Starting phenix.real_space_refine on Sat Oct 24 11:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9shv_54916/10_2026/9shv_54916.cif Found real_map, /net/cci-nas-00/data/ceres_data/9shv_54916/10_2026/9shv_54916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9shv_54916/10_2026/9shv_54916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9shv_54916/10_2026/9shv_54916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9shv_54916/10_2026/9shv_54916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9shv_54916/10_2026/9shv_54916.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 8145 2.51 5 N 2133 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s 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: 12891 Number of models: 1 Model: "" Number of chains: 6 Chain: "Aa" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3386 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 15, 'TRANS': 425} Chain breaks: 1 Chain: "Ab" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3386 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 15, 'TRANS': 425} Chain breaks: 1 Chain: "Ac" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3386 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 15, 'TRANS': 425} Chain breaks: 1 Chain: "Ba" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 911 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "Bb" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 911 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "Bc" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 911 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Time building chain proxies: 2.76, per 1000 atoms: 0.21 Number of scatterers: 12891 At special positions: 0 Unit cell: (110.808, 112.752, 108.864, 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 2535 8.00 N 2133 7.00 C 8145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 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 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 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: 0.82 Conformation dependent library (CDL) restraints added in 483.4 milliseconds 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3144 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 24 sheets defined 34.6% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'Aa' and resid 29 through 36 removed outlier: 3.687A pdb=" N ILEAa 36 " --> pdb=" O LYSAa 32 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 65 through 72 removed outlier: 3.523A pdb=" N SERAa 69 " --> pdb=" O SERAa 66 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYSAa 70 " --> pdb=" O ASNAa 67 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 74 through 99 removed outlier: 3.643A pdb=" N ILEAa 86 " --> pdb=" O ARGAa 82 " (cutoff:3.500A) Proline residue: Aa 89 - end of helix removed outlier: 3.764A 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 146 removed outlier: 4.035A pdb=" N LYSAa 139 " --> pdb=" O TYRAa 135 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASNAa 140 " --> pdb=" O GLUAa 136 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASNAa 143 " --> pdb=" O LYSAa 139 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 147 through 154 Processing helix chain 'Aa' and resid 175 through 182 Processing helix chain 'Aa' and resid 191 through 215 removed outlier: 4.453A pdb=" N PHEAa 212 " --> pdb=" O SERAa 208 " (cutoff:3.500A) removed outlier: 4.795A 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 245 removed outlier: 3.750A pdb=" N LEUAa 242 " --> pdb=" O ASNAa 238 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THRAa 245 " --> pdb=" O THRAa 241 " (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 359 through 363 Processing helix chain 'Aa' and resid 437 through 441 Processing helix chain 'Aa' and resid 452 through 474 Processing helix chain 'Ab' and resid 29 through 36 removed outlier: 3.662A pdb=" N ILEAb 36 " --> pdb=" O LYSAb 32 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 65 through 72 removed outlier: 3.507A pdb=" N SERAb 69 " --> pdb=" O SERAb 66 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYSAb 70 " --> pdb=" O ASNAb 67 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 74 through 99 removed outlier: 3.610A pdb=" N ILEAb 86 " --> pdb=" O ARGAb 82 " (cutoff:3.500A) Proline residue: Ab 89 - end of helix removed outlier: 3.760A 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 145 removed outlier: 4.063A pdb=" N LYSAb 139 " --> pdb=" O TYRAb 135 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASNAb 140 " --> pdb=" O GLUAb 136 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASNAb 143 " --> pdb=" O LYSAb 139 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 147 through 154 Processing helix chain 'Ab' and resid 175 through 182 Processing helix chain 'Ab' and resid 191 through 215 removed outlier: 4.424A pdb=" N PHEAb 212 " --> pdb=" O SERAb 208 " (cutoff:3.500A) removed outlier: 4.737A 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 removed outlier: 3.503A pdb=" N GLYAb 236 " --> pdb=" O GLNAb 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ab' and resid 233 through 236' Processing helix chain 'Ab' and resid 238 through 245 removed outlier: 3.768A pdb=" N LEUAb 242 " --> pdb=" O ASNAb 238 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THRAb 245 " --> pdb=" O THRAb 241 " (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 359 through 363 Processing helix chain 'Ab' and resid 437 through 441 Processing helix chain 'Ab' and resid 452 through 474 Processing helix chain 'Ac' and resid 29 through 36 removed outlier: 3.655A pdb=" N ILEAc 36 " --> pdb=" O LYSAc 32 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 65 through 72 removed outlier: 3.507A pdb=" N SERAc 69 " --> pdb=" O SERAc 66 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYSAc 70 " --> pdb=" O ASNAc 67 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 74 through 99 removed outlier: 3.512A pdb=" N ILEAc 86 " --> pdb=" O ARGAc 82 " (cutoff:3.500A) Proline residue: Ac 89 - end of helix removed outlier: 3.765A 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 145 removed outlier: 3.995A pdb=" N LYSAc 139 " --> pdb=" O TYRAc 135 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASNAc 140 " --> pdb=" O GLUAc 136 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASNAc 143 " --> pdb=" O LYSAc 139 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 147 through 154 Processing helix chain 'Ac' and resid 175 through 182 Processing helix chain 'Ac' and resid 191 through 215 removed outlier: 4.426A pdb=" N PHEAc 212 " --> pdb=" O SERAc 208 " (cutoff:3.500A) removed outlier: 4.748A 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 245 removed outlier: 3.755A pdb=" N LEUAc 242 " --> pdb=" O ASNAc 238 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THRAc 245 " --> pdb=" O THRAc 241 " (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 359 through 363 Processing helix chain 'Ac' and resid 437 through 441 Processing helix chain 'Ac' and resid 452 through 474 Processing helix chain 'Ba' and resid 61 through 63 No H-bonds generated for 'chain 'Ba' and resid 61 through 63' Processing helix chain 'Ba' and resid 85 through 89 Processing helix chain 'Ba' and resid 102 through 106 removed outlier: 3.519A pdb=" N LYSBa 106 " --> pdb=" O ALABa 103 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 61 through 63 No H-bonds generated for 'chain 'Bb' and resid 61 through 63' Processing helix chain 'Bb' and resid 85 through 89 Processing helix chain 'Bb' and resid 102 