.047 0.169 3327 Planarity : 0.006 0.060 3756 Dihedral : 5.437 53.835 2898 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.42 % Favored : 96.43 % Rotamer: Outliers : 3.50 % Allowed : 18.53 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.16), residues: 2664 helix: 1.62 (0.14), residues: 1326 sheet: 0.27 (0.24), residues: 429 loop : -0.32 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPBc 65 HIS 0.006 0.002 HISBb 173 PHE 0.025 0.002 PHEAc 200 TYR 0.028 0.002 TYRCb 157 ARG 0.014 0.001 ARGAa 298 Details of bonding type rmsd hydrogen bonds : bond 0.05913 ( 1212) hydrogen bonds : angle 5.03312 ( 3519) covalent geometry : bond 0.00464 (22128) covalent geometry : angle 0.65341 (30219) *********************** 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 355 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 277 time to evaluate : 2.843 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8244 (tpt) REVERT: Ba 247 LYS cc_start: 0.8377 (tttt) cc_final: 0.8011 (ttmm) REVERT: Aa 172 SER cc_start: 0.8776 (OUTLIER) cc_final: 0.8462 (p) REVERT: Aa 256 ARG cc_start: 0.7596 (mtm110) cc_final: 0.7017 (mtp180) REVERT: Aa 274 GLU cc_start: 0.8250 (tp30) cc_final: 0.8029 (tp30) REVERT: Aa 287 GLU cc_start: 0.8372 (tp30) cc_final: 0.7759 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7107 (ptp-170) REVERT: Aa 362 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: Aa 367 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8546 (mp) REVERT: Aa 400 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7217 (tttm) REVERT: Ca 19 VAL cc_start: 0.8033 (m) cc_final: 0.7626 (t) REVERT: Ca 43 GLN cc_start: 0.8456 (tp40) cc_final: 0.8090 (tp-100) REVERT: Ca 59 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7778 (mp10) REVERT: Ca 67 TRP cc_start: 0.6748 (m100) cc_final: 0.5981 (m100) REVERT: Ca 68 THR cc_start: 0.8776 (m) cc_final: 0.8525 (m) REVERT: Ca 92 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7489 (p) REVERT: Ca 253 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7418 (tt) REVERT: Da 1 MET cc_start: 0.8683 (mmm) cc_final: 0.8343 (tpp) REVERT: Bb 206 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8500 (pt0) REVERT: Bb 247 LYS cc_start: 0.8032 (tttt) cc_final: 0.7648 (ttmm) REVERT: Bc 58 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: Ab 160 LYS cc_start: 0.8636 (pttt) cc_final: 0.8332 (pttp) REVERT: Ab 256 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.6989 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8087 (tt0) cc_final: 0.7534 (tm-30) REVERT: Ab 353 THR cc_start: 0.8690 (m) cc_final: 0.8423 (t) REVERT: Ab 366 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7854 (mtpp) REVERT: Ac 59 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: Ac 60 GLU cc_start: 0.7739 (tp30) cc_final: 0.7528 (tt0) REVERT: Ac 172 SER cc_start: 0.8693 (t) cc_final: 0.8298 (p) REVERT: Ac 256 ARG cc_start: 0.8085 (mpp-170) cc_final: 0.7066 (mmt180) REVERT: Ac 272 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: Ac 330 ASP cc_start: 0.8371 (m-30) cc_final: 0.8153 (m-30) REVERT: Ac 400 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7530 (mtpp) REVERT: Ac 415 VAL cc_start: 0.8034 (p) cc_final: 0.7739 (m) REVERT: Cb 22 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7601 (mtp85) REVERT: Cb 87 THR cc_start: 0.8462 (m) cc_final: 0.8170 (p) REVERT: Cb 214 VAL cc_start: 0.7798 (t) cc_final: 0.7487 (m) REVERT: Cc 57 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6964 (pm20) REVERT: Cc 86 LYS cc_start: 0.8022 (tttt) cc_final: 0.7565 (ttmt) REVERT: Db 1 MET cc_start: 0.8190 (mmm) cc_final: 0.7856 (mmm) REVERT: Db 19 THR cc_start: 0.7608 (m) cc_final: 0.7176 (p) outliers start: 78 outliers final: 32 residues processed: 330 average time/residue: 1.7658 time to fit residues: 663.1750 Evaluate side-chains 298 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Aa residue 47 ASP Chi-restraints excluded: chain Aa residue 54 THR Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 172 SER Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 362 GLU Chi-restraints excluded: chain Aa residue 367 ILE Chi-restraints excluded: chain Aa residue 406 ILE Chi-restraints excluded: chain Ca residue 92 VAL Chi-restraints excluded: chain Ca residue 118 ILE Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Ca residue 253 LEU Chi-restraints excluded: chain Bb residue 44 