Starting phenix.real_space_refine on Sat Oct 24 10:55:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sf4_54813/10_2026/9sf4_54813.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sf4_54813/10_2026/9sf4_54813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sf4_54813/10_2026/9sf4_54813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sf4_54813/10_2026/9sf4_54813.map" model { file = "/net/cci-nas-00/data/ceres_data/9sf4_54813/10_2026/9sf4_54813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sf4_54813/10_2026/9sf4_54813.cif" } resolution = 2.6 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= 0.011 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 69 5.16 5 C 8076 2.51 5 N 2115 2.21 5 O 2514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12774 Number of models: 1 Model: "" Number of chains: 6 Chain: "Aa" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3349 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 15, 'TRANS': 421} Chain breaks: 1 Chain: "Ab" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3349 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 15, 'TRANS': 421} Chain breaks: 1 Chain: "Ac" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3349 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 15, 'TRANS': 421} Chain breaks: 1 Chain: "Ba" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 909 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "Bb" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 909 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "Bc" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 909 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Time building chain proxies: 2.70, per 1000 atoms: 0.21 Number of scatterers: 12774 At special positions: 0 Unit cell: (111.456, 115.344, 102.384, 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 69 16.00 O 2514 8.00 N 2115 7.00 C 8076 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYSAc 387 " - pdb=" SG CYSAc 392 " distance=2.03 Simple disulfide: pdb=" SG CYSBa 22 " - pdb=" SG CYSBa 96 " distance=2.03 Simple disulfide: pdb=" SG CYSBb 22 " - pdb=" SG CYSBb 96 " distance=2.03 Simple disulfide: pdb=" SG CYSBc 22 " - pdb=" SG CYSBc 96 " 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: 0.91 Conformation dependent library (CDL) restraints added in 595.6 milliseconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3126 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 24 sheets defined 33.6% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'Aa' and resid 29 through 35 removed outlier: 3.591A pdb=" N LYSAa 35 " --> pdb=" O GLUAa 31 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 65 through 72 removed outlier: 3.650A pdb=" N SERAa 69 " --> pdb=" O SERAa 66 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYSAa 70 " --> pdb=" O ASNAa 67 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THRAa 72 " --> pdb=" O SERAa 69 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 74 through 100 Proline residue: Aa 89 - end of helix removed outlier: 3.774A 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: 4.088A pdb=" N LYSAa 139 " --> pdb=" O TYRAa 135 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASNAa 140 " --> pdb=" O GLUAa 136 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASNAa 143 " --> pdb=" O LYSAa 139 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 147 through 153 Processing helix chain 'Aa' and resid 175 through 182 Processing helix chain 'Aa' and resid 191 through 215 removed outlier: 4.384A pdb=" N PHEAa 212 " --> pdb=" O SERAa 208 " (cutoff:3.500A) removed outlier: 4.723A 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: 3.719A pdb=" N LEUAa 242 " --> pdb=" O ASNAa 238 " (cutoff:3.500A) removed outlier: 4.030A 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 358 Processing helix chain 'Aa' and resid 359 through 363 Processing helix chain 'Aa' and resid 452 through 470 removed outlier: 3.500A pdb=" N SERAa 457 " --> pdb=" O LYSAa 453 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 29 through 36 removed outlier: 3.591A pdb=" N LYSAb 35 " --> pdb=" O GLUAb 31 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILEAb 36 " --> pdb=" O LYSAb 32 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 65 through 72 removed outlier: 3.647A pdb=" N SERAb 69 " --> pdb=" O SERAb 66 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYSAb 70 " --> pdb=" O ASNAb 67 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THRAb 72 " --> pdb=" O SERAb 69 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 74 through 100 Proline residue: Ab 89 - end of helix removed outlier: 3.757A 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 146 removed outlier: 4.092A pdb=" N LYSAb 139 " --> pdb=" O TYRAb 135 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASNAb 140 " --> pdb=" O GLUAb 136 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASNAb 143 " --> pdb=" O LYSAb 139 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 147 through 153 Processing helix chain 'Ab' and resid 175 through 182 Processing helix chain 'Ab' and resid 191 through 215 removed outlier: 4.397A pdb=" N PHEAb 212 " --> pdb=" O SERAb 208 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VALAb 213 " --> pdb=" O ASPAb 209 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 227 through 232 Processing helix chain 'Ab' and resid 233 through 236 Processing helix chain 'Ab' and resid 238 through 245 removed outlier: 3.742A pdb=" N LEUAb 242 " --> pdb=" O ASNAb 238 " (cutoff:3.500A) removed outlier: 4.029A 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 358 Processing helix chain 'Ab' and resid 359 through 363 Processing helix chain 'Ab' and resid 452 through 470 Processing helix chain 'Ac' and resid 29 through 36 removed outlier: 3.575A pdb=" N LYSAc 35 " --> pdb=" O GLUAc 31 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILEAc 36 " --> pdb=" O LYSAc 32 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 65 through 72 removed outlier: 3.607A pdb=" N SERAc 69 " --> pdb=" O SERAc 66 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LYSAc 70 " --> pdb=" O ASNAc 67 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THRAc 72 " --> pdb=" O SERAc 69 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 74 through 100 Proline residue: Ac 89 - end of helix removed outlier: 3.753A 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 146 removed outlier: 4.098A pdb=" N LYSAc 139 " --> pdb=" O TYRAc 135 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASNAc 140 " --> pdb=" O GLUAc 136 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASNAc 143 " --> pdb=" O LYSAc 139 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 147 through 153 Processing helix chain 'Ac' and resid 175 through 182 Processing helix chain 'Ac' and resid 191 through 215 removed outlier: 4.362A pdb=" N PHEAc 212 " --> pdb=" O SERAc 208 " (cutoff:3.500A) removed outlier: 4.700A 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: 3.729A pdb=" N LEUAc 242 " --> pdb=" O ASNAc 238 " (cutoff:3.500A) removed outlier: 4.036A 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 358 Processing helix chain 'Ac' and resid 359 through 363 Processing helix chain 'Ac' and resid 452 through 470 Processing helix chain 'Ba' and resid 28 through 32 removed outlier: 4.076A pdb=" N ARGBa 31 " --> pdb=" O THRBa 28 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 63 through 65 No H-bonds generated for 'chain 'Ba' and resid 63 through 65' Processing helix chain 'Ba' and resid 87 through 91 Processing helix chain 'Bb' and resid 28 through 32 removed outlier: 4.005A pdb=" N ARGBb 31 " --> pdb=" O THRBb 28 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 63 through 65 No H-bonds generated for 'chain 'Bb' and resid 63 through 65' Processing helix chain 'Bb' and resid 87 through 91 Processing helix chain 'Bc' and resid 28 through 32 removed outlier: 4.150A pdb=" N ARGBc 31 " --> pdb=" O THRBc 28 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 63 through 65 No H-bonds generated for 'chain 'Bc' and resid 63 through 65' Processing helix chain 'Bc' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 158 through 162 removed outlier: 10.777A pdb=" N THRAa 168 " --> pdb=" O THRAa 54 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASPAa 56 " --> pdb=" O THRAa 168 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYRAa 170 " --> pdb=" O ASPAa 56 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VALAa 39 " --> pdb=" O LEUAa 296 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEUAa 296 " --> pdb=" O VALAa 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLYAa 41 " --> pdb=" O GLNAa 294 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLNAa 294 " --> pdb=" O GLYAa 41 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N THRAa 43 " --> pdb=" O TYRAa 292 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N TYRAa 292 " --> pdb=" O THRAa 43 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N LYSAa 45 " --> pdb=" O GLNAa 290 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N GLNAa 290 " --> pdb=" O LYSAa 45 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYSAa 47 " --> pdb=" O ILEAa 288 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILEAa 288 " --> pdb=" O LYSAa 47 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYSAa 49 " --> pdb=" O THRAa 286 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N THRAa 286 " --> pdb=" O LYSAa 49 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASNAa 51 " --> pdb=" O ILEAa 284 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILEAa 284 " --> pdb=" O ASNAa 51 " (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: 6.520A pdb=" N ILEAa 277 " --> pdb=" O VALAa 267 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VALAa 269 " --> pdb=" O TYRAa 275 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TYRAa 275 " --> pdb=" O VALAa 269 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILEAa 284 " --> pdb=" O ASNAa 51 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASNAa 51 " --> pdb=" O ILEAa 284 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N THRAa 286 " --> pdb=" O LYSAa 49 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LYSAa 49 " --> pdb=" O THRAa 286 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILEAa 288 " --> pdb=" O LYSAa 47 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYSAa 47 " --> pdb=" O ILEAa 288 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N GLNAa 290 " --> pdb=" O LYSAa 45 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N LYSAa 45 " --> pdb=" O GLNAa 290 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N TYRAa 292 " --> pdb=" O THRAa 43 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N THRAa 43 " --> pdb=" O TYRAa 292 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLNAa 294 " --> pdb=" O GLYAa 41 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLYAa 41 " --> pdb=" O GLNAa 294 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEUAa 296 " --> pdb=" O VALAa 39 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VALAa 39 " --> pdb=" O LEUAa 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Aa' and resid 38 through 60 current: chain 'Aa' and resid 323 through 326 Processing sheet with id=AA3, first strand: chain 'Aa' and resid 101 through 102 removed outlier: 5.908A pdb=" N VALAa 113 " --> pdb=" O ILEAb 426 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SERAb 428 " --> pdb=" O VALAa 113 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N METAa 115 " --> pdb=" O SERAb 428 " (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: 7.399A pdb=" N ILEBa 48 " --> pdb=" O ALABa 61 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHEBa 47 " --> pdb=" O ARGBa 38 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARGBa 38 " --> pdb=" O PHEBa 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Aa' and resid 248 through 250 removed outlier: 7.399A pdb=" N ILEBa 48 " --> pdb=" O ALABa 61 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHEBa 47 " --> pdb=" O ARGBa 38 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARGBa 38 " --> pdb=" O PHEBa 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Aa' and resid 301 through 302 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 393 through 394 Processing sheet with id=AB1, first strand: chain 'Ab' and resid 158 through 162 removed outlier: 10.786A pdb=" N THRAb 168 " --> pdb=" O THRAb 54 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASPAb 56 " --> pdb=" O THRAb 168 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYRAb 170 " --> pdb=" O ASPAb 56 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VALAb 39 " --> pdb=" O LEUAb 296 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEUAb 296 " --> pdb=" O VALAb 39 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLYAb 41 " --> pdb=" O GLNAb 294 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLNAb 294 " --> pdb=" O GLYAb 41 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N THRAb 43 " --> pdb=" O TYRAb 292 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N TYRAb 292 " --> pdb=" O THRAb 43 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N LYSAb 45 " --> pdb=" O GLNAb 290 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N GLNAb 290 " --> pdb=" O LYSAb 45 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYSAb 47 " --> pdb=" O ILEAb 288 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILEAb 288 " --> pdb=" O LYSAb 47 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LYSAb 49 " --> pdb=" O THRAb 286 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THRAb 286 " --> pdb=" O LYSAb 49 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASNAb 51 " --> pdb=" O ILEAb 284 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILEAb 284 " --> pdb=" O ASNAb 51 " (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: 6.516A pdb=" N ILEAb 277 " --> pdb=" O VALAb 267 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VALAb 269 " --> pdb=" O TYRAb 275 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYRAb 275 " --> pdb=" O VALAb 