through 106 removed outlier: 3.550A pdb=" N LYSBb 106 " --> pdb=" O ALABb 103 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 61 through 63 No H-bonds generated for 'chain 'Bc' and resid 61 through 63' Processing helix chain 'Bc' and resid 85 through 89 Processing helix chain 'Bc' and resid 102 through 106 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 158 through 162 removed outlier: 10.870A pdb=" N THRAa 168 " --> pdb=" O THRAa 54 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASPAa 56 " --> pdb=" O THRAa 168 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYRAa 170 " --> pdb=" O ASPAa 56 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLUAa 295 " --> pdb=" O GLYAa 41 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THRAa 43 " --> pdb=" O VALAa 293 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VALAa 293 " --> pdb=" O THRAa 43 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LYSAa 45 " --> pdb=" O ALAAa 291 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ALAAa 291 " --> pdb=" O LYSAa 45 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N LYSAa 47 " --> pdb=" O GLNAa 289 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N GLNAa 289 " --> pdb=" O LYSAa 47 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N LYSAa 49 " --> pdb=" O GLUAa 287 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N GLUAa 287 " --> pdb=" O LYSAa 49 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ASNAa 51 " --> pdb=" O LEUAa 285 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEUAa 285 " --> pdb=" O ASNAa 51 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEUAa 53 " --> pdb=" O PROAa 283 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LYSAa 55 " --> pdb=" O TYRAa 281 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYRAa 281 " --> pdb=" O LYSAa 55 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILEAa 57 " --> pdb=" O ARGAa 279 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ARGAa 279 " --> pdb=" O ILEAa 57 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILEAa 59 " --> pdb=" O ILEAa 277 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILEAa 277 " --> pdb=" O ILEAa 59 " (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: 6.467A pdb=" N ILEAa 277 " --> pdb=" O VALAa 267 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VALAa 269 " --> pdb=" O TYRAa 275 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYRAa 275 " --> pdb=" O VALAa 269 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILEAa 277 " --> pdb=" O ILEAa 59 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILEAa 59 " --> pdb=" O ILEAa 277 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ARGAa 279 " --> pdb=" O ILEAa 57 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILEAa 57 " --> pdb=" O ARGAa 279 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYRAa 281 " --> pdb=" O LYSAa 55 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LYSAa 55 " --> pdb=" O TYRAa 281 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEUAa 53 " --> pdb=" O PROAa 283 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEUAa 285 " --> pdb=" O ASNAa 51 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ASNAa 51 " --> pdb=" O LEUAa 285 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N GLUAa 287 " --> pdb=" O LYSAa 49 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N LYSAa 49 " --> pdb=" O GLUAa 287 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N GLNAa 289 " --> pdb=" O LYSAa 47 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N LYSAa 47 " --> pdb=" O GLNAa 289 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ALAAa 291 " --> pdb=" O LYSAa 45 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LYSAa 45 " --> pdb=" O ALAAa 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VALAa 293 " --> pdb=" O THRAa 43 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THRAa 43 " --> pdb=" O VALAa 293 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLUAa 295 " --> pdb=" O GLYAa 41 " (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 102 removed outlier: 6.690A pdb=" N METAa 115 " --> pdb=" O SERAb 428 " (cutoff:3.500A) removed outlier: 4.646A 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 248 through 250 removed outlier: 7.347A pdb=" N VALBa 47 " --> pdb=" O ALABa 59 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEUBa 46 " --> pdb=" O ARGBa 37 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARGBa 37 " --> pdb=" O LEUBa 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Aa' and resid 248 through 250 removed outlier: 7.347A pdb=" N VALBa 47 " --> pdb=" O ALABa 59 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEUBa 46 " --> pdb=" O ARGBa 37 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARGBa 37 " --> pdb=" O LEUBa 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Aa' and resid 301 through 302 removed outlier: 5.956A pdb=" N ARGAa 365 " --> pdb=" O VALAa 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Aa' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'Aa' and resid 400 through 401 removed outlier: 4.639A pdb=" N CYSAa 392 " --> pdb=" O ILEAa 401 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Ab' and resid 158 through 162 removed outlier: 10.858A pdb=" N THRAb 168 " --> pdb=" O THRAb 54 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASPAb 56 " --> pdb=" O THRAb 168 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYRAb 170 " --> pdb=" O ASPAb 56 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLUAb 295 " --> pdb=" O GLYAb 41 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THRAb 43 " --> pdb=" O VALAb 293 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VALAb 293 " --> pdb=" O THRAb 43 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYSAb 45 " --> pdb=" O ALAAb 291 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ALAAb 291 " --> pdb=" O LYSAb 45 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N LYSAb 47 " --> pdb=" O GLNAb 289 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N GLNAb 289 " --> pdb=" O LYSAb 47 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LYSAb 49 " --> pdb=" O GLUAb 287 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLUAb 287 " --> pdb=" O LYSAb 49 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ASNAb 51 " --> pdb=" O LEUAb 285 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEUAb 285 " --> pdb=" O ASNAb 51 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEUAb 53 " --> pdb=" O PROAb 283 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYSAb 55 " --> pdb=" O TYRAb 281 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TYRAb 281 " --> pdb=" O LYSAb 55 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILEAb 57 " --> pdb=" O ARGAb 279 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ARGAb 279 " --> pdb=" O ILEAb 57 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILEAb 59 " --> pdb=" O ILEAb 277 " (cutoff:3.500A) removed outlier: 5.694A 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=AB2, first strand: chain 'Ab' and resid 263 through 270 removed outlier: 6.466A pdb=" N ILEAb 277 " --> pdb=" O VALAb 267 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VALAb 269 " --> pdb=" O TYRAb 275 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYRAb 275 " --> pdb=" O VALAb 269 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILEAb 277 " --> pdb=" O ILEAb 59 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILEAb 59 " --> pdb=" O ILEAb 277 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ARGAb 279 " --> pdb=" O ILEAb 57 