VAL Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Bb residue 206 GLU Chi-restraints excluded: chain Bc residue 29 MET Chi-restraints excluded: chain Bc residue 58 ASP 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 256 ARG Chi-restraints excluded: chain Ab residue 274 GLU 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 Ab residue 367 ILE Chi-restraints excluded: chain Ac residue 47 ASP Chi-restraints excluded: chain Ac residue 53 THR Chi-restraints excluded: chain Ac residue 59 GLU Chi-restraints excluded: chain Ac residue 272 GLU Chi-restraints excluded: chain Ac residue 274 GLU Chi-restraints excluded: chain Ac residue 287 GLU Chi-restraints excluded: chain Ac residue 292 VAL Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Ac residue 406 ILE Chi-restraints excluded: chain Cb residue 22 ARG Chi-restraints excluded: chain Cb residue 118 ILE Chi-restraints excluded: chain Cb residue 183 PHE Chi-restraints excluded: chain Cb residue 217 LEU Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cc residue 118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 235 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 164 ASN Aa 308 ASN Aa 368 GLN Bb 14 ASN Bc 164 ASN Ac 68 HIS ** Ac 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 308 ASN Ac 312 GLN ** Cb 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 109 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.087950 restraints weight = 25854.285| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.41 r_work: 0.2900 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.9807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22128 Z= 0.132 Angle : 0.566 10.028 30219 Z= 0.295 Chirality : 0.043 0.140 3327 Planarity : 0.005 0.058 3756 Dihedral : 5.137 52.089 2898 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Rotamer: Outliers : 2.83 % Allowed : 18.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2664 helix: 1.80 (0.14), residues: 1335 sheet: 0.26 (0.24), residues: 429 loop : -0.23 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPAa 198 HIS 0.005 0.001 HISBb 173 PHE 0.028 0.001 PHEAc 200 TYR 0.024 0.002 TYRCb 157 ARG 0.011 0.000 ARGAa 298 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 1212) hydrogen bonds : angle 4.83875 ( 3519) covalent geometry : bond 0.00302 (22128) covalent geometry : angle 0.56579 (30219) *********************** 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 340 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 277 time to evaluate : 2.252 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8236 (tpt) REVERT: Ba 247 LYS cc_start: 0.8364 (tttt) cc_final: 0.7965 (ttmm) REVERT: Aa 160 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8485 (pttm) REVERT: Aa 256 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7014 (mmt180) REVERT: Aa 274 GLU cc_start: 0.8166 (tp30) cc_final: 0.7935 (tp30) REVERT: Aa 287 GLU cc_start: 0.8446 (tp30) cc_final: 0.7824 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7657 (mtm110) cc_final: 0.7209 (ptp-170) REVERT: Aa 362 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: Aa 400 LYS cc_start: 0.7968 (ttmt) cc_final: 0.7207 (tttm) REVERT: Ca 19 VAL cc_start: 0.8051 (m) cc_final: 0.7662 (t) REVERT: Ca 43 GLN cc_start: 0.8517 (tp40) cc_final: 0.8189 (tp-100) REVERT: Ca 59 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7863 (mp10) REVERT: Ca 67 TRP cc_start: 0.6705 (m100) cc_final: 0.5921 (m100) REVERT: Ca 87 THR cc_start: 0.8343 (m) cc_final: 0.8028 (p) REVERT: Ca 253 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7570 (tt) REVERT: Da 1 MET cc_start: 0.8801 (mmm) cc_final: 0.8496 (tpp) REVERT: Bb 206 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8483 (pt0) REVERT: Bb 247 LYS cc_start: 0.8069 (tttt) cc_final: 0.7733 (ttmm) REVERT: Bc 118 TYR cc_start: 0.9115 (m-80) cc_final: 0.8913 (m-80) REVERT: Ab 53 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7657 (p) REVERT: Ab 160 LYS cc_start: 0.8594 (pttt) cc_final: 0.8327 (pttp) REVERT: Ab 256 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.6943 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8126 (tt0) cc_final: 0.7552 (tm-30) REVERT: Ab 353 THR cc_start: 0.8692 (m) cc_final: 0.8443 (t) REVERT: Ab 366 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7855 (mtpp) REVERT: Ac 59 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: Ac 172 SER cc_start: 0.8858 (t) cc_final: 0.8447 (m) REVERT: Ac 256 ARG cc_start: 0.8046 (mpp-170) cc_final: 0.7107 (mmt180) REVERT: Ac 299 GLU cc_start: 0.7262 (mp0) cc_final: 0.6993 (mt-10) REVERT: Ac 330 ASP cc_start: 0.8385 (m-30) cc_final: 0.8167 (m-30) REVERT: Ac 362 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: Ac 400 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7588 (mtpp) REVERT: Ac 415 VAL cc_start: 0.8040 (p) cc_final: 0.7667 (m) REVERT: Cb 87 THR cc_start: 0.8421 (m) cc_final: 0.8135 (p) REVERT: Cb 210 GLU cc_start: 0.7197 (mp0) cc_final: 0.6629 (mp0) REVERT: Cb 214 VAL cc_start: 0.7719 (t) cc_final: 0.7406 (m) REVERT: Cc 57 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6954 (pm20) REVERT: Cc 59 GLN cc_start: 0.8336 (tp40) cc_final: 0.7529 (mm-40) REVERT: Cc 86 LYS cc_start: 0.8084 (tttt) cc_final: 0.7655 (ttmt) REVERT: Db 1 MET cc_start: 0.8235 (mmm) cc_final: 0.7999 (mmm) REVERT: Db 19 THR cc_start: 0.7675 (m) cc_final: 0.7245 (p) outliers start: 63 outliers final: 26 residues processed: 320 average time/residue: 1.3617 time to fit residues: 495.0964 Evaluate side-chains 292 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 257 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 164 ASN Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Aa residue 47 ASP 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 362 GLU Chi-restraints excluded: chain Aa residue 406 ILE Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Ca residue 253 LEU Chi-restraints excluded: chain Bb residue 44 VAL Chi-restraints excluded: chain Bb residue 202 ILE Chi-restraints excluded: chain Bb residue 206 GLU 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 95 VAL Chi-restraints excluded: chain Ab residue 256 ARG 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 Ab residue 367 ILE 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 292 VAL 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 217 LEU Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cb residue 253 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 256 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 219 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 14 ASN Bc 164 ASN Bc 178 GLN ** Ac 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3281 r_free = 0.3281 target = 0.108074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.086848 restraints weight = 25923.860| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.44 r_work: 0.2887 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.9882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22128 Z= 0.138 Angle : 0.568 10.195 30219 Z= 0.296 Chirality : 0.044 0.145 3327 Planarity : 0.005 0.058 3756 Dihedral : 5.101 52.652 2898 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.30 % Favored : 96.58 % Rotamer: Outliers : 2.78 % Allowed : 18.98 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.16), residues: 2664 helix: 1.86 (0.14), residues: 1332 sheet: 0.38 (0.25), residues: 396 loop : -0.14 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPAa 198 HIS 0.007 0.001 HISCa 133 PHE 0.027 0.002 PHEAc 200 TYR 0.024 0.002 TYRCb 157 ARG 0.008 0.000 ARGAa 298 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 1212) hydrogen bonds : angle 4.83091 ( 3519) covalent geometry : bond 0.00320 (22128) covalent geometry : angle 0.56822 (30219) *********************** 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 329 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 267 time to evaluate : 2.753 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8232 (tpt) REVERT: Ba 247 LYS cc_start: 0.8365 (tttt) cc_final: 0.7980 (ttmm) REVERT: Aa 172 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8669 (p) REVERT: Aa 256 ARG cc_start: 0.7557 (mtm110) cc_final: 0.6976 (mmt180) REVERT: Aa 274 GLU cc_start: 0.8134 (tp30) cc_final: 0.7906 (tp30) REVERT: Aa 287 GLU cc_start: 0.8407 (tp30) cc_final: 0.7764 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7675 (mtm110) cc_final: 0.7230 (ptp-170) REVERT: Aa 362 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: Aa 366 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7717 (tmtm) REVERT: Aa 400 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7148 (tttm) REVERT: Ca 19 VAL cc_start: 0.8180 (m) cc_final: 0.7823 (t) REVERT: Ca 43 GLN cc_start: 0.8507 (tp40) cc_final: 0.8198 (tp-100) REVERT: Ca 59 