Starting phenix.real_space_refine on Sat Sep 12 01:45:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26fe_80609/09_2026/26fe_80609.cif Found real_map, /net/cci-nas-00/data/ceres_data/26fe_80609/09_2026/26fe_80609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26fe_80609/09_2026/26fe_80609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26fe_80609/09_2026/26fe_80609.map" model { file = "/net/cci-nas-00/data/ceres_data/26fe_80609/09_2026/26fe_80609.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26fe_80609/09_2026/26fe_80609.cif" } resolution = 3.04 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 37 5.16 5 C 8046 2.51 5 N 2044 2.21 5 O 2458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12585 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4193 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 527, 4193 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Chain: "B" Number of atoms: 4193 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 527, 4193 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Chain: "C" Number of atoms: 4199 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 527, 4185 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 527, 4193 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 bond proxies already assigned to first conformer: 4268 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS C 94 " occ=0.34 ... (10 atoms not shown) pdb=" SG BCYS C 94 " occ=0.66 Time building chain proxies: 3.16, per 1000 atoms: 0.25 Number of scatterers: 12585 At special positions: 0 Unit cell: (102.05, 94.9, 106.6, 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 37 16.00 O 2458 8.00 N 2044 7.00 C 8046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 586.7 milliseconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3014 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 33 sheets defined 18.5% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.675A pdb=" N VAL A 164 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.929A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.696A pdb=" N TRP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.701A pdb=" N VAL B 164 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.912A pdb=" N ASP B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.649A pdb=" N TRP B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 112 through 119 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.985A pdb=" N VAL C 164 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 removed outlier: 3.752A pdb=" N VAL C 191 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 removed outlier: 4.017A pdb=" N PHE C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.974A pdb=" N ASP C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'C' and resid 389 through 395 Processing helix chain 'C' and resid 396 through 402 removed outlier: 3.666A pdb=" N TRP C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 516 through 521 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 39 removed outlier: 4.253A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 69 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 39 removed outlier: 4.253A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.510A pdb=" N HIS A 97 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.518A pdb=" N VAL A 78 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 141 removed outlier: 5.777A pdb=" N ARG A 83 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 193 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 236 removed outlier: 7.205A pdb=" N GLN A 522 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN A 524 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 259 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 526 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 257 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 528 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 255 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 530 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA A 251 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 252 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.037A pdb=" N ALA A 251 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 530 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 255 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 528 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 257 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL A 526 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 259 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN A 524 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLN A 522 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 247 removed outlier: 6.880A pdb=" N LEU A 443 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER A 454 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 445 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 296 through 299 Processing sheet with id=AB1, first strand: chain 'A' and resid 320 through 323 removed outlier: 6.574A pdb=" N ASP A 327 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE A 368 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR A 329 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLY A 370 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS A 331 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TYR A 372 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP A 333 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A 365 " --> pdb=" O HIS A 386 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS A 386 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 367 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 384 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR A 369 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AB3, first strand: chain 'B' and resid 34 through 40 removed outlier: 4.177A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU B 69 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 34 through 40 removed outlier: 4.177A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 44 removed outlier: 4.201A pdb=" N ALA B 52 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 97 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 98 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU B 109 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 100 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY B 105 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.675A pdb=" N VAL B 78 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 139 through 140 removed outlier: 6.182A pdb=" N ARG B 83 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 194 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 193 " --> pdb=" O PHE B 422 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 227 through 236 removed outlier: 7.255A pdb=" N GLN B 522 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN B 524 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 259 " --> pdb=" O GLN B 524 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 526 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B 257 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 528 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 255 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN B 530 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA B 251 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 252 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 475 through 476 removed outlier: 3.521A pdb=" N ARG B 475 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA B 251 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN B 530 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 255 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 528 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B 257 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 526 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 259 " --> pdb=" O GLN B 524 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN B 524 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLN B 522 " --> pdb=" O PRO B 261 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 243 through 247 removed outlier: 5.660A pdb=" N PHE B 447 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 296 through 299 Processing sheet with id=AC3, first strand: chain 'B' and resid 320 through 323 removed outlier: 5.153A pdb=" N SER B 366 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER B 385 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE B 368 " --> pdb=" O HIS B 383 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N HIS B 383 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY B 370 " --> pdb=" O PHE B 381 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE B 381 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B 372 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B 379 " --> pdb=" O TYR B 372 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AC5, first strand: chain 'C' and resid 32 through 39 removed outlier: 3.630A pdb=" N MET C 218 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU C 69 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 32 through 39 removed outlier: 3.630A pdb=" N MET C 218 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.154A pdb=" N SER C 102 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AC9, first strand: chain 'C' and resid 82 through 84 Processing sheet with id=AD1, first strand: chain 'C' and resid 193 through 194 Processing sheet with id=AD2, first strand: chain 'C' and resid 227 through 236 removed outlier: 4.129A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 530 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA C 252 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 475 through 476 removed outlier: 3.618A pdb=" N ARG C 475 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 530 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 243 through 246 removed outlier: 3.548A pdb=" N ARG C 442 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 443 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER C 454 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL C 445 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 296 through 299 Processing sheet with id=AD6, first strand: chain 'C' and resid 320 through 323 removed outlier: 4.975A pdb=" N SER C 366 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER C 385 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE C 368 " --> pdb=" O HIS C 383 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N HIS C 383 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY C 370 " --> pdb=" O PHE C 381 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE C 381 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR C 372 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR C 379 " --> pdb=" O TYR C 372 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1236 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: 2.08 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4029 1.34 - 1.46: 2779 1.46 - 1.58: 5993 