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILEAb 57 " --> pdb=" O ARGAb 279 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TYRAb 281 " --> pdb=" O LYSAb 55 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYSAb 55 " --> pdb=" O TYRAb 281 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEUAb 53 " --> pdb=" O PROAb 283 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N LEUAb 285 " --> pdb=" O ASNAb 51 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ASNAb 51 " --> pdb=" O LEUAb 285 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLUAb 287 " --> pdb=" O LYSAb 49 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LYSAb 49 " --> pdb=" O GLUAb 287 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N GLNAb 289 " --> pdb=" O LYSAb 47 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N LYSAb 47 " --> pdb=" O GLNAb 289 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ALAAb 291 " --> pdb=" O LYSAb 45 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYSAb 45 " --> pdb=" O ALAAb 291 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VALAb 293 " --> pdb=" O THRAb 43 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THRAb 43 " --> pdb=" O VALAb 293 " (cutoff:3.500A) removed outlier: 5.358A 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=AB3, first strand: chain 'Ab' and resid 101 through 102 removed outlier: 6.713A pdb=" N METAb 115 " --> pdb=" O SERAc 428 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N CYSAc 392 " --> pdb=" O ILEAc 401 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ab' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'Ab' and resid 248 through 250 removed outlier: 7.353A pdb=" N VALBb 47 " --> pdb=" O ALABb 59 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRPBb 35 " --> pdb=" O VALBb 47 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARGBb 49 " --> pdb=" O METBb 33 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N METBb 33 " --> pdb=" O ARGBb 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Ab' and resid 248 through 250 removed outlier: 7.353A pdb=" N VALBb 47 " --> pdb=" O ALABb 59 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRPBb 35 " --> pdb=" O VALBb 47 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARGBb 49 " --> pdb=" O METBb 33 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N METBb 33 " --> pdb=" O ARGBb 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ab' and resid 301 through 302 removed outlier: 6.005A pdb=" N ARGAb 365 " --> pdb=" O VALAb 449 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Ac' and resid 158 through 162 removed outlier: 10.879A pdb=" N THRAc 168 " --> pdb=" O THRAc 54 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASPAc 56 " --> pdb=" O THRAc 168 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYRAc 170 " --> pdb=" O ASPAc 56 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLUAc 295 " --> pdb=" O GLYAc 41 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THRAc 43 " --> pdb=" O VALAc 293 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VALAc 293 " --> pdb=" O THRAc 43 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LYSAc 45 " --> pdb=" O ALAAc 291 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALAAc 291 " --> pdb=" O LYSAc 45 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N LYSAc 47 " --> pdb=" O GLNAc 289 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N GLNAc 289 " --> pdb=" O LYSAc 47 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N LYSAc 49 " --> pdb=" O GLUAc 287 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLUAc 287 " --> pdb=" O LYSAc 49 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N ASNAc 51 " --> pdb=" O LEUAc 285 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEUAc 285 " --> pdb=" O ASNAc 51 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEUAc 53 " --> pdb=" O PROAc 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYSAc 55 " --> pdb=" O TYRAc 281 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYRAc 281 " --> pdb=" O LYSAc 55 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILEAc 57 " --> pdb=" O ARGAc 279 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARGAc 279 " --> pdb=" O ILEAc 57 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILEAc 59 " --> pdb=" O ILEAc 277 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILEAc 277 " --> pdb=" O ILEAc 59 " (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=AB9, first strand: chain 'Ac' and resid 263 through 270 removed outlier: 6.488A pdb=" N ILEAc 277 " --> pdb=" O VALAc 267 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VALAc 269 " --> pdb=" O TYRAc 275 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYRAc 275 " --> pdb=" O VALAc 269 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILEAc 277 " --> pdb=" O ILEAc 59 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILEAc 59 " --> pdb=" O ILEAc 277 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARGAc 279 " --> pdb=" O ILEAc 57 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILEAc 57 " --> pdb=" O ARGAc 279 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYRAc 281 " --> pdb=" O LYSAc 55 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYSAc 55 " --> pdb=" O TYRAc 281 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEUAc 53 " --> pdb=" O PROAc 283 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEUAc 285 " --> pdb=" O ASNAc 51 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N ASNAc 51 " --> pdb=" O LEUAc 285 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLUAc 287 " --> pdb=" O LYSAc 49 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N LYSAc 49 " --> pdb=" O GLUAc 287 " (cutoff:3.500A) removed outlier: 9.768A pdb=" N GLNAc 289 " --> pdb=" O LYSAc 47 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N LYSAc 47 " --> pdb=" O GLNAc 289 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALAAc 291 " --> pdb=" O LYSAc 45 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LYSAc 45 " --> pdb=" O ALAAc 291 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VALAc 293 " --> pdb=" O THRAc 43 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THRAc 43 " --> pdb=" O VALAc 293 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLUAc 295 " --> pdb=" O GLYAc 41 " (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=AC1, first strand: chain 'Ac' and resid 248 through 250 removed outlier: 7.355A pdb=" N VALBc 47 " --> pdb=" O ALABc 59 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEUBc 46 " --> pdb=" O ARGBc 37 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARGBc 37 " --> pdb=" O LEUBc 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Ac' and resid 248 through 250 removed outlier: 7.355A pdb=" N VALBc 47 " --> pdb=" O ALABc 59 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEUBc 46 " --> pdb=" O ARGBc 37 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARGBc 37 " --> pdb=" O LEUBc 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Ac' and resid 301 through 302 removed outlier: 6.013A pdb=" N ARGAc 365 " --> pdb=" O VALAc 449 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Ba' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'Bb' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'Bc' and resid 4 through 7 620 hydrogen bonds defined for protein. 