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7828 (mp10) REVERT: Ca 67 TRP cc_start: 0.6737 (m100) cc_final: 0.5969 (m100) REVERT: Ca 87 THR cc_start: 0.8359 (m) cc_final: 0.8110 (p) REVERT: Ca 253 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7773 (tt) REVERT: Bb 239 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8491 (mtp) REVERT: Bb 247 LYS cc_start: 0.8085 (tttt) cc_final: 0.7733 (ttmm) REVERT: Bc 58 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: Ab 160 LYS cc_start: 0.8616 (pttt) cc_final: 0.8364 (pttm) REVERT: Ab 256 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6945 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8079 (tt0) cc_final: 0.7559 (tm-30) REVERT: Ab 353 THR cc_start: 0.8666 (m) cc_final: 0.8424 (t) REVERT: Ab 366 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7829 (mtpp) REVERT: Ac 59 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: Ac 172 SER cc_start: 0.8799 (t) cc_final: 0.8465 (m) REVERT: Ac 256 ARG cc_start: 0.8016 (mpp-170) cc_final: 0.7069 (mmt180) REVERT: Ac 272 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: Ac 299 GLU cc_start: 0.7173 (mp0) cc_final: 0.6888 (mt-10) REVERT: Ac 330 ASP cc_start: 0.8359 (m-30) cc_final: 0.8131 (m-30) REVERT: Ac 400 LYS cc_start: 0.8038 (ttmt) cc_final: 0.7605 (mtpp) REVERT: Ac 415 VAL cc_start: 0.8010 (p) cc_final: 0.7639 (m) REVERT: Cb 87 THR cc_start: 0.8403 (m) cc_final: 0.8123 (p) REVERT: Cb 210 GLU cc_start: 0.7319 (mp0) cc_final: 0.6388 (mp0) REVERT: Cb 214 VAL cc_start: 0.7615 (t) cc_final: 0.7319 (m) REVERT: Cc 57 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6940 (pm20) REVERT: Cc 59 GLN cc_start: 0.8269 (tp40) cc_final: 0.7574 (mm-40) REVERT: Cc 86 LYS cc_start: 0.8070 (tttt) cc_final: 0.7629 (ttmt) REVERT: Db 19 THR cc_start: 0.7729 (m) cc_final: 0.7291 (p) outliers start: 62 outliers final: 31 residues processed: 306 average time/residue: 1.5904 time to fit residues: 556.0204 Evaluate side-chains 298 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 256 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Aa residue 47 ASP Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 172 SER Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 362 GLU Chi-restraints excluded: chain Aa residue 366 LYS Chi-restraints excluded: chain Aa residue 406 ILE 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 Ca residue 253 LEU Chi-restraints excluded: chain Bb residue 44 VAL Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Bb residue 239 MET Chi-restraints excluded: chain Bc residue 58 ASP 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 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 Ab residue 367 ILE 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 272 GLU Chi-restraints excluded: chain Ac residue 287 GLU Chi-restraints excluded: chain Ac residue 292 VAL Chi-restraints excluded: chain Ac residue 334 THR Chi-restraints excluded: chain Ac residue 350 VAL Chi-restraints excluded: chain Cb residue 196 ASN Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cb residue 253 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 165 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 164 ASN Aa 308 ASN Ca 196 ASN Bb 14 ASN ** Ac 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 59 GLN Cb 196 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.088050 restraints weight = 25866.307| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.41 r_work: 0.2902 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.9932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22128 Z= 0.123 Angle : 0.558 10.171 30219 Z= 0.289 Chirality : 0.043 0.152 3327 Planarity : 0.005 0.058 3756 Dihedral : 5.037 52.179 2898 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Rotamer: Outliers : 2.51 % Allowed : 19.43 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.17), residues: 2664 helix: 1.95 (0.14), residues: 1329 sheet: 0.32 (0.24), residues: 429 loop : -0.18 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPAc 198 HIS 0.008 0.001 HISCa 133 PHE 0.024 0.001 PHEAc 200 TYR 0.023 0.002 TYRCb 157 ARG 0.008 0.000 ARGAa 298 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 1212) hydrogen bonds : angle 4.79372 ( 3519) covalent geometry : bond 0.00277 (22128) covalent geometry : angle 0.55784 (30219) *********************** 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 321 