Starting phenix.real_space_refine on Thu Feb 5 01:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dlb_46862/02_2026/9dlb_46862.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dlb_46862/02_2026/9dlb_46862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dlb_46862/02_2026/9dlb_46862.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dlb_46862/02_2026/9dlb_46862.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dlb_46862/02_2026/9dlb_46862.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dlb_46862/02_2026/9dlb_46862.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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 40 5.16 5 C 9153 2.51 5 N 2437 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14375 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3598 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "B" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3598 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3581 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 21, 'TRANS': 450} Chain: "D" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3598 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Time building chain proxies: 2.69, per 1000 atoms: 0.19 Number of scatterers: 14375 At special positions: 0 Unit cell: (110.39, 111.22, 105.41, 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 40 16.00 O 2745 8.00 N 2437 7.00 C 9153 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: 0.98 Conformation dependent library (CDL) restraints added in 548.1 milliseconds 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3476 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 27 sheets defined 45.9% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 37 through 58 Proline residue: A 53 - end of helix removed outlier: 3.501A pdb=" N LEU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 77 Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 92 through 116 removed outlier: 3.713A pdb=" N LEU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 removed outlier: 4.151A pdb=" N LYS A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 181 through 196 removed outlier: 3.565A pdb=" N GLY A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 removed outlier: 4.231A pdb=" N GLY A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 278 through 281 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 326 through 343 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 455 through 463 Processing helix chain 'B' and resid 37 through 57 Proline residue: B 53 - end of helix Processing helix chain 'B' and resid 59 through 77 Processing helix chain 'B' and resid 77 through 90 removed outlier: 3.834A pdb=" N ILE B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 115 removed outlier: 3.625A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.501A pdb=" N SER B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 132 " --> pdb=" O ALA B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 156 through 168 removed outlier: 4.805A pdb=" N LYS B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.528A pdb=" N ALA B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 4.300A pdb=" N GLY B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 278 through 281 Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 326 through 343 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 389 through 399 Processing helix chain 'B' and resid 412 through 423 removed outlier: 3.573A pdb=" N GLU B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 455 through 463 Processing helix chain 'C' and resid 37 through 57 Proline residue: C 53 - end of helix Processing helix chain 'C' and resid 59 through 77 removed outlier: 3.549A pdb=" N ARG C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 90 removed outlier: 3.825A pdb=" N ILE C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 114 Processing helix chain 'C' and resid 156 through 169 Proline residue: C 165 - end of helix removed outlier: 3.607A pdb=" N ALA C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 Processing helix chain 'C' and resid 230 through 242 removed outlier: 3.762A pdb=" N ARG C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 278 through 281 Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 326 through 343 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 389 through 399 Processing helix chain 'C' and resid 412 through 423 Processing helix chain 'C' and resid 455 through 463 Processing helix chain 'D' and resid 37 through 57 Proline residue: D 53 - end of helix Processing helix chain 'D' and resid 59 through 77 Processing helix chain 'D' and resid 77 through 90 Processing helix chain 'D' and resid 92 through 115 Processing helix chain 'D' and resid 128 through 132 removed outlier: 3.607A pdb=" N LYS D 132 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 4.206A pdb=" N LYS D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Proline residue: D 165 - end of helix Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 215 through 219 removed outlier: 3.669A pdb=" N HIS D 219 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 4.247A pdb=" N GLY D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 295 through 309 Processing helix chain 'D' and resid 314 through 318 Processing helix chain 'D' and resid 326 through 343 