1647 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: 2.46 Time building geometry restraints manager: 1.15 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: 4180 1.34 - 1.45: 1898 1.45 - 1.57: 6897 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 13089 Sorted by residual: bond pdb=" CB GLUAa 166 " pdb=" CG GLUAa 166 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" CB GLUAc 166 " pdb=" CG GLUAc 166 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.38e+00 bond pdb=" CB THRAc 129 " pdb=" CG2 THRAc 129 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 bond pdb=" CB THRAa 129 " pdb=" CG2 THRAa 129 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.27e+00 bond pdb=" CB THRAb 129 " pdb=" CG2 THRAb 129 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 ... (remaining 13084 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 17549 1.69 - 3.37: 183 3.37 - 5.06: 34 5.06 - 6.75: 13 6.75 - 8.44: 5 Bond angle restraints: 17784 Sorted by residual: angle pdb=" CA GLUAc 166 " pdb=" CB GLUAc 166 " pdb=" CG GLUAc 166 " ideal model delta sigma weight residual 114.10 121.26 -7.16 2.00e+00 2.50e-01 1.28e+01 angle pdb=" CA GLUAa 166 " pdb=" CB GLUAa 166 " pdb=" CG GLUAa 166 " ideal model delta sigma weight residual 114.10 121.11 -7.01 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA GLUBc 87 " pdb=" CB GLUBc 87 " pdb=" CG GLUBc 87 " ideal model delta sigma weight residual 114.10 120.98 -6.88 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CA GLUBa 87 " pdb=" CB GLUBa 87 " pdb=" CG GLUBa 87 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CB GLUAa 166 " pdb=" CG GLUAa 166 " pdb=" CD GLUAa 166 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.70e+00 3.46e-01 1.10e+01 ... (remaining 17779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 7321 17.43 - 34.87: 445 34.87 - 52.30: 155 52.30 - 69.73: 44 69.73 - 87.17: 6 Dihedral angle restraints: 7971 sinusoidal: 3069 harmonic: 4902 Sorted by residual: dihedral pdb=" CA SERAc 337 " pdb=" C SERAc 337 " pdb=" N VALAc 338 " pdb=" CA VALAc 338 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CG ARGAb 244 " pdb=" CD ARGAb 244 " pdb=" NE ARGAb 244 " pdb=" CZ ARGAb 244 " ideal model delta sinusoidal sigma weight residual -90.00 -39.85 -50.15 2 1.50e+01 4.44e-03 1.26e+01 dihedral pdb=" CG ARGAa 244 " pdb=" CD ARGAa 244 " pdb=" NE ARGAa 244 " pdb=" CZ ARGAa 244 " ideal model delta sinusoidal sigma weight residual -90.00 -39.88 -50.12 2 1.50e+01 4.44e-03 1.26e+01 ... (remaining 7968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1003 0.028 - 0.055: 635 0.055 - 0.083: 273 0.083 - 0.111: 173 0.111 - 0.139: 55 Chirality restraints: 2139 Sorted by residual: chirality pdb=" CA VALAb 312 " pdb=" N VALAb 312 " pdb=" C VALAb 312 " pdb=" CB VALAb 312 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA VALAc 312 " pdb=" N VALAc 312 " pdb=" C VALAc 312 " pdb=" CB VALAc 312 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA VALAa 312 " pdb=" N VALAa 312 " pdb=" C VALAa 312 " pdb=" CB VALAa 312 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 2136 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLUBb 87 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" CD GLUBb 87 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLUBb 87 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLUBb 87 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLUBa 87 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" CD GLUBa 87 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLUBa 87 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLUBa 87 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLUBc 87 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" CD GLUBc 87 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLUBc 87 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLUBc 87 " -0.010 2.00e-02 2.50e+03 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 6025 2.96 - 3.45: 12208 3.45 - 3.93: 22156 3.93 - 4.42: 25737 4.42 - 4.90: 41636 Nonbonded interactions: 107762 Sorted by model distance: nonbonded pdb=" N GLUBc 87 " pdb=" OE1 GLUBc 87 " model vdw 2.480 3.120 nonbonded pdb=" N GLUAa 166 " pdb=" OE1 GLUAa 166 " model vdw 2.484 3.120 nonbonded pdb=" N GLUAc 166 " pdb=" OE1 GLUAc 166 " model vdw 2.486 3.120 nonbonded pdb=" N GLUBb 87 " pdb=" OE1 GLUBb 87 " model vdw 2.488 3.120 nonbonded pdb=" N GLUBa 87 " pdb=" OE1 GLUBa 87 " model vdw 2.495 3.120 ... (remaining 107757 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: 0.01 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: 5.340 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.820 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:8.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9467 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13101 Z= 0.251 Angle : 0.545 8.436 17808 Z= 0.281 Chirality : 0.048 0.139 2139 Planarity : 0.004 0.053 2250 Dihedral : 14.040 87.167 4791 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.41 % Allowed : 9.84 % Favored : 89.75 % 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: 0.39 (0.20), residues: 1665 helix: 0.75 (0.24), residues: 429 sheet: -0.39 (0.24), residues: 405 loop : 0.54 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGAc 244 TYR 0.014 0.001 TYRAc 46 PHE 0.009 0.001 PHEAc 301 TRP 0.016 0.002 TRPBa 100 HIS 0.004 0.001 HISAa 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.25 (13089) covalent geometry : angle 0.54402 / 0.28 (17784) SS BOND : bond 0.00394 / 0.22 ( 12) SS BOND : angle 0.86066 / 0.56 ( 24) hydrogen bonds : bond 0.19261 / 12.63 ( 561) hydrogen bonds : angle 7.81173 / 5.40 ( 1647) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 0.518 Fit side-chains REVERT: Aa 453 LYS cc_start: 0.9210 (tttt) cc_final: 0.8903 (ttpp) REVERT: Ab 453 LYS cc_start: 0.9132 (ttmt) cc_final: 0.8764 (tttm) REVERT: Ab 465 GLN cc_start: 0.8125 (mt0) cc_final: 0.7900 (mm-40) REVERT: Ac 453 LYS cc_start: 0.9191 (tttt) cc_final: 0.8842 (tttm) REVERT: Ac 465 GLN cc_start: 0.8045 (mt0) cc_final: 0.7817 (mm-40) REVERT: Ba 3 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8470 (mm110) REVERT: Ba 71 ASP cc_start: 0.9062 (t0) cc_final: 0.8753 (t70) REVERT: Ba 75 ASN cc_start: 0.9025 (m110) cc_final: 0.8773 (m-40) REVERT: Bb 71 ASP cc_start: 0.9080 (t0) cc_final: 0.8597 (t0) REVERT: Bb 74 LYS cc_start: 0.9389 (mtpp) cc_final: 0.9091 (mtpp) REVERT: Bb 108 MET cc_start: 0.8772 (ttp) cc_final: 0.8483 (tpp) outliers start: 6 outliers final: 4 residues processed: 194 average time/residue: 0.6115 time to fit residues: 128.7216 Evaluate side-chains 188 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 220 ASP Chi-restraints excluded: chain Ab residue 49 LYS Chi-restraints excluded: chain Ac residue 49 LYS Chi-restraints excluded: chain Ac residue 220 ASP 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: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 290 GLN Aa 303 ASN Aa 320 ASN Aa 393 GLN Ab 290 GLN Ab 320 ASN Ab 393 GLN Ac 290 GLN Ac 320 ASN Ac 393 GLN Ba 38 GLN Ba 75 ASN Bb 43 GLN Bb 52 ASN Bc 52 ASN Bc 75 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.070980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2362 r_free = 0.2362 target = 0.053487 restraints weight = 20710.001| |-----------------------------------------------------------------------------| r_work (start): 0.2359 rms_B_bonded: 2.16 r_work: 0.2213 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2071 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9375 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13101 Z= 0.150 Angle : 0.479 5.844 17808 Z= 0.260 Chirality : 0.046 0.137 2139 Planarity : 0.004 0.032 2250 Dihedral : 4.784 46.552 1818 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.25 % Allowed : 8.06 % Favored : 89.69 % 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: 