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 2.636 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8230 (tpt) REVERT: Ba 247 LYS cc_start: 0.8402 (tttt) cc_final: 0.8029 (ttmm) REVERT: Aa 160 LYS cc_start: 0.8512 (pttm) cc_final: 0.8217 (ptmm) REVERT: Aa 172 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8687 (p) REVERT: Aa 256 ARG cc_start: 0.7589 (mtm110) cc_final: 0.7019 (mmt180) REVERT: Aa 287 GLU cc_start: 0.8420 (tp30) cc_final: 0.7789 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7676 (mtm110) cc_final: 0.7374 (ptp-170) REVERT: Aa 362 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: Aa 366 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7763 (tttm) REVERT: Aa 400 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7567 (mtpp) REVERT: Ca 19 VAL cc_start: 0.8199 (m) cc_final: 0.7848 (t) REVERT: Ca 43 GLN cc_start: 0.8530 (tp40) cc_final: 0.8213 (tp-100) REVERT: Ca 59 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7860 (mp10) REVERT: Ca 67 TRP cc_start: 0.6702 (m100) cc_final: 0.5962 (m100) REVERT: Ca 87 THR cc_start: 0.8368 (m) cc_final: 0.8139 (p) REVERT: Ca 213 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7365 (m-10) REVERT: Ca 253 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7896 (tt) REVERT: Bb 239 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8518 (mtp) REVERT: Bb 247 LYS cc_start: 0.8108 (tttt) cc_final: 0.7771 (ttmm) REVERT: Ab 53 THR cc_start: 0.8188 (OUTLIER) cc_final: 0.7679 (p) REVERT: Ab 160 LYS cc_start: 0.8671 (pttt) cc_final: 0.8376 (pttp) REVERT: Ab 256 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6954 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8035 (tt0) cc_final: 0.7565 (tm-30) REVERT: Ab 330 ASP cc_start: 0.8463 (m-30) cc_final: 0.8229 (m-30) REVERT: Ab 353 THR cc_start: 0.8664 (m) cc_final: 0.8436 (t) REVERT: Ab 366 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7835 (mtpp) REVERT: Ac 59 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: Ac 172 SER cc_start: 0.8814 (t) cc_final: 0.8504 (m) REVERT: Ac 256 ARG cc_start: 0.8037 (mpp-170) cc_final: 0.7111 (mmt180) REVERT: Ac 272 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: Ac 299 GLU cc_start: 0.7183 (mp0) cc_final: 0.6897 (mt-10) REVERT: Ac 330 ASP cc_start: 0.8365 (m-30) cc_final: 0.8138 (m-30) REVERT: Ac 400 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7599 (mtpp) REVERT: Ac 415 VAL cc_start: 0.8041 (p) cc_final: 0.7686 (m) REVERT: Cb 22 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7543 (mtp85) REVERT: Cb 87 THR cc_start: 0.8402 (m) cc_final: 0.8143 (p) REVERT: Cb 210 GLU cc_start: 0.7401 (mp0) cc_final: 0.6552 (mp0) REVERT: Cb 214 VAL cc_start: 0.7600 (t) cc_final: 0.7312 (m) REVERT: Cb 253 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7398 (tm) REVERT: Cc 57 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6969 (pm20) REVERT: Cc 59 GLN cc_start: 0.8297 (tp40) cc_final: 0.7552 (mm-40) REVERT: Cc 86 LYS cc_start: 0.8117 (tttt) cc_final: 0.7646 (ttmt) REVERT: Db 19 THR cc_start: 0.7777 (m) cc_final: 0.7361 (p) outliers start: 56 outliers final: 32 residues processed: 299 average time/residue: 1.4295 time to fit residues: 484.9520 Evaluate side-chains 302 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 256 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 15 SER Chi-restraints excluded: chain Ba residue 164 ASN Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Aa residue 47 ASP Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 172 SER Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 362 GLU Chi-restraints excluded: chain Aa residue 366 LYS Chi-restraints excluded: chain Aa residue 406 ILE Chi-restraints excluded: chain Ca residue 118 ILE Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 213 PHE Chi-restraints excluded: chain Ca residue 217 LEU Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Ca residue 253 LEU Chi-restraints excluded: chain Bb residue 44 VAL Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Bb residue 239 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 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 Ab residue 367 ILE 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 272 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 Cb residue 22 ARG Chi-restraints excluded: chain Cb residue 217 LEU Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cb residue 253 LEU