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 389 through 399 Processing helix chain 'D' and resid 412 through 423 Processing helix chain 'D' and resid 455 through 463 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 22 removed outlier: 3.967A pdb=" N GLY A 31 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 468 Processing sheet with id=AA4, first strand: chain 'A' and resid 464 through 468 removed outlier: 6.484A pdb=" N VAL C 428 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER C 406 " --> pdb=" O HIS C 429 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA C 255 " --> pdb=" O GLN C 405 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASP C 254 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL C 289 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA C 256 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL C 291 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 258 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS C 287 " --> pdb=" O PRO C 383 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ILE C 385 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL C 289 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL C 387 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL C 291 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 365 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG C 386 " --> pdb=" O GLN C 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.596A pdb=" N ILE A 145 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 228 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N MET A 247 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 225 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLU A 249 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE A 227 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.985A pdb=" N LEU A 382 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP A 364 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE A 384 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG A 386 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LYS A 287 " --> pdb=" O PRO A 383 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ILE A 385 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 289 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL A 387 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL A 291 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP A 254 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 288 " --> pdb=" O ASP A 254 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA A 255 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE A 409 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 257 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 406 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.868A pdb=" N LEU A 357 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 443 through 444 Processing sheet with id=AA9, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.217A pdb=" N ILE B 19 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR B 32 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 21 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 120 through 123 Processing sheet with id=AB3, first strand: chain 'B' and resid 120 through 123 Processing sheet with id=AB4, first strand: chain 'B' and resid 202 through 204 removed outlier: 6.356A pdb=" N VAL B 146 " --> pdb=" O MET B 174 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LYS B 176 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA B 148 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE B 145 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 224 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 346 through 347 removed outlier: 6.156A pdb=" N VAL B 289 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL B 387 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 291 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA B 255 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE B 409 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 257 " --> pdb=" O PHE B 409 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N SER B 406 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'B' and resid 443 through 444 Processing sheet with id=AB8, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB9, first strand: chain 'C' and resid 17 through 22 removed outlier: 7.577A pdb=" N GLN C 17 " --> pdb=" O PRO C 34 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE C 19 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR C 32 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 21 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.610A pdb=" N SER D 406 " --> pdb=" O HIS D 429 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA D 255 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N PHE D 409 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU D 257 " --> pdb=" O PHE D 409 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP D 254 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS D 287 " --> pdb=" O PRO D 383 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE D 385 " --> pdb=" O LYS D 287 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL D 289 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL D 387 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL D 291 