Starting phenix.real_space_refine on Sat Oct 24 13:10:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9shw_54918/10_2026/9shw_54918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9shw_54918/10_2026/9shw_54918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9shw_54918/10_2026/9shw_54918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9shw_54918/10_2026/9shw_54918.map" model { file = "/net/cci-nas-00/data/ceres_data/9shw_54918/10_2026/9shw_54918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9shw_54918/10_2026/9shw_54918.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 8262 2.51 5 N 2187 2.21 5 O 2568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13095 Number of models: 1 Model: "" Number of chains: 6 Chain: "Aa" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3468 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 16, 'TRANS': 433} Chain breaks: 1 Chain: "Ab" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3468 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 16, 'TRANS': 433} Chain breaks: 1 Chain: "Ac" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3468 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 16, 'TRANS': 433} Chain breaks: 1 Chain: "Ba" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "Bb" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "Bc" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Time building chain proxies: 2.91, per 1000 atoms: 0.22 Number of scatterers: 13095 At special positions: 0 Unit cell: (116.748, 116.748, 123.372, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 2568 8.00 N 2187 7.00 C 8262 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYSAa 104 " - pdb=" SG CYSAa 114 " distance=2.03 Simple disulfide: pdb=" SG CYSAa 331 " - pdb=" SG CYSAa 340 " distance=2.03 Simple disulfide: pdb=" SG CYSAa 355 " - pdb=" SG CYSAa 363 " distance=2.02 Simple disulfide: pdb=" SG CYSAa 387 " - pdb=" SG CYSAa 392 " distance=2.03 Simple disulfide: pdb=" SG CYSAb 104 " - pdb=" SG CYSAb 114 " distance=2.03 Simple disulfide: pdb=" SG CYSAb 331 " - pdb=" SG CYSAb 340 " distance=2.03 Simple disulfide: pdb=" SG CYSAb 355 " - pdb=" SG CYSAb 363 " distance=2.02 Simple disulfide: pdb=" SG CYSAb 387 " - pdb=" SG CYSAb 392 " distance=2.03 Simple disulfide: pdb=" SG CYSAc 104 " - pdb=" SG CYSAc 114 " distance=2.03 Simple disulfide: pdb=" SG CYSAc 331 " - pdb=" SG CYSAc 340 " distance=2.03 Simple disulfide: pdb=" SG CYSAc 355 " - pdb=" SG CYSAc 363 " distance=2.02 Simple disulfide: pdb=" SG CYSAc 387 " - pdb=" SG CYSAc 392 " distance=2.03 Simple disulfide: pdb=" SG CYSBa 22 " - pdb=" SG CYSBa 94 " distance=2.03 Simple disulfide: pdb=" SG CYSBb 22 " - pdb=" SG CYSBb 94 " distance=2.03 Simple disulfide: pdb=" SG CYSBc 22 " - pdb=" SG CYSBc 94 " distance=2.03 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: 0.97 Conformation dependent library (CDL) restraints added in 611.5 milliseconds 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3174 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 24 sheets defined 34.6% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'Aa' and resid 29 through 36 removed outlier: 3.517A pdb=" N LYSAa 35 " --> pdb=" O GLUAa 31 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILEAa 36 " --> pdb=" O LYSAa 32 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 65 through 72 removed outlier: 3.729A pdb=" N SERAa 69 " --> pdb=" O SERAa 66 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLNAa 70 " --> pdb=" O ASNAa 67 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THRAa 72 " --> pdb=" O SERAa 69 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 74 through 99 Proline residue: Aa 89 - end of helix removed outlier: 4.176A pdb=" N TYRAa 97 " --> pdb=" O ALAAa 93 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 117 through 121 Processing helix chain 'Aa' and resid 125 through 137 Processing helix chain 'Aa' and resid 137 through 146 Processing helix chain 'Aa' and resid 147 through 153 Processing helix chain 'Aa' and resid 175 through 182 Processing helix chain 'Aa' and resid 183 through 187 Processing helix chain 'Aa' and resid 191 through 215 removed outlier: 4.348A pdb=" N PHEAa 212 " --> pdb=" O SERAa 208 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VALAa 213 " --> pdb=" O ASPAa 209 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 227 through 232 Processing helix chain 'Aa' and resid 233 through 236 Processing helix chain 'Aa' and resid 238 through 247 removed outlier: 3.736A pdb=" N LEUAa 242 " --> pdb=" O ASNAa 238 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 252 through 259 Processing helix chain 'Aa' and resid 328 through 331 Processing helix chain 'Aa' and resid 349 through 357 Processing helix chain 'Aa' and resid 358 through 363 removed outlier: 5.404A pdb=" N GLUAa 361 " --> pdb=" O GLYAa 358 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 452 through 481 removed outlier: 3.678A pdb=" N SERAa 457 " --> pdb=" O LYSAa 453 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 29 through 36 removed outlier: 3.640A pdb=" N ILEAb 36 " --> pdb=" O LYSAb 32 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 65 through 72 removed outlier: 3.717A pdb=" N SERAb 69 " --> pdb=" O SERAb 66 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLNAb 70 " --> pdb=" O ASNAb 67 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THRAb 72 " --> pdb=" O SERAb 69 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 74 through 99 Proline residue: Ab 89 - end of helix removed outlier: 4.138A pdb=" N TYRAb 97 " --> pdb=" O ALAAb 93 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 117 through 121 Processing helix chain 'Ab' and resid 125 through 137 Processing helix chain 'Ab' and resid 137 through 146 Processing helix chain 'Ab' and resid 147 through 153 Processing helix chain 'Ab' and resid 175 through 182 Processing helix chain 'Ab' and resid 183 through 187 Processing helix chain 'Ab' and resid 191 through 215 removed outlier: 4.315A pdb=" N PHEAb 212 " --> pdb=" O SERAb 208 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VALAb 213 " --> pdb=" O ASPAb 209 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 227 through 232 Processing helix chain 'Ab' and resid 233 through 236 Processing helix chain 'Ab' and resid 238 through 246 removed outlier: 3.699A pdb=" N LEUAb 242 " --> pdb=" O ASNAb 238 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 252 through 259 Processing helix chain 'Ab' and resid 328 through 331 Processing helix chain 'Ab' and resid 349 through 357 Processing helix chain 'Ab' and resid 358 through 363 removed outlier: 5.391A pdb=" N GLUAb 361 " --> pdb=" O GLYAb 358 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 452 through 481 removed outlier: 3.686A pdb=" N SERAb 457 " --> pdb=" O LYSAb 453 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 29 through 36 removed outlier: 3.538A pdb=" N LYSAc 35 " --> pdb=" O GLUAc 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILEAc 36 " --> pdb=" O LYSAc 32 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 65 through 72 removed outlier: 3.674A pdb=" N SERAc 69 " --> pdb=" O SERAc 66 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLNAc 70 " --> pdb=" O ASNAc 67 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THRAc 