269 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILEAb 284 " --> pdb=" O ASNAb 51 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ASNAb 51 " --> pdb=" O ILEAb 284 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THRAb 286 " --> pdb=" O LYSAb 49 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LYSAb 49 " --> pdb=" O THRAb 286 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILEAb 288 " --> pdb=" O LYSAb 47 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYSAb 47 " --> pdb=" O ILEAb 288 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N GLNAb 290 " --> pdb=" O LYSAb 45 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N LYSAb 45 " --> pdb=" O GLNAb 290 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N TYRAb 292 " --> pdb=" O THRAb 43 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N THRAb 43 " --> pdb=" O TYRAb 292 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLNAb 294 " --> pdb=" O GLYAb 41 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLYAb 41 " --> pdb=" O GLNAb 294 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEUAb 296 " --> pdb=" O VALAb 39 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VALAb 39 " --> pdb=" O LEUAb 296 " (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 323 through 326 Processing sheet with id=AB3, first strand: chain 'Ab' and resid 101 through 102 removed outlier: 5.917A pdb=" N VALAb 113 " --> pdb=" O ILEAc 426 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N SERAc 428 " --> pdb=" O VALAb 113 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N METAb 115 " --> pdb=" O SERAc 428 " (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: 7.416A pdb=" N ILEBb 48 " --> pdb=" O ALABb 61 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRPBb 36 " --> pdb=" O ILEBb 48 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARGBb 50 " --> pdb=" O VALBb 34 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VALBb 34 " --> pdb=" O ARGBb 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Ab' and resid 248 through 250 removed outlier: 7.416A pdb=" N ILEBb 48 " --> pdb=" O ALABb 61 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRPBb 36 " --> pdb=" O ILEBb 48 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARGBb 50 " --> pdb=" O VALBb 34 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VALBb 34 " --> pdb=" O ARGBb 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ab' and resid 301 through 303 Processing sheet with id=AB8, first strand: chain 'Ac' and resid 158 through 162 removed outlier: 10.767A pdb=" N THRAc 168 " --> pdb=" O THRAc 54 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASPAc 56 " --> pdb=" O THRAc 168 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TYRAc 170 " --> pdb=" O ASPAc 56 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VALAc 39 " --> pdb=" O LEUAc 296 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEUAc 296 " --> pdb=" O VALAc 39 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLYAc 41 " --> pdb=" O GLNAc 294 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLNAc 294 " --> pdb=" O GLYAc 41 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N THRAc 43 " --> pdb=" O TYRAc 292 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N TYRAc 292 " --> pdb=" O THRAc 43 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N LYSAc 45 " --> pdb=" O GLNAc 290 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N GLNAc 290 " --> pdb=" O LYSAc 45 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYSAc 47 " --> pdb=" O ILEAc 288 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILEAc 288 " --> pdb=" O LYSAc 47 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYSAc 49 " --> pdb=" O THRAc 286 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N THRAc 286 " --> pdb=" O LYSAc 49 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASNAc 51 " --> pdb=" O ILEAc 284 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILEAc 284 " --> pdb=" O ASNAc 51 " (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: 6.516A pdb=" N ILEAc 277 " --> pdb=" O VALAc 267 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VALAc 269 " --> pdb=" O TYRAc 275 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYRAc 275 " --> pdb=" O VALAc 269 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILEAc 284 " --> pdb=" O ASNAc 51 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASNAc 51 " --> pdb=" O ILEAc 284 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N THRAc 286 " --> pdb=" O LYSAc 49 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYSAc 49 " --> pdb=" O THRAc 286 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILEAc 288 " --> pdb=" O LYSAc 47 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYSAc 47 " --> pdb=" O ILEAc 288 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N GLNAc 290 " --> pdb=" O LYSAc 45 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N LYSAc 45 " --> pdb=" O GLNAc 290 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N TYRAc 292 " --> pdb=" O THRAc 43 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N THRAc 43 " --> pdb=" O TYRAc 292 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLNAc 294 " --> pdb=" O GLYAc 41 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLYAc 41 " --> pdb=" O GLNAc 294 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEUAc 296 " --> pdb=" O VALAc 39 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VALAc 39 " --> pdb=" O LEUAc 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Ac' and resid 38 through 60 current: chain 'Ac' and resid 323 through 326 Processing sheet with id=AC1, first strand: chain 'Ac' and resid 248 through 250 removed outlier: 7.411A pdb=" N ILEBc 48 " --> pdb=" O ALABc 61 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRPBc 36 " --> pdb=" O ILEBc 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARGBc 50 " --> pdb=" O VALBc 34 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VALBc 34 " --> pdb=" O ARGBc 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Ac' and resid 248 through 250 removed outlier: 7.411A pdb=" N ILEBc 48 " --> pdb=" O ALABc 61 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRPBc 36 " --> pdb=" O ILEBc 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARGBc 50 " --> pdb=" O VALBc 34 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VALBc 34 " --> pdb=" O ARGBc 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Ac' and resid 301 through 302 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 5 through 7 Processing sheet with id=AC6, first strand: chain 'Bc' and resid 5 through 7 630 hydrogen bonds defined for protein. 