0.79 (0.21), residues: 1665 helix: 1.72 (0.26), residues: 438 sheet: -0.20 (0.24), residues: 423 loop : 0.41 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAc 244 TYR 0.016 0.001 TYRAa 438 PHE 0.008 0.001 PHEAa 376 TRP 0.014 0.001 TRPBa 100 HIS 0.002 0.001 HISAa 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (13089) covalent geometry : angle 0.47948 / 0.26 (17784) SS BOND : bond 0.00286 / 0.15 ( 12) SS BOND : angle 0.41872 / 0.27 ( 24) hydrogen bonds : bond 0.04573 / 2.93 ( 561) hydrogen bonds : angle 5.28251 / 3.70 ( 1647) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.579 Fit side-chains REVERT: Aa 103 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: Aa 166 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8589 (pm20) REVERT: Ab 453 LYS cc_start: 0.8230 (ttmt) cc_final: 0.8016 (ttpp) REVERT: Ab 465 GLN cc_start: 0.7871 (mt0) cc_final: 0.7666 (mm-40) REVERT: Ac 453 LYS cc_start: 0.8343 (tttt) cc_final: 0.8101 (ttpp) REVERT: Ac 465 GLN cc_start: 0.7834 (mt0) cc_final: 0.7624 (mm-40) REVERT: Ba 3 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8423 (mm110) REVERT: Ba 71 ASP cc_start: 0.8795 (t0) cc_final: 0.8198 (t0) REVERT: Ba 74 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9125 (mtpt) REVERT: Ba 75 ASN cc_start: 0.8935 (m-40) cc_final: 0.8705 (m-40) REVERT: Bb 71 ASP cc_start: 0.8793 (t0) cc_final: 0.8095 (t0) REVERT: Bb 108 MET cc_start: 0.8910 (ttp) cc_final: 0.8426 (tpp) REVERT: Bc 71 ASP cc_start: 0.8520 (t70) cc_final: 0.8303 (t0) outliers start: 33 outliers final: 15 residues processed: 203 average time/residue: 0.5752 time to fit residues: 127.3290 Evaluate side-chains 202 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 49 LYS Chi-restraints excluded: chain Aa residue 103 ASP Chi-restraints excluded: chain Aa residue 166 GLU Chi-restraints excluded: chain Aa residue 396 THR Chi-restraints excluded: chain Aa residue 427 ILE Chi-restraints excluded: chain Ab residue 49 LYS Chi-restraints excluded: chain Ab residue 396 THR Chi-restraints excluded: chain Ab residue 427 ILE Chi-restraints excluded: chain Ac residue 49 LYS Chi-restraints excluded: chain Ac residue 167 LYS Chi-restraints excluded: chain Ac residue 396 THR Chi-restraints excluded: chain Ac residue 427 ILE Chi-restraints excluded: chain Ba residue 43 GLN Chi-restraints excluded: chain Ba residue 74 LYS Chi-restraints excluded: chain Bb residue 61 SER Chi-restraints excluded: chain Bb residue 83 SER Chi-restraints excluded: chain Bb residue 118 THR Chi-restraints excluded: chain Bc residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [23, 55, 68, 110, 152, 125, 9, 163, 104, 3, 95] chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 290 GLN Ba 38 GLN Bb 43 GLN Bc 3 GLN Bc 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.072065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.054526 restraints weight = 20935.659| |-----------------------------------------------------------------------------| r_work (start): 0.2382 rms_B_bonded: 2.19 r_work: 0.2236 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2094 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9361 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13101 Z= 0.123 Angle : 0.448 8.263 17808 Z= 0.239 Chirality : 0.045 0.132 2139 Planarity : 0.004 0.037 2250 Dihedral : 4.328 46.481 1814 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 2.05 % Allowed : 8.54 % 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: 1.00 (0.21), residues: 1665 helix: 2.07 (0.26), residues: 438 sheet: -0.11 (0.23), residues: 423 loop : 0.45 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAc 244 TYR 0.010 0.001 TYRAa 438 PHE 0.007 0.001 PHEAa 376 TRP 0.011 0.001 TRPBa 100 HIS 0.002 0.001 HISAa 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (13089) covalent geometry : angle 0.44783 / 0.24 (17784) SS BOND : bond 0.00272 / 0.15 ( 12) SS BOND : angle 0.41416 / 0.28 ( 24) hydrogen bonds : bond 0.03792 / 2.44 ( 561) hydrogen bonds : angle 4.72860 / 3.31 ( 1647) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.536 Fit side-chains REVERT: Aa 103 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: Ac 465 GLN cc_start: 0.7812 (mt0) cc_final: 0.7605 (mm-40) REVERT: Ba 3 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8494 (mp10) REVERT: Ba 71 ASP cc_start: 0.8744 (t0) cc_final: 0.8089 (t0) REVERT: Bb 71 ASP cc_start: 0.8809 (t0) cc_final: 0.8131 (t0) REVERT: Bb 108 MET cc_start: 0.8871 (ttp) cc_final: 0.8383 (tpp) REVERT: Bc 71 ASP cc_start: 0.8524 (t70) cc_final: 0.8207 (t0) outliers start: 30 outliers final: 14 residues processed: 203 average time/residue: 0.5906 time to fit residues: 130.2555 Evaluate side-chains 198 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 49 LYS Chi-restraints excluded: chain Aa residue 103 ASP Chi-restraints excluded: chain Aa residue 220 ASP Chi-restraints excluded: chain Aa residue 427 ILE Chi-restraints excluded: chain Ab residue 49 LYS Chi-restraints excluded: chain Ab residue 427 ILE Chi-restraints excluded: chain Ac residue 49 LYS Chi-restraints excluded: chain Ac residue 167 LYS Chi-restraints excluded: chain Ac residue 220 ASP Chi-restraints excluded: chain Ac residue 427 ILE Chi-restraints excluded: chain Ba residue 83 SER Chi-restraints excluded: chain Ba residue 118 THR Chi-restraints excluded: chain Bb residue 7 SER Chi-restraints excluded: chain Bb residue 63 LYS Chi-restraints excluded: chain Bb residue 83 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [10, 24, 4, 36, 131, 144, 60, 42, 106, 121, 135] chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 290 GLN Ba 38 GLN Bc 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.071140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.053537 restraints weight = 20877.535| |-----------------------------------------------------------------------------| r_work (start): 0.2364 rms_B_bonded: 2.19 r_work: 0.2216 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2073 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9370 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13101 Z= 0.176 Angle : 0.465 8.080 17808 Z= 0.246 Chirality : 0.046 0.132 2139 Planarity : 0.004 0.040 2250 Dihedral : 4.393 47.106 1814 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 2.25 % Allowed : 9.15 % Favored : 88.59 % 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: 1.06 (0.21), residues: 1665 helix: 2.14 (0.26), residues: 438 sheet: -0.05 (0.24), residues: 423 loop : 0.46 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAa 244 TYR 0.015 0.001 TYRBa 93 PHE 0.007 0.001 PHEAc 376 TRP 0.011 0.001 TRPBa 100 HIS 0.002 0.001 HISAa 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (13089) covalent geometry : angle 0.46446 / 0.25 (17784) SS BOND : bond 0.00251 / 0.13 ( 12) SS BOND : angle 0.56294 / 0.38 ( 24) hydrogen bonds : bond 0.03865 / 2.49 ( 561) hydrogen bonds : angle 4.63580 / 3.26 ( 1647) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.503 Fit side-chains REVERT: Aa 103 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: Aa 443 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9068 (pp) REVERT: Ac 465 GLN cc_start: 0.7799 (mt0) cc_final: 0.7593 (mm-40) REVERT: Ba 71 ASP cc_start: 0.8749 (t0) cc_final: 0.8115 (t0) REVERT: Ba 75 ASN cc_start: 0.8919 (m110) cc_final: 0.8719 (m-40) REVERT: Bb 71 ASP cc_start: 0.8775 (t0) cc_final: 0.8098 (t0) REVERT: Bb 108 MET cc_start: 0.8882 (ttp) cc_final: 0.8375 (tpp) REVERT: Bc 71 ASP cc_start: 0.8537 (t70) cc_final: 0.8201 (t0) outliers start: 33 outliers final: 20 residues