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 12862 Sorted by residual: bond pdb=" CA ASN C 50 " pdb=" CB ASN C 50 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.82e-01 bond pdb=" CA TYR B 131 " pdb=" C TYR B 131 " ideal model delta sigma weight residual 1.530 1.522 0.009 1.08e-02 8.57e+03 6.62e-01 bond pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.29e-01 bond pdb=" CA ASN B 50 " pdb=" CB ASN B 50 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 5.16e-01 bond pdb=" N TYR B 131 " pdb=" CA TYR B 131 " ideal model delta sigma weight residual 1.465 1.457 0.009 1.31e-02 5.83e+03 4.27e-01 ... (remaining 12857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 17369 1.88 - 3.77: 121 3.77 - 5.65: 10 5.65 - 7.54: 0 7.54 - 9.42: 1 Bond angle restraints: 17501 Sorted by residual: angle pdb=" C ASP C 49 " pdb=" N ASN C 50 " pdb=" CA ASN C 50 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.18e+00 angle pdb=" C ASP B 49 " pdb=" N ASN B 50 " pdb=" CA ASN B 50 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 7.99e+00 angle pdb=" C ASP A 49 " pdb=" N ASN A 50 " pdb=" CA ASN A 50 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.55e+00 angle pdb=" C LYS A 484 " pdb=" N ILE A 485 " pdb=" CA ILE A 485 " ideal model delta sigma weight residual 121.97 125.84 -3.87 1.80e+00 3.09e-01 4.62e+00 angle pdb=" C LYS C 484 " pdb=" N ILE C 485 " pdb=" CA ILE C 485 " ideal model delta sigma weight residual 121.97 125.67 -3.70 1.80e+00 3.09e-01 4.22e+00 ... (remaining 17496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 7133 17.44 - 34.88: 484 34.88 - 52.33: 80 52.33 - 69.77: 14 69.77 - 87.21: 13 Dihedral angle restraints: 7724 sinusoidal: 3037 harmonic: 4687 Sorted by residual: dihedral pdb=" CA VAL B 164 " pdb=" C VAL B 164 " pdb=" N GLU B 165 " pdb=" CA GLU B 165 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASP B 333 " pdb=" CB ASP B 333 " pdb=" CG ASP B 333 " pdb=" OD1 ASP B 333 " ideal model delta sinusoidal sigma weight residual -30.00 -89.93 59.93 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA TYR A 92 " pdb=" C TYR A 92 " pdb=" N LYS A 93 " pdb=" CA LYS A 93 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 7721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1151 0.028 - 0.056: 524 0.056 - 0.085: 117 0.085 - 0.113: 168 0.113 - 0.141: 57 Chirality restraints: 2017 Sorted by residual: chirality pdb=" CA ASN B 50 " pdb=" N ASN B 50 " pdb=" C ASN B 50 " pdb=" CB ASN B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ASN A 50 " pdb=" N ASN A 50 " pdb=" C ASN A 50 " pdb=" CB ASN A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE A 100 " pdb=" N ILE A 100 " pdb=" C ILE A 100 " pdb=" CB ILE A 100 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 2014 not shown) Planarity restraints: 2237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 425 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 426 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 426 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 426 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 425 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.08e+00 pdb=" N PRO A 426 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 426 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 426 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 425 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO C 426 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 426 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 426 " 0.019 5.00e-02 4.00e+02 ... (remaining 2234 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 7153 3.02 - 3.49: 11772 3.49 - 3.96: 20305 3.96 - 4.43: 23936 4.43 - 4.90: 39602 Nonbonded interactions: 102768 Sorted by model distance: nonbonded pdb=" O ASP C 49 " pdb=" OD1 ASN C 50 " model vdw 2.552 3.040 nonbonded pdb=" O ASP A 410 " pdb=" OD1 ASP A 410 " model vdw 2.559 3.040 nonbonded pdb=" O ASP B 49 " pdb=" OD1 ASN B 50 " model vdw 2.569 3.040 nonbonded pdb=" O ASP A 49 " pdb=" OD1 ASN A 50 " model vdw 2.571 3.040 nonbonded pdb=" O SER A 387 " pdb=" OG SER A 387 " model vdw 2.607 3.040 ... (remaining 102763 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'B' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'C' and (resid 18 through 93 or resid 95 through 356 or resid 358 through \ 547)) } 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=0.34 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.070 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 0.027 12862 Z= 0.091 Angle : 0.427 9.423 17501 Z= 0.227 Chirality : 0.046 0.141 2017 Planarity : 0.003 0.038 2237 Dihedral : 12.342 87.209 4710 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.05 (0.21), residues: 1572 helix: -0.18 (0.34), residues: 233 sheet: 0.63 (0.24), residues: 507 loop : -0.33 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 404 TYR 0.008 0.001 TYR C 519 PHE 0.010 0.001 PHE B 422 TRP 0.005 0.001 TRP A 108 HIS 0.002 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (12862) covalent geometry : angle 0.42728 / 0.23 (17501) hydrogen bonds : bond 0.16503 / 10.65 ( 431) hydrogen bonds : angle 7.67487 / 5.41 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8442 (t) cc_final: 0.8116 (p) REVERT: A 146 ASP cc_start: 0.8005 (t0) cc_final: 0.7665 (m-30) REVERT: A 221 ASN cc_start: 0.7520 (m-40) cc_final: 0.7263 (t0) REVERT: A 238 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7896 (mm-40) REVERT: A 281 LYS cc_start: 0.7658 (tttp) cc_final: 0.7063 (ttpp) REVERT: A 359 TYR cc_start: 0.8105 (t80) cc_final: 0.7772 (t80) REVERT: B 33 MET cc_start: 