72 " --> pdb=" O SERAc 69 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 74 through 99 Proline residue: Ac 89 - end of helix removed outlier: 4.152A pdb=" N TYRAc 97 " --> pdb=" O ALAAc 93 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 117 through 121 Processing helix chain 'Ac' and resid 125 through 137 Processing helix chain 'Ac' and resid 137 through 146 Processing helix chain 'Ac' and resid 147 through 153 Processing helix chain 'Ac' and resid 175 through 182 Processing helix chain 'Ac' and resid 183 through 187 Processing helix chain 'Ac' and resid 191 through 215 removed outlier: 4.316A pdb=" N PHEAc 212 " --> pdb=" O SERAc 208 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VALAc 213 " --> pdb=" O ASPAc 209 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 227 through 232 Processing helix chain 'Ac' and resid 233 through 236 Processing helix chain 'Ac' and resid 238 through 246 removed outlier: 3.657A pdb=" N LEUAc 242 " --> pdb=" O ASNAc 238 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 252 through 259 Processing helix chain 'Ac' and resid 328 through 331 Processing helix chain 'Ac' and resid 349 through 357 Processing helix chain 'Ac' and resid 358 through 363 removed outlier: 5.395A pdb=" N GLUAc 361 " --> pdb=" O GLYAc 358 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 452 through 481 removed outlier: 3.674A pdb=" N SERAc 457 " --> pdb=" O LYSAc 453 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 85 through 89 Processing helix chain 'Bb' and resid 85 through 89 Processing helix chain 'Bc' and resid 85 through 89 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 158 through 162 removed outlier: 16.933A pdb=" N THRAa 168 " --> pdb=" O PROAa 52 " (cutoff:3.500A) removed outlier: 11.473A pdb=" N THRAa 54 " --> pdb=" O THRAa 168 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N TYRAa 170 " --> pdb=" O THRAa 54 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASPAa 56 " --> pdb=" O TYRAa 170 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N PHEAa 172 " --> pdb=" O ASPAa 56 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VALAa 58 " --> pdb=" O PHEAa 172 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEUAa 38 " --> pdb=" O LEUAa 296 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEUAa 296 " --> pdb=" O LEUAa 38 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LYSAa 40 " --> pdb=" O GLNAa 294 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N GLNAa 294 " --> pdb=" O LYSAa 40 " (cutoff:3.500A) removed outlier: 11.081A pdb=" N VALAa 42 " --> pdb=" O TYRAa 292 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N TYRAa 292 " --> pdb=" O VALAa 42 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N ARGAa 44 " --> pdb=" O GLNAa 290 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N GLNAa 290 " --> pdb=" O ARGAa 44 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYRAa 46 " --> pdb=" O ILEAa 288 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N PHEAa 282 " --> pdb=" O PROAa 52 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THRAa 54 " --> pdb=" O VALAa 280 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VALAa 280 " --> pdb=" O THRAa 54 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASPAa 56 " --> pdb=" O VALAa 278 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VALAa 278 " --> pdb=" O ASPAa 56 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VALAa 58 " --> pdb=" O ILEAa 276 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILEAa 276 " --> pdb=" O VALAa 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Aa' and resid 275 through 298 current: chain 'Aa' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'Aa' and resid 263 through 270 removed outlier: 3.513A pdb=" N THRAa 263 " --> pdb=" O TYRAa 281 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILEAa 277 " --> pdb=" O ILEAa 267 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VALAa 269 " --> pdb=" O TYRAa 275 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYRAa 275 " --> pdb=" O VALAa 269 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILEAa 276 " --> pdb=" O VALAa 58 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VALAa 58 " --> pdb=" O ILEAa 276 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VALAa 278 " --> pdb=" O ASPAa 56 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASPAa 56 " --> pdb=" O VALAa 278 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VALAa 280 " --> pdb=" O THRAa 54 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THRAa 54 " --> pdb=" O VALAa 280 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N PHEAa 282 " --> pdb=" O PROAa 52 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYRAa 46 " --> pdb=" O ILEAa 288 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N GLNAa 290 " --> pdb=" O ARGAa 44 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N ARGAa 44 " --> pdb=" O GLNAa 290 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N TYRAa 292 " --> pdb=" O VALAa 42 " (cutoff:3.500A) removed outlier: 11.081A pdb=" N VALAa 42 " --> pdb=" O TYRAa 292 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N GLNAa 294 " --> pdb=" O LYSAa 40 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LYSAa 40 " --> pdb=" O GLNAa 294 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEUAa 296 " --> pdb=" O LEUAa 38 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEUAa 38 " --> pdb=" O LEUAa 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Aa' and resid 38 through 60 current: chain 'Aa' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'Aa' and resid 101 through 103 removed outlier: 6.011A pdb=" N VALAa 113 " --> pdb=" O ILEAb 426 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N SERAb 428 " --> pdb=" O VALAa 113 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N METAa 115 " --> pdb=" O SERAb 428 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYSAb 392 " --> pdb=" O ILEAb 401 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Aa' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'Aa' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'Aa' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'Aa' and resid 393 through 394 Processing sheet with id=AA8, first strand: chain 'Ab' and resid 158 through 162 removed outlier: 10.061A pdb=" N THRAb 168 " --> pdb=" O THRAb 54 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASPAb 56 " --> pdb=" O THRAb 168 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYRAb 170 " --> pdb=" O ASPAb 56 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLUAb 295 " --> pdb=" O GLYAb 41 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THRAb 43 " --> pdb=" O ILEAb 293 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILEAb 293 " --> pdb=" O THRAb 43 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LYSAb 45 " --> pdb=" O ALAAb 291 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ALAAb 291 " --> pdb=" O LYSAb 45 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N LYSAb 47 " --> pdb=" O GLNAb 289 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N GLNAb 289 " --> pdb=" O LYSAb 47 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N LYSAb 49 " --> pdb=" O GLUAb 287 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLUAb 287 " --> pdb=" O LYSAb 49 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N ASNAb 51 " --> pdb=" O LEUAb 285 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEUAb 285 " --> pdb=" O ASNAb 51 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEUAb 53 " --> pdb=" O PROAb 283 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYSAb 55 " --> pdb=" O TYRAb 281 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYRAb 281 " --> pdb=" O LYSAb 55 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILEAb 57 " --> pdb=" O ARGAb 279 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ARGAb 279 " --> pdb=" O ILEAb 57 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILEAb 59 " --> pdb=" O ILEAb 277 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILEAb 277 " --> pdb=" O ILEAb 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Ab' and resid 275 through 298 current: chain 'Ab' and resid 332 through 333 Processing sheet with id=AA9, first strand: chain 'Ab' and resid 263 through 270 removed outlier: 3.520A pdb=" N THRAb 263 " --> pdb=" O TYRAb 281 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILEAb 277 " --> pdb=" O ILEAb 267 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VALAb 269 " --> pdb=" O TYRAb 275 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYRAb 275 " --> pdb=" O VALAb 269 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILEAb 277 " --> pdb=" O ILEAb 59 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILEAb 59 " --> pdb=" O ILEAb 277 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ARGAb 279 " --> pdb=" O ILEAb 57 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILEAb 57 " --> pdb=" O ARGAb 279 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYRAb 281 " --> pdb=" O LYSAb 55 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYSAb 55 " --> pdb=" O TYRAb 281 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEUAb 53 " --> pdb=" O PROAb 283 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEUAb 285 " --> pdb=" O ASNAb 51 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N ASNAb 51 " --> pdb=" O LEUAb 285 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLUAb 287 " --> pdb=" O LYSAb 49 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N LYSAb 49 " --> pdb=" O GLUAb 287 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N GLNAb 289 " --> pdb=" O LYSAb 47 " (cutoff:3.500A) removed outlier: 9.646A pdb=" N LYSAb 47 " --> pdb=" O GLNAb 289 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ALAAb 291 " --> pdb=" O LYSAb 45 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LYSAb 45 " --> pdb=" O ALAAb 291 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILEAb 293 " --> pdb=" O THRAb 43 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THRAb 43 " --> pdb=" O ILEAb 293 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLUAb 295 " --> pdb=" O GLYAb 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Ab' and resid 38 through 60 current: chain 'Ab' and resid 322 through 326 Processing sheet with id=AB1, first strand: chain 'Ab' and resid 101 through 103 removed outlier: 6.031A pdb=" N VALAb 113 " --> pdb=" O ILEAc 426 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N SERAc 428 " --> pdb=" O VALAb 113 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N METAb 115 " --> pdb=" O SERAc 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Ab' and resid 123 through 124 Processing sheet with id=AB3, first strand: chain 'Ab' and resid 301 through 302 Processing sheet with id=AB4, first strand: chain 'Ac' and resid 158 through 162 removed outlier: 10.061A pdb=" N THRAc 168 " --> pdb=" O THRAc 54 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ASPAc 56 " --> pdb=" O THRAc 168 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYRAc 170 " --> pdb=" O ASPAc 56 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEUAc 38 " --> pdb=" O LEUAc 296 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEUAc 296 " --> pdb=" O LEUAc 38 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N LYSAc 40 " --> pdb=" O GLNAc 294 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N GLNAc 294 " --> pdb=" O LYSAc 40 " (cutoff:3.500A) removed outlier: 11.058A pdb=" N VALAc 42 " --> pdb=" O TYRAc 292 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N TYRAc 292 " --> pdb=" O VALAc 42 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N ARGAc 44 " --> pdb=" O GLNAc 290 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N GLNAc 290 " --> pdb=" O ARGAc 44 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TYRAc 46 " --> pdb=" O ILEAc 288 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHEAc 282 " --> pdb=" O PROAc 52 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THRAc 54 " --> pdb=" O VALAc 280 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VALAc 280 " --> pdb=" O THRAc 54 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASPAc 56 " --> pdb=" O VALAc 278 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VALAc 278 " --> pdb=" O ASPAc 56 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VALAc 58 " --> pdb=" O ILEAc 276 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILEAc 276 " --> pdb=" O VALAc 58 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Ac' and resid 275 through 298 current: chain 'Ac' and resid 332 through 333 Processing sheet with id=AB5, first strand: chain 'Ac' and resid 263 through 270 removed outlier: 3.519A pdb=" N THRAc 263 " --> pdb=" O TYRAc 281 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILEAc 277 " --> pdb=" O ILEAc 267 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VALAc 269 " --> pdb=" O TYRAc 275 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYRAc 275 " --> pdb=" O VALAc 269 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILEAc 276 " --> pdb=" O VALAc 58 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VALAc 58 " --> pdb=" O ILEAc 276 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VALAc 278 " --> pdb=" O ASPAc 56 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASPAc 56 " --> pdb=" O VALAc 278 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VALAc 280 " --> pdb=" O THRAc 54 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THRAc 54 " --> pdb=" O VALAc 280 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHEAc 282 " --> pdb=" O PROAc 52 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TYRAc 46 " --> pdb=" O ILEAc 288 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N GLNAc 290 " --> pdb=" O ARGAc 44 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N ARGAc 44 " --> pdb=" O GLNAc 290 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N TYRAc 292 " --> pdb=" O VALAc 42 " (cutoff:3.500A) removed outlier: 11.058A pdb=" N VALAc 42 " --> pdb=" O TYRAc 292 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N GLNAc 294 " --> pdb=" O LYSAc 40 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N LYSAc 40 " --> pdb=" O GLNAc 294 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEUAc 296 " --> pdb=" O LEUAc 38 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEUAc 38 " --> pdb=" O LEUAc 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Ac' and resid 38 through 60 current: chain 'Ac' and resid 322 through 326 Processing sheet with id=AB6, first strand: chain 'Ac' and resid 301 