Chi-restraints excluded: chain Cc residue 63 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 253 optimal weight: 0.0870 chunk 60 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ca 200 ASN Bb 14 ASN Bc 164 ASN Cb 59 GLN Cb 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.087894 restraints weight = 25778.898| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.43 r_work: 0.2901 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.9972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22128 Z= 0.125 Angle : 0.556 11.076 30219 Z= 0.288 Chirality : 0.043 0.142 3327 Planarity : 0.005 0.058 3756 Dihedral : 5.004 52.133 2898 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.43 % Rotamer: Outliers : 2.69 % Allowed : 19.11 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.17), residues: 2664 helix: 1.97 (0.14), residues: 1314 sheet: 0.33 (0.24), residues: 429 loop : -0.14 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPAc 198 HIS 0.009 0.001 HISCa 133 PHE 0.025 0.001 PHEAc 200 TYR 0.023 0.002 TYRCb 157 ARG 0.007 0.000 ARGAa 298 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 1212) hydrogen bonds : angle 4.77578 ( 3519) covalent geometry : bond 0.00283 (22128) covalent geometry : angle 0.55636 (30219) *********************** 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 322 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 262 time to evaluate : 2.259 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8205 (tpt) REVERT: Ba 247 LYS cc_start: 0.8360 (tttt) cc_final: 0.7992 (ttmm) REVERT: Aa 160 LYS cc_start: 0.8596 (pttm) cc_final: 0.8302 (pttp) REVERT: Aa 172 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8657 (p) REVERT: Aa 256 ARG cc_start: 0.7598 (mtm110) cc_final: 0.7026 (mmt180) REVERT: Aa 287 GLU cc_start: 0.8410 (tp30) cc_final: 0.7757 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7392 (ptp-170) REVERT: Aa 362 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: Aa 366 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7797 (tttm) REVERT: Aa 400 LYS cc_start: 0.7968 (ttmt) cc_final: 0.7575 (mtpp) REVERT: Ca 19 VAL cc_start: 0.8173 (m) cc_final: 0.7840 (t) REVERT: Ca 43 GLN cc_start: 0.8505 (tp40) cc_final: 0.8184 (tp-100) REVERT: Ca 59 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7849 (mp10) REVERT: Ca 67 TRP cc_start: 0.6669 (m100) cc_final: 0.5947 (m100) REVERT: Ca 87 THR cc_start: 0.8353 (m) cc_final: 0.8124 (p) REVERT: Ca 213 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: Ca 253 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7855 (tt) REVERT: Bb 239 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8483 (mtp) REVERT: Bb 247 LYS cc_start: 0.8082 (tttt) cc_final: 0.7736 (ttmm) REVERT: Ab 53 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7658 (p) REVERT: Ab 160 LYS cc_start: 0.8642 (pttt) cc_final: 0.8318 (pttp) REVERT: Ab 256 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6949 (mmp-170) REVERT: Ab 287 GLU cc_start: 0.8019 (tt0) cc_final: 0.7534 (tm-30) REVERT: Ab 315 ARG cc_start: 0.7374 (mtm180) cc_final: 0.7102 (mtm180) REVERT: Ab 330 ASP cc_start: 0.8435 (m-30) cc_final: 0.8200 (m-30) REVERT: Ab 366 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7819 (mtpp) REVERT: Ac 59 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: Ac 172 SER cc_start: 0.8771 (t) cc_final: 0.8523 (m) REVERT: Ac 256 ARG cc_start: 0.8020 (mpp-170) cc_final: 0.7084 (mmt180) REVERT: Ac 272 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: Ac 299 GLU cc_start: 0.7125 (mp0) cc_final: 0.6860 (mt-10) REVERT: Ac 330 ASP cc_start: 0.8352 (m-30) cc_final: 0.8119 (m-30) REVERT: Ac 400 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7576 (mtpp) REVERT: Ac 415 VAL cc_start: 0.8006 (p) cc_final: 0.7655 (m) REVERT: Cb 22 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7486 (mtp85) REVERT: Cb 59 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7941 (mm-40) REVERT: Cb 87 THR cc_start: 0.8349 (m) cc_final: 0.8102 (p) REVERT: Cb 210 GLU cc_start: 0.7472 (mp0) cc_final: 0.6483 (mp0) REVERT: Cb 214 VAL cc_start: 0.7638 (t) cc_final: 0.7346 (m) REVERT: Cb 253 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7368 (tm) REVERT: Cc 57 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6937 (pm20) REVERT: Cc 59 GLN cc_start: 0.8268 (tp40) cc_final: 0.7531 (mm-40) REVERT: Cc 86 LYS cc_start: 0.8091 (tttt) cc_final: 