0.8546 (tpt) cc_final: 0.8153 (tpt) REVERT: B 57 GLU cc_start: 0.7990 (tt0) cc_final: 0.7634 (tp30) REVERT: B 92 TYR cc_start: 0.8497 (m-80) cc_final: 0.8292 (m-80) REVERT: B 204 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7346 (mtmm) REVERT: B 358 ILE cc_start: 0.8364 (mm) cc_final: 0.8010 (tt) REVERT: C 111 GLU cc_start: 0.8032 (mm-30) cc_final: 0.6927 (mp0) REVERT: C 218 MET cc_start: 0.8452 (ptm) cc_final: 0.8171 (ttm) REVERT: C 223 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7775 (mm-40) REVERT: C 241 GLN cc_start: 0.7724 (mm110) cc_final: 0.7513 (mm-40) REVERT: C 281 LYS cc_start: 0.7745 (tttp) cc_final: 0.7388 (tmmt) REVERT: C 311 GLU cc_start: 0.8022 (tt0) cc_final: 0.7297 (mt-10) REVERT: C 339 MET cc_start: 0.8076 (mtt) cc_final: 0.7593 (mtt) REVERT: C 353 ARG cc_start: 0.8029 (ptm-80) cc_final: 0.7023 (ptp90) REVERT: C 415 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7395 (mp0) REVERT: C 544 THR cc_start: 0.8527 (m) cc_final: 0.8087 (p) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1022 time to fit residues: 36.8485 Evaluate side-chains 172 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 ASN A 495 ASN B 20 ASN B 408 ASN B 411 ASN B 464 ASN C 539 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.114632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.088065 restraints weight = 16794.881| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.42 r_work: 0.2778 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 12862 Z= 0.353 Angle : 0.646 10.543 17501 Z= 0.345 Chirality : 0.054 0.174 2017 Planarity : 0.005 0.038 2237 Dihedral : 4.481 21.749 1727 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.99 % Allowed : 5.91 % Favored : 92.10 % 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: -0.46 (0.20), residues: 1572 helix: -0.47 (0.34), residues: 210 sheet: 0.17 (0.24), residues: 465 loop : -0.46 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 412 TYR 0.021 0.002 TYR C 520 PHE 0.032 0.002 PHE C 479 TRP 0.009 0.002 TRP A 108 HIS 0.008 0.002 HIS B 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00894 / 0.35 (12862) covalent geometry : angle 0.64610 / 0.35 (17501) hydrogen bonds : bond 0.04990 / 3.38 ( 431) hydrogen bonds : angle 6.02231 / 4.20 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 146 ASP cc_start: 0.8043 (t0) cc_final: 0.7669 (m-30) REVERT: A 220 LYS cc_start: 0.8120 (mptt) cc_final: 0.7447 (mppt) REVERT: A 221 ASN cc_start: 0.7594 (m-40) cc_final: 0.7292 (t0) REVERT: A 230 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8022 (mt-10) REVERT: A 281 LYS cc_start: 0.7708 (tttp) cc_final: 0.7039 (ttpp) REVERT: A 339 MET cc_start: 0.7803 (mtt) cc_final: 0.7567 (mtt) REVERT: A 377 LYS cc_start: 0.8392 (mmtp) cc_final: 0.8154 (mmtp) REVERT: A 421 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8175 (pp) REVERT: B 57 GLU cc_start: 0.8054 (tt0) cc_final: 0.7545 (tp30) REVERT: B 177 LYS cc_start: 0.7599 (mppt) cc_final: 0.7027 (mmtp) REVERT: B 285 ASP cc_start: 0.8252 (m-30) cc_final: 0.7966 (m-30) REVERT: B 293 ASP cc_start: 0.8151 (m-30) cc_final: 0.7923 (m-30) REVERT: B 327 ASP cc_start: 0.8741 (p0) cc_final: 0.8506 (p0) REVERT: B 358 ILE cc_start: 0.8506 (mm) cc_final: 0.8278 (tt) REVERT: C 218 MET cc_start: 0.8240 (ptm) cc_final: 0.7932 (ttm) REVERT: C 223 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7896 (mm-40) REVERT: C 239 ILE cc_start: 0.8421 (mm) cc_final: 0.8188 (mm) REVERT: C 281 LYS cc_start: 0.7768 (tttp) cc_final: 0.7310 (tmmt) REVERT: C 311 GLU cc_start: 0.8009 (tt0) cc_final: 0.7331 (mt-10) REVERT: C 339 MET cc_start: 0.8069 (mtt) cc_final: 0.7578 (mtt) REVERT: C 353 ARG cc_start: 0.8159 (ptm-80) cc_final: 0.7094 (ptp90) REVERT: C 415 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7660 (mp0) REVERT: C 512 MET cc_start: 0.8064 (mtt) cc_final: 0.7716 (mtt) outliers start: 29 outliers final: 22 residues processed: 194 average time/residue: 0.0985 time to fit residues: 28.1439 Evaluate side-chains 186 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 349 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 0.7980 chunk 24 optimal weight: 0.0030 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN B 480 ASN C 128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.120405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.092359 restraints weight = 25725.812| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.01 r_work: 0.2813 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12862 Z= 0.098 Angle : 0.455 9.748 17501 Z= 0.244 Chirality : 0.047 0.147 2017 Planarity : 0.004 0.037 2237 Dihedral : 3.920 18.773 1727 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.17 % Allowed : 8.10 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1572 helix: -0.34 (0.34), residues: 230 sheet: 0.21 (0.23), residues: 492 loop : -0.39 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 404 TYR 0.015 0.001 TYR C 520 PHE 0.007 0.001 PHE B 422 TRP 0.007 0.001 TRP A 108 HIS 0.002 0.000 HIS C 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (12862) covalent geometry : angle 0.45521 / 0.24 (17501) hydrogen bonds : bond 0.03119 / 2.08 ( 431) hydrogen bonds : angle 5.31874 / 3.71 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.429 Fit side-chains REVERT: A 146 ASP cc_start: 0.8053 (t0) cc_final: 0.7766 (m-30) REVERT: A 220 LYS cc_start: 0.8118 (mptt) cc_final: 0.7495 (mppt) REVERT: A 221 ASN cc_start: 0.7467 (m-40) cc_final: 0.7247 (t0) REVERT: A 281 LYS cc_start: 0.7569 (tttp) cc_final: 0.6956 (ttpp) REVERT: A 339 MET cc_start: 0.7781 (mtt) cc_final: 