processed: 204 average time/residue: 0.5791 time to fit residues: 128.9756 Evaluate side-chains 202 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 49 LYS Chi-restraints excluded: chain Aa residue 96 LEU Chi-restraints excluded: chain Aa residue 103 ASP Chi-restraints excluded: chain Aa residue 220 ASP Chi-restraints excluded: chain Aa residue 396 THR Chi-restraints excluded: chain Aa residue 427 ILE Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 49 LYS Chi-restraints excluded: chain Ab residue 396 THR Chi-restraints excluded: chain Ab residue 427 ILE Chi-restraints excluded: chain Ac residue 49 LYS Chi-restraints excluded: chain Ac residue 139 LYS Chi-restraints excluded: chain Ac residue 167 LYS Chi-restraints excluded: chain Ac residue 220 ASP Chi-restraints excluded: chain Ac residue 396 THR Chi-restraints excluded: chain Ac residue 427 ILE Chi-restraints excluded: chain Ba residue 83 SER Chi-restraints excluded: chain Ba residue 118 THR Chi-restraints excluded: chain Bb residue 7 SER Chi-restraints excluded: chain Bb residue 61 SER Chi-restraints excluded: chain Bb residue 63 LYS Chi-restraints excluded: chain Bb residue 83 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [83, 31, 39, 67, 106, 80, 32, 117, 61, 125, 13] chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 0.0570 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 290 GLN Ba 3 GLN Ba 38 GLN Bc 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.070792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.053412 restraints weight = 21069.906| |-----------------------------------------------------------------------------| r_work (start): 0.2365 rms_B_bonded: 2.17 r_work: 0.2219 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2076 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9379 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13101 Z= 0.170 Angle : 0.465 8.302 17808 Z= 0.246 Chirality : 0.046 0.133 2139 Planarity : 0.004 0.044 2250 Dihedral : 4.391 47.078 1814 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.60 % Allowed : 9.43 % Favored : 87.98 % 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: 1.08 (0.21), residues: 1665 helix: 2.14 (0.26), residues: 438 sheet: -0.03 (0.24), residues: 423 loop : 0.48 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAb 244 TYR 0.009 0.001 TYRAa 438 PHE 0.007 0.001 PHEAa 376 TRP 0.011 0.001 TRPBa 100 HIS 0.002 0.001 HISAa 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (13089) covalent geometry : angle 0.46467 / 0.25 (17784) SS BOND : bond 0.00247 / 0.13 ( 12) SS BOND : angle 0.54667 / 0.37 ( 24) hydrogen bonds : bond 0.03757 / 2.42 ( 561) hydrogen bonds : angle 4.56090 / 3.20 ( 1647) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.485 Fit side-chains REVERT: Aa 103 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: Aa 443 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9044 (pp) REVERT: Ab 443 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9174 (pp) REVERT: Ac 443 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9146 (pp) REVERT: Ba 71 ASP cc_start: 0.8767 (t0) cc_final: 0.8150 (t0) REVERT: Bb 71 ASP cc_start: 0.8751 (t0) cc_final: 0.8077 (t0) REVERT: Bb 108 MET cc_start: 0.8909 (ttp) cc_final: 0.8404 (tpp) REVERT: Bc 71 ASP cc_start: 0.8611 (t70) cc_final: 0.8214 (t0) outliers start: 38 outliers final: 21 residues processed: 205 average time/residue: 0.5807 time to fit residues: 129.7901 Evaluate side-chains 204 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 49 LYS Chi-restraints excluded: chain Aa residue 96 LEU Chi-restraints excluded: chain Aa residue 103 ASP Chi-restraints excluded: chain Aa residue 220 ASP Chi-restraints excluded: chain Aa residue 396 THR Chi-restraints excluded: chain Aa residue 427 ILE Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 49 LYS Chi-restraints excluded: chain Ab residue 220 ASP Chi-restraints excluded: chain Ab residue 396 THR Chi-restraints excluded: chain Ab residue 443 ILE Chi-restraints excluded: chain Ac residue 49 LYS Chi-restraints excluded: chain Ac residue 139 LYS Chi-restraints excluded: chain Ac residue 167 LYS Chi-restraints excluded: chain Ac residue 220 ASP Chi-restraints excluded: chain Ac residue 396 THR Chi-restraints excluded: chain Ac residue 443 ILE Chi-restraints excluded: chain Ba residue 7 SER Chi-restraints excluded: chain Ba residue 83 SER Chi-restraints excluded: chain Ba residue 118 THR Chi-restraints excluded: chain Bb residue 7 SER Chi-restraints excluded: chain Bb residue 61 SER Chi-restraints excluded: chain Bb residue 63 LYS Chi-restraints excluded: chain Bb residue 83 SER Chi-restraints excluded: chain Bc residue 81 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [99, 33, 146, 153, 38, 103, 139, 102, 144, 100, 54] chunk 99 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 chunk 139 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 290 GLN Ab 303 ASN Ba 3 GLN Bc 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.072107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.054761 restraints weight = 20775.622| |-----------------------------------------------------------------------------| r_work (start): 0.2387 rms_B_bonded: 2.18 r_work: 0.2244 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2104 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9356 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13101 Z= 0.112 Angle : 0.440 8.295 17808 Z= 0.233 Chirality : 0.044 0.133 2139 Planarity : 0.004 0.039 2250 Dihedral : 4.256 46.480 1814 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.66 % Allowed : 9.43 % Favored : 87.91 % 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 (0.21), residues: 1665 helix: 2.20 (0.26), residues: 444 sheet: 0.05 (0.24), residues: 426 loop : 0.57 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAc 244 TYR 0.016 0.001 TYRBa 93 PHE 0.008 0.001 PHEAa 376 TRP 0.009 0.001 TRPBa 100 HIS 0.001 0.000 HISAa 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (13089) covalent geometry : angle 0.43989 / 0.23 (17784) SS BOND : bond 0.00222 / 0.12 ( 12) SS BOND : angle 0.39057 / 0.26 ( 24) hydrogen bonds : bond 0.03332 / 2.15 ( 561) hydrogen bonds : angle 4.39270 / 3.08 ( 1647) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.542 Fit side-chains REVERT: Aa 103 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8310 (m-30) REVERT: Ac 443 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9114 (pp) REVERT: Ba 3 GLN cc_start: 0.8673 (mp-120) cc_final: 0.8340 (mp10) REVERT: Ba 71 ASP cc_start: 0.8756 (t0) cc_final: 0.8090 (t0) REVERT: Bb 71 ASP cc_start: 0.8728 (t0) cc_final: 0.8053 (t0) REVERT: Bb 108 MET cc_start: 0.8872 (ttp) cc_final: 0.8378 (tpp) REVERT: Bc 71 ASP cc_start: 0.8595 (t70) cc_final: 0.8221 (t70) outliers start: 39 outliers final: 20 residues processed: 212 average time/residue: 0.5826 time to fit residues: 134.5387 Evaluate side-chains 207 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 49 LYS Chi-restraints excluded: chain Aa residue 103 ASP Chi-restraints excluded: chain Aa residue 220 ASP Chi-restraints excluded: chain Aa residue 427 ILE Chi-restraints excluded: chain Ab residue 49 LYS Chi-restraints excluded: chain Ab residue 220 ASP Chi-restraints excluded: chain Ab residue 396 THR Chi-restraints excluded: chain Ab residue 427 ILE Chi-restraints excluded: chain Ac residue 49 LYS Chi-restraints excluded: chain Ac residue 139 LYS Chi-restraints excluded: chain Ac residue 167 LYS Chi-restraints excluded: chain Ac residue 220 ASP Chi-restraints excluded: chain Ac residue 396 