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL D 361 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE D 384 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE D 363 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ARG D 386 " --> pdb=" O PHE D 363 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLN D 365 " --> pdb=" O ARG D 386 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 202 through 204 removed outlier: 6.540A pdb=" N ILE C 145 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AC4, first strand: chain 'C' and resid 402 through 403 removed outlier: 3.589A pdb=" N GLY C 403 " --> pdb=" O VAL C 446 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AC6, first strand: chain 'D' and resid 18 through 22 removed outlier: 3.801A pdb=" N GLY D 31 " --> pdb=" O ILE D 21 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 202 through 204 removed outlier: 6.226A pdb=" N VAL D 146 " --> pdb=" O MET D 174 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 353 through 354 removed outlier: 3.558A pdb=" N LEU D 357 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 402 through 403 removed outlier: 3.513A pdb=" N GLY D 403 " --> pdb=" O VAL D 446 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 2082 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: 2.11 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 2525 1.25 - 1.39: 3149 1.39 - 1.53: 8370 1.53 - 1.67: 499 1.67 - 1.81: 76 Bond restraints: 14619 Sorted by residual: bond pdb=" C MET C 122 " pdb=" O MET C 122 " ideal model delta sigma weight residual 1.234 1.113 0.121 1.40e-02 5.10e+03 7.46e+01 bond pdb=" C LYS C 134 " pdb=" O LYS C 134 " ideal model delta sigma weight residual 1.232 1.118 0.113 1.32e-02 5.74e+03 7.34e+01 bond pdb=" CA SER C 131 " pdb=" CB SER C 131 " ideal model delta sigma weight residual 1.531 1.408 0.123 1.51e-02 4.39e+03 6.61e+01 bond pdb=" C ASN C 133 " pdb=" O ASN C 133 " ideal model delta sigma weight residual 1.235 1.139 0.096 1.34e-02 5.57e+03 5.12e+01 bond pdb=" C GLY C 126 " pdb=" O GLY C 126 " ideal model delta sigma weight residual 1.235 1.159 0.077 1.14e-02 7.69e+03 4.51e+01 ... (remaining 14614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 19105 2.73 - 5.46: 622 5.46 - 8.19: 63 8.19 - 10.91: 11 10.91 - 13.64: 4 Bond angle restraints: 19805 Sorted by residual: angle pdb=" C LYS C 134 " pdb=" N LEU C 135 " pdb=" CA LEU C 135 " ideal model delta sigma weight residual 120.95 131.43 -10.48 1.40e+00 5.10e-01 5.60e+01 angle pdb=" C GLY B 448 " pdb=" N SER B 449 " pdb=" CA SER B 449 " ideal model delta sigma weight residual 122.54 110.44 12.10 1.65e+00 3.67e-01 5.37e+01 angle pdb=" N ARG B 436 " pdb=" CA ARG B 436 " pdb=" C ARG B 436 " ideal model delta sigma weight residual 111.71 103.97 7.74 1.15e+00 7.56e-01 4.53e+01 angle pdb=" CA LYS C 134 " pdb=" C LYS C 134 " pdb=" O LYS C 134 " ideal model delta sigma weight residual 121.39 114.37 7.02 1.12e+00 7.97e-01 3.93e+01 angle pdb=" N SER B 159 " pdb=" CA SER B 159 " pdb=" C SER B 159 " ideal model delta sigma weight residual 113.55 105.91 7.64 1.26e+00 6.30e-01 3.68e+01 ... (remaining 19800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 8073 17.85 - 35.70: 637 35.70 - 53.55: 119 53.55 - 71.39: 36 71.39 - 89.24: 15 Dihedral angle restraints: 8880 sinusoidal: 3482 harmonic: 5398 Sorted by residual: dihedral pdb=" C GLU C 128 " pdb=" N GLU C 128 " pdb=" CA GLU C 128 " pdb=" CB GLU C 128 " ideal model delta harmonic sigma weight residual -122.60 -109.44 -13.16 0 2.50e+00 1.60e-01 2.77e+01 dihedral pdb=" CA VAL D 473 " pdb=" C VAL D 473 " pdb=" N LYS D 474 " pdb=" CA LYS D 474 " ideal model delta harmonic sigma weight residual -180.00 -153.93 -26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA GLY C 170 " pdb=" C GLY C 170 " pdb=" N ASN C 171 " pdb=" CA ASN C 171 " ideal model delta harmonic sigma weight residual -180.00 -156.04 -23.96 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 8877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1706 0.066 - 0.132: 479 0.132 - 0.198: 88 0.198 - 0.264: 13 0.264 - 0.330: 3 Chirality restraints: 2289 Sorted by residual: chirality pdb=" CB VAL D 425 " pdb=" CA VAL D 425 " pdb=" CG1 VAL D 425 " pdb=" CG2 VAL D 425 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB VAL C 425 " pdb=" CA VAL C 425 " pdb=" CG1 VAL C 425 " pdb=" CG2 VAL C 425 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA MET B 174 " pdb=" N MET B 174 " pdb=" C MET B 174 " pdb=" CB MET B 174 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 2286 not shown) Planarity restraints: 2581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 134 " 0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C LYS C 134 " -0.055 2.00e-02 2.50e+03 pdb=" O LYS C 134 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU C 135 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 211 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.85e+00 pdb=" C GLU D 211 " 0.051 2.00e-02 2.50e+03 pdb=" O GLU D 211 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE D 212 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 378 " 0.024 2.00e-02 2.50e+03 2.09e-02 7.62e+00 pdb=" CG PHE C 378 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE C 378 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 378 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 378 