0.7526 (mtt) REVERT: A 377 LYS cc_start: 0.8396 (mmtp) cc_final: 0.8136 (mmtp) REVERT: B 33 MET cc_start: 0.8576 (tpt) cc_final: 0.8159 (tpt) REVERT: B 57 GLU cc_start: 0.7880 (tt0) cc_final: 0.7482 (tp30) REVERT: B 177 LYS cc_start: 0.7610 (mppt) cc_final: 0.7127 (mmtp) REVERT: B 241 GLN cc_start: 0.7804 (mm110) cc_final: 0.6707 (tt0) REVERT: B 293 ASP cc_start: 0.8095 (m-30) cc_final: 0.7765 (m-30) REVERT: B 534 LYS cc_start: 0.8383 (tptm) cc_final: 0.7605 (ttpt) REVERT: C 79 LYS cc_start: 0.8644 (ptpp) cc_final: 0.8253 (ptpp) REVERT: C 218 MET cc_start: 0.8106 (ptm) cc_final: 0.7805 (ttm) REVERT: C 223 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7783 (mm-40) REVERT: C 230 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7981 (mt-10) REVERT: C 239 ILE cc_start: 0.8278 (mm) cc_final: 0.8049 (mm) REVERT: C 281 LYS cc_start: 0.7652 (tttp) cc_final: 0.7266 (tmmt) REVERT: C 311 GLU cc_start: 0.7875 (tt0) cc_final: 0.7184 (mt-10) REVERT: C 339 MET cc_start: 0.8098 (mtt) cc_final: 0.7652 (mtt) REVERT: C 353 ARG cc_start: 0.8160 (ptm-80) cc_final: 0.7177 (ptp90) REVERT: C 415 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7621 (mp0) outliers start: 17 outliers final: 11 residues processed: 190 average time/residue: 0.0999 time to fit residues: 27.9140 Evaluate side-chains 177 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 19 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN A 471 ASN C 539 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.116499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.089019 restraints weight = 20640.247| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.67 r_work: 0.2746 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12862 Z= 0.214 Angle : 0.528 9.440 17501 Z= 0.280 Chirality : 0.049 0.151 2017 Planarity : 0.004 0.039 2237 Dihedral : 4.115 21.007 1727 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.06 % Allowed : 9.00 % Favored : 88.94 % 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: -0.48 (0.20), residues: 1572 helix: -0.20 (0.36), residues: 210 sheet: 0.11 (0.23), residues: 492 loop : -0.54 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 404 TYR 0.022 0.001 TYR C 520 PHE 0.021 0.002 PHE C 479 TRP 0.008 0.001 TRP A 108 HIS 0.005 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.21 (12862) covalent geometry : angle 0.52776 / 0.28 (17501) hydrogen bonds : bond 0.03852 / 2.60 ( 431) hydrogen bonds : angle 5.38256 / 3.75 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.396 Fit side-chains REVERT: A 146 ASP cc_start: 0.7998 (t0) cc_final: 0.7739 (m-30) REVERT: A 220 LYS cc_start: 0.8114 (mptt) cc_final: 0.7475 (mppt) REVERT: A 281 LYS cc_start: 0.7581 (tttp) cc_final: 0.6961 (ttpp) REVERT: A 339 MET cc_start: 0.7795 (mtt) cc_final: 0.7548 (mtt) REVERT: A 377 LYS cc_start: 0.8395 (mmtp) cc_final: 0.8129 (mmtp) REVERT: A 421 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8025 (pp) REVERT: B 57 GLU cc_start: 0.7844 (tt0) cc_final: 0.7359 (tp30) REVERT: B 127 LYS cc_start: 0.8113 (tptt) cc_final: 0.7472 (ttpp) REVERT: B 177 LYS cc_start: 0.7591 (mppt) cc_final: 0.7119 (mmtp) REVERT: B 241 GLN cc_start: 0.7810 (mm110) cc_final: 0.6770 (tt0) REVERT: B 293 ASP cc_start: 0.8071 (m-30) cc_final: 0.7738 (m-30) REVERT: B 534 LYS cc_start: 0.8329 (tptm) cc_final: 0.7613 (ttpt) REVERT: C 218 MET cc_start: 0.8051 (ptm) cc_final: 0.7740 (ttm) REVERT: C 223 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7829 (mm-40) REVERT: C 230 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7926 (mt-10) REVERT: C 281 LYS cc_start: 0.7677 (tttp) cc_final: 0.7228 (tmmt) REVERT: C 311 GLU cc_start: 0.7786 (tt0) cc_final: 0.7123 (mt-10) REVERT: C 339 MET cc_start: 0.8091 (mtt) cc_final: 0.7598 (mtt) REVERT: C 353 ARG cc_start: 0.8174 (ptm-80) cc_final: 0.7193 (ptp90) REVERT: C 415 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7637 (mp0) outliers start: 30 outliers final: 26 residues processed: 185 average time/residue: 0.1002 time to fit residues: 27.4864 Evaluate side-chains 189 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 544 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 56 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN A 471 ASN C 539 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.119718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.093999 restraints weight = 15427.572| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.30 r_work: 0.2788 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12862 Z= 0.115 Angle : 0.457 9.010 17501 Z= 0.243 Chirality : 0.047 0.147 2017 Planarity : 0.003 0.041 2237 Dihedral : 3.841 19.159 1727 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.65 % Allowed : 9.62 % Favored : 88.74 % 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: -0.41 (0.20), residues: 1572 helix: -0.28 (0.35), residues: 230 sheet: 0.12 (0.23), residues: 492 loop : -0.42 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 404 TYR 0.016 0.001 TYR C 520 PHE 0.009 0.001 PHE C 479 TRP 0.008 0.001 TRP A 108 HIS 0.003 0.000 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (12862) covalent geometry : angle 0.45691 / 0.24 (17501) hydrogen bonds : bond 0.03059 / 2.04 ( 431) hydrogen bonds : angle 5.05730 / 3.52 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.438 Fit side-chains REVERT: A 146 ASP cc_start: 0.7946 (t0) cc_final: 0.7579 (m-30) REVERT: A 220 LYS cc_start: 0.8130 (mptt) cc_final: 0.7454 (mppt) REVERT: A 281 LYS cc_start: 0.7554 (tttp) cc_final: 0.6894 (ttpp) REVERT: A 339 MET cc_start: 0.7742 (mtt) cc_final: 0.7468 (mtt) REVERT: A 377 LYS cc_start: 0.8328 (mmtp) cc_final: 0.8063 (mmtp) REVERT: A 421 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8030 (pp) REVERT: B 33 MET cc_start: 0.8616 (tpt) cc_final: 0.8170 (tpt) REVERT: B 57 GLU cc_start: 0.7974 (tt0) cc_final: 0.7521 (tp30) REVERT: B 127 LYS cc_start: 0.8267 (tptt) cc_final: 0.7607 (ttpp) REVERT: B 177 LYS cc_start: 0.7600 (mppt) cc_final: 0.7087 (mmtp) REVERT: B 241 GLN cc_start: 0.7745 (mm110) cc_final: 0.6541 (tt0) REVERT: B 293 ASP cc_start: 0.8118 (m-30) cc_final: 0.7800 (m-30) REVERT: B 534 LYS cc_start: 0.8316 (tptm) cc_final: 0.7623 (ttpt) REVERT: C 145 ASN cc_start: 0.8738 (m-40) cc_final: 0.7658 (m110) REVERT: C 218 MET cc_start: 0.8250 (ptm) cc_final: 0.7906 (ttm) REVERT: C 223 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7757 (mm-40) REVERT: C 230 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8048 (mt-10) REVERT: C 281 LYS cc_start: 0.7678 (tttp) cc_final: 0.7229 (tmmt) REVERT: C 311 GLU cc_start: 0.7871 (tt0) cc_final: 0.7153 (mt-10) REVERT: C 339 MET cc_start: 0.7994 (mtt) cc_final: 0.7501 (mtt) REVERT: C 415 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7733 (mp0) outliers start: 24 outliers final: 18 residues processed: 184 average time/residue: 0.0960 time to fit residues: 26.2779 Evaluate side-chains 185 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 76 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 150 optimal weight: 0.0020 chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN A 471 ASN C 539 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.119624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.091694 restraints weight = 28249.597| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.08 r_work: 0.2698 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12862 Z= 0.124 Angle : 0.459 8.639 17501 Z= 0.243 Chirality : 0.047 0.147 2017 Planarity : 0.003 0.041 2237 Dihedral : 3.786 19.277 1727 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.85 % Allowed : 9.96 % Favored : 88.19 % 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: -0.34 (0.20), residues: 1572 helix: 0.10 (0.37), residues: 210 sheet: 0.16 (0.23), residues: 492 loop : -0.46 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 404 TYR 0.016 0.001 TYR B 92 PHE 0.011 0.001 PHE C 479 TRP 0.008 0.001 TRP A 108 HIS 0.003 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (12862) covalent geometry : angle 0.45864 / 0.24 (17501) hydrogen bonds : bond 0.03068 / 2.05 ( 431) hydrogen bonds : angle 4.96529 / 3.46 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.341 Fit side-chains REVERT: A 146 ASP cc_start: 0.7900 (t0) cc_final: 0.7550 (m-30) REVERT: A 220 LYS cc_start: 0.8146 (mptt) cc_final: 0.7481 (mppt) REVERT: A 281 LYS cc_start: 0.7496 (tttp) cc_final: 0.6843 (ttpp) REVERT: A 339 MET cc_start: 0.7724 (mtt) cc_final: 0.7447 (mtt) REVERT: A 377 LYS cc_start: 0.8311 (mmtp) cc_final: 0.8037 (mmtp) REVERT: A 421 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7968 (pp) REVERT: B 57 GLU cc_start: 0.7886 (tt0) cc_final: 0.7421 (tp30) REVERT: B 127 LYS cc_start: 0.8195 (tptt) cc_final: 0.7564 (ttpp) REVERT: B 177 LYS cc_start: 0.7557 (mppt) cc_final: 0.7107 (mmtp) REVERT: B 241 GLN cc_start: 0.7734 (mm110) cc_final: 0.6519 (tt0) REVERT: B 293 ASP cc_start: 0.8060 (m-30) cc_final: 0.7725 (m-30) REVERT: B 534 LYS cc_start: 0.8254 (tptm) cc_final: 0.7595 (ttpt) REVERT: C 145 ASN cc_start: 0.8734 (m-40) cc_final: 0.7651 (m110) REVERT: C 218 MET cc_start: 0.8102 (ptm) cc_final: 0.7795 (ttm) REVERT: C 223 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7753 (mm-40) REVERT: C 230 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7991 (mt-10) REVERT: C 281 LYS cc_start: 0.7614 (tttp) cc_final: 0.7178 (tmmt) REVERT: C 311 GLU cc_start: 0.7786 (tt0) cc_final: 0.7079 (mt-10) REVERT: C 339 MET cc_start: 0.7992 (mtt) cc_final: 0.7532 (mtt) REVERT: C 415 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7671 (mp0) outliers start: 27 outliers final: 22 residues processed: 184 average time/residue: 0.1007 time to fit residues: 27.5468 Evaluate side-chains 186 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 155 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 0.0000 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN C 539 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.118862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.091788 restraints weight = 19145.044| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.60 r_work: 0.2753 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12862 Z= 0.127 Angle : 0.461 8.507 17501 Z= 0.245 Chirality : 0.047 0.147 2017 Planarity : 0.003 0.043 2237 Dihedral : 3.765 19.111 1727 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.13 % Allowed : 10.16 % Favored : 87.71 % 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: -0.34 (0.20), residues: 1572 helix: 0.11 (0.37), residues: 210 sheet: 0.17 (0.23), residues: 492 loop : -0.48 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 404 TYR 0.016 0.001 TYR B 92 PHE 0.011 0.001 PHE C 479 TRP 0.008 0.001 TRP A 108 HIS 0.004 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (12862) covalent geometry : angle 0.46098 / 0.24 (17501) hydrogen bonds : bond 0.03058 / 2.05 ( 431) hydrogen bonds : angle 4.92758 / 3.43 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.499 Fit side-chains REVERT: A 142 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8132 (mm) REVERT: A 146 ASP cc_start: 0.7986 (t0) cc_final: 0.7539 (m-30) REVERT: A 220 LYS cc_start: 0.8156 (mptt) cc_final: 