0.7610 (ttmt) REVERT: Db 19 THR cc_start: 0.7761 (m) cc_final: 0.7349 (p) outliers start: 60 outliers final: 32 residues processed: 300 average time/residue: 1.3893 time to fit residues: 473.7266 Evaluate side-chains 302 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 15 SER Chi-restraints excluded: chain Ba residue 164 ASN Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Aa residue 47 ASP Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 172 SER Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 362 GLU Chi-restraints excluded: chain Aa residue 366 LYS Chi-restraints excluded: chain Aa residue 406 ILE Chi-restraints excluded: chain Ca residue 118 ILE Chi-restraints excluded: chain Ca residue 145 SER Chi-restraints excluded: chain Ca residue 213 PHE Chi-restraints excluded: chain Ca residue 217 LEU Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Ca residue 253 LEU Chi-restraints excluded: chain Bb residue 44 VAL Chi-restraints excluded: chain Bb residue 198 MET Chi-restraints excluded: chain Bb residue 204 MET Chi-restraints excluded: chain Bb residue 239 MET Chi-restraints excluded: chain Ab residue 47 ASP Chi-restraints excluded: chain Ab residue 53 THR 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 Ab residue 367 ILE 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 272 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 Cb residue 22 ARG Chi-restraints excluded: chain Cb residue 59 GLN Chi-restraints excluded: chain Cb residue 196 ASN Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cb residue 253 LEU 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 60 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 209 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 164 ASN Ca 200 ASN Bb 14 ASN Bc 164 ASN ** Ac 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 59 GLN Cb 196 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.107418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.086304 restraints weight = 25950.352| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.43 r_work: 0.2902 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 1.0024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22128 Z= 0.145 Angle : 0.581 12.811 30219 Z= 0.300 Chirality : 0.044 0.146 3327 Planarity : 0.005 0.057 3756 Dihedral : 5.080 52.725 2898 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.55 % Rotamer: Outliers : 2.33 % Allowed : 19.61 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.16), residues: 2664 helix: 1.93 (0.14), residues: 1314 sheet: 0.29 (0.24), residues: 429 loop : -0.17 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAc 198 HIS 0.010 0.001 HISCa 133 PHE 0.027 0.002 PHEAc 200 TYR 0.024 0.002 TYRCb 157 ARG 0.007 0.000 ARGAa 298 Details of bonding type rmsd hydrogen bonds : bond 0.04963 ( 1212) hydrogen bonds : angle 4.81171 ( 3519) covalent geometry : bond 0.00341 (22128) covalent geometry : angle 0.58066 (30219) ********************** 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 304 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 2.508 Fit side-chains REVERT: Ba 198 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8242 (tpt) REVERT: Ba 247 LYS cc_start: 0.8345 (tttt) cc_final: 0.7992 (ttmm) REVERT: Aa 172 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8623 (p) REVERT: Aa 256 ARG cc_start: 0.7658 (mtm110) cc_final: 0.7017 (mtp180) REVERT: Aa 287 GLU cc_start: 0.8372 (tp30) cc_final: 0.7714 (tm-30) REVERT: Aa 298 ARG cc_start: 0.7811 (mtm110) cc_final: 0.7418 (ptp-170) REVERT: Aa 362 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: Aa 366 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7800 (tttm) REVERT: Aa 400 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7578 (mtpp) REVERT: Ca 19 VAL cc_start: 0.8178 (m) cc_final: 0.7848 (t) REVERT: Ca 43 GLN cc_start: 0.8529 (tp40) cc_final: 0.8206 (tp-100) REVERT: Ca 59 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7873 (mp10) REVERT: Ca 67 TRP cc_start: 0.6693 (m100) cc_final: 0.5981 (m100) REVERT: Ca 87 THR cc_start: 0.8400 (m) cc_final: 0.8190 (p) REVERT: Ca 213 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: Ca 253 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7901 (tt) REVERT: Bb 247 LYS cc_start: 0.8100 (tttt) cc_final: 0.7757 (ttmm) REVERT: Ab 160 LYS cc_start: 0.8628 (pttt) cc_final: 0.8328 (pttp) REVERT: Ab 256 