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 378 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 378 " 0.006 2.00e-02 2.50e+03 ... (remaining 2578 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 644 2.71 - 3.26: 14008 3.26 - 3.80: 23832 3.80 - 4.35: 32130 4.35 - 4.90: 54072 Nonbonded interactions: 124686 Sorted by model distance: nonbonded pdb=" O GLU D 112 " pdb=" NH1 ARG D 116 " model vdw 2.160 3.120 nonbonded pdb=" O PHE C 402 " pdb=" NZ LYS C 447 " model vdw 2.193 3.120 nonbonded pdb=" O PRO A 178 " pdb=" OG SER A 182 " model vdw 2.200 3.040 nonbonded pdb=" OE2 GLU A 123 " pdb=" NH1 ARG D 139 " model vdw 2.224 3.120 nonbonded pdb=" NH2 ARG B 282 " pdb=" O THR B 284 " model vdw 2.231 3.120 ... (remaining 124681 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 1 through 472) selection = (chain 'B' and resid 1 through 472) selection = chain 'C' selection = (chain 'D' and resid 1 through 472) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.060 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 : 0.010 0.123 14619 Z= 0.537 Angle : 1.134 13.644 19805 Z= 0.723 Chirality : 0.064 0.330 2289 Planarity : 0.005 0.054 2581 Dihedral : 14.084 89.242 5404 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 1.61 % Allowed : 1.20 % Favored : 97.19 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 1886 helix: 0.14 (0.18), residues: 800 sheet: -1.52 (0.24), residues: 409 loop : -1.55 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 140 TYR 0.030 0.003 TYR D 458 PHE 0.048 0.003 PHE C 378 TRP 0.023 0.002 TRP B 359 HIS 0.008 0.003 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.01035 (14619) covalent geometry : angle 1.13381 (19805) hydrogen bonds : bond 0.16145 ( 733) hydrogen bonds : angle 6.39142 ( 2082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7262 (mtm110) cc_final: 0.6973 (mtp-110) REVERT: A 427 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8454 (m) REVERT: B 146 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8660 (t) outliers start: 24 outliers final: 5 residues processed: 201 average time/residue: 0.6701 time to fit residues: 145.6151 Evaluate side-chains 127 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain D residue 378 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS A 465 ASN B 26 ASN B 46 GLN C 26 ASN C 38 GLN C 46 GLN C 219 HIS D 465 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116812 restraints weight = 16198.870| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.63 r_work: 0.3326 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14619 Z= 0.141 Angle : 0.585 10.070 19805 Z= 0.304 Chirality : 0.044 0.169 2289 Planarity : 0.005 0.055 2581 Dihedral : 6.224 77.359 2015 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.41 % Allowed : 8.03 % Favored : 89.56 % 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: -0.66 (0.20), residues: 1886 helix: 0.66 (0.19), residues: 808 sheet: -1.18 (0.26), residues: 399 loop : -1.18 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 236 TYR 0.014 0.001 TYR D 458 PHE 0.012 0.001 PHE C 378 TRP 0.011 0.001 TRP D 55 HIS 0.004 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00320 (14619) covalent geometry : angle 0.58521 (19805) hydrogen bonds : bond 0.05083 ( 733) hydrogen bonds : angle 4.83856 ( 2082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.609 Fit side-chains REVERT: A 236 ARG cc_start: 0.7422 (mtp-110) cc_final: 0.7002 (ttt90) REVERT: A 320 ASP cc_start: 0.8026 (m-30) cc_final: 0.7793 (m-30) REVERT: A 421 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6667 (mt-10) REVERT: B 218 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8012 (mt-10) REVERT: B 378 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8783 (m-80) REVERT: C 29 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 153 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7801 (p0) REVERT: C 282 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7589 (ptm-80) REVERT: C 433 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7835 (ptmt) REVERT: D 154 TYR cc_start: 0.7963 (m-80) cc_final: 0.7685 (m-80) outliers start: 36 outliers final: 17 residues processed: 186 average time/residue: 0.6556 time to fit residues: 132.5367 Evaluate side-chains 145 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 417 PHE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 378 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 35 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 88 optimal weight: 0.0370 overall best weight: 1.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN B 26 ASN B 46 GLN C 219 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.113627 restraints weight = 16365.407| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.64 r_work: 0.3287 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14619 Z= 0.181 Angle : 0.597 10.890 19805 Z= 0.305 Chirality : 0.045 0.179 2289 Planarity : 0.005 0.047 2581 Dihedral : 5.848 72.458 2009 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.41 % Allowed : 10.44 % Favored : 86.14 % 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: -0.47 (0.20), residues: 1886 helix: 0.76 (0.19), residues: 811 sheet: -1.05 (0.26), residues: 399 loop : -1.01 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 236 TYR 0.014 0.001 TYR D 458 PHE 0.018 0.002 PHE C 378 TRP 0.009 