0.7483 (mppt) REVERT: A 281 LYS cc_start: 0.7584 (tttp) cc_final: 0.6913 (ttpp) REVERT: A 339 MET cc_start: 0.7766 (mtt) cc_final: 0.7499 (mtt) REVERT: A 377 LYS cc_start: 0.8337 (mmtp) cc_final: 0.8069 (mmtp) REVERT: A 421 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8041 (pp) REVERT: B 57 GLU cc_start: 0.8020 (tt0) cc_final: 0.7561 (tp30) REVERT: B 92 TYR cc_start: 0.8760 (m-80) cc_final: 0.8554 (m-80) REVERT: B 127 LYS cc_start: 0.8234 (tptt) cc_final: 0.7625 (ttpp) REVERT: B 177 LYS cc_start: 0.7620 (mppt) cc_final: 0.7156 (mmtp) REVERT: B 241 GLN cc_start: 0.7746 (mm110) cc_final: 0.6649 (tt0) REVERT: B 293 ASP cc_start: 0.8143 (m-30) cc_final: 0.7791 (m-30) REVERT: B 534 LYS cc_start: 0.8287 (tptm) cc_final: 0.7630 (ttpt) REVERT: C 145 ASN cc_start: 0.8725 (m-40) cc_final: 0.8003 (m110) REVERT: C 218 MET cc_start: 0.8290 (ptm) cc_final: 0.7965 (ttm) REVERT: C 223 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7726 (mm-40) REVERT: C 230 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8092 (mt-10) REVERT: C 281 LYS cc_start: 0.7716 (tttp) cc_final: 0.7261 (tmmt) REVERT: C 311 GLU cc_start: 0.7908 (tt0) cc_final: 0.7174 (mt-10) REVERT: C 339 MET cc_start: 0.8015 (mtt) cc_final: 0.7565 (mtt) REVERT: C 415 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7769 (mp0) outliers start: 31 outliers final: 26 residues processed: 180 average time/residue: 0.1013 time to fit residues: 27.3741 Evaluate side-chains 188 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 55 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN C 408 ASN C 539 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.114135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.086708 restraints weight = 22617.264| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.77 r_work: 0.2749 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 12862 Z= 0.313 Angle : 0.594 9.080 17501 Z= 0.315 Chirality : 0.052 0.148 2017 Planarity : 0.004 0.044 2237 Dihedral : 4.299 21.868 1727 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.34 % Allowed : 10.65 % Favored : 87.02 % 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: -0.54 (0.20), residues: 1572 helix: -0.37 (0.35), residues: 210 sheet: 0.08 (0.23), residues: 462 loop : -0.53 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 404 TYR 0.019 0.002 TYR C 520 PHE 0.025 0.002 PHE C 479 TRP 0.009 0.002 TRP A 108 HIS 0.008 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00789 / 0.31 (12862) covalent geometry : angle 0.59419 / 0.31 (17501) hydrogen bonds : bond 0.04340 / 2.94 ( 431) hydrogen bonds : angle 5.39867 / 3.76 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.482 Fit side-chains REVERT: A 142 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8197 (mm) REVERT: A 146 ASP cc_start: 0.7972 (t0) cc_final: 0.7639 (m-30) REVERT: A 241 GLN cc_start: 0.7825 (mm110) cc_final: 0.7243 (mt0) REVERT: A 281 LYS cc_start: 0.7630 (tttp) cc_final: 0.6978 (ttpp) REVERT: A 339 MET cc_start: 0.7808 (mtt) cc_final: 0.7518 (mtt) REVERT: A 421 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8020 (pp) REVERT: B 57 GLU cc_start: 0.7884 (tt0) cc_final: 0.7347 (tp30) REVERT: B 127 LYS cc_start: 0.8229 (tptt) cc_final: 0.7633 (ttpp) REVERT: B 177 LYS cc_start: 0.7645 (mppt) cc_final: 0.7200 (mmtp) REVERT: B 241 GLN cc_start: 0.7856 (mm110) cc_final: 0.6747 (tt0) REVERT: B 285 ASP cc_start: 0.8132 (m-30) cc_final: 0.7827 (m-30) REVERT: B 293 ASP cc_start: 0.8110 (m-30) cc_final: 0.7765 (m-30) REVERT: B 534 LYS cc_start: 0.8257 (tptm) cc_final: 0.7572 (ttpt) REVERT: C 145 ASN cc_start: 0.8777 (m-40) cc_final: 0.7924 (m110) REVERT: C 218 MET cc_start: 0.8102 (ptm) cc_final: 0.7746 (ttm) REVERT: C 223 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7921 (mm-40) REVERT: C 230 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7944 (mt-10) REVERT: C 281 LYS cc_start: 0.7712 (tttp) cc_final: 0.7243 (tmmt) REVERT: C 311 GLU cc_start: 0.7814 (tt0) cc_final: 0.7256 (mt-10) REVERT: C 339 MET cc_start: 0.8074 (mtt) cc_final: 0.7631 (mtt) REVERT: C 415 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7788 (mp0) outliers start: 34 outliers final: 27 residues processed: 181 average time/residue: 0.0993 time to fit residues: 27.1184 Evaluate side-chains 185 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 58 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 120 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN A 344 HIS B 408 ASN B 411 ASN C 539 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.122276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.094118 restraints weight = 23354.669| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.88 r_work: 0.2824 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12862 Z= 0.094 Angle : 0.447 8.342 17501 Z= 0.238 Chirality : 0.046 0.146 2017 Planarity : 0.003 0.044 2237 Dihedral : 3.770 18.976 1727 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.65 % Allowed : 11.47 % Favored : 86.88 % 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: -0.44 (0.20), residues: 1572 helix: -0.25 (0.35), residues: 230 sheet: 0.10 (0.23), residues: 492 loop : -0.45 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.017 0.001 TYR B 92 PHE 0.007 0.001 PHE C 184 TRP 0.009 0.001 TRP C 108 HIS 0.003 0.000 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 (12862) covalent geometry : angle 0.44698 / 0.24 (17501) hydrogen bonds : bond 0.02696 / 1.78 ( 431) hydrogen bonds : angle 4.88742 / 3.41 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.467 Fit side-chains REVERT: A 142 