through 302 removed outlier: 6.118A pdb=" N ARGAc 365 " --> pdb=" O VALAc 449 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ba' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'Ba' and resid 11 through 12 removed outlier: 3.581A pdb=" N ALABa 33 " --> pdb=" O ASNBa 97 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASNBa 99 " --> pdb=" O ILEBa 31 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILEBa 31 " --> pdb=" O ASNBa 99 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N ASNBa 32 " --> pdb=" O SERBa 52 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SERBa 52 " --> pdb=" O ASNBa 32 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N METBa 34 " --> pdb=" O VALBa 50 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VALBa 50 " --> pdb=" O METBa 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRPBa 36 " --> pdb=" O VALBa 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Ba' and resid 11 through 12 removed outlier: 6.615A pdb=" N THRBa 100 " --> pdb=" O TRPBa 104 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TRPBa 104 " --> pdb=" O THRBa 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Bb' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'Bb' and resid 11 through 12 removed outlier: 3.582A pdb=" N ALABb 33 " --> pdb=" O ASNBb 97 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASNBb 99 " --> pdb=" O ILEBb 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILEBb 31 " --> pdb=" O ASNBb 99 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N ASNBb 32 " --> pdb=" O SERBb 52 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SERBb 52 " --> pdb=" O ASNBb 32 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N METBb 34 " --> pdb=" O VALBb 50 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VALBb 50 " --> pdb=" O METBb 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRPBb 36 " --> pdb=" O VALBb 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Bb' and resid 11 through 12 removed outlier: 6.605A pdb=" N THRBb 100 " --> pdb=" O TRPBb 104 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TRPBb 104 " --> pdb=" O THRBb 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Bc' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'Bc' and resid 11 through 12 removed outlier: 3.528A pdb=" N ALABc 33 " --> pdb=" O ASNBc 97 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASNBc 99 " --> pdb=" O ILEBc 31 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILEBc 31 " --> pdb=" O ASNBc 99 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N ASNBc 32 " --> pdb=" O SERBc 52 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SERBc 52 " --> pdb=" O ASNBc 32 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N METBc 34 " --> pdb=" O VALBc 50 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VALBc 50 " --> pdb=" O METBc 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRPBc 36 " --> pdb=" O VALBc 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Bc' and resid 11 through 12 removed outlier: 6.604A pdb=" N THRBc 100 " --> pdb=" O TRPBc 104 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRPBc 104 " --> pdb=" O THRBc 100 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1611 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: 1.73 Time building geometry restraints manager: 1.36 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: 4296 1.34 - 1.46: 2846 1.46 - 1.58: 6040 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 13296 Sorted by residual: bond pdb=" N LEUAa 28 " pdb=" CA LEUAa 28 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N LEUAb 28 " pdb=" CA LEUAb 28 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N LEUAc 28 " pdb=" CA LEUAc 28 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N VALBb 2 " pdb=" CA VALBb 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N VALBc 2 " pdb=" CA VALBc 2 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.73e+00 ... (remaining 13291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 17187 0.84 - 1.67: 723 1.67 - 2.51: 74 2.51 - 3.35: 40 3.35 - 4.18: 24 Bond angle restraints: 18048 Sorted by residual: angle pdb=" N VALBa 48 " pdb=" CA VALBa 48 " pdb=" C VALBa 48 " ideal model delta sigma weight residual 111.56 108.90 2.66 8.60e-01 1.35e+00 9.60e+00 angle pdb=" N VALBc 48 " pdb=" CA VALBc 48 " pdb=" C VALBc 48 " ideal model delta sigma weight residual 111.56 109.10 2.46 8.60e-01 1.35e+00 8.16e+00 angle pdb=" CA GLYBc 26 " pdb=" C GLYBc 26 " pdb=" N SERBc 27 " ideal model delta sigma weight residual 115.34 116.85 -1.51 8.40e-01 1.42e+00 3.25e+00 angle pdb=" CA GLYBc 26 " pdb=" C GLYBc 26 " pdb=" O GLYBc 26 " ideal model delta sigma weight residual 122.14 120.47 1.67 1.05e+00 9.07e-01 2.52e+00 angle pdb=" N ILEAc 426 " pdb=" CA ILEAc 426 " pdb=" C ILEAc 426 " ideal model delta sigma weight residual 108.11 106.08 2.03 1.40e+00 5.10e-01 2.11e+00 ... (remaining 18043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 7336 15.14 - 30.29: 597 30.29 - 45.43: 111 45.43 - 60.58: 47 60.58 - 75.72: 12 Dihedral angle restraints: 8103 sinusoidal: 3156 harmonic: 4947 Sorted by residual: dihedral pdb=" CB CYSAb 104 " pdb=" SG CYSAb 104 " pdb=" SG CYSAb 114 " pdb=" CB CYSAb 114 " ideal model delta sinusoidal sigma weight residual 93.00 128.60 -35.60 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" CB CYSAa 355 " pdb=" SG CYSAa 355 " pdb=" SG CYSAa 363 " pdb=" CB CYSAa 363 " ideal model delta sinusoidal sigma weight residual 93.00 123.96 -30.96 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CB CYSAc 355 " pdb=" SG CYSAc 355 " pdb=" SG CYSAc 363 " pdb=" CB CYSAc 363 " ideal model delta sinusoidal sigma weight residual 93.00 123.56 -30.56 1 1.00e+01 1.00e-02 1.33e+01 ... (remaining 8100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1293 0.029 - 0.059: 553 0.059 - 0.088: 95 0.088 - 0.118: 153 0.118 - 0.147: 51 Chirality restraints: 2145 Sorted by residual: chirality pdb=" CA ILEAc 426 " pdb=" N ILEAc 426 " pdb=" C ILEAc 426 " pdb=" CB ILEAc 426 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILEAc 293 " pdb=" N ILEAc 293 " pdb=" C ILEAc 293 " pdb=" CB ILEAc 293 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ILEAa 293 " pdb=" N ILEAa 293 " pdb=" C ILEAa 293 " pdb=" CB ILEAa 293 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 2142 not shown) Planarity restraints: 2304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLYAc 446 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PROAc 447 " -0.082 5.00e-02 4.00e+02 pdb=" CA PROAc 447 " 0.025 5.00e-02 4.00e+02 pdb=" CD PROAc 447 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLYAa 446 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PROAa 447 " -0.080 5.00e-02 4.00e+02 pdb=" CA PROAa 447 " 0.024 5.00e-02 4.00e+02 pdb=" CD PROAa 447 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLYAb 446 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PROAb 447 " -0.080 5.00e-02 4.00e+02 pdb=" CA PROAb 447 " 0.024 5.00e-02 4.00e+02 pdb=" CD PROAb 447 " 0.025 5.00e-02 4.00e+02 ... (remaining 2301 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 6336 2.98 - 3.46: 12580 3.46 - 3.94: 22058 3.94 - 4.42: 25028 4.42 - 4.90: 40676 Nonbonded interactions: 106678 Sorted by model distance: nonbonded pdb=" O LYSAa 35 " pdb=" OG1 THRAa 408 " model