1674 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: 2.22 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4158 1.34 - 1.46: 2836 1.46 - 1.58: 5879 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 12969 Sorted by residual: bond pdb=" CB GLNAc 289 " pdb=" CG GLNAc 289 " ideal model delta sigma weight residual 1.520 1.538 -0.018 3.00e-02 1.11e+03 3.48e-01 bond pdb=" C SERAc 88 " pdb=" N PROAc 89 " ideal model delta sigma weight residual 1.335 1.341 -0.007 1.28e-02 6.10e+03 2.84e-01 bond pdb=" C SERAa 88 " pdb=" N PROAa 89 " ideal model delta sigma weight residual 1.335 1.341 -0.007 1.28e-02 6.10e+03 2.76e-01 bond pdb=" CA LEUBb 20 " pdb=" C LEUBb 20 " ideal model delta sigma weight residual 1.523 1.529 -0.006 1.19e-02 7.06e+03 2.22e-01 bond pdb=" C VALAa 184 " pdb=" N PROAa 185 " ideal model delta sigma weight residual 1.335 1.341 -0.006 1.28e-02 6.10e+03 2.20e-01 ... (remaining 12964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 17225 0.99 - 1.98: 327 1.98 - 2.97: 56 2.97 - 3.96: 14 3.96 - 4.95: 9 Bond angle restraints: 17631 Sorted by residual: angle pdb=" CA LEUAa 409 " pdb=" CB LEUAa 409 " pdb=" CG LEUAa 409 " ideal model delta sigma weight residual 116.30 121.25 -4.95 3.50e+00 8.16e-02 2.00e+00 angle pdb=" CA LEUAc 409 " pdb=" CB LEUAc 409 " pdb=" CG LEUAc 409 " ideal model delta sigma weight residual 116.30 121.20 -4.90 3.50e+00 8.16e-02 1.96e+00 angle pdb=" CA LEUAb 409 " pdb=" CB LEUAb 409 " pdb=" CG LEUAb 409 " ideal model delta sigma weight residual 116.30 121.20 -4.90 3.50e+00 8.16e-02 1.96e+00 angle pdb=" C ASNAa 320 " pdb=" N THRAa 321 " pdb=" CA THRAa 321 " ideal model delta sigma weight residual 122.08 123.99 -1.91 1.47e+00 4.63e-01 1.69e+00 angle pdb=" CB GLNAc 289 " pdb=" CG GLNAc 289 " pdb=" CD GLNAc 289 " ideal model delta sigma weight residual 112.60 114.64 -2.04 1.70e+00 3.46e-01 1.44e+00 ... (remaining 17626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 7311 17.07 - 34.14: 444 34.14 - 51.20: 98 51.20 - 68.27: 33 68.27 - 85.34: 10 Dihedral angle restraints: 7896 sinusoidal: 3030 harmonic: 4866 Sorted by residual: dihedral pdb=" CA ASPAc 452 " pdb=" CB ASPAc 452 " pdb=" CG ASPAc 452 " pdb=" OD1 ASPAc 452 " ideal model delta sinusoidal sigma weight residual -30.00 -87.75 57.75 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASPAb 452 " pdb=" CB ASPAb 452 " pdb=" CG ASPAb 452 " pdb=" OD1 ASPAb 452 " ideal model delta sinusoidal sigma weight residual -30.00 -87.71 57.71 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASPAa 452 " pdb=" CB ASPAa 452 " pdb=" CG ASPAa 452 " pdb=" OD1 ASPAa 452 " ideal model delta sinusoidal sigma weight residual -30.00 -87.62 57.62 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 7893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1314 0.029 - 0.058: 480 0.058 - 0.087: 139 0.087 - 0.116: 182 0.116 - 0.145: 18 Chirality restraints: 2133 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 2.59 -0.15 2.00e-01 2.50e+01 5.27e-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 2.57 -0.13 2.00e-01 2.50e+01 4.43e-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 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 2130 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLYAb 446 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PROAb 447 " -0.049 5.00e-02 4.00e+02 pdb=" CA PROAb 447 " 0.015 5.00e-02 4.00e+02 pdb=" CD PROAb 447 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLYAc 446 " 0.018 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PROAc 447 " -0.048 5.00e-02 4.00e+02 pdb=" CA PROAc 447 " 0.015 5.00e-02 4.00e+02 pdb=" CD PROAc 447 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLYAa 446 " 0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PROAa 447 " -0.048 5.00e-02 4.00e+02 pdb=" CA PROAa 447 " 0.014 5.00e-02 4.00e+02 pdb=" CD PROAa 447 " 0.015 5.00e-02 4.00e+02 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 8770 3.09 - 3.54: 12709 3.54 - 3.99: 20839 3.99 - 4.45: 24715 4.45 - 4.90: 38489 Nonbonded interactions: 105522 Sorted by model distance: nonbonded pdb=" N ALABc 92 " pdb=" O ALABc 92 " model vdw 2.637 2.496 nonbonded pdb=" N LEUAa 409 " pdb=" O LEUAa 409 " model vdw 2.638 2.496 nonbonded pdb=" N ALABa 92 " pdb=" O ALABa 92 " model vdw 2.640 2.496 nonbonded pdb=" N LEUAb 409 " pdb=" O LEUAb 409 " model vdw 2.640 2.496 nonbonded pdb=" N ASPAa 413 " pdb=" O ASPAa 413 " model vdw 2.640 2.496 ... (remaining 105517 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: 0.03 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: 7.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.290 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 12981 Z= 0.071 Angle : 0.385 4.949 17655 Z= 0.203 Chirality : 0.043 0.145 2133 Planarity : 0.003 0.028 2235 Dihedral : 12.580 85.338 4734 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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 (0.21), residues: 1650 helix: 1.28 (0.25), residues: 420 sheet: -0.46 (0.25), residues: 402 loop : 0.26 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGBc 31 TYR 0.011 0.001 TYRBa 94 PHE 0.010 0.001 PHEBa 47 TRP 0.003 0.001 TRPBa 36 HIS 0.003 0.001 HISAb 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00153 / 0.07 (12969) covalent geometry : angle 0.38349 / 0.20 (17631) SS BOND : bond 0.00274 / 0.14 ( 12) SS BOND : angle 1.04910 / 0.51 ( 24) hydrogen bonds : bond 0.19081 / 12.96 ( 557) hydrogen bonds : angle 8.35552 / 6.14 ( 1674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.580 Fit side-chains REVERT: Aa 167 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7962 (mtpp) REVERT: Aa 220 ASP cc_start: 0.8501 (t0) cc_final: 0.8298 (m-30) REVERT: Aa 289 GLN cc_start: 0.8837 (mm110) cc_final: 0.8615 (mm110) REVERT: Aa 393 GLN cc_start: 0.8666 (tt0) cc_final: 0.8353 (tm-30) REVERT: Aa 399 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8194 (mtm110) REVERT: Ab 393 GLN cc_start: 0.8635 (tt0) cc_final: 0.8289 (tm-30) REVERT: Ab 399 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8231 (mtm110) REVERT: Ac 399 ARG cc_start: 0.8456 (mtp85) cc_final: 0.8200 (mtm110) REVERT: Ba 106 SER cc_start: 0.8243 (m) cc_final: 0.8032 (p) REVERT: Bb 106 SER cc_start: 0.8247 (m) cc_final: 0.7889 (p) REVERT: Bb 109 ASP cc_start: 0.8059 (m-30) cc_final: 0.7482 (m-30) REVERT: Bc 20 LEU cc_start: 0.8699 (mp) cc_final: 0.8493 (mt) REVERT: Bc 106 SER cc_start: 0.8244 (m) cc_final: 0.7833 (p) REVERT: Bc 109 ASP cc_start: 0.7997 (m-30) cc_final: 0.7371 (m-30) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.6038 time to fit residues: 143.9235 Evaluate side-chains 165 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 140 ASN Ab 424 ASN Ba 99 GLN Bb 99 GLN Bc 39 GLN Bc 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.071848 restraints weight = 18190.640| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 1.92 r_work: 0.2584 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9237 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12981 Z= 0.220 Angle : 0.532 5.180 17655 Z= 0.287 Chirality : 0.048 0.160 2133 Planarity : 0.004 0.035 2235 Dihedral : 4.356 20.721 1791 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.86 % Allowed : 6.61 % Favored : 91.53 % 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: 0.70 (0.21), residues: 1650 helix: 1.69 (0.26), residues: 417 sheet: -0.30 (0.24), residues: 435 loop : 0.42 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGBa 19 TYR 0.012 0.001 TYRBb 95 PHE 0.017 0.002 