THR Chi-restraints excluded: chain Ac residue 427 ILE Chi-restraints excluded: chain Ac residue 443 ILE Chi-restraints excluded: chain Ba residue 7 SER Chi-restraints excluded: chain Bb residue 7 SER Chi-restraints excluded: chain Bb residue 61 SER Chi-restraints excluded: chain Bb residue 63 LYS Chi-restraints excluded: chain Bb residue 83 SER Chi-restraints excluded: chain Bc residue 75 ASN Chi-restraints excluded: chain Bc residue 81 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [62, 167, 35, 158, 25, 132, 107, 90, 37, 157, 70] chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 132 optimal weight: 5.9990 chunk 107 optimal weight: 0.0040 chunk 90 optimal weight: 0.7980 chunk 37 optimal weight: 0.0670 chunk 157 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 290 GLN Ac 303 ASN Ba 75 ASN ** Bc 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.073044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.055754 restraints weight = 20609.509| |-----------------------------------------------------------------------------| r_work (start): 0.2411 rms_B_bonded: 2.18 r_work: 0.2267 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2125 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9343 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13101 Z= 0.093 Angle : 0.439 7.781 17808 Z= 0.232 Chirality : 0.044 0.134 2139 Planarity : 0.004 0.040 2250 Dihedral : 4.167 46.482 1814 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.12 % Allowed : 10.38 % Favored : 87.50 % 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: 1.26 (0.21), residues: 1665 helix: 2.24 (0.26), residues: 444 sheet: 0.10 (0.24), residues: 426 loop : 0.60 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAb 244 TYR 0.010 0.001 TYRBc 78 PHE 0.007 0.001 PHEAa 376 TRP 0.008 0.001 TRPBa 100 HIS 0.001 0.000 HISAc 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (13089) covalent geometry : angle 0.43896 / 0.23 (17784) SS BOND : bond 0.00242 / 0.13 ( 12) SS BOND : angle 0.59156 / 0.32 ( 24) hydrogen bonds : bond 0.03070 / 1.98 ( 561) hydrogen bonds : angle 4.26700 / 2.99 ( 1647) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: Aa 103 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: Ac 443 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9096 (pp) REVERT: Ba 3 GLN cc_start: 0.8662 (mp-120) cc_final: 0.8422 (mp10) REVERT: Ba 71 ASP cc_start: 0.8720 (t0) cc_final: 0.8068 (t0) REVERT: Bb 71 ASP cc_start: 0.8706 (t0) cc_final: 0.8036 (t0) REVERT: Bb 108 MET cc_start: 0.8870 (ttp) cc_final: 0.8376 (tpp) REVERT: Bc 71 ASP cc_start: 0.8567 (t70) cc_final: 0.8133 (t0) outliers start: 31 outliers final: 15 residues processed: 202 average time/residue: 0.5394 time to fit residues: 119.3738 Evaluate side-chains 205 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 49 LYS Chi-restraints excluded: chain Aa residue 103 ASP Chi-restraints excluded: chain Aa residue 427 ILE Chi-restraints excluded: chain Ab residue 49 LYS Chi-restraints excluded: chain Ab residue 427 ILE Chi-restraints excluded: chain Ac residue 49 LYS Chi-restraints excluded: chain Ac residue 167 LYS Chi-restraints excluded: chain Ac residue 220 ASP Chi-restraints excluded: chain Ac residue 427 ILE Chi-restraints excluded: chain Ac residue 443 ILE Chi-restraints excluded: chain Ba residue 7 SER Chi-restraints excluded: chain Ba residue 75 ASN Chi-restraints excluded: chain Bb residue 7 SER Chi-restraints excluded: chain Bb residue 43 GLN Chi-restraints excluded: chain Bb residue 83 SER Chi-restraints excluded: chain Bc residue 76 THR Chi-restraints excluded: chain Bc residue 81 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [131, 88, 78, 24, 32, 130, 158, 45, 12, 105, 59] chunk 131 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 290 GLN Ba 75 ASN Bc 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.072021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.054659 restraints weight = 20740.465| |-----------------------------------------------------------------------------| r_work (start): 0.2389 rms_B_bonded: 2.18 r_work: 0.2243 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2101 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9357 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13101 Z= 0.141 Angle : 0.453 7.600 17808 Z= 0.237 Chirality : 0.045 0.137 2139 Planarity : 0.004 0.042 2250 Dihedral : 4.231 47.045 1814 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.78 % Allowed : 11.27 % Favored : 86.95 % 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: 1.24 (0.21), residues: 1665 helix: 2.20 (0.26), residues: 444 sheet: 0.11 (0.24), residues: 426 loop : 0.59 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAb 244 TYR 0.010 0.001 TYRBb 93 PHE 0.007 0.001 PHEAa 376 TRP 0.009 0.001 TRPBa 100 HIS 0.002 0.001 HISAc 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (13089) covalent geometry : angle 0.45309 / 0.24 (17784) SS BOND : bond 0.00311 / 0.17 ( 12) SS BOND : angle 0.58290 / 0.37 ( 24) hydrogen bonds : bond 0.03340 / 2.17 ( 561) hydrogen bonds : angle 4.32673 / 3.04 ( 1647) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.577 Fit side-chains REVERT: Aa 103 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8331 (m-30) REVERT: Ab 152 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8552 (tm-30) REVERT: Ac 443 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9098 (pp) REVERT: Ba 3 GLN cc_start: 0.8727 (mp-120) cc_final: 0.8461 (mm110) REVERT: Ba 71 ASP cc_start: 0.8739 (t0) cc_final: 0.8109 (t0) REVERT: Bb 71 ASP cc_start: 0.8731 (t0) cc_final: 0.8056 (t0) REVERT: Bb 108 MET cc_start: 0.8887 (ttp) cc_final: 0.8379 (tpp) REVERT: Bc 71 ASP cc_start: 0.8618 (t70) cc_final: 0.8221 (t70) outliers start: 26 outliers final: 19 residues processed: 201 average time/residue: 0.5625 time to fit residues: 123.5826 Evaluate side-chains 208 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 49 LYS Chi-restraints excluded: chain Aa residue 103 ASP Chi-restraints excluded: chain Aa residue 427 ILE Chi-restraints excluded: chain Ab residue 49 LYS Chi-restraints excluded: chain Ab residue 152 GLU Chi-restraints excluded: chain Ab residue 396 THR Chi-restraints excluded: chain Ab residue 427 ILE Chi-restraints excluded: chain Ac residue 49 LYS Chi-restraints excluded: chain Ac residue 167 LYS Chi-restraints excluded: chain Ac residue 220 ASP Chi-restraints excluded: chain Ac residue 396 THR Chi-restraints excluded: chain Ac residue 427 ILE Chi-restraints excluded: chain Ac residue 443 ILE Chi-restraints excluded: chain Ba residue 7 SER Chi-restraints excluded: chain Ba residue 75 ASN Chi-restraints excluded: chain Ba residue 76 THR Chi-restraints excluded: chain Bb residue 7 SER Chi-restraints excluded: chain Bb residue 43 GLN Chi-restraints excluded: chain Bb residue 63 LYS Chi-restraints excluded: chain Bb residue 83 SER Chi-restraints excluded: chain Bc residue 75 ASN Chi-restraints excluded: chain Bc residue 81 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [99, 42, 85, 27, 87, 93, 53, 101, 141, 165, 10] chunk 99 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 290 GLN ** Ba 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bc 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.072108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.054661 restraints weight = 20964.278| |-----------------------------------------------------------------------------| r_work (start): 0.2389 rms_B_bonded: 2.20 r_work: 0.2242 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2100 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9356 