vdw 2.506 3.040 nonbonded pdb=" O LYSAb 35 " pdb=" OG1 THRAb 408 " model vdw 2.513 3.040 nonbonded pdb=" O LYSAc 35 " pdb=" OG1 THRAc 408 " model vdw 2.528 3.040 nonbonded pdb=" NH1 ARGAa 365 " pdb=" O GLYAa 446 " model vdw 2.541 3.120 nonbonded pdb=" O CYSAb 387 " pdb=" O VALAb 390 " model vdw 2.545 3.040 ... (remaining 106673 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: 0.02 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' } ncs_group { reference = chain 'Ba' selection = chain 'Bb' selection = chain 'Bc' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.750 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 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 : 0.002 0.033 13311 Z= 0.109 Angle : 0.424 4.184 18078 Z= 0.230 Chirality : 0.044 0.147 2145 Planarity : 0.003 0.047 2304 Dihedral : 12.356 75.723 4884 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1686 helix: 1.49 (0.24), residues: 468 sheet: 0.36 (0.27), residues: 393 loop : 0.14 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAc 244 TYR 0.006 0.001 TYRAb 248 PHE 0.006 0.001 PHEBb 66 TRP 0.008 0.001 TRPBc 104 HIS 0.004 0.001 HISAc 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (13296) covalent geometry : angle 0.42217 / 0.23 (18048) SS BOND : bond 0.00343 / 0.20 ( 15) SS BOND : angle 1.10317 / 0.71 ( 30) hydrogen bonds : bond 0.20512 / 13.27 ( 580) hydrogen bonds : angle 7.99575 / 5.68 ( 1611) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.516 Fit side-chains REVERT: Aa 189 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8353 (mmtm) REVERT: Aa 251 GLU cc_start: 0.8500 (pm20) cc_final: 0.8214 (pm20) REVERT: Aa 335 LYS cc_start: 0.9163 (tttt) cc_final: 0.8636 (tptp) REVERT: Aa 352 MET cc_start: 0.9206 (tpp) cc_final: 0.8931 (tpp) REVERT: Ab 251 GLU cc_start: 0.8562 (pm20) cc_final: 0.8267 (pm20) REVERT: Ab 335 LYS cc_start: 0.9213 (tttt) cc_final: 0.8597 (tptp) REVERT: Ac 335 LYS cc_start: 0.9268 (tttt) cc_final: 0.8652 (tptp) REVERT: Ba 46 GLU cc_start: 0.9054 (pt0) cc_final: 0.8805 (pt0) REVERT: Ba 71 ASP cc_start: 0.8202 (t70) cc_final: 0.7919 (t70) REVERT: Ba 80 GLN cc_start: 0.8959 (tp40) cc_final: 0.8688 (tp40) REVERT: Bb 18 LEU cc_start: 0.8583 (tp) cc_final: 0.8324 (tp) REVERT: Bb 25 LEU cc_start: 0.9178 (mt) cc_final: 0.8895 (mt) REVERT: Bb 71 ASP cc_start: 0.8450 (t70) cc_final: 0.8080 (t70) REVERT: Bb 108 TYR cc_start: 0.9069 (m-80) cc_final: 0.8794 (m-80) REVERT: Bc 71 ASP cc_start: 0.8529 (t0) cc_final: 0.7927 (t70) REVERT: Bc 106 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7855 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.7690 time to fit residues: 160.4428 Evaluate side-chains 170 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ba 57 ASN Bb 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.079383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.058057 restraints weight = 20585.776| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 1.85 r_work: 0.2345 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2211 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9474 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13311 Z= 0.232 Angle : 0.523 5.708 18078 Z= 0.280 Chirality : 0.048 0.151 2145 Planarity : 0.004 0.045 2304 Dihedral : 4.309 15.882 1830 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.35 % Allowed : 5.67 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1686 helix: 2.27 (0.25), residues: 450 sheet: 0.43 (0.26), residues: 417 loop : -0.03 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAa 365 TYR 0.012 0.001 TYRAa 275 PHE 0.010 0.001 PHEBb 105 TRP 0.013 0.002 TRPBc 104 HIS 0.001 0.000 HISAa 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.23 (13296) covalent geometry : angle 0.51684 / 0.28 (18048) SS BOND : bond 0.00321 / 0.19 ( 15) SS BOND : angle 2.06435 / 1.21 ( 30) hydrogen bonds : bond 0.04976 / 3.20 ( 580) hydrogen bonds : angle 5.61265 / 3.99 ( 1611) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.508 Fit side-chains REVERT: Aa 335 LYS cc_start: 0.9253 (tttt) cc_final: 0.8967 (tptp) REVERT: Ab 244 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8644 (ttp-170) REVERT: Ab 335 LYS cc_start: 0.9283 (tttt) cc_final: 0.8995 (tptp) REVERT: Ac 335 LYS cc_start: 0.9313 (tttt) cc_final: 0.9014 (tptp) REVERT: Ac 395 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: Ba 46 GLU cc_start: 0.9092 (pt0) cc_final: 0.8875 (pt0) REVERT: Ba 71 ASP cc_start: 0.8295 (t70) cc_final: 0.8014 (t70) REVERT: Bb 13 GLN cc_start: 0.8624 (tp40) cc_final: 0.8396 (mm-40) REVERT: Bb 71 ASP cc_start: 0.8493 (t70) cc_final: 0.8115 (t70) outliers start: 20 outliers final: 8 residues processed: 183 average time/residue: 0.7537 time to fit residues: 147.5490 Evaluate side-chains 181 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 114 CYS Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 244 ARG Chi-restraints excluded: chain Ab residue 327 GLU Chi-restraints excluded: chain Ab residue 443 ILE Chi-restraints excluded: chain Ac residue 114 CYS Chi-restraints excluded: chain Ac residue 395 GLN Chi-restraints excluded: chain Bb residue 67 THR Chi-restraints excluded: chain Bb residue 116 THR Chi-restraints excluded: chain Bc residue 67 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [114, 112, 153, 127, 76, 3, 126, 31, 33, 44, 29] chunk 114 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 0.0170 chunk 126 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 224 ASN Ac 320 ASN ** Bb 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.079741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.058385 restraints weight = 20734.552| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 1.85 r_work: 0.2353 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2217 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9470 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13311 Z= 0.190 Angle : 0.488 5.309 18078 Z= 0.262 Chirality : 0.047 0.152 2145 Planarity : 0.004 0.037 2304 Dihedral : 4.262 15.905 1830 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.62 % Allowed : 6.88 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1686 helix: 2.48 (0.25), residues: 450 sheet: 0.52 (0.25), residues: 417 loop : -0.06 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGBc 19 TYR 0.010 0.001 TYRAa 275 PHE 0.009 0.001 PHEBb 105 TRP 0.010 0.002 TRPBc 104 HIS 0.001 0.000 HISAb 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 (13296) covalent geometry : angle 0.48422 / 0.26 (18048) SS BOND : bond 0.00246 / 0.15 ( 15) SS BOND : angle 1.62243 / 0.94 ( 30) hydrogen bonds : bond 0.04347 / 2.81 ( 580) hydrogen bonds : angle 5.22495 / 3.72 ( 1611) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.525 Fit side-chains REVERT: Aa 335 LYS cc_start: 0.9245 (tttt) cc_final: 0.8958 (tptp) REVERT: Ab 335 LYS cc_start: 0.9282 (tttt) cc_final: 0.8986 (tptp) REVERT: Ac 335 LYS cc_start: 0.9310 (tttt) cc_final: 0.9015 (tptp) REVERT: Ac 395 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: Ba 46 GLU cc_start: 0.9092 (pt0) cc_final: 0.8886 (pt0) REVERT: Ba 71 ASP cc_start: 0.8209 (t70) cc_final: 0.7886 (t70) REVERT: Bb 13 GLN cc_start: 0.8612 (tp40) cc_final: 0.8382 (mm-40) REVERT: Bb 71 ASP cc_start: 0.8408 (t70) cc_final: 0.8171 (t70) outliers start: 24 outliers final: 5 