PHEBb 27 TRP 0.005 0.001 TRPBb 112 HIS 0.002 0.001 HISAb 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 (12969) covalent geometry : angle 0.53212 / 0.29 (17631) SS BOND : bond 0.00285 / 0.16 ( 12) SS BOND : angle 0.71930 / 0.38 ( 24) hydrogen bonds : bond 0.04855 / 3.25 ( 557) hydrogen bonds : angle 5.50287 / 3.97 ( 1674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Aa 152 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8374 (tm-30) REVERT: Aa 167 LYS cc_start: 0.8398 (mtmt) cc_final: 0.8160 (mtpp) REVERT: Aa 443 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8131 (pp) REVERT: Aa 453 LYS cc_start: 0.8266 (tttt) cc_final: 0.7831 (ttpt) REVERT: Ab 152 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8459 (tm-30) REVERT: Ac 152 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: Ac 393 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: Ac 399 ARG cc_start: 0.8586 (mtp85) cc_final: 0.8310 (mtm110) REVERT: Ba 82 GLN cc_start: 0.8684 (tp40) cc_final: 0.8201 (tp40) REVERT: Ba 106 SER cc_start: 0.8439 (m) cc_final: 0.8100 (p) REVERT: Ba 109 ASP cc_start: 0.8401 (m-30) cc_final: 0.7914 (m-30) REVERT: Bb 19 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8201 (tmm-80) REVERT: Bc 82 GLN cc_start: 0.8709 (tp40) cc_final: 0.8286 (tp40) REVERT: Bc 106 SER cc_start: 0.8501 (m) cc_final: 0.8290 (p) outliers start: 27 outliers final: 8 residues processed: 188 average time/residue: 0.5568 time to fit residues: 114.1754 Evaluate side-chains 178 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 152 GLU Chi-restraints excluded: chain Aa residue 309 ILE Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 152 GLU Chi-restraints excluded: chain Ab residue 309 ILE Chi-restraints excluded: chain Ab residue 322 LEU Chi-restraints excluded: chain Ac residue 152 GLU Chi-restraints excluded: chain Ac residue 309 ILE Chi-restraints excluded: chain Ac residue 393 GLN Chi-restraints excluded: chain Ba residue 71 SER Chi-restraints excluded: chain Bb residue 19 ARG Chi-restraints excluded: chain Bb residue 71 SER Chi-restraints excluded: chain Bc residue 21 SER Chi-restraints excluded: chain Bc residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [5, 58, 128, 57, 118, 87, 90, 111, 141, 88, 83] chunk 5 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 83 optimal weight: 0.0770 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.074323 restraints weight = 18133.676| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 1.89 r_work: 0.2632 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9189 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12981 Z= 0.113 Angle : 0.442 4.624 17655 Z= 0.240 Chirality : 0.045 0.154 2133 Planarity : 0.004 0.059 2235 Dihedral : 4.026 18.033 1791 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.52 % Allowed : 8.26 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1650 helix: 2.01 (0.26), residues: 417 sheet: -0.17 (0.24), residues: 429 loop : 0.43 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGAb 399 TYR 0.011 0.001 TYRBa 95 PHE 0.013 0.001 PHEBc 47 TRP 0.005 0.001 TRPBa 36 HIS 0.001 0.000 HISAc 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (12969) covalent geometry : angle 0.44228 / 0.24 (17631) SS BOND : bond 0.00189 / 0.10 ( 12) SS BOND : angle 0.28956 / 0.17 ( 24) hydrogen bonds : bond 0.03906 / 2.60 ( 557) hydrogen bonds : angle 4.92728 / 3.55 ( 1674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: Aa 167 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8156 (ttmt) REVERT: Aa 453 LYS cc_start: 0.8190 (tttt) cc_final: 0.7731 (ttpt) REVERT: Ab 152 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8470 (tm-30) REVERT: Ac 322 LEU cc_start: 0.8576 (tp) cc_final: 0.8045 (mt) REVERT: Ac 399 ARG cc_start: 0.8543 (mtp85) cc_final: 0.8322 (mtm110) REVERT: Ba 82 GLN cc_start: 0.8647 (tp40) cc_final: 0.8066 (tp40) REVERT: Ba 106 SER cc_start: 0.8394 (m) cc_final: 0.8070 (p) REVERT: Ba 109 ASP cc_start: 0.8353 (m-30) cc_final: 0.7886 (m-30) REVERT: Bb 19 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8286 (tmm-80) REVERT: Bb 82 GLN cc_start: 0.8561 (tp40) cc_final: 0.7993 (tp40) REVERT: Bb 109 ASP cc_start: 0.8383 (m-30) cc_final: 0.8046 (m-30) REVERT: Bc 82 GLN cc_start: 0.8707 (tp40) cc_final: 0.8302 (tp40) outliers start: 22 outliers final: 5 residues processed: 185 average time/residue: 0.5308 time to fit residues: 107.5088 Evaluate side-chains 175 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 309 ILE Chi-restraints excluded: chain Ab residue 152 GLU Chi-restraints excluded: chain Ac residue 309 ILE Chi-restraints excluded: chain Bb residue 19 ARG Chi-restraints excluded: chain Bc residue 28 THR Chi-restraints excluded: chain Bc residue 71 SER Chi-restraints excluded: chain Bc residue 95 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [99, 77, 62, 123, 82, 89, 66, 148, 47, 103, 63] chunk 99 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 393 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.070986 restraints weight = 18303.395| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 1.85 r_work: 0.2570 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9229 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12981 Z= 0.231 Angle : 0.529 5.320 17655 Z= 0.283 Chirality : 0.048 0.160 2133 Planarity : 0.004 0.042 2235 Dihedral : 4.437 21.753 1791 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.38 % Allowed : 9.02 % Favored : 89.60 % 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: 0.81 (0.21), residues: 1650 helix: 1.92 (0.25), residues: 417 sheet: -0.27 (0.25), residues: 405 loop : 0.38 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAa 399 TYR 0.014 0.001 TYRBc 80 PHE 0.016 0.002 PHEBb 27 TRP 0.004 0.001 TRPBc 112 HIS 0.001 0.000 HISAc 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (12969) covalent geometry : angle 0.52897 / 0.28 (17631) SS BOND : bond 0.00189 / 0.10 ( 12) SS BOND : angle 0.33817 / 0.18 ( 24) hydrogen bonds : bond 0.04699 / 3.14 ( 557) hydrogen bonds : angle 5.05816 / 3.63 ( 1674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.446 Fit side-chains REVERT: Aa 152 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8502 (tm-30) REVERT: Aa 167 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8162 (ttmt) REVERT: Aa 453 LYS cc_start: 0.8329 (tttt) cc_final: 0.7845 (ttpt) REVERT: Ab 152 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8527 (tm-30) REVERT: Ac 139 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8522 (mptp) REVERT: Ac 152 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8369 (tm-30) REVERT: Ac 393 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: Ba 106 SER cc_start: 0.8451 (m) cc_final: 0.8062 (p) REVERT: Ba 109 ASP cc_start: 0.8501 (m-30) cc_final: 0.8017 (m-30) REVERT: Bb 19 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8109 (tmm-80) REVERT: Bb 82 GLN cc_start: 0.8638 (tp40) cc_final: 0.8391 (tp40) REVERT: Bb 109 ASP cc_start: 0.8510 (m-30) cc_final: 0.8077 (m-30) REVERT: Bc 20 LEU cc_start: 0.8842 (mp) cc_final: 0.8595 (mt) REVERT: Bc 82 GLN cc_start: 0.8774 (tp40) cc_final: 0.8347 (tp40) REVERT: Bc 109 ASP cc_start: 0.8418 (m-30) cc_final: 0.7944 (m-30) outliers start: 20 outliers final: 4 residues processed: 184 average time/residue: 0.5475 time to fit residues: 110.2058 Evaluate side-chains 177 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 152 GLU Chi-restraints excluded: chain Aa residue 309 ILE Chi-restraints excluded: chain Ab residue 152 GLU Chi-restraints excluded: chain Ac residue 152 GLU Chi-restraints excluded: chain Ac residue 309 ILE Chi-restraints excluded: chain Ac residue 393 GLN Chi-restraints excluded: chain Bb residue 19 ARG Chi-restraints excluded: chain Bc residue 28 THR Chi-restraints excluded: chain Bc residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [26, 44, 139, 100, 14, 119, 7, 27, 55, 158, 93] chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.072955 restraints weight = 18393.523| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 1.94 r_work: 0.2607 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9222 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12981 Z= 0.120 Angle : 0.461 8.240 17655 Z= 0.247 Chirality : 0.045 0.155 2133 Planarity : 0.004 0.066 2235 Dihedral : 4.138 18.737 1791 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.24 % Allowed : 9.57 % Favored : 89.19 % 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: 0.93 (0.21), residues: 1650 helix: 2.13 (0.25), residues: 417 sheet: -0.18 (0.25), residues: 399 loop : 0.37 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGAc 399 TYR 0.011 0.001 TYRBc 95 PHE 0.014 0.001 PHEBc 27 TRP 0.004 0.001 TRPBa 36 HIS 0.000 0.000 HISAc 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (12969) covalent geometry : angle 0.46121 / 0.25 (17631) SS BOND : bond 0.00150 / 0.08 ( 12) SS BOND : angle 0.26190 / 0.16 ( 24) hydrogen bonds : bond 0.03752 / 2.49 ( 557) hydrogen bonds : angle 4.69531 / 3.36 ( 1674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.460 Fit side-chains REVERT: Aa 152 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8509 (tm-30) REVERT: Aa 167 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8179 (ttmt) REVERT: Aa 443 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8107 (pp) REVERT: Aa 453 LYS cc_start: 0.8230 (tttt) cc_final: 0.7745 (ttpt) REVERT: Ab 152 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8571 (tm-30) REVERT: Ab 167 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8110 (tttm) REVERT: Ac 139 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8428 (mptp) REVERT: Ac 322 LEU cc_start: 0.8585 (tp) cc_final: 0.8083 (mt) REVERT: Ac 393 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: Ac 399 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7930 (mtm110) REVERT: Ba 106 SER cc_start: 0.8397 (m) cc_final: 0.8051 (p) REVERT: Ba 109 ASP cc_start: 0.8472 (m-30) cc_final: 0.8030 (m-30) REVERT: Bb 82 GLN cc_start: 0.8629 (tp40) cc_final: 0.8023 (tp40) REVERT: Bb 109 ASP cc_start: 0.8500 (m-30) cc_final: 0.8125 (m-30) REVERT: Bc 82 GLN cc_start: 0.8785 (tp40) cc_final: 0.8378 (tp40) REVERT: Bc 109 ASP cc_start: 0.8408 (m-30) cc_final: 0.7968 (m-30) outliers start: 18 outliers final: 4 residues processed: 179 average time/residue: 0.5776 time to fit residues: 112.6365 Evaluate side-chains 172 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 152 GLU Chi-restraints excluded: chain Aa residue 309 ILE Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 152 GLU Chi-restraints excluded: chain Ac residue 309 ILE Chi-restraints excluded: chain Ac residue 393 GLN Chi-restraints excluded: chain Bc residue 21 SER Chi-restraints excluded: chain Bc residue 28 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [76, 9, 149, 101, 143, 129, 19, 156, 47, 34, 124] chunk 76 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 101 optimal weight: 0.0370 chunk 143 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Aa 393 GLN Bc 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.095767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.070786 restraints weight = 18162.435| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 1.92 r_work: 0.2563 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9249 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12981 Z= 0.231 Angle : 0.527 8.042 17655 Z= 0.280 Chirality : 0.048 0.159 2133 Planarity : 0.004 0.051 2235 Dihedral : 4.444 21.479 1791 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.03 % Allowed : 9.92 % Favored : 89.05 % 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: 0.80 (0.21), residues: 1650 helix: 1.96 (0.25), residues: 417 sheet: -0.26 (0.25), residues: 399 loop : 0.33 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGAa 399 TYR 0.013 0.001 TYRBc 80 PHE 0.017 0.002 PHEBb 27 TRP 0.004 0.001 TRPBb 112 HIS 0.001 0.000 HISAc 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (12969) covalent geometry : angle 0.52676 / 0.28 (17631) SS BOND : bond 0.00164 / 0.09 ( 12) SS BOND : angle 0.31554 / 0.18 ( 24) hydrogen bonds : bond 0.04528 / 3.03 ( 557) hydrogen bonds : angle 4.90517 / 3.51 ( 1674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.504 Fit side-chains REVERT: Aa 152 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8524 (tm-30) REVERT: Aa 167 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8176 (ttmm) REVERT: Aa 443 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8162 (pp) REVERT: Aa 453 LYS cc_start: 0.8343 (tttt) cc_final: 0.7860 (ttpt) REVERT: Ab 152 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8546 (tm-30) REVERT: Ac 139 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8446 (mptp) REVERT: Ac 152 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8436 (tm-30) REVERT: Ac 393 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: Ba 106 SER cc_start: 0.8440 (m) cc_final: 0.8047 (p) REVERT: Ba 109 ASP cc_start: 0.8556 (m-30) cc_final: 0.8118 (m-30) REVERT: Bb 109 ASP cc_start: 0.8550 (m-30) cc_final: 0.8128 (m-30) REVERT: Bc 20 LEU cc_start: 0.8832 (mp) cc_final: 0.8589 (mt) REVERT: Bc 82 GLN cc_start: 0.8801 (tp40) cc_final: 0.8294 (tp40) REVERT: Bc 109 ASP cc_start: 0.8469 (m-30) cc_final: 0.8037 (m-30) outliers start: 15 outliers final: 6 residues processed: 181 average time/residue: 0.5472 time to fit residues: 108.2731 Evaluate side-chains 180 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 152 GLU Chi-restraints excluded: chain Aa residue 309 ILE Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 152 GLU Chi-restraints excluded: chain Ab residue 309 ILE Chi-restraints excluded: chain Ac residue 152 GLU Chi-restraints excluded: chain Ac residue 309 ILE Chi-restraints excluded: chain Ac residue 393 GLN Chi-restraints excluded: chain Bb residue 21 SER Chi-restraints excluded: chain Bc residue 21 SER Chi-restraints excluded: chain Bc residue 28 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [100, 58, 46, 127, 16, 147, 76, 34, 20, 66, 141] chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 127 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.098520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.073641 