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6926 (mmp-170) REVERT: Ab 274 GLU cc_start: 0.8517 (tp30) cc_final: 0.8270 (tp30) REVERT: Ab 287 GLU cc_start: 0.8002 (tt0) cc_final: 0.7532 (tm-30) REVERT: Ab 315 ARG cc_start: 0.7441 (mtm180) cc_final: 0.7181 (mtm180) REVERT: Ab 330 ASP cc_start: 0.8425 (m-30) cc_final: 0.8195 (m-30) REVERT: Ab 366 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7840 (mtpp) REVERT: Ac 59 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: Ac 172 SER cc_start: 0.8755 (t) cc_final: 0.8532 (m) REVERT: Ac 256 ARG cc_start: 0.8011 (mpp-170) cc_final: 0.7102 (mmt180) REVERT: Ac 272 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: Ac 299 GLU cc_start: 0.7222 (mp0) cc_final: 0.6938 (mt-10) REVERT: Ac 330 ASP cc_start: 0.8365 (m-30) cc_final: 0.8163 (m-30) REVERT: Ac 400 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7578 (mtpp) REVERT: Ac 415 VAL cc_start: 0.8047 (p) cc_final: 0.7842 (m) REVERT: Cb 22 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7539 (mtp85) REVERT: Cb 87 THR cc_start: 0.8367 (m) cc_final: 0.8116 (p) REVERT: Cb 210 GLU cc_start: 0.7573 (mp0) cc_final: 0.6650 (mp0) REVERT: Cb 214 VAL cc_start: 0.7644 (t) cc_final: 0.7368 (m) REVERT: Cb 253 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7404 (tm) REVERT: Cc 57 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7003 (pm20) REVERT: Cc 59 GLN cc_start: 0.8284 (tp40) cc_final: 0.7556 (mm-40) REVERT: Cc 86 LYS cc_start: 0.8110 (tttt) cc_final: 0.7642 (ttmt) REVERT: Db 19 THR cc_start: 0.7872 (m) cc_final: 0.7558 (p) outliers start: 52 outliers final: 34 residues processed: 284 average time/residue: 1.4365 time to fit residues: 464.4017 Evaluate side-chains 297 residues out of total 2229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ba residue 15 SER Chi-restraints excluded: chain Ba residue 164 ASN Chi-restraints excluded: chain Ba residue 198 MET Chi-restraints excluded: chain Aa residue 47 ASP Chi-restraints excluded: chain Aa residue 170 ASP Chi-restraints excluded: chain Aa residue 172 SER Chi-restraints excluded: chain Aa residue 320 THR Chi-restraints excluded: chain Aa residue 350 VAL Chi-restraints excluded: chain Aa residue 362 GLU Chi-restraints excluded: chain Aa residue 366 LYS Chi-restraints excluded: chain Aa residue 406 ILE 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 213 PHE Chi-restraints excluded: chain Ca residue 217 LEU Chi-restraints excluded: chain Ca residue 246 VAL Chi-restraints excluded: chain Ca residue 253 LEU Chi-restraints excluded: chain Bb residue 44 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 Ab residue 47 ASP Chi-restraints excluded: chain Ab residue 53 THR 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 Ab residue 367 ILE 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 272 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 Cb residue 22 ARG Chi-restraints excluded: chain Cb residue 246 VAL Chi-restraints excluded: chain Cb residue 253 LEU 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 62 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 173 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ba 164 ASN Bb 14 ASN ** Ac 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 59 GLN Cb 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.086265 restraints weight = 25580.652| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.43 r_work: 0.2881 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 1.0017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 22128 Z= 0.196 Angle : 0.802 59.085 30219 Z= 0.470 Chirality : 0.046 0.686 3327 Planarity : 0.005 0.106 3756 Dihedral : 5.115 52.737 2898 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 2.29 % Allowed : 19.69 % Favored : 78.02 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.16), residues: 2664 helix: 1.91 (0.14), residues: 1314 sheet: 0.29 (0.24), residues: 429 loop : -0.17 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAc 198 HIS 0.010 0.001 HISCa 133 PHE 0.025 0.002 PHEAc 200 TYR 0.024 0.002 TYRCb 157 ARG 0.006 0.000 ARGAa 298 Details of bonding type rmsd hydrogen bonds : bond 0.05058 ( 1212) hydrogen bonds : angle 4.82597 ( 3519) covalent geometry : bond 0.00400 (22128) covalent geometry : angle 0.80214 (30219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15866.67 seconds wall clock time: 277 minutes 5.92 seconds (16625.92 seconds total)