residues processed: 179 average time/residue: 0.7880 time to fit residues: 150.6588 Evaluate side-chains 171 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 165 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 443 ILE Chi-restraints excluded: chain Ac residue 395 GLN Chi-restraints excluded: chain Ba residue 18 LEU Chi-restraints excluded: chain Ba residue 67 THR Chi-restraints excluded: chain Bb residue 67 THR Chi-restraints excluded: chain Bc residue 67 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [47, 6, 37, 28, 60, 59, 131, 90, 76, 87, 138] chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 138 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 320 ASN Bb 3 GLN Bc 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.081562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.060280 restraints weight = 20832.530| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 1.87 r_work: 0.2398 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2265 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9444 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13311 Z= 0.106 Angle : 0.446 7.911 18078 Z= 0.239 Chirality : 0.044 0.152 2145 Planarity : 0.003 0.036 2304 Dihedral : 4.011 16.362 1830 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.55 % Allowed : 8.23 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.20), residues: 1686 helix: 2.72 (0.25), residues: 450 sheet: 0.55 (0.26), residues: 405 loop : 0.03 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGBa 19 TYR 0.007 0.001 TYRAc 438 PHE 0.007 0.001 PHEAc 376 TRP 0.006 0.001 TRPBc 104 HIS 0.002 0.000 HISAb 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (13296) covalent geometry : angle 0.44402 / 0.24 (18048) SS BOND : bond 0.00187 / 0.12 ( 15) SS BOND : angle 1.20860 / 0.71 ( 30) hydrogen bonds : bond 0.03414 / 2.22 ( 580) hydrogen bonds : angle 4.83889 / 3.45 ( 1611) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.440 Fit side-chains REVERT: Aa 335 LYS cc_start: 0.9209 (tttt) cc_final: 0.8930 (tptp) REVERT: Ab 335 LYS cc_start: 0.9262 (tttt) cc_final: 0.8948 (tptp) REVERT: Ac 226 MET cc_start: 0.9207 (ttp) cc_final: 0.8881 (ttp) REVERT: Ac 335 LYS cc_start: 0.9285 (tttt) cc_final: 0.9076 (tptp) REVERT: Ac 395 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: Ba 71 ASP cc_start: 0.8088 (t70) cc_final: 0.7787 (OUTLIER) REVERT: Bb 13 GLN cc_start: 0.8605 (tp40) cc_final: 0.8368 (mm-40) REVERT: Bb 71 ASP cc_start: 0.8298 (t70) cc_final: 0.7926 (t70) REVERT: Bb 81 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8836 (mtm) REVERT: Bc 70 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8142 (ttp80) REVERT: Bc 71 ASP cc_start: 0.8386 (t70) cc_final: 0.8060 (t70) outliers start: 23 outliers final: 10 residues processed: 186 average time/residue: 0.7625 time to fit residues: 151.5959 Evaluate side-chains 181 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 114 CYS Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ac residue 114 CYS Chi-restraints excluded: chain Ac residue 395 GLN Chi-restraints excluded: chain Ba residue 18 LEU Chi-restraints excluded: chain Ba residue 67 THR Chi-restraints excluded: chain Bb residue 67 THR Chi-restraints excluded: chain Bb residue 81 MET Chi-restraints excluded: chain Bc residue 2 VAL Chi-restraints excluded: chain Bc residue 18 LEU Chi-restraints excluded: chain Bc residue 67 THR Chi-restraints excluded: chain Bc residue 70 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [10, 0, 112, 141, 88, 84, 34, 116, 152, 107, 160] chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Bb 3 GLN Bc 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.078810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.057392 restraints weight = 20913.881| |-----------------------------------------------------------------------------| r_work (start): 0.2477 rms_B_bonded: 1.85 r_work: 0.2330 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2195 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9483 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13311 Z= 0.275 Angle : 0.542 5.576 18078 Z= 0.288 Chirality : 0.049 0.154 2145 Planarity : 0.004 0.037 2304 Dihedral : 4.424 16.881 1830 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.69 % Allowed : 8.91 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1686 helix: 2.51 (0.25), residues: 468 sheet: 0.50 (0.25), residues: 420 loop : -0.03 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGBa 19 TYR 0.013 0.002 TYRAa 275 PHE 0.012 0.001 PHEBb 105 TRP 0.014 0.002 TRPBc 104 HIS 0.002 0.000 HISAb 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.28 (13296) covalent geometry : angle 0.53834 / 0.29 (18048) SS BOND : bond 0.00303 / 0.19 ( 15) SS BOND : angle 1.61281 / 0.93 ( 30) hydrogen bonds : bond 0.04646 / 3.00 ( 580) hydrogen bonds : angle 5.13496 / 3.65 ( 1611) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.529 Fit side-chains REVERT: Aa 335 LYS cc_start: 0.9233 (tttt) cc_final: 0.8959 (tptp) REVERT: Ab 335 LYS cc_start: 0.9252 (tttt) cc_final: 0.8993 (tptp) REVERT: Ac 335 LYS cc_start: 0.9304 (tttt) cc_final: 0.9101 (tptp) REVERT: Ac 395 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: Ba 71 ASP cc_start: 0.8170 (t70) cc_final: 0.7841 (t70) REVERT: Bb 13 GLN cc_start: 0.8636 (tp40) cc_final: 0.8420 (mm-40) REVERT: Bb 71 ASP cc_start: 0.8357 (t70) cc_final: 0.8046 (t70) REVERT: Bc 29 TYR cc_start: 0.8909 (m-10) cc_final: 0.8656 (m-80) REVERT: Bc 70 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8291 (ttp80) REVERT: Bc 71 ASP cc_start: 0.8329 (t70) cc_final: 0.7862 (t70) REVERT: Bc 74 LYS cc_start: 0.9121 (pttm) cc_final: 0.8684 (pmtt) outliers start: 25 outliers final: 10 residues processed: 173 average time/residue: 0.7931 time to fit residues: 146.5365 Evaluate side-chains 173 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 114 CYS Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 443 ILE Chi-restraints excluded: chain Ac residue 114 CYS Chi-restraints excluded: chain Ac residue 395 GLN Chi-restraints excluded: chain Ba residue 18 LEU Chi-restraints excluded: chain Ba residue 67 THR Chi-restraints excluded: chain Bb residue 67 THR Chi-restraints excluded: chain Bc residue 2 VAL Chi-restraints excluded: chain Bc residue 18 LEU Chi-restraints excluded: chain Bc residue 67 THR Chi-restraints excluded: chain Bc residue 70 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [17, 94, 35, 70, 63, 122, 33, 53, 13, 162, 103] chunk 17 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Bb 3 GLN Bc 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.080488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.059157 restraints weight = 20626.760| |-----------------------------------------------------------------------------| r_work (start): 0.2505 rms_B_bonded: 1.85 r_work: 0.2364 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2232 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9457 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13311 Z= 0.143 Angle : 0.470 8.473 18078 Z= 0.250 Chirality : 0.045 0.153 2145 Planarity : 0.003 0.037 2304 Dihedral : 4.151 15.176 1830 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.21 % Allowed : 10.05 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1686 helix: 2.76 (0.25), residues: 450 sheet: 0.52 (0.25), residues: 420 loop : -0.08 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGBa 19 TYR 0.008 0.001 TYRAc 248 PHE 0.008 0.001 PHEAc 376 TRP 0.007 0.001 TRPBc 104 HIS 0.001 0.000 HISAb 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (13296) covalent geometry : angle 0.46797 / 0.25 (18048) SS BOND : bond 0.00261 / 0.15 ( 15) SS BOND : angle 1.20285 / 0.71 ( 30) hydrogen bonds : bond 0.03645 / 2.36 ( 580) hydrogen bonds : angle 4.82089 / 3.43 ( 1611) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.417 Fit side-chains REVERT: Aa 335 LYS cc_start: 0.9206 (tttt) cc_final: 0.8940 (tptp) REVERT: Ab 335 LYS cc_start: 0.9259 (tttt) cc_final: 0.8950 (tptp) REVERT: Ac 335 LYS cc_start: 0.9291 (tttt) cc_final: 0.9010 (tptp) REVERT: Ac 395 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: Ba 71 ASP cc_start: 0.8131 (t70) cc_final: 0.7850 (t70) REVERT: Bb 71 ASP cc_start: 0.8226 (t70) cc_final: 0.7922 (t70) REVERT: Bc 29 TYR cc_start: 0.8863 (m-10) cc_final: 0.8583 (m-80) outliers start: 18 outliers final: 9 residues processed: 170 average time/residue: 0.7775 time to fit residues: 141.1671 Evaluate side-chains 170 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 443 ILE Chi-restraints excluded: chain Ab residue 445 ILE Chi-restraints excluded: chain Ac residue 114 CYS Chi-restraints excluded: chain Ac residue 395 GLN Chi-restraints excluded: chain Ba residue 18 LEU Chi-restraints excluded: chain Bb residue 67 THR Chi-restraints excluded: chain Bc residue 2 VAL Chi-restraints excluded: chain Bc residue 18 LEU Chi-restraints excluded: chain Bc residue 67 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [56, 153, 71, 21, 155, 141, 19, 74, 77, 46, 22] chunk 56 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 22 optimal weight: 0.0970 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Bb 3 GLN Bc 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.080675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.059332 restraints weight = 20728.246| |-----------------------------------------------------------------------------| r_work (start): 0.2519 rms_B_bonded: 1.86 r_work: 0.2375 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2240 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9458 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13311 Z= 0.136 Angle : 0.468 6.292 18078 Z= 0.249 Chirality : 0.045 0.155 2145 Planarity : 0.003 0.036 2304 Dihedral : 4.105 14.992 1830 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.48 % Allowed : 10.12 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1686 helix: 2.82 (0.25), residues: 450 sheet: 0.53 (0.25), residues: 420 loop : -0.07 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGBa 55 TYR 0.010 0.001 TYRAc 248 PHE 0.008 0.001 PHEAc 376 TRP 0.007 0.001 TRPBc 104 HIS 0.001 0.000 HISAb 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (13296) covalent geometry : angle 0.46553 / 0.25 (18048) SS BOND : bond 0.00181 / 0.11 ( 15) SS BOND : angle 1.29356 / 0.76 ( 30) hydrogen bonds : bond 0.03573 / 2.32 ( 580) hydrogen bonds : angle 4.74982 / 3.38 ( 1611) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.537 Fit side-chains REVERT: Aa 335 LYS cc_start: 0.9220 (tttt) cc_final: 0.8940 (tptp) REVERT: Ab 335 LYS cc_start: 0.9275 (tttt) cc_final: 0.8979 (tptp) REVERT: Ac 335 LYS cc_start: 0.9310 (tttt) cc_final: 0.9012 (tptp) REVERT: Ac 395 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: Ba 71 ASP cc_start: 0.8109 (t70) cc_final: 0.7764 (t70) REVERT: Ba 74 LYS cc_start: 0.9109 (pttm) cc_final: 0.8868 (pmtt) REVERT: Bb 6 GLU cc_start: 0.8703 (mp0) cc_final: 0.8278 (mt-10) REVERT: Bb 71 ASP cc_start: 0.8126 (t70) cc_final: 0.7709 (t70) REVERT: Bb 74 LYS cc_start: 0.9169 (pttm) cc_final: 0.8816 (pmtt) REVERT: Bc 29 TYR cc_start: 0.8879 (m-10) cc_final: 0.8598 (m-80) outliers start: 22 outliers final: 8 residues processed: 171 average time/residue: 0.7838 time to fit residues: 143.1509 Evaluate side-chains 167 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 114 CYS Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 443 ILE Chi-restraints excluded: chain Ac residue 114 CYS Chi-restraints excluded: chain Ac residue 395 GLN Chi-restraints excluded: chain Ba residue 18 LEU Chi-restraints excluded: chain Bb residue 67 THR Chi-restraints excluded: chain Bc residue 2 VAL Chi-restraints excluded: chain Bc residue 67 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [101, 93, 27, 116, 57, 147, 66, 55, 89, 148, 51] chunk 101 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 116 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Bb 3 GLN Bc 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.079633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.058235 restraints weight = 20610.743| |-----------------------------------------------------------------------------| r_work (start): 0.2485 rms_B_bonded: 1.86 r_work: 0.2342 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2207 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9472 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13311 Z= 0.206 Angle : 0.509 8.540 18078 Z= 0.269 Chirality : 0.047 0.167 2145 Planarity : 0.004 0.036 2304 Dihedral : 4.275 16.408 1830 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.35 % Allowed : 10.32 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1686 helix: 2.77 (0.25), residues: 450 sheet: 0.49 (0.24), residues: 420 loop : -0.12 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGBa 55 TYR 0.012 0.001 TYRAc 248 PHE 0.010 0.001 PHEBb 105 TRP 0.011 0.002 TRPBc 104 HIS 0.002 0.000 HISAb 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (13296) covalent geometry : angle 0.50603 / 0.27 (18048) SS BOND : bond 0.00207 / 0.13 ( 15) SS BOND : angle 1.40345 / 0.83 ( 30) hydrogen bonds : bond 0.04077 / 2.64 ( 580) hydrogen bonds : angle 4.89081 / 3.47 ( 1611) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.520 Fit side-chains REVERT: Aa 335 LYS cc_start: 0.9233 (tttt) cc_final: 0.8957 (tptp) REVERT: Ab 335 LYS cc_start: 0.9264 (tttt) cc_final: 0.8989 (tptp) REVERT: Ac 335 LYS cc_start: 0.9299 (tttt) cc_final: 0.9022 (tptp) REVERT: Ac 395 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: Ba 71 ASP cc_start: 0.8131 (t70) cc_final: 0.7823 (t70) REVERT: Bb 6 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: Bb 71 ASP cc_start: 0.8203 (t70) cc_final: 0.7868 (t70) REVERT: Bc 29 TYR cc_start: 0.8889 (m-10) cc_final: 0.8630 (m-80) outliers start: 20 outliers final: 12 residues processed: 168 average time/residue: 0.7837 time to fit residues: 140.6932 Evaluate side-chains 173 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 114 CYS Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Aa residue 469 GLN Chi-restraints excluded: chain Ab residue 443 ILE Chi-restraints excluded: chain Ab residue 469 GLN Chi-restraints excluded: chain Ac residue 114 CYS Chi-restraints excluded: chain Ac residue 187 ILE Chi-restraints excluded: chain Ac residue 395 GLN Chi-restraints excluded: chain Ba residue 18 LEU Chi-restraints excluded: chain Ba residue 67 THR Chi-restraints excluded: chain Bb residue 6 GLU Chi-restraints excluded: chain Bb residue 67 THR Chi-restraints excluded: chain Bc residue 2 VAL Chi-restraints excluded: chain Bc residue 