restraints weight = 18058.207| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.93 r_work: 0.2619 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12981 Z= 0.113 Angle : 0.467 7.081 17655 Z= 0.249 Chirality : 0.045 0.155 2133 Planarity : 0.004 0.075 2235 Dihedral : 4.086 18.014 1791 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.90 % Allowed : 10.74 % Favored : 88.36 % 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: 0.84 (0.21), residues: 1650 helix: 2.08 (0.25), residues: 432 sheet: -0.17 (0.25), residues: 399 loop : 0.23 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARGAc 399 TYR 0.012 0.001 TYRBc 95 PHE 0.014 0.001 PHEBc 47 TRP 0.005 0.001 TRPBa 36 HIS 0.000 0.000 HISAa 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (12969) covalent geometry : angle 0.46753 / 0.25 (17631) SS BOND : bond 0.00138 / 0.07 ( 12) SS BOND : angle 0.28124 / 0.18 ( 24) hydrogen bonds : bond 0.03563 / 2.37 ( 557) hydrogen bonds : angle 4.55414 / 3.24 ( 1674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.480 Fit side-chains REVERT: Aa 152 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: Aa 167 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8221 (ttmm) REVERT: Aa 393 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8444 (tt0) REVERT: Aa 453 LYS cc_start: 0.8215 (tttt) cc_final: 0.7731 (ttpt) REVERT: Ab 152 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8560 (tm-30) REVERT: Ab 167 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8180 (tttm) REVERT: Ab 322 LEU cc_start: 0.8571 (tp) cc_final: 0.8101 (mt) REVERT: Ac 139 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8356 (mptp) REVERT: Ac 167 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8296 (mttt) REVERT: Ac 322 LEU cc_start: 0.8590 (tp) cc_final: 0.8098 (mt) REVERT: Ac 399 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7848 (mtm110) REVERT: Ba 106 SER cc_start: 0.8397 (m) cc_final: 0.8047 (p) REVERT: Ba 109 ASP cc_start: 0.8486 (m-30) cc_final: 0.8069 (m-30) REVERT: Bb 19 ARG cc_start: 0.8561 (tmm-80) cc_final: 0.8278 (mmm-85) REVERT: Bb 82 GLN cc_start: 0.8492 (tp40) cc_final: 0.7908 (tp40) REVERT: Bb 109 ASP cc_start: 0.8487 (m-30) cc_final: 0.8111 (m-30) REVERT: Bc 19 ARG cc_start: 0.8702 (tmm-80) cc_final: 0.8489 (mmm-85) REVERT: Bc 82 GLN cc_start: 0.8767 (tp40) cc_final: 0.8291 (tp40) REVERT: Bc 109 ASP cc_start: 0.8439 (m-30) cc_final: 0.7995 (m-30) outliers start: 13 outliers final: 2 residues processed: 175 average time/residue: 0.5677 time to fit residues: 108.5642 Evaluate side-chains 166 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 152 GLU Chi-restraints excluded: chain Aa residue 393 GLN Chi-restraints excluded: chain Ab residue 152 GLU Chi-restraints excluded: chain Bb residue 21 SER Chi-restraints excluded: chain Bc residue 21 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [100, 71, 114, 24, 127, 1, 0, 156, 96, 55, 159] chunk 100 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 156 optimal weight: 0.0270 chunk 96 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.072431 restraints weight = 17966.057| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 1.94 r_work: 0.2595 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9237 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12981 Z= 0.157 Angle : 0.491 6.970 17655 Z= 0.261 Chirality : 0.046 0.155 2133 Planarity : 0.005 0.068 2235 Dihedral : 4.204 19.926 1791 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.96 % Allowed : 11.23 % Favored : 87.81 % 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: 0.90 (0.21), residues: 1650 helix: 2.17 (0.25), residues: 417 sheet: -0.21 (0.25), residues: 399 loop : 0.33 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGAc 399 TYR 0.012 0.001 TYRBb 95 PHE 0.016 0.001 PHEBb 27 TRP 0.004 0.001 TRPBa 36 HIS 0.001 0.000 HISAc 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (12969) covalent geometry : angle 0.49137 / 0.26 (17631) SS BOND : bond 0.00152 / 0.08 ( 12) SS BOND : angle 0.29261 / 0.18 ( 24) hydrogen bonds : bond 0.03921 / 2.61 ( 557) hydrogen bonds : angle 4.63731 / 3.30 ( 1674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.458 Fit side-chains REVERT: Aa 139 LYS cc_start: 0.8806 (mptt) cc_final: 0.8537 (mptp) REVERT: Aa 152 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8506 (tm-30) REVERT: Aa 167 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8220 (ttmm) REVERT: Aa 443 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8147 (pp) REVERT: Aa 453 LYS cc_start: 0.8280 (tttt) cc_final: 0.7800 (ttpt) REVERT: Ab 152 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8538 (tm-30) REVERT: Ab 167 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8175 (tttm) REVERT: Ac 139 LYS cc_start: 0.8682 (mtmm) cc_final: 0.8354 (mptp) REVERT: Ac 152 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8444 (tm-30) REVERT: Ac 167 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8301 (mttt) REVERT: Ac 322 LEU cc_start: 0.8592 (tp) cc_final: 0.8101 (mt) REVERT: Ac 393 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: Ba 82 GLN cc_start: 0.8532 (tp40) cc_final: 0.8224 (tp40) REVERT: Ba 106 SER cc_start: 0.8399 (m) cc_final: 0.8027 (p) REVERT: Ba 109 ASP cc_start: 0.8516 (m-30) cc_final: 0.8090 (m-30) REVERT: Bb 109 ASP cc_start: 0.8522 (m-30) cc_final: 0.8124 (m-30) REVERT: Bc 20 LEU cc_start: 0.8841 (mp) cc_final: 0.8606 (mt) REVERT: Bc 82 GLN cc_start: 0.8802 (tp40) cc_final: 0.8314 (tp40) REVERT: Bc 109 ASP cc_start: 0.8474 (m-30) cc_final: 0.8027 (m-30) outliers start: 14 outliers final: 4 residues processed: 175 average time/residue: 0.5759 time to fit residues: 109.8806 Evaluate side-chains 174 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 152 GLU Chi-restraints excluded: chain Aa residue 309 ILE Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 152 GLU Chi-restraints excluded: chain Ac residue 152 GLU Chi-restraints excluded: chain Ac residue 309 ILE Chi-restraints excluded: chain Ac residue 393 GLN Chi-restraints excluded: chain Bb residue 21 SER Chi-restraints excluded: chain Bc residue 21 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [65, 24, 68, 44, 64, 135, 81, 79, 67, 126, 134] chunk 65 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 134 optimal weight: 0.0570 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.074688 restraints weight = 18061.068| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 1.94 r_work: 0.2637 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12981 Z= 0.103 Angle : 0.452 6.389 17655 Z= 0.241 Chirality : 0.045 0.152 2133 Planarity : 0.004 0.077 2235 Dihedral : 3.942 17.310 1791 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.62 % Allowed : 11.50 % Favored : 87.88 % 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: 0.96 (0.21), residues: 1650 helix: 2.26 (0.25), residues: 420 sheet: -0.24 (0.25), residues: 384 loop : 0.35 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGAc 399 TYR 0.014 0.001 TYRBc 80 PHE 0.014 0.001 PHEBc 47 TRP 0.007 0.001 TRPBa 36 HIS 0.000 0.000 HISAc 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (12969) covalent geometry : angle 0.45244 / 0.24 (17631) SS BOND : bond 0.00136 / 0.07 ( 12) SS BOND : angle 0.31097 / 0.20 ( 24) hydrogen bonds : bond 0.03361 / 2.23 ( 557) hydrogen bonds : angle 4.40893 / 3.14 ( 1674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 0.380 Fit side-chains REVERT: Aa 139 LYS cc_start: 0.8753 (mptt) cc_final: 0.8501 (mptp) REVERT: Aa 152 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8520 (tm-30) REVERT: Aa 167 LYS cc_start: 0.8501 (mtmt) cc_final: 0.8215 (ttmm) REVERT: Aa 322 LEU cc_start: 0.8543 (tp) cc_final: 0.8082 (mp) REVERT: Aa 443 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8100 (pp) REVERT: Aa 453 LYS cc_start: 0.8221 (tttt) cc_final: 0.7737 (ttpt) REVERT: Ab 152 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: Ab 167 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8183 (tttm) REVERT: Ab 322 LEU cc_start: 0.8562 (tp) cc_final: 0.8095 (mt) REVERT: Ac 139 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8307 (mptp) REVERT: Ac 152 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8448 (tm-30) REVERT: Ac 167 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8315 (mttt) REVERT: Ac 322 LEU cc_start: 0.8621 (tp) cc_final: 0.8118 (mt) REVERT: Ac 393 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: Ac 399 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7836 (mtm110) REVERT: Ba 82 GLN cc_start: 0.8435 (tp40) cc_final: 0.8002 (tp40) REVERT: Ba 106 SER cc_start: 0.8359 (m) cc_final: 0.8007 (p) REVERT: Ba 109 ASP cc_start: 0.8471 (m-30) cc_final: 0.8069 (m-30) REVERT: Bb 109 ASP cc_start: 0.8493 (m-30) cc_final: 0.8134 (m-30) REVERT: Bc 20 LEU cc_start: 0.8811 (mp) cc_final: 0.8570 (mt) REVERT: Bc 109 ASP cc_start: 0.8418 (m-30) cc_final: 0.7964 (m-30) outliers start: 9 outliers final: 1 residues processed: 172 average time/residue: 0.5865 time to fit residues: 109.6342 Evaluate side-chains 169 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 152 GLU Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 152 GLU Chi-restraints excluded: chain Ac residue 152 GLU Chi-restraints excluded: chain Ac residue 393 GLN Chi-restraints excluded: chain Bc residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [98, 20, 18, 139, 71, 66, 67, 146, 44, 72, 101] chunk 98 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Ab 393 GLN Bb 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.073118 restraints weight = 18016.880| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 1.94 r_work: 0.2610 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9228 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12981 Z= 0.144 Angle : 0.487 6.691 17655 Z= 0.259 Chirality : 0.046 0.153 2133 Planarity : 0.005 0.084 2235 Dihedral : 4.116 19.540 1791 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.69 % Allowed : 11.43 % Favored : 87.88 % 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: 0.97 (0.21), residues: 1650 helix: 2.26 (0.25), residues: 417 sheet: -0.15 (0.25), residues: 399 loop : 0.34 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARGAc 399 TYR 0.015 0.001 TYRBc 80 PHE 0.016 0.001 PHEBb 27 TRP 0.004 0.001 TRPBa 36 HIS 0.001 0.000 HISAc 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (12969) covalent geometry : angle 0.48703 / 0.26 (17631) SS BOND : bond 0.00144 / 0.08 ( 12) SS BOND : angle 0.32469 / 0.21 ( 24) hydrogen bonds : bond 0.03780 / 2.52 ( 557) hydrogen bonds : angle 4.54710 / 3.23 ( 1674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.491 Fit side-chains REVERT: Aa 139 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8510 (mptp) REVERT: Aa 152 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8515 (tm-30) REVERT: Aa 167 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8225 (ttmm) REVERT: Aa 443 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8120 (pp) REVERT: Aa 453 LYS cc_start: 0.8256 (tttt) cc_final: 0.7772 (ttpt) REVERT: Ab 152 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8543 (tm-30) REVERT: Ab 167 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8203 (tttm) REVERT: Ab 322 LEU cc_start: 0.8579 (tp) cc_final: 0.8118 (mt) REVERT: Ab 393 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: Ac 139 LYS cc_start: 0.8664 (mtmm) cc_final: 0.8331 (mptp) REVERT: Ac 152 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8438 (tm-30) REVERT: Ac 167 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8332 (mttt) REVERT: Ac 322 LEU cc_start: 0.8609 (tp) cc_final: 0.8114 (mt) REVERT: Ac 393 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: Ac 399 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7846 (mtm110) REVERT: Ba 106 SER cc_start: 0.8379 (m) cc_final: 0.8019 (p) REVERT: Ba 109 ASP cc_start: 0.8529 (m-30) cc_final: 0.8115 (m-30) REVERT: Bb 109 ASP cc_start: 0.8523 (m-30) cc_final: 0.8156 (m-30) REVERT: Bc 20 LEU cc_start: 0.8809 (mp) cc_final: 0.8567 (mt) REVERT: Bc 109 ASP cc_start: 0.8468 (m-30) cc_final: 0.8029 (m-30) outliers start: 10 outliers final: 2 residues processed: 171 average time/residue: 0.5526 time to fit residues: 103.1261 Evaluate side-chains 172 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 139 LYS Chi-restraints excluded: chain Aa residue 152 GLU Chi-restraints excluded: chain Aa residue 309 ILE Chi-restraints excluded: chain Aa residue 443 ILE Chi-restraints excluded: chain Ab residue 152 GLU Chi-restraints excluded: chain Ab residue 393 GLN Chi-restraints excluded: chain Ac residue 152 GLU Chi-restraints excluded: chain Ac residue 393 GLN Chi-restraints excluded: chain Bc residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: [77, 51, 103, 136, 69, 21, 42, 112, 87, 33, 160] chunk 77 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 21 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.074388 restraints weight = 18034.584| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 1.92 r_work: 0.2633 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9210 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12981 Z= 0.107 Angle : 0.457 6.299 17655 Z= 0.244 Chirality : 0.045 0.150 2133 Planarity : 0.005 0.079 2235 Dihedral : 3.968 17.857 1791 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.55 % Allowed : 11.64 % Favored : 87.81 % 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: 0.97 (0.21), residues: 1650 helix: 2.28 (0.25), residues: 420 sheet: -0.23 (0.25), residues: 384 loop : 0.36 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARGAc 399 TYR 0.014 0.001 TYRBc 80 PHE 0.014 0.001 PHEBc 47 TRP 0.006 0.001 TRPBa 36 HIS 0.000 0.000 HISAa 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (12969) covalent geometry : angle 0.45754 / 0.24 (17631) SS BOND : bond 0.00152 / 0.08 ( 12) SS BOND : angle 0.34796 / 0.23 ( 24) hydrogen bonds : bond 0.03428 / 2.28 ( 557) hydrogen bonds : angle 4.41612 / 3.14 ( 1674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4387.74 seconds wall clock time: 75 minutes 37.95 seconds (4537.95 seconds total)