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8028 (mm) REVERT: A 146 ASP cc_start: 0.7940 (t0) cc_final: 0.7591 (m-30) REVERT: A 198 ASP cc_start: 0.7339 (p0) cc_final: 0.7058 (p0) REVERT: A 230 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7535 (mm-30) REVERT: A 281 LYS cc_start: 0.7553 (tttp) cc_final: 0.6926 (ttpp) REVERT: A 339 MET cc_start: 0.7771 (mtt) cc_final: 0.7476 (mtt) REVERT: A 377 LYS cc_start: 0.8388 (mmtp) cc_final: 0.8100 (mmtp) REVERT: A 421 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8014 (pp) REVERT: B 33 MET cc_start: 0.8560 (tpt) cc_final: 0.8121 (tpt) REVERT: B 57 GLU cc_start: 0.7805 (tt0) cc_final: 0.7346 (tp30) REVERT: B 127 LYS cc_start: 0.8250 (tptt) cc_final: 0.7649 (ttpp) REVERT: B 177 LYS cc_start: 0.7631 (mppt) cc_final: 0.7217 (mmtp) REVERT: B 241 GLN cc_start: 0.7765 (mm110) cc_final: 0.6722 (tt0) REVERT: B 293 ASP cc_start: 0.8069 (m-30) cc_final: 0.7733 (m-30) REVERT: B 534 LYS cc_start: 0.8320 (tptm) cc_final: 0.7631 (ttpt) REVERT: C 145 ASN cc_start: 0.8723 (m-40) cc_final: 0.8016 (m110) REVERT: C 218 MET cc_start: 0.8094 (ptm) cc_final: 0.7786 (ttm) REVERT: C 230 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7932 (mt-10) REVERT: C 281 LYS cc_start: 0.7642 (tttp) cc_final: 0.7223 (tmmt) REVERT: C 311 GLU cc_start: 0.7802 (tt0) cc_final: 0.7262 (mt-10) REVERT: C 339 MET cc_start: 0.8077 (mtt) cc_final: 0.7552 (mtt) REVERT: C 415 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7782 (mp0) outliers start: 24 outliers final: 20 residues processed: 179 average time/residue: 0.0972 time to fit residues: 26.3843 Evaluate side-chains 183 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 138 optimal weight: 0.6980 chunk 151 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN C 539 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.115579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.088814 restraints weight = 18028.500| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.50 r_work: 0.2808 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12862 Z= 0.230 Angle : 0.535 8.663 17501 Z= 0.284 Chirality : 0.050 0.147 2017 Planarity : 0.004 0.044 2237 Dihedral : 4.073 21.210 1727 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.72 % Allowed : 11.68 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.20), residues: 1572 helix: -0.16 (0.36), residues: 210 sheet: 0.02 (0.22), residues: 492 loop : -0.58 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 404 TYR 0.021 0.001 TYR B 92 PHE 0.020 0.002 PHE C 479 TRP 0.008 0.002 TRP A 108 HIS 0.006 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.23 (12862) covalent geometry : angle 0.53540 / 0.28 (17501) hydrogen bonds : bond 0.03793 / 2.56 ( 431) hydrogen bonds : angle 5.18547 / 3.61 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.339 Fit side-chains REVERT: A 142 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8134 (mm) REVERT: A 146 ASP cc_start: 0.7992 (t0) cc_final: 0.7544 (m-30) REVERT: A 198 ASP cc_start: 0.7435 (p0) cc_final: 0.7166 (p0) REVERT: A 241 GLN cc_start: 0.7758 (mm110) cc_final: 0.7208 (mt0) REVERT: A 281 LYS cc_start: 0.7684 (tttp) cc_final: 0.7004 (ttpp) REVERT: A 339 MET cc_start: 0.7801 (mtt) cc_final: 0.7505 (mtt) REVERT: A 421 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8079 (pp) REVERT: B 57 GLU cc_start: 0.8056 (tt0) cc_final: 0.7544 (tp30) REVERT: B 127 LYS cc_start: 0.8282 (tptt) cc_final: 0.7676 (ttpp) REVERT: B 177 LYS cc_start: 0.7622 (mppt) cc_final: 0.7169 (mmtp) REVERT: B 241 GLN cc_start: 0.7841 (mm110) cc_final: 0.6656 (tt0) REVERT: B 293 ASP cc_start: 0.8151 (m-30) cc_final: 0.7810 (m-30) REVERT: B 534 LYS cc_start: 0.8294 (tptm) cc_final: 0.7624 (ttpt) REVERT: C 145 ASN cc_start: 0.8738 (m-40) cc_final: 0.8069 (m110) REVERT: C 218 MET cc_start: 0.8331 (ptm) cc_final: 0.7970 (ttm) REVERT: C 230 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8107 (mt-10) REVERT: C 281 LYS cc_start: 0.7778 (tttp) cc_final: 0.7304 (tmmt) REVERT: C 311 GLU cc_start: 0.7923 (tt0) cc_final: 0.7342 (mt-10) REVERT: C 339 MET cc_start: 0.8042 (mtt) cc_final: 0.7526 (mtt) REVERT: C 415 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7914 (mp0) outliers start: 25 outliers final: 22 residues processed: 172 average time/residue: 0.0978 time to fit residues: 25.2884 Evaluate side-chains 178 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 472 ASN Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 544 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 GLN C 539 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.093484 restraints weight = 19003.636| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.58 r_work: 0.2772 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12862 Z= 0.111 Angle : 0.456 8.364 17501 Z= 0.242 Chirality : 0.047 0.146 2017 Planarity : 0.003 0.045 2237 Dihedral : 3.791 19.345 1727 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.72 % Allowed : 11.61 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1572 helix: -0.26 (0.35), residues: 230 sheet: 0.08 (0.23), residues: 492 loop : -0.45 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 404 TYR 0.021 0.001 TYR B 92 PHE 0.007 0.001 PHE C 479 TRP 0.009 0.001 TRP A 108 HIS 0.003 0.000 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (12862) covalent geometry : angle 0.45624 / 0.24 (17501) hydrogen bonds : bond 0.02879 / 1.91 ( 431) hydrogen bonds : angle 4.89985 / 3.42 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3085.59 seconds wall clock time: 53 minutes 43.77 seconds (3223.77 seconds total)