67 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [47, 121, 26, 165, 39, 159, 120, 32, 90, 83, 22] chunk 47 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 120 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Bb 3 GLN Bc 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.079755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.058349 restraints weight = 20690.599| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 1.86 r_work: 0.2351 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2215 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9473 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13311 Z= 0.193 Angle : 0.505 6.981 18078 Z= 0.269 Chirality : 0.046 0.163 2145 Planarity : 0.003 0.036 2304 Dihedral : 4.276 16.253 1830 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.62 % Allowed : 10.39 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1686 helix: 2.77 (0.25), residues: 450 sheet: 0.49 (0.24), residues: 420 loop : -0.13 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGBc 19 TYR 0.013 0.001 TYRAc 248 PHE 0.009 0.001 PHEBb 105 TRP 0.010 0.002 TRPBc 104 HIS 0.001 0.000 HISAb 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 (13296) covalent geometry : angle 0.50274 / 0.27 (18048) SS BOND : bond 0.00197 / 0.12 ( 15) SS BOND : angle 1.36307 / 0.81 ( 30) hydrogen bonds : bond 0.03993 / 2.58 ( 580) hydrogen bonds : angle 4.86893 / 3.45 ( 1611) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.589 Fit side-chains REVERT: Aa 335 LYS cc_start: 0.9221 (tttt) cc_final: 0.8955 (tptp) REVERT: Ab 335 LYS cc_start: 0.9256 (tttt) cc_final: 0.8980 (tptp) REVERT: Ac 335 LYS cc_start: 0.9291 (tttt) cc_final: 0.9022 (tptp) REVERT: Ac 395 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: Ba 71 ASP cc_start: 0.8112 (t70) cc_final: 0.7789 (t70) REVERT: Ba 74 LYS cc_start: 0.9130 (pttm) cc_final: 0.8915 (pmtt) REVERT: Bb 6 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: Bb 71 ASP cc_start: 0.8162 (t70) cc_final: 0.7761 (t70) REVERT: Bb 74 LYS cc_start: 0.9185 (pttm) cc_final: 0.8901 (pmtt) REVERT: Bc 29 TYR cc_start: 0.8896 (m-10) cc_final: 0.8645 (m-80) outliers start: 24 outliers final: 13 residues processed: 169 average time/residue: 0.7883 time to fit residues: 142.0443 Evaluate side-chains 172 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 114 CYS Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Aa residue 469 GLN Chi-restraints excluded: chain Ab residue 443 ILE Chi-restraints excluded: chain Ab residue 469 GLN Chi-restraints excluded: chain Ac residue 114 CYS Chi-restraints excluded: chain Ac residue 187 ILE Chi-restraints excluded: chain Ac residue 395 GLN Chi-restraints excluded: chain Ba residue 18 LEU Chi-restraints excluded: chain Ba residue 67 THR Chi-restraints excluded: chain Bb residue 6 GLU Chi-restraints excluded: chain Bb residue 67 THR Chi-restraints excluded: chain Bc residue 2 VAL Chi-restraints excluded: chain Bc residue 18 LEU Chi-restraints excluded: chain Bc residue 67 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [48, 15, 56, 141, 12, 77, 52, 135, 32, 35, 76] chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 0.0060 chunk 141 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.5114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 395 GLN Bb 3 GLN Bb 13 GLN Bc 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.082114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.060925 restraints weight = 20634.672| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 1.86 r_work: 0.2412 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2279 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9436 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13311 Z= 0.097 Angle : 0.449 6.792 18078 Z= 0.240 Chirality : 0.044 0.153 2145 Planarity : 0.003 0.036 2304 Dihedral : 3.924 14.480 1830 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.81 % Allowed : 11.40 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1686 helix: 2.87 (0.25), residues: 450 sheet: 0.56 (0.25), residues: 405 loop : -0.03 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGBc 19 TYR 0.012 0.001 TYRAc 248 PHE 0.008 0.001 PHEAa 376 TRP 0.004 0.001 TRPBc 104 HIS 0.001 0.000 HISAa 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (13296) covalent geometry : angle 0.44763 / 0.24 (18048) SS BOND : bond 0.00202 / 0.09 ( 15) SS BOND : angle 1.06325 / 0.63 ( 30) hydrogen bonds : bond 0.03022 / 1.97 ( 580) hydrogen bonds : angle 4.55354 / 3.23 ( 1611) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.482 Fit side-chains REVERT: Aa 335 LYS cc_start: 0.9187 (tttt) cc_final: 0.8914 (tptp) REVERT: Ab 335 LYS cc_start: 0.9220 (tttt) cc_final: 0.8935 (tptp) REVERT: Ac 335 LYS cc_start: 0.9269 (tttt) cc_final: 0.8986 (tptp) REVERT: Ba 71 ASP cc_start: 0.8084 (t70) cc_final: 0.7761 (t70) REVERT: Ba 74 LYS cc_start: 0.9105 (pttm) cc_final: 0.8873 (pmtt) REVERT: Bb 6 GLU cc_start: 0.8666 (mp0) cc_final: 0.8235 (mt-10) REVERT: Bb 71 ASP cc_start: 0.8094 (t70) cc_final: 0.7677 (t70) REVERT: Bb 74 LYS cc_start: 0.9086 (pttm) cc_final: 0.8832 (pmtt) REVERT: Bc 29 TYR cc_start: 0.8863 (m-10) cc_final: 0.8621 (m-80) REVERT: Bc 70 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8149 (tpp80) outliers start: 12 outliers final: 6 residues processed: 168 average time/residue: 0.7871 time to fit residues: 141.1726 Evaluate side-chains 164 residues out of total 1482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 114 CYS Chi-restraints excluded: chain Ab residue 443 ILE Chi-restraints excluded: chain Ac residue 114 CYS Chi-restraints excluded: chain Ba residue 67 THR Chi-restraints excluded: chain Bc residue 2 VAL Chi-restraints excluded: chain Bc residue 67 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [152, 34, 26, 82, 146, 37, 21, 137, 106, 30, 123] chunk 152 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 395 GLN Bb 3 GLN Bc 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.079564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.058129 restraints weight = 20529.647| |-----------------------------------------------------------------------------| r_work (start): 0.2492 rms_B_bonded: 1.85 r_work: 0.2347 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2211 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9475 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13311 Z= 0.220 Angle : 0.524 7.299 18078 Z= 0.277 Chirality : 0.047 0.164 2145 Planarity : 0.004 0.036 2304 Dihedral : 4.281 16.530 1830 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.81 % Allowed : 11.54 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1686 helix: 2.75 (0.25), residues: 450 sheet: 0.52 (0.25), residues: 420 loop : -0.14 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGBa 55 TYR 0.014 0.001 TYRAc 248 PHE 0.010 0.001 PHEBb 105 TRP 0.011 0.002 TRPBc 104 HIS 0.001 0.000 HISAb 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (13296) covalent geometry : angle 0.52111 / 0.28 (18048) SS BOND : bond 0.00217 / 0.13 ( 15) SS BOND : angle 1.39239 / 0.82 ( 30) hydrogen bonds : bond 0.04155 / 2.69 ( 580) hydrogen bonds : angle 4.87904 / 3.46 ( 1611) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4548.67 seconds wall clock time: 78 minutes 14.64 seconds (4694.64 seconds total)