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13101 Z= 0.130 Angle : 0.452 7.522 17808 Z= 0.236 Chirality : 0.045 0.133 2139 Planarity : 0.004 0.042 2250 Dihedral : 4.230 47.007 1814 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 1.57 % Allowed : 11.82 % Favored : 86.61 % 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: 1.24 (0.21), residues: 1665 helix: 2.18 (0.26), residues: 444 sheet: 0.12 (0.24), residues: 426 loop : 0.60 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAb 244 TYR 0.009 0.001 TYRAa 438 PHE 0.007 0.001 PHEAa 376 TRP 0.009 0.001 TRPBa 100 HIS 0.001 0.001 HISAc 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (13089) covalent geometry : angle 0.45205 / 0.24 (17784) SS BOND : bond 0.00276 / 0.15 ( 12) SS BOND : angle 0.51465 / 0.34 ( 24) hydrogen bonds : bond 0.03308 / 2.14 ( 561) hydrogen bonds : angle 4.32304 / 3.04 ( 1647) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.521 Fit side-chains REVERT: Aa 103 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8326 (m-30) REVERT: Ab 152 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8544 (tm-30) REVERT: Ac 443 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9097 (pp) REVERT: Ba 3 GLN cc_start: 0.8746 (mp-120) cc_final: 0.8472 (mm110) REVERT: Ba 71 ASP cc_start: 0.8739 (t0) cc_final: 0.8111 (t0) REVERT: Bb 71 ASP cc_start: 0.8724 (t0) cc_final: 0.8045 (t0) REVERT: Bb 108 MET cc_start: 0.8897 (ttp) cc_final: 0.8386 (tpp) REVERT: Bc 71 ASP cc_start: 0.8621 (t70) cc_final: 0.8241 (t70) outliers start: 23 outliers final: 16 residues processed: 198 average time/residue: 0.5790 time to fit residues: 125.0866 Evaluate side-chains 205 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 49 LYS Chi-restraints excluded: chain Aa residue 103 ASP Chi-restraints excluded: chain Aa residue 427 ILE Chi-restraints excluded: chain Ab residue 49 LYS Chi-restraints excluded: chain Ab residue 152 GLU Chi-restraints excluded: chain Ab residue 396 THR Chi-restraints excluded: chain Ab residue 427 ILE Chi-restraints excluded: chain Ac residue 49 LYS Chi-restraints excluded: chain Ac residue 167 LYS Chi-restraints excluded: chain Ac residue 220 ASP Chi-restraints excluded: chain Ac residue 396 THR Chi-restraints excluded: chain Ac residue 427 ILE Chi-restraints excluded: chain Ac residue 443 ILE Chi-restraints excluded: chain Ba residue 7 SER Chi-restraints excluded: chain Bb residue 7 SER Chi-restraints excluded: chain Bb residue 43 GLN Chi-restraints excluded: chain Bb residue 63 LYS Chi-restraints excluded: chain Bb residue 83 SER Chi-restraints excluded: chain Bc residue 81 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [57, 111, 92, 90, 34, 61, 54, 151, 91, 98, 71] chunk 57 optimal weight: 0.2980 chunk 111 optimal weight: 0.0170 chunk 92 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 98 optimal weight: 0.0370 chunk 71 optimal weight: 1.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 290 GLN Ba 38 GLN Ba 75 ASN ** Bc 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.074202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.057121 restraints weight = 20686.609| |-----------------------------------------------------------------------------| r_work (start): 0.2441 rms_B_bonded: 2.16 r_work: 0.2297 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2156 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9333 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 : 0.002 0.021 13101 Z= 0.084 Angle : 0.429 7.542 17808 Z= 0.224 Chirality : 0.044 0.133 2139 Planarity : 0.003 0.040 2250 Dihedral : 4.055 46.319 1814 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.09 % Allowed : 12.23 % Favored : 86.68 % 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: 1.35 (0.21), residues: 1665 helix: 2.26 (0.26), residues: 441 sheet: 0.20 (0.24), residues: 426 loop : 0.66 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAb 244 TYR 0.016 0.001 TYRBa 93 PHE 0.007 0.001 PHEAa 376 TRP 0.007 0.001 TRPBa 100 HIS 0.001 0.000 HISAb 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.08 (13089) covalent geometry : angle 0.42907 / 0.22 (17784) SS BOND : bond 0.00237 / 0.13 ( 12) SS BOND : angle 0.38417 / 0.24 ( 24) hydrogen bonds : bond 0.02836 / 1.83 ( 561) hydrogen bonds : angle 4.12868 / 2.89 ( 1647) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.477 Fit side-chains REVERT: Aa 103 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8307 (m-30) REVERT: Aa 152 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8632 (tm-30) REVERT: Ac 443 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9086 (pp) REVERT: Ac 468 GLN cc_start: 0.7851 (tp40) cc_final: 0.7611 (mm110) REVERT: Ba 3 GLN cc_start: 0.8766 (mp-120) cc_final: 0.8509 (mm110) REVERT: Ba 71 ASP cc_start: 0.8728 (t0) cc_final: 0.8099 (t0) REVERT: Bb 71 ASP cc_start: 0.8698 (t0) cc_final: 0.8247 (t70) REVERT: Bb 108 MET cc_start: 0.8881 (ttp) cc_final: 0.8390 (tpp) REVERT: Bc 71 ASP cc_start: 0.8587 (t70) cc_final: 0.7693 (t70) REVERT: Bc 74 LYS cc_start: 0.9376 (mtpp) cc_final: 0.8890 (mtmm) REVERT: Bc 85 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8394 (mtmp) outliers start: 16 outliers final: 9 residues processed: 207 average time/residue: 0.5661 time to fit residues: 127.8431 Evaluate side-chains 202 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 49 LYS Chi-restraints excluded: chain Aa residue 103 ASP Chi-restraints excluded: chain Aa residue 152 GLU Chi-restraints excluded: chain Ab residue 49 LYS Chi-restraints excluded: chain Ab residue 427 ILE Chi-restraints excluded: chain Ac residue 49 LYS Chi-restraints excluded: chain Ac residue 167 LYS Chi-restraints excluded: chain Ac residue 220 ASP Chi-restraints excluded: chain Ac residue 427 ILE Chi-restraints excluded: chain Ac residue 443 ILE Chi-restraints excluded: chain Ba residue 75 ASN Chi-restraints excluded: chain Bb residue 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: [96, 98, 131, 84, 60, 59, 102, 106, 11, 80, 115] chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 102 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 290 GLN Ba 75 ASN ** Bc 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.073495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.056293 restraints weight = 20675.756| |-----------------------------------------------------------------------------| r_work (start): 0.2423 rms_B_bonded: 2.16 r_work: 0.2279 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2138 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9342 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13101 Z= 0.108 Angle : 0.437 7.120 17808 Z= 0.228 Chirality : 0.044 0.133 2139 Planarity : 0.003 0.041 2250 Dihedral : 4.085 46.801 1814 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.09 % Allowed : 12.23 % Favored : 86.68 % 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: 1.39 (0.21), residues: 1665 helix: 2.31 (0.26), residues: 441 sheet: 0.26 (0.24), residues: 426 loop : 0.66 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAb 244 TYR 0.010 0.001 TYRBc 93 PHE 0.007 0.001 PHEAa 376 TRP 0.008 0.001 TRPBa 100 HIS 0.001 0.000 HISAc 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (13089) covalent geometry : angle 0.43677 / 0.23 (17784) SS BOND : bond 0.00255 / 0.14 ( 12) SS BOND : angle 0.43538 / 0.29 ( 24) hydrogen bonds : bond 0.03003 / 1.95 ( 561) hydrogen bonds : angle 4.13911 / 2.91 ( 1647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4197.00 seconds wall clock time: 72 minutes 26.40 seconds (4346.40 seconds total)