0.001 TRP D 55 HIS 0.004 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00443 (14619) covalent geometry : angle 0.59702 (19805) hydrogen bonds : bond 0.05167 ( 733) hydrogen bonds : angle 4.66582 ( 2082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7922 (m-30) cc_final: 0.7631 (m-30) REVERT: A 113 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: A 157 ASN cc_start: 0.8723 (t0) cc_final: 0.8396 (t160) REVERT: A 216 ILE cc_start: 0.8323 (mm) cc_final: 0.7380 (pt) REVERT: A 236 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.6970 (ttt90) REVERT: A 421 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6653 (mt-10) REVERT: A 463 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7864 (mpp) REVERT: B 218 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8033 (mt-10) REVERT: B 318 ASN cc_start: 0.8557 (m-40) cc_final: 0.8347 (m-40) REVERT: B 378 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8906 (m-80) REVERT: C 18 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7373 (mt-10) REVERT: C 128 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8376 (mt-10) REVERT: C 139 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7095 (mtp85) REVERT: C 220 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6796 (mptt) REVERT: C 282 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7618 (ptm-80) REVERT: C 433 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8134 (pttp) REVERT: D 3 ARG cc_start: 0.7464 (mmm-85) cc_final: 0.7230 (mmm-85) REVERT: D 154 TYR cc_start: 0.7997 (m-80) cc_final: 0.7762 (m-80) REVERT: D 239 ARG cc_start: 0.7823 (ttm170) cc_final: 0.7515 (ttm-80) outliers start: 51 outliers final: 20 residues processed: 174 average time/residue: 0.7022 time to fit residues: 132.0759 Evaluate side-chains 156 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 433 LYS Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 378 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 152 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN B 46 GLN B 465 ASN C 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113372 restraints weight = 16301.029| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.63 r_work: 0.3286 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14619 Z= 0.177 Angle : 0.581 10.805 19805 Z= 0.297 Chirality : 0.045 0.200 2289 Planarity : 0.005 0.046 2581 Dihedral : 5.703 70.971 2009 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.35 % Allowed : 11.91 % Favored : 84.74 % 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: -0.34 (0.20), residues: 1886 helix: 0.86 (0.19), residues: 811 sheet: -0.99 (0.26), residues: 399 loop : -0.94 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 236 TYR 0.011 0.001 TYR D 458 PHE 0.011 0.001 PHE B 316 TRP 0.010 0.001 TRP D 55 HIS 0.004 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00434 (14619) covalent geometry : angle 0.58072 (19805) hydrogen bonds : bond 0.04999 ( 733) hydrogen bonds : angle 4.55657 ( 2082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7953 (m-30) cc_final: 0.7708 (m-30) REVERT: A 157 ASN cc_start: 0.8761 (t0) cc_final: 0.8443 (t160) REVERT: A 216 ILE cc_start: 0.8251 (mm) cc_final: 0.7792 (pt) REVERT: A 218 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8001 (mt-10) REVERT: A 236 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.6970 (ttt90) REVERT: A 421 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6597 (mt-10) REVERT: A 463 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.7865 (mpp) REVERT: B 218 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8031 (mt-10) REVERT: B 318 ASN cc_start: 0.8587 (m-40) cc_final: 0.8379 (m-40) REVERT: B 320 ASP cc_start: 0.8138 (m-30) cc_final: 0.7901 (m-30) REVERT: B 378 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8868 (m-80) REVERT: C 18 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7434 (mt-10) REVERT: C 36 MET cc_start: 0.8426 (mtp) cc_final: 0.8217 (mtm) REVERT: C 139 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7068 (mtp85) REVERT: C 220 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6778 (mptt) REVERT: C 249 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8343 (pt0) REVERT: C 282 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7746 (ptm-80) REVERT: D 154 TYR cc_start: 0.8032 (m-80) cc_final: 0.7749 (m-80) REVERT: D 239 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7561 (ttm-80) REVERT: D 354 GLU cc_start: 0.7517 (tt0) cc_final: 0.6490 (mp0) outliers start: 50 outliers final: 31 residues processed: 175 average time/residue: 0.6609 time to fit residues: 125.3091 Evaluate side-chains 166 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 378 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 0.1980 chunk 129 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN B 46 GLN C 26 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115257 restraints weight = 16209.363| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.64 r_work: 0.3307 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14619 Z= 0.135 Angle : 0.538 10.304 19805 Z= 0.275 Chirality : 0.043 0.202 2289 Planarity : 0.004 0.046 2581 Dihedral : 5.468 69.121 2009 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.21 % Allowed : 13.25 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1886 helix: 1.03 (0.19), residues: 813 sheet: -0.90 (0.26), residues: 399 loop : -0.79 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 236 TYR 0.008 0.001 TYR D 458 PHE 0.008 0.001 PHE B 316 TRP 0.008 0.001 TRP D 55 HIS 0.002 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00319 (14619) covalent geometry : angle 0.53788 (19805) hydrogen bonds : bond 0.04511 ( 733) hydrogen bonds : angle 4.41150 ( 2082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7813 (m-30) cc_final: 0.7602 (m-30) REVERT: A 216 ILE cc_start: 0.8116 (mm) cc_final: 0.7835 (pt) REVERT: A 236 ARG cc_start: 0.7296 (mtp-110) cc_final: 0.6927 (ttt90) REVERT: A 286 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.6985 (mt) REVERT: A 421 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6499 (mt-10) REVERT: A 463 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7802 (mpp) REVERT: B 43 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6913 (mt-10) REVERT: B 146 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8190 (t) REVERT: B 218 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7986 (mt-10) REVERT: B 318 ASN cc_start: 0.8541 (m-40) cc_final: 0.8341 (m-40) REVERT: B 320 ASP cc_start: 0.8115 (m-30) cc_final: 0.7891 (m-30) REVERT: B 378 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8803 (m-80) REVERT: C 36 MET cc_start: 0.8357 (mtp) cc_final: 0.8109 (mtm) REVERT: C 249 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: C 282 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7666 (ptm-80) REVERT: D 239 ARG cc_start: 0.7798 (ttm170) cc_final: 0.7521 (ttm-80) REVERT: D 354 GLU cc_start: 0.7539 (tt0) cc_final: 0.6496 (mp0) outliers start: 48 outliers final: 24 residues processed: 176 average time/residue: 0.6846 time to fit residues: 130.4706 Evaluate side-chains 154 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 378 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 182 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN B 46 GLN B 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112198 restraints weight = 16245.958| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.63 r_work: 0.3267 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14619 Z= 0.208 Angle : 0.602 11.012 19805 Z= 0.306 Chirality : 0.046 0.211 2289 Planarity : 0.005 0.056 2581 Dihedral : 5.613 67.791 2009 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.82 % Allowed : 13.72 % Favored : 82.46 % 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: -0.19 (0.20), residues: 1886 helix: 0.95 (0.19), residues: 814 sheet: -0.95 (0.25), residues: 423 loop : -0.77 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 3 TYR 0.011 0.001 TYR D 458 PHE 0.014 0.002 PHE B 316 TRP 0.008 0.001 TRP B 359 HIS 0.004 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00514 (14619) covalent geometry : angle 0.60238 (19805) hydrogen bonds : bond 0.05118 ( 733) hydrogen bonds : angle 4.51578 ( 2082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 127 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 157 ASN cc_start: 0.8760 (t0) cc_final: 0.8443 (t160) REVERT: A 286 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7096 (mt) REVERT: A 421 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6607 (mt-10) REVERT: B 1 MET cc_start: 0.3789 (OUTLIER) cc_final: 0.2630 (tpt) REVERT: B 146 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8234 (t) REVERT: B 218 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8071 (mt-10) REVERT: B 320 ASP cc_start: 0.8115 (m-30) cc_final: 0.7897 (m-30) REVERT: B 378 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8892 (m-80) REVERT: B 414 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7975 (tttt) REVERT: C 36 MET cc_start: 0.8431 (mtp) cc_final: 0.8184 (mtm) REVERT: C 249 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8311 (pt0) REVERT: C 282 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7800 (ptm-80) REVERT: D 154 TYR cc_start: 0.8093 (m-80) cc_final: 0.7825 (m-80) REVERT: D 239 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7505 (ttm-80) REVERT: D 354 GLU cc_start: 0.7641 (tt0) cc_final: 0.6641 (mp0) outliers start: 57 outliers final: 33 residues processed: 172 average time/residue: 0.6828 time to fit residues: 127.8183 Evaluate side-chains 159 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 464 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 101 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 176 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116094 restraints weight = 16215.786| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.63 r_work: 0.3315 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14619 Z= 0.125 Angle : 0.525 11.236 19805 Z= 0.268 Chirality : 0.043 0.217 2289 Planarity : 0.004 0.047 2581 Dihedral : 5.324 67.162 2009 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.01 % Allowed : 14.86 % Favored : 82.13 % 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: 0.02 (0.20), residues: 1886 helix: 1.15 (0.19), residues: 813 sheet: -0.87 (0.25), residues: 414 loop : -0.68 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 3 TYR 0.006 0.001 TYR D 458 PHE 0.008 0.001 PHE C 409 TRP 0.009 0.001 TRP D 55 HIS 0.003 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00294 (14619) covalent geometry : angle 0.52533 (19805) hydrogen bonds : bond 0.04256 ( 733) hydrogen bonds : angle 4.34060 ( 2082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7949 (m-30) cc_final: 0.7693 (m-30) REVERT: A 286 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.7061 (mt) REVERT: A 421 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6544 (mt-10) REVERT: A 463 MET cc_start: 0.8959 (mtm) cc_final: 0.8265 (mtt) REVERT: B 1 MET cc_start: 0.3705 (OUTLIER) cc_final: 0.2704 (tpt) REVERT: B 3 ARG cc_start: 0.7457 (mtp85) cc_final: 0.7052 (mtp85) REVERT: B 43 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6913 (mt-10) REVERT: B 146 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8343 (t) REVERT: B 320 ASP cc_start: 0.8121 (m-30) cc_final: 0.7876 (m-30) REVERT: B 378 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8830 (m-80) REVERT: C 128 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7911 (mt-10) REVERT: C 249 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8191 (pt0) REVERT: C 282 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7719 (ptm-80) REVERT: D 239 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7580 (ttm-80) REVERT: D 354 GLU cc_start: 0.7620 (tt0) cc_final: 0.7388 (mt-10) outliers start: 45 outliers final: 24 residues processed: 172 average time/residue: 0.6656 time to fit residues: 124.4918 Evaluate side-chains 153 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 417 PHE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 464 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 145 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN B 26 ASN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.112766 restraints weight = 16281.051| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.62 r_work: 0.3273 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14619 Z= 0.194 Angle : 0.599 11.639 19805 Z= 0.303 Chirality : 0.045 0.234 2289 Planarity : 0.005 0.055 2581 Dihedral : 5.495 64.805 2009 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.21 % Allowed : 15.46 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1886 helix: 1.06 (0.19), residues: 814 sheet: -0.92 (0.25), residues: 435 loop : -0.61 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 236 TYR 0.010 0.001 TYR D 458 PHE 0.012 0.002 PHE B 316 TRP 0.008 0.001 TRP B 359 HIS 0.004 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00479 (14619) covalent geometry : angle 0.59934 (19805) hydrogen bonds : bond 0.04915 ( 733) hydrogen bonds : angle 4.45962 ( 2082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 174 MET cc_start: 0.8494 (mmm) cc_final: 0.8279 (tpp) REVERT: A 286 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7147 (mt) REVERT: A 421 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6591 (mt-10) REVERT: A 463 MET cc_start: 0.8954 (mtm) cc_final: 0.8348 (mtt) REVERT: B 1 MET cc_start: 0.3778 (OUTLIER) cc_final: 0.2814 (tpt) REVERT: B 3 ARG cc_start: 0.7484 (mtp85) cc_final: 0.7054 (mtp85) REVERT: B 146 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8343 (t) REVERT: B 320 ASP cc_start: 0.8107 (m-30) cc_final: 0.7876 (m-30) REVERT: B 378 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8889 (m-80) REVERT: C 3 ARG cc_start: 0.7633 (mtp85) cc_final: 0.7326 (mtp85) REVERT: C 128 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7881 (mt-10) REVERT: C 249 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8301 (pt0) REVERT: C 282 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7632 (ptm-80) REVERT: D 38 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.6483 (mt0) REVERT: D 154 TYR cc_start: 0.8112 (m-80) cc_final: 0.7811 (m-80) REVERT: D 239 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7541 (ttm-80) REVERT: D 354 GLU cc_start: 0.7722 (tt0) cc_final: 0.7483 (mt-10) outliers start: 48 outliers final: 28 residues processed: 162 average time/residue: 0.7240 time to fit residues: 127.0665 Evaluate side-chains 155 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 464 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 139 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113360 restraints weight = 16205.069| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.63 r_work: 0.3280 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14619 Z= 0.174 Angle : 0.587 12.029 19805 Z= 0.296 Chirality : 0.045 0.230 2289 Planarity : 0.005 0.055 2581 Dihedral : 5.469 66.026 2009 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.15 % Allowed : 15.66 % Favored : 81.19 % 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: -0.01 (0.20), residues: 1886 helix: 1.08 (0.18), residues: 811 sheet: -0.97 (0.24), residues: 450 loop : -0.51 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 236 TYR 0.009 0.001 TYR D 458 PHE 0.010 0.001 PHE B 316 TRP 0.007 0.001 TRP D 334 HIS 0.003 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00427 (14619) covalent geometry : angle 0.58730 (19805) hydrogen bonds : bond 0.04780 ( 733) hydrogen bonds : angle 4.43808 ( 2082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8001 (m-30) cc_final: 0.7788 (m-30) REVERT: A 174 MET cc_start: 0.8517 (mmm) cc_final: 0.8282 (tpp) REVERT: A 286 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7157 (mt) REVERT: A 378 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8416 (t80) REVERT: A 421 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6613 (mt-10) REVERT: A 463 MET cc_start: 0.8946 (mtm) cc_final: 0.8387 (mtt) REVERT: B 1 MET cc_start: 0.4001 (OUTLIER) cc_final: 0.3092 (tpt) REVERT: B 3 ARG cc_start: 0.7497 (mtp85) cc_final: 0.7041 (mtp85) REVERT: B 43 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6925 (mt-10) REVERT: B 146 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8380 (t) REVERT: B 320 ASP cc_start: 0.8068 (m-30) cc_final: 0.7830 (m-30) REVERT: B 378 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8775 (m-80) REVERT: C 128 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7884 (mt-10) REVERT: C 174 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7530 (mmm) REVERT: C 249 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8264 (pt0) REVERT: C 282 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7793 (ptm-80) REVERT: D 38 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.6397 (mt0) REVERT: D 154 TYR cc_start: 0.8139 (m-80) cc_final: 0.7812 (m-80) REVERT: D 239 ARG cc_start: 0.7858 (ttm170) cc_final: 0.7558 (ttm-80) REVERT: D 354 GLU cc_start: 0.7754 (tt0) cc_final: 0.7523 (mt-10) outliers start: 47 outliers final: 29 residues processed: 162 average time/residue: 0.7199 time to fit residues: 126.2361 Evaluate side-chains 160 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 417 PHE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 136 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 160 optimal weight: 0.2980 chunk 81 optimal weight: 7.9990 chunk 133 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN B 318 ASN C 26 ASN C 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115978 restraints weight = 16233.948| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.63 r_work: 0.3311 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14619 Z= 0.129 Angle : 0.546 10.048 19805 Z= 0.276 Chirality : 0.043 0.245 2289 Planarity : 0.004 0.051 2581 Dihedral : 5.277 64.626 2009 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.41 % Allowed : 16.40 % Favored : 81.19 % 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: 0.15 (0.20), residues: 1886 helix: 1.21 (0.19), residues: 815 sheet: -0.85 (0.25), residues: 435 loop : -0.47 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 3 TYR 0.006 0.001 TYR D 458 PHE 0.008 0.001 PHE D 471 TRP 0.008 0.001 TRP D 55 HIS 0.002 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00302 (14619) covalent geometry : angle 0.54598 (19805) hydrogen bonds : bond 0.04277 ( 733) hydrogen bonds : angle 4.31256 ( 2082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7422 (mm-30) REVERT: A 42 ASP cc_start: 0.8047 (m-30) cc_final: 0.7801 (m-30) REVERT: A 286 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.7086 (mt) REVERT: A 378 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8442 (t80) REVERT: A 421 GLU cc_start: 0.7346 (tm-30) cc_final: 0.6588 (mt-10) REVERT: A 463 MET cc_start: 0.8968 (mtm) cc_final: 0.8360 (mtt) REVERT: B 1 MET cc_start: 0.4092 (OUTLIER) cc_final: 0.3022 (tpt) REVERT: B 3 ARG cc_start: 0.7461 (mtp85) cc_final: 0.7005 (mtp85) REVERT: B 43 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6897 (mt-10) REVERT: B 146 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8400 (t) REVERT: B 320 ASP cc_start: 0.8037 (m-30) cc_final: 0.7809 (m-30) REVERT: B 378 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8700 (m-80) REVERT: C 123 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: C 128 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7922 (mt-10) REVERT: C 174 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7428 (mmm) REVERT: C 249 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8223 (pt0) REVERT: C 282 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7707 (ptm-80) REVERT: D 239 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7570 (ttm-80) REVERT: D 354 GLU cc_start: 0.7711 (tt0) cc_final: 0.7483 (mt-10) outliers start: 36 outliers final: 23 residues processed: 154 average time/residue: 0.6828 time to fit residues: 113.8180 Evaluate side-chains 153 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 153 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 282 ARG Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 378 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 47 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 ASN C 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117159 restraints weight = 16290.367| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.62 r_work: 0.3325 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14619 Z= 0.121 Angle : 0.537 11.358 19805 Z= 0.270 Chirality : 0.043 0.238 2289 Planarity : 0.004 0.050 2581 Dihedral : 5.168 62.508 2009 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.48 % Allowed : 16.60 % Favored : 80.92 % 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: 0.27 (0.20), residues: 1886 helix: 1.30 (0.19), residues: 815 sheet: -0.84 (0.25), residues: 450 loop : -0.33 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 3 TYR 0.006 0.001 TYR D 458 PHE 0.010 0.001 PHE A 396 TRP 0.008 0.001 TRP D 55 HIS 0.002 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00284 (14619) covalent geometry : angle 0.53689 (19805) hydrogen bonds : bond 0.04115 ( 733) hydrogen bonds : angle 4.25689 ( 2082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4074.86 seconds